Post hoc deconvolution of human mitochondrial DNA mixtures by EMMA 2 using fine-tuned Phylotree nomenclature.

In this paper we present a new algorithm for splitting (partial) human mitogenomes into components with high similarity to haplogroup motifs of Phylotree. The algorithm reads a (partial) mitogenome coded by the differences to the reference (rCRS) and outputs the estimated haplogroups of the putative components. The algorithm requires no special information on the raw data of the sequencing process and is therefore suited for the post hoc analysis of mixtures of any sequencing technology.

On the Role of Polymer Viscoelasticity in Enhanced Oil Recovery: Extensive Laboratory Data and Review.

Polymer flooding most commonly uses partially hydrolyzed polyacrylamides (HPAM) injected to increase the declining oil production from mature fields. Apart from the improved mobility ratio, also the viscoelasticity-associated flow effects yield additional oil recovery. Viscoelasticity is defined as the ability of particular polymer solutions to behave as a solid and liquid simultaneously if certain flow conditions, e.

Optimizing Management of Otophyma: A Case Series Highlighting the Role of Surgical and Retinoid Therapy.

Otophyma is a rare condition that can result in conductive hearing loss. Current otophyma literature does not examine validated treatment outcomes for patients. Utilizing a medical and surgical approach to maintain a patent canal can lead to significant objective improvements.

Doravirine and Its Potential in the Treatment of HIV: An Evidence-Based Review of the Emerging Data.

The utility of doravirine in the management of HIV-1 infection is approved for use in patients who are antiretroviral-naïve as well as patients who have achieved stable virologic suppression and are interested in replacing their current antiretroviral therapy. The role of doravirine continues to evolve as data emerges on the potential for new combination therapy with the investigational agent, islatravir, as well as a potential strategy to minimize post-marketing safety concerns with recommended first-line agents, such as integrase inhibitors. The goal of this review is to assess recent and emerging data on the non-nucleoside reverse transcriptase inhibitor, doravirine.

MicroRNA Expression Profiling of Cutaneous Squamous Cell Carcinomas Arising in Different Sites.

Objective: To examine the microRNA (miRNA) expression profile of cutaneous squamous cell carcinoma (cSCC) tumors from aggressive head and neck locations compared with nonaggressive anatomic sites and normal controls.

Study Design: Retrospective analysis of miRNA expression.

Setting: Tertiary care center.

Comparison of Opioid Prescription Patterns and Consumption Following Otologic Surgery.

Objective: To examine opioid prescribing patterns and consumption among patients undergoing common otologic surgeries.

Study Design: Retrospective cohort study with chart review and telephone survey.

Setting: Tertiary academic medical center.

Postoperative Prescriptions and Corresponding Opioid Consumption After Septoplasty or Rhinoplasty.

The objective of our study was to assess the relationship between postoperative opioid prescribing patterns and opioid consumption among patients who underwent septoplasty or rhinoplasty. A chart review of patients who underwent either septoplasty or rhinoplasty by 3 surgeons between July 2016 and June 2017 was performed, and pertinent clinical data were collected including the amount of narcotic pain medications prescribed. A telephone interview was then conducted to assess opioid usage and pain control regimen postoperatively.

Lack of gene-language correlation due to reciprocal female but directional male admixture in Austronesians and non-Austronesians of East Timor.

Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene-language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene-language correlation in this region. Aiming to investigate gene-language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN- and NAN-speaking groups.

Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity.

Background: Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice.

Full mtGenome reference data: development and characterization of 588 forensic-quality haplotypes representing three U.S. populations.

Though investigations into the use of massively parallel sequencing technologies for the generation of complete mitochondrial genome (mtGenome) profiles from difficult forensic specimens are well underway in multiple laboratories, the high quality population reference data necessary to support full mtGenome typing in the forensic context are lacking. To address this deficiency, we have developed 588 complete mtGenome haplotypes, spanning three U.S.

Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia.

A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.

Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software.

Aim: To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors.

Method: We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; www.empop.

Development of forensic-quality full mtGenome haplotypes: success rates with low template specimens.

Forensic mitochondrial DNA (mtDNA) testing requires appropriate, high quality reference population data for estimating the rarity of questioned haplotypes and, in turn, the strength of the mtDNA evidence. Available reference databases (SWGDAM, EMPOP) currently include information from the mtDNA control region; however, novel methods that quickly and easily recover mtDNA coding region data are becoming increasingly available. Though these assays promise to both facilitate the acquisition of mitochondrial genome (mtGenome) data and maximize the general utility of mtDNA testing in forensics, the appropriate reference data and database tools required for their routine application in forensic casework are lacking.

Mass spectrometric base composition profiling: Implications for forensic mtDNA databasing.

In forensic genetics mitochondrial DNA (mtDNA) is usually analyzed by direct Sanger-type sequencing (STS). This method is known to be laborious and sometimes prone to human error. Alternative methods have been proposed that lead to faster results.

Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA).

The assignment of haplogroups to mitochondrial DNA haplotypes contributes substantial value for quality control, not only in forensic genetics but also in population and medical genetics. The availability of Phylotree, a widely accepted phylogenetic tree of human mitochondrial DNA lineages, led to the development of several (semi-)automated software solutions for haplogrouping. However, currently existing haplogrouping tools only make use of haplogroup-defining mutations, whereas private mutations (beyond the haplogroup level) can be additionally informative allowing for enhanced haplogroup assignment.

Forensic and phylogeographic characterisation of mtDNA lineages from Somalia.

The African mitochondrial (mt) phylogeny is coarsely resolved but the majority of population data generated so far is limited to the analysis of the first hypervariable segment (HVS-1) of the control region (CR). Therefore, this study aimed on the investigation of the entire CR of 190 unrelated Somali individuals to enrich the severely underrepresented African mtDNA pool. The majority (60.

Prosthetic and surgical management of oronasal communications secondary to cocaine abuse.

Oronasal communications are serious sequelae of chronic cocaine abuse. If left untreated, these communications can severely limit a patient's quality of life. The defects can be rehabilitated successfully utilizing either maxillofacial prosthetics or various surgical techniques.

Mitochondrial DNA control region data from indigenous Angolan Khoe-San lineages.

Here we provide 129 complete mitochondrial control region sequences of indigenous Khoe-San individuals from Angola to contribute to the still underrepresented pool of data from Africa. The dataset consists of exclusively African lineages with a majority of Sub-Saharan haplogroups. The probability of a random match was calculated as 0.

Rapid coastal spread of First Americans: novel insights from South America's Southern Cone mitochondrial genomes.

It is now widely agreed that the Native American founders originated from a Beringian source population ~15-18 thousand years ago (kya) and rapidly populated all of the New World, probably mainly following the Pacific coastal route. However, details about the migration into the Americas and the routes pursued on the continent still remain unresolved, despite numerous genetic, archaeological, and linguistic investigations. To examine the pioneering peopling phase of the South American continent, we screened literature and mtDNA databases and identified two novel mitochondrial DNA (mtDNA) clades, here named D1g and D1j, within the pan-American haplogroup D1.

MtDNA diversity of Ghana: a forensic and phylogeographic view.

West Africa is characterized by a migration history spanning more than 150,000 years. Climate changes but also political circumstances were responsible for several early but also recent population movements that shaped the West African mitochondrial landscape. The aim of the study was to establish a Ghanaian mtDNA dataset for forensic purposes and to investigate the diversity of the Ghanaian population sample with respect to surrounding populations.

Southeast Asian diversity: first insights into the complex mtDNA structure of Laos.

Background: Vast migrations and subsequent assimilation processes have shaped the genetic composition of Southeast Asia, an area of close contact between several major ethnic groups. To better characterize the genetic variation of this region, we analyzed the entire mtDNA control region of 214 unrelated donors from Laos according to highest forensic quality standards. To detail the phylogeny, we inspected selected SNPs from the mtDNA coding region.

Application of a west Eurasian-specific filter for quasi-median network analysis: Sharpening the blade for mtDNA error detection.

The application of quasi-median networks provides an effective tool to check the quality of mtDNA data. Filtering of highly recurrent mutations prior to network analysis is required to simplify the data set and reduce the complexity of the network. The phylogenetic background determines those mutations that need to be filtered.

SAM: String-based sequence search algorithm for mitochondrial DNA database queries.

The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA.

Accumulation of mutations over the entire mitochondrial genome of breast cancer cells obtained by tissue microdissection.

The occurrence of heteroplasmy and mixtures is technically challenging for the analysis of mitochondrial DNA. More than that, observed mutations need to be carefully interpreted in the light of the phylogeny as mitochondrial DNA is a uniparental marker reflecting human evolution. Earlier attempts to explain the role of mtDNA in cancerous tissues led to substantial confusion in medical genetics mainly due to the presentation of low sequence data quality and misinterpretation of mutations representing a particular haplogroup background rather than being cancer-specific.