The ReAct (Recovery, Activity) project is an ENFSI (European Network of Forensic Science Institutes) supported initiative comprising a large consortium of laboratories. Here, the results from more than 23 laboratories are presented. The primary purpose was to design experiments simulating typical casework circumstances; collect data and to implement Bayesian networks to assess the value (i.e., likelihood ratio) of DNA results given activity level propositions. Two different experimental designs were used to simulate a robbery, where a screwdriver was used to force a door or window. Propositions and case information were chosen following laboratory feedback listing typical casework circumstances (included in the paper). In a direct transfer experiment, the defendant owned and used the screwdriver, but he did not force the door/window in question. An unknown person used the defendant's stolen screwdriver. In an indirect transfer experiment, the defendant neither owned, saw, nor used the screwdriver, nor did they force the door or window. For the second experiment, given the defence view, the defendant never held the screwdriver. We envisaged the situation where an object manipulated by the defendant (or the defendant himself/herself) would be touched by the unknown offender who would then force the window. It was found for the direct transfer experiment that unless a single contributor profile aligning with the known person's of interest profile was retrieved, the results did not allow to discriminate between propositions. On the other hand, for the indirect transfer experiment, both single and major contributor profiles that aligned with the person of interest (POI) supported the proposition that the person used the tool rather than an unknown person who had touched an object, when indeed the former was true. There was considerable variation in median recoveries of DNA between laboratories (between 200pg-5ng) for a given experiment if quantities are taken into account. These differences affect the likelihood ratios given activity level propositions. More than 2700 samples were analysed in the course of this study. Two different Bayesian Networks are made available via an open source application written in Shiny R: Shiny_React(). For comparison, all datasets were analysed using a qualitative method categorised into absent, single, major or other given contributors. The importance of standardising methods is emphasised, alongside the necessity of developing new approaches to assign the probability of laboratory-dependent DNA recovery. Freely accessible open databases play a crucial role in supporting these efforts.
- MeSH
- Bayes Theorem * MeSH
- DNA Fingerprinting * MeSH
- DNA * genetics MeSH
- Laboratories * MeSH
- Humans MeSH
- Microsatellite Repeats MeSH
- Likelihood Functions MeSH
- Forensic Genetics methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
Verifying the speaker of a speech fragment can be crucial in attributing a crime to a suspect. The question can be addressed given disputed and reference speech material, adopting the recommended and scientifically accepted likelihood ratio framework for reporting evidential strength in court. In forensic practice, usually, auditory and acoustic analyses are performed to carry out such a verification task considering a diversity of features, such as language competence, pronunciation, or other linguistic features. Automated speaker comparison systems can also be used alongside those manual analyses. State-of-the-art automatic speaker comparison systems are based on deep neural networks that take acoustic features as input. Additional information, though, may be obtained from linguistic analysis. In this paper, we aim to answer if, when and how modern acoustic-based systems can be complemented by an authorship technique based on frequent words, within the likelihood ratio framework. We consider three different approaches to derive a combined likelihood ratio: using a support vector machine algorithm, fitting bivariate normal distributions, and passing the score of the acoustic system as additional input to the frequent-word analysis. We apply our method to the forensically relevant dataset FRIDA and the FISHER corpus, and we explore under which conditions fusion is valuable. We evaluate our results in terms of log likelihood ratio cost (Cllr) and equal error rate (EER). We show that fusion can be beneficial, especially in the case of intercepted phone calls with noise in the background.
- MeSH
- Speech Acoustics MeSH
- Algorithms MeSH
- Humans MeSH
- Linguistics MeSH
- Likelihood Functions MeSH
- Speech MeSH
- Forensic Sciences * methods MeSH
- Support Vector Machine MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
Objectives. This study aimed to assess the psychometric properties of the Czech adaptation of the Comprehensive Assessment of Acceptance and Commitment Therapy Processes (CompACT) questionnaire, which assesses three psychological flexibility processes consistent with the ACT Triflex. Participants. The data was collected from 299 participants (209 females, 87 males, and 3 other/did not specify) aged 18 to 70 years (M = 29.27, SD = 10.51). Statistical analyses. Confirmatory factor analysis (CFA) with a robust maximum likelihood estimation method was used to assess factor validity. Furthermore, the authors used structural equation modelling (SEM) to assess convergent, concurrent, and incremental validity. Finally, the authors used McDonald’s omega for the assessment of internal consistency. Results. The CFA showed that the original 23-item model did not fit the data well. Through a series of confirmatory factor analyses and modification indices, the authors found an alternative 17-item model. However, the model did not fit with the data acceptably. Moderate to high correlations (-.81 to -.54) between the latent factors of the 17-item CompACT and the Action and Acceptance Questionnaire-II (AAQ-II) indicate good convergent validity. Low to moderate correlations (-.64 to -.33) between the latent factors of the 17-item CompACT and a shorter version of the Depression Anxiety Stress Scale (DASS-21) and Satisfaction With Life Scale (SWLS) indicate acceptable concurrent validity. Partial regression coefficients of the CompACT latent factors were not alongside the AAQ-II questionnaire significant predictors of distress outcomes. Of the CompACT latent factors, only the Valued Actions subscale was a significant predictor of subjective well-being, indicating the poor incremental validity of CompACT over the AAQ-II. The questionnaire had good internal consistency, with McDonald’s omega ranging from .75 to .85.
BACKGROUND: We provide an overview of Bayesian estimation, hypothesis testing, and model-averaging and illustrate how they benefit parametric survival analysis. We contrast the Bayesian framework to the currently dominant frequentist approach and highlight advantages, such as seamless incorporation of historical data, continuous monitoring of evidence, and incorporating uncertainty about the true data generating process. METHODS: We illustrate the application of the outlined Bayesian approaches on an example data set, retrospective re-analyzing a colon cancer trial. We assess the performance of Bayesian parametric survival analysis and maximum likelihood survival models with AIC/BIC model selection in fixed-n and sequential designs with a simulation study. RESULTS: In the retrospective re-analysis of the example data set, the Bayesian framework provided evidence for the absence of a positive treatment effect of adding Cetuximab to FOLFOX6 regimen on disease-free survival in patients with resected stage III colon cancer. Furthermore, the Bayesian sequential analysis would have terminated the trial 10.3 months earlier than the standard frequentist analysis. In a simulation study with sequential designs, the Bayesian framework on average reached a decision in almost half the time required by the frequentist counterparts, while maintaining the same power, and an appropriate false-positive rate. Under model misspecification, the Bayesian framework resulted in higher false-negative rate compared to the frequentist counterparts, which resulted in a higher proportion of undecided trials. In fixed-n designs, the Bayesian framework showed slightly higher power, slightly elevated error rates, and lower bias and RMSE when estimating treatment effects in small samples. We found no noticeable differences for survival predictions. We have made the analytic approach readily available to other researchers in the RoBSA R package. CONCLUSIONS: The outlined Bayesian framework provides several benefits when applied to parametric survival analyses. It uses data more efficiently, is capable of considerably shortening the length of clinical trials, and provides a richer set of inferences.
- MeSH
- Bayes Theorem MeSH
- Humans MeSH
- Colonic Neoplasms * drug therapy MeSH
- Disease-Free Survival MeSH
- Retrospective Studies MeSH
- Research Design * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Specimens of Neoechinorhynchus (Neoechinorhynchus) poonchensis sp. n. are described from Schizothorax richardsonii (Gray) in the Poonch River, Jammu and Kashmir. Specimens are thick-walled with dissimilar dorsal and ventral para-receptacle structures, anteriorly manubriated hooks, two giant nuclei in each lemniscus and many subcutaneousy. The lemnisci barely overlap the larger anterior testis, the cement gland has eight giant nuclei, and the seminal vesicle is large with thin walls. The vagina is unremarkable but the long uterus is made up of four specialised regions. Neoechinorhynchus rigidus (Van Cleave, 1928), resembles N. poonchensis sp. n. It is distinguished from N. poonchensis sp. n. by having smaller trunk, proboscis, and male reproductive structures, equal testes, unequal lemnisci with three giant nuclei each, and much larger anterior proboscis hook (130 μm in males) than that originally described by Van Cleave (1928) (70 μm in a female). Anterior hook length alone is sufficient to conclude that the N. rigidus of Datta (1937) is not the same species as the N. rigidus of Van Cleave (1928). Van Cleave's (1928) species remains valid and that of Datta (1937) is considered a different species named Neoechinorhynchus pseudorigidus sp. n., herein. Micropores of N. poonchensis sp. n. have variable distribution in different trunk regions and the Energy Dispersive X-ray analysis demonstrated higher levels of sulfur and lower levels of calcium and phosphorus. Sequences of the 18S rDNA gene from nuclear DNA, and cytochrome c oxidase subunit I (cox1) from mitochondrial DNA of N. poonchensis sp. n. were amplified and aligned with other sequences available on GenBank. Maximum likelihood (ML) and Bayesian inference (BI) analyses inferred for 18S rDNA and cox1 showed that N. poonchensis sp. n. was nested in a separate clade.
- MeSH
- Acanthocephala * MeSH
- Bayes Theorem MeSH
- Cyprinidae * MeSH
- Helminthiasis, Animal * MeSH
- Fish Diseases * MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
The African continent has a rich diversity of fish and amphibians in its inland water systems that serve as hosts for monogeneans of seven genera of the Gyrodactylidae van Beneden et Hesse, 1832. In August 2011, eight gyrodactylid parasites were collected from the gills of two specimens of bulldog, Marcusenius macrolepidotus (Peters), from Lake Kariba, Zimbabwe. Morphometric evaluation and sequencing of 18S rDNA confirmed that the specimens represented a species of a new viviparous genus, Tresuncinidactylus wilmienae gen. et sp. n. The attachment apparatus consists of a single pair of large slender hamuli with prominently flattened roots that are connected by a simple, narrow dorsal bar. The ventral bar is small and possesses a thin lingulate membrane but no evident anterolateral processes. There are 16 marginal hooks of one morphological type, but of three different sizes, with large falculate sickles that are proportionaly equal in length to the length of their handles. The two largest pairs of marginal hooks are positioned closest to the opisthaptoral peduncle, the neighbouring two pairs of medium-sized marginal hook sickles are situated along the lateral margins of the opisthaptor. Four pairs of smallest marginal hooks are positioned along the posterior margin of the opisthaptor. The male copulatory organ consists of a muscular pouch armed with approximately 30 gracile spines. Phylogenetic analyses of partial sequences of the 18S rDNA using Maximum Likelihood and Bayesian Inference placed the new genus within the lineage of solely African genera and suggests Afrogyrodactylus Paperna, 1968, Citharodactylus Přikrylová, Shinn et Paladini, 2017 and Mormyrogyrodactylus Luus-Powell, Mashego et Khalil, 2003 as genera most closely related to the new genus.
A rod-shaped and Gram-stain-negative bacterial strain 9AT, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9AT belongs to the genus Hymenobacter and shows the highest similarity to Hymenobacter coccineus CCM 8649T (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9AT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth is observed at 0-20 °C (optimum 10 °C), pH 6.0-8.0 (optimum pH 7.0), and in the absence of NaCl. The predominant menaquinone of strain 9AT is MK-7 and the major fatty acids comprise Summed Feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 25.2 %), iso-C15 : 0 (23.2 %), C16 : 1 ω5c (11.6 %), Summed Feature 4 (anteiso-C17 : 1 B/iso-C17 : 1 I) (9.6 %) and anteiso-C15 : 0 (9.6 %). The polar lipid profile consists of the major lipid phosphatidylethanolamine and moderate to minor amounts of phosphatidylserine, unidentified aminolipids, aminophospholipids, aminophosphoglycolipids, polar lipids lacking a functional group and an unidentified phospholipid and a glycolipid. In the polyamine pattern sym-homospermidine is predominant. On the basis of the results obtained, strain 9AT is proposed as a novel species of the genus Hymenobacter, for which the name Hymenobacter caeli sp. nov. is suggested. The type strain is 9AT (=CCM 8971T=LMG 32109T=DSM 111653T).
- MeSH
- Bacteroidetes classification genetics isolation & purification MeSH
- DNA, Bacterial genetics MeSH
- Phylogeny MeSH
- Genome, Bacterial MeSH
- Air Microbiology * MeSH
- Islands * MeSH
- Likelihood Functions MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Base Composition MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Antarctic Regions MeSH
- Islands * MeSH
The bovine genes TLR1, TLR2 and TLR6, which encode Toll-like receptors, key components of the innate immune system, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle, and the different variants present in the population were tested for association with reproductive and fitness traits. Diversity was investigated in a group of 164 bulls using hybrid resequencing of pooled amplicons with PacBio technology and of pooled genomic DNA using HiSeq X-Ten technology. The validated single nucleotide polymorphisms (SNPs) were genotyped in individual animals using the primer extension technique. The association of genotypic classes of 16 polymorphisms with six phenotypic traits were estimated with one-way analysis of variance (ANOVA) and with restricted maximum likelihood (REML) algorithm. The evaluated traits included the incidence of cystic ovaries, index of early reproductive disorders, paternal and maternal indicators of calving ease, production longevity and calf vitality index. The estimated breeding values were used for combined trait quantification. Early traits, namely, cystic ovaries and early reproductive disorders, were not associated with any of the tested polymorphisms according to the general ANOVA test. By contrast, five variants of all three genes were associated with calving ease, both paternal and maternal. The production longevity correlated with two variants of TLR1 and the calf vitality index correlated with the 1044 T > C (rs68268249) polymorphism in TLR2. The false discovery rate (FDR) according to Benjamini-Hochberg was favourable for the calving ease trait (0.221) and maternal calving ease (0.214), which allows to consider the observed associations real, regardless of the error arising from the multiple comparisons. These results were supported by REML only partially, probably in view of the additivity assumption. Two mechanisms of action on calving are conceivable, either via infection resistance or via the involvement of TLR2 in signalling in the myometrium. The known formation of heterodimers by the TLR1, -2 and -6 products might be responsible for the shared pattern of action in these genes. The association of the calf vitality index with TLR2 variation might reflect the increased role of infections in calves compared to adult animals.
- MeSH
- Breeding MeSH
- Longevity genetics MeSH
- Phenotype MeSH
- Genotype MeSH
- Polymorphism, Single Nucleotide * MeSH
- Reproduction genetics MeSH
- Cattle genetics MeSH
- Toll-Like Receptor 1 genetics MeSH
- Toll-Like Receptor 2 genetics MeSH
- Toll-Like Receptor 6 genetics MeSH
- Toll-Like Receptors genetics MeSH
- Age Factors MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Cattle genetics MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Clonal growth of plants is attained by a number of morphologically different organs (e.g. stolons, rhizomes, and roots), which are not functionally equivalent. Consequently, these clonal growth organ (CGO) types can determine functional traits that are associated with clonality, although little is known about their evolutionary flexibility or the constraining role they play on clonal traits. We investigated the rates of evolutionary change by which individual CGOs are acquired and lost using a set of 2652 species of Central European flora. Furthermore, we asked how these individual CGOs constrain functionally relevant clonal traits, such as lateral spread, number of offspring, and persistence of connections. We show that plants can easily switch in evolution among individual types of CGO and between clonal and nonclonal habits. However, not all these transitions are equally probable. Namely, stem-based clonal growth and root-based clonal growth constitute evolutionarily separate forms of clonal growth. Clonal traits are strongly constrained by individual CGO types. Specifically, fast lateral spread is attained by stolons or hypogeogenous rhizomes, and persistent connections are attained by all rhizome types. However, the ease with which clonal organs appear and disappear in evolution implies that plants can overcome these constraints by adjusting their morphologies.
Morphological and molecular evaluation of tapeworms of the genus Bothriocephalus Rudolphi, 1808 (Cestoda: Bothriocephalidea), based on newly collected and uniformly fixed worms from freshwater fishes in Canada and the United States has revealed unexpected diversity. With a combination of selected morphological features and 4 molecular markers (18S rDNA V8 region, ITS1, ITS2, and COI gene sequences), the following morphotypes and lineages of the Bothriocephalus cuspidatus Cooper, 1917 complex were identified, several of which are specific to their respective fish definitive hosts and may represent separate species: B. cuspidatus sensu stricto from walleye, Sander vitreus (type host), which likely includes a miniature morphotype from Johnny darter, Etheostoma nigrum (both Percidae); Bothriocephalus morphotype from pumpkinseed, Lepomis gibbosus (Centrarchidae); and Bothriocephalus morphotype from rock bass, Ambloplites rupestris (Centrarchidae). The Bothriocephalus morphotype from goldeye, Hiodon alosoides (Hiodontidae), may also represent a separate lineage (possibly Bothriocephalus texomensisSelf, 1954) but requires additional studies. A morphotype from smallmouth bass, Micropterus dolomieu, based on a single specimen, is morphologically and genetically very similar to the morphotype from rock bass. Morphological study of the scolex and strobila of heat-killed and fixed specimens has revealed consistent differences, often subtle, that allowed us to differentiate between these morphotypes.
- MeSH
- Cestoda anatomy & histology genetics ultrastructure MeSH
- Cestode Infections parasitology veterinary MeSH
- Microscopy, Electron, Scanning veterinary MeSH
- Fish Diseases parasitology MeSH
- Perches parasitology MeSH
- Perciformes parasitology MeSH
- Likelihood Functions MeSH
- DNA, Ribosomal analysis chemistry MeSH
- RNA, Ribosomal, 18S genetics MeSH
- Fishes MeSH
- Base Sequence MeSH
- Sequence Alignment veterinary MeSH
- Fresh Water MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Canada MeSH
- United States MeSH
