Cryptic Contamination and Phylogenetic Nonsense

Ancient human DNA has been treated cautiously ever since the problems related to this type of material were exposed in the early 1990s, but as sequential genetic data from ancient specimens have been key components in several evolutionary and ecological studies, interest in ancient human DNA is on the increase again. It is especially tempting to approach archaeological and anthropological questions through this type of material, but DNA from ancient human tissue is notoriously complicated to work with due to the risk of contamination with modern human DNA. Various ways of authenticating results based on ancient human DNA have been developed to circumvent the problems. One commonly used method is to predict what the contamination is expected to look like and then test whether the ancient human DNA fulfils this prediction. If it does, the results are rejected as contamination, while if it does not, they are often considered authentic. We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists. We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material

Barking up the wrong tree: Modern northern European dogs fail to explain their origin

<p>Abstract</p> <p>Background</p> <p>Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlying presumption is that phylogeographic patterns among domesticates were established during, or shortly after the domestication. Human activities are assumed not to have altered the haplogroup frequencies to any great extent. We studied this hypothesis by analyzing 24 mtDNA sequences in ancient Scandinavian dogs. Breeds originating in northern Europe are characterized by having a high frequency of mtDNA sequences belonging to a haplogroup rare in other populations (HgD). This has been suggested to indicate a possible origin of the haplogroup (perhaps even a separate domestication) in central or northern Europe.</p> <p>Results</p> <p>The sequences observed in the ancient samples do not include the haplogroup indicative for northern European breeds (HgD). Instead, several of them correspond to haplogroups that are uncommon in the region today and that are supposed to have Asian origin.</p> <p>Conclusion</p> <p>We find no evidence for local domestication. We conclude that interpretation of the processes responsible for current domestic haplogroup frequencies should be carried out with caution if based only on contemporary data. They do not only tell their own story, but also that of humans.</p

Return-to-work : Exploring professionals' experiences of support for persons with spinal cord injury

Purpose: To generate knowledge about how professional stakeholders organise and experience the support of the return-to-work (RTW) process for persons with spinal cord injury (SCI). Methods: Constructivist grounded theory approach. Professional stakeholders (n = 34) involved in the RTW process and representing three Swedish Regions were recruited into seven focus groups. Analysis followed initial, focussed, and theoretical coding. Findings: The core category - mediating intentions to support work and possibilities of working through social, labour market, and societal context - illustrates complexities of when and how to support a person with SCI in the RTW process, and a risk of delayed, unequal, or absent RTW processes. Analysis outlines: (1) Assessment of ability to work - uncertainty of how and when; (2) Planning RTW - divide between dynamic and rule-based perspectives; (3) Work re-entry - unequal paths towards viable solutions. Conclusions: In RTW after SCI, it is critical to acknowledge how the RTW process is situated in relation to the person and context. A possible direction - grounded in an occupational perspective - through early identification of needs and resources and coordination derived from the SCI rehabilitation setting within healthcare is suggested. This can facilitate a time-sensitive and equal RTW process

Presumption of innocence and media rights to inform society about legal proceedings

Par nevainīguma prezumpciju var runāt kā par sākotnēju pieņēmumu, ka persona nav vainīga noziedzīga nodarījuma izdarīšanā, kamēr tās vaina nav pierādīta saskaņā ar likumu. Tomēr plašsaziņas līdzekļi, informējot sabiedrību par tiesu procesiem, bieži publicē ziņas par vienas vai otras personas “notiesāšanu” pirms šīs, patiesībā tikai iespējami vainīgās, personas saukšanas pie atbildības un notiesājoša sprieduma taisīšanas. Ievērojot minēto, darba mērķi ir noskaidrot, vai plašsaziņas līdzekļi, informējot sabiedrību par tiesas procesiem, var pārkāpt personas tiesības uz nevainīguma prezumpciju un, ja var, tad kā līdzsvarot plašsaziņas līdzekļu pienākumu informēt sabiedrību par tiesas procesiem ar citām cilvēka tiesībām. Maģistra darba ietvaros Autore secina, ka plašsaziņas līdzekļi nevar pārkāpt nevainīguma prezumpciju kā kriminālprocesu organizējošu principu, jo plašsaziņas līdzekļu izteikumi par personas vainu nevar ietekmēt kriminālprocesa norisi. Tomēr nevainīguma prezumpcijas principam nevar piešķirt tik šauru nozīmi, jo goda un cieņas, arī reputācijas aizsardzība ir viens no nevainīguma prezumpcijas aspektiem. Plašsaziņas līdzekļi var pārkāpt nevainīguma prezumpcijas reputācijas aizsardzības aspektu. Savukārt līdzsvarojot plašsaziņas līdzekļu izteikumus un nevainīguma prezumpcijas principu, Eiropas Cilvēktiesību tiesas praksē tiek vērtēti šādi kritēriji: veids, kādā informācija tika iegūta; apstrīdētā raksta saturs; raksta aktualitāte sabiedriskai diskusijai; raksta ietekme uz kriminālprocesu; privātās dzīves aizskāruma nopietnība; soda samērīgums.The presumption of innocence could be expressed as an initial presumption that a person is not guilty of a criminal offense until guilt is proven in accordance with the law. However, it has been observed that media while informing public about court proceedings often “convict” one or another person before the prosecution and conviction of that person, who is only allegedly guilty, has been made. Thus, the purposes of the Master’s thesis are to find out whether the media may violate a person's rights of the presumption of innocence by informing the public about court proceedings and, if so, how to balance the media's obligation to inform the public about court proceedings and other human rights. The author concludes that media cannot violate the presumption of innocence as a principle of criminal proceeding organization because media’s statements about guilt cannot affect the process of criminal proceedings. However, the principle of the presumption of innocence cannot be given such a narrow meaning, because the protection of honour and dignity, as well reputation, is one of the aspects of the presumption of innocence. The media may violate the reputation protection aspect of the presumption of innocence. In balancing the statements of the media and the principle of the presumption of innocence, the European Court of Human Rights assesses the following criteria: the way in which the information was obtained; the content of the impugned article; contribution of the impugned article to a public-interest debate; influence of the impugned article on the criminal proceedings; infringement of the accused’s private life; proportionality of the penalty imposed

A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures

Species identification can be interesting in a wide range of areas, for example, in forensic applications, food monitoring and in archeology. The vast majority of existing DNA typing methods developed for species determination, mainly focuses on a single species source. There are, however, many instances where all species from mixed sources need to be determined, even when the species in minority constitutes less than 1 % of the sample. The introduction of next generation sequencing opens new possibilities for such challenging samples. In this study we present a universal deep sequencing method using 454 GS Junior sequencing of a target on the mitochondrial gene 16S rRNA. The method was designed through phylogenetic analyses of DNA reference sequences from more than 300 mammal species. Experiments were performed on artificial species-species mixture samples in order to verify the method's robustness and its ability to detect all species within a mixture. The method was also tested on samples from authentic forensic casework. The results showed to be promising, discriminating over 99.9 % of mammal species and the ability to detect multiple donors within a mixture and also to detect minor components as low as 1 % of a mixed sample

Evaluating the feasibility of ReWork-SCI : a person-centred intervention for return-to-work after spinal cord injury

Objectives To evaluate the feasibility of: (1) ReWork-SCI with regard to adherence and acceptability and (2) a study design for evaluating ReWork-SCI with regard to recruitment, retention and outcome measures. Design Pre-test and post-test, single group, feasibility study. Setting Spinal cord injury (SCI) unit at a regional rehabilitation centre in Sweden. Participants Two women and five men (n=7). Eligible criteria: (1) sustained traumatic or non-traumatic SCI; (2) completed the first acute care episode in a hospital; (3) between 18 to 65 years of age; (4) assessed by a physician as approachable for participation in the intervention; (5) history of permanent or temporary employment; (6) self-reported desire to return to work; and (7) ability to communicate in English or Swedish. Intervention ReWork-SCI is a person-centred intervention for return-to-work (RTW), developed and evaluated using the Medical Research Council's guidelines. ReWork-SCI follows a person-centred, structured and coordinated intervention process led by a coordinator within a SCI rehabilitation team. Outcome measures The feasibility of ReWork-SCI and a study design was evaluated using a set of outcome measurement tools, vocational data, logbooks and semi-structured interviews. Results All eligible participants accepted enrolment and follow-up. All participants had a plan for RTW after 3 months and four participants had initiated part-time work or work trial 6 months after commencement of intervention. Adherence and acceptability were overall good. Challenges of the intervention related to the person-centred follow-up, staff shortage and rootedness in the SCI team. Conclusions ReWork-SCI was feasible and can contribute to a systematic design of an individualised plan, facilitate decision-making and build trust in the RTW process after SCI. Core features of the intervention was the systematic structure, use of a person-centred approach and dialogue with the employer. For the effectiveness of ReWork-SCI, modifications and considerations of study design are needed

Analysis of linkage and linkage disequilibrium for eight X-STR markers

X-chromosomal short tandem repeats (X-STR) have proven to be informative and useful in complex relationship testing. Themain feature of X-STR markers, compared to autosomal forensicmarkers, is that all loci are located on the same chromosome. Thus, linkage and linkage disequilibrium may occur. The aim of this work was to study population genetic parameters of eight X-STR markers, located in four linkage groups. We present haplotype frequencies, based on 718 Swedish males, for the four linkage groups included in the Argus X-8 kit. Forensic efficiency parameters have been calculated as well as the allelic association between the tested markers for detection of linkage disequilibrium. To study the occurrences of recombination between the loci, both Swedish and Somali families were typed. A mathematical model for the estimation of recombination frequencies is presented and applied on the family samples. Our study showed that the tested markers all have highly informative forensic values and that there is a significant degree of linkage disequilibrium between the STR markers within the four linkage groups. Furthermore, based on the tested families, we also demonstrated that two of the linkage groups are partially linked. A consequence of these findings is that both linkage and linkage disequilibrium should be accounted for when producing likelihood ratios in relationship testing with XSTR markers

Distribution of the number of pairwise differences (in base pairs) for the target sequence among 334 mammal species.

<p>Distribution of the number of pairwise differences (in base pairs) for the target sequence among 334 mammal species.</p

Results from experiments with DNA samples from authentic forensic cases using the 454 deep sequencing method.

<p>The number of reads obtained after analyses of five samples from authentic forensic casework are presented. Case 1 was a sample taken from a human accused of animal cruelty and case 2 was four samples taken from a human corpse with multiple bite marks.</p

Distribution of the length (in base pairs) of the target sequence among 334 mammal species.

<p>Distribution of the length (in base pairs) of the target sequence among 334 mammal species.</p