Putative Cases Research Articles

Morphological differences between ‘Mangrove White-eye’ and montane Abyssinian White-eye (Zosterops abyssinicus arabs) in Arabia despite no differentiation in mitochondrial DNA: incipient speciation via niche divergence?

The Arabian population of the Abyssinian White-eye Zosterops abyssinicus arabs occurs in the Asir Mountains in southwest Saudi Arabia, the highlands of Yemen, and southwest Oman. In Saudi Arabia, a recently discovered, very small, and enigmatic population of white-eyes Zosterops sp. indet. occurs in stands of mature mangroves on the Kingdom’s southern Red Sea coast 80–100 km west of the nearest locality of Z. a. arabs in the Asir Mountains. We obtained biometric data and blood samples from individuals of both populations, in the Asir Mountains and the Red Sea mangroves, complemented by measurements from museum specimens from throughout the range of Z. a. arabs. The mangrove-dwelling white-eyes were found to differ in morphometrics and several plumage characters from montane Abyssinian White-eyes Z. a. arabs. However, no differences were revealed by one mitochondrial marker between four ‘Mangrove White-eyes’ and five Z. a. arabs from the Asir Mountains. ‘Mangrove White-eyes’ might thus represent the result of a recent colonization followed by niche divergence, and a putative case of incipient speciation in one of the fastest-radiating vertebrate lineages. A review of the scant available literature and our own surveys indicate that the ‘Mangrove White-eye’ is very scarce within a highly restricted and threatened range, and presumably at risk of extinction.

An outbreak of abortions, stillbirths and malformations in a Spanish sheep flock associated with a bovine viral diarrhoea virus 2-contaminated orf vaccine.

Bovine viral diarrhoea virus (BVDV) is a pestivirus that affects both cattle and sheep, causing an array of clinical signs, which include abortions and malformations in the offspring. Manufacturing of modified live virus (MLV) vaccines often includes the use of bovine-derived products, which implies a risk of contamination with viable BVDV. Recently, the circulation of a specific strain of BVDV2b among Spanish sheep flocks, associated with outbreaks of abortions and malformations, and whose origin was not determined, has been observed. On February 2018, a MLV orf vaccine was applied to a 1,600 highly prolific sheep flock in the Northeast of Spain that included 550 pregnant ewes. In May 2018, during the lambing season, an unusual high rate (72.7%) of abortions, stillbirths, congenital malformations and neurological signs in the offspring was observed. It was estimated that about 1,000 lambs were lost. Three 1- to 3-day-old affected lambs and a sealed vial of the applied vaccine were studied. Lambs showed variable degrees of central nervous system malformations and presence of pestiviral antigen in the brain. Molecular studies demonstrated the presence of exactly the same BVDV2b in the tissues of the three lambs and in the orf vaccine, thus pointing to a pestivirus contamination in the applied vaccine as the cause of the outbreak. Interestingly, sequencing at the 5'-untranslated region-(UTR) of the contaminating virus showed a complete match with the virus described in the previously reported outbreaks in Spain, thus indicating that the same contaminated vaccine could have also played a role in those cases. This communication provides a clear example of the effects of the application of this contaminated product in a sheep flock. The information presented here can be of interest in putative future cases of suspected circulation of this or other BVDV strains in ruminants.

Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity

The investigation on the genetic diversity of grapevine germplasm is crucial for a more efficient use of grapevine genetic resources in light of changing environmental conditions. Here, we used simple sequence repeats (SSRs) coupled with single nucleotide polymorphism (SNP) markers to disclose grapevine genetic diversity of a collection of Apulian minor/neglected genotypes. Their relationships with national or international cultivars were also examined. Genetic diversity was investigated using 10 SSR markers and 1,178 SNPs generated by genotyping by sequencing (GBS). Based on the SSR data, the 128 genotypes were classified into six main genetic clusters. Twenty-four putative cases of synonymy and 2 of misnamings were detected. Ten “unknown” autochthonous genotypes did not show high similarity to Apulian, national, or international varieties. We took advantage of available GBS-derived SNP data points for only forty genotypes to better investigate the genetic distance among them, identify private SNP alleles, and divergent loci putatively under selection. Based on SNP alleles, two interesting gene pools of minor/neglected Apulian samples were identified. Genetic divergence was investigated by FST and allowed the detection of loci capable of differentiating the gene pools. Overall, this work emphasizes the need for recovering the untapped genetic variability that characterizes minor/neglected grapevine Apulian genotypes and the requirement to preserve and use more efficiently grapevine genetic resources in breeding programs.

The role of head shape and trophic variation in the diversification of the genus Herichthys in sympatry and allopatry

In the present study we evaluate the putative cases of sympatric speciation in the genus Herichthys by studying the variation of the head shape using principal component analysis, phylomorphospace and reconstructions of the ancestral states of feeding preferences. Herichthys includes both allopatric as well as sympatric sister-species, as well as sympatric unrelated species and offers thus great potential for evolutionary studies of putatively sympatric speciation. Herichthys is the northernmost group of cichlids in America and one of the most ecologically disparate genera within Middle American cichlids. Fifteen anatomical points were recorded on the heads of 293 specimens of the 11 species recognized within the genus. The results showed that in spite of having wide variation in consumed diets, most species of Herichthys are close in morphospace. However, morphological variation was great among the two pairs of sympatric sister species in agreement with the suggested sympatric model of speciation. This article is protected by copyright. All rights reserved.

Colour Relations in Black and White

I argue that it is possible to perceptually represent colour relations between two objects, without perceptually representing their colours. Such primitive relational colour representation (PRCR) goes against the orthodox view that we represent colour relations by virtue of representing colours. I first argue that under certain assumptions, PRCR is conceptually and even nomically possible. I then compare two possible models of PRCR: the linguaform model and chromatic edge model, the latter involving iconic rather than discursive representation. I argue that the chromatic edge model gives a better account of putative cases of PRCR in cerebral achromatopsia, a rare disorder of colour consciousness.

Putative Equine Neorickettsiosis in a Mare from Southern Brazil

Background: This report describes the occurrence of equine neorickettsiosis (EN) in the northern region of Paraná, southern Brazil. EN is a non-contagious infectious disease caused by the Gram-negative bacterium, Neorickettsia risticii. Equine neorickettsiosis was previously known as Potomac horse fever and monocytic ehrlichiosis. The disease occurs predominantly in the USA and Canada; data relative to EN in Brazil is scarce. The aim of this study was to report the first case of putative EN in the state of Paraná due to a combination of IHC and molecular testing.Case: A 2-year-old Quarter Horse was referred to a Veterinary Hospital with episodes of abdominal discomfort, fever, anorexia, tachycardia, and tachypnea. The animal reportedly demonstrated episodes of blackened and fetid diarrhea after the ingestion of hay. A treatment was established upon arrival at the veterinary hospital, but the mare died after 12 hours of monitoring. An autopsy examination performed soon after death revealed severe hyperemia of the mucosa of the cecum and colon, with multifocal cecal erosions and ulcerations. The principal histological lesion observed was necrotizing enterocolitis. Additional significant histopathologic lesions included widespread lymphoid depletion affecting the spleen, tonsils, and lymph nodes. An IHC assay designed to identify the antigens of N. helminthoeca (NH) in formalin fixed paraffin embedded (FFPE) tissues, identified antigens of intralesional neorickettsial organisms within macrophages of the mucosa of the colon. Additionally, a PCR assay designed to amplify the 16S rRNA gene of Neorickettsia, amplified the desired amplicon, but sequencing was frustrating.Discussion: A putative diagnosis of equine neorickettsiosis was established due to the combination of epidemiological evidence, pathologic findings, immunohistochemical identification of intralesional antigens of neorickettsial agents, and amplification of the 16S gene of Neorickettsia spp. by PCR. The gross and microscopic lesions described must be differentiated from lesions observed in equine salmonellosis and Clostridium difficile associated disease of horses. IHC was performed on FFPE intestinal tissue using an anti-NH hyperimmune serum as primary antibody due to high antigenic cross-reactivity between Neorickettsia spp. There was positive intracytoplasmic immunolabeling of macrophages in the mucosa of the large colon indicating the presence of neorickettsial antigens. The PCR amplified the desired amplicon from the colon fragment, but sequencing was frustrating due to poor quality product that resulted in an organism consistent with Methylobacterium spp., probably, a contaminant. EN show a seasonal and endemic tendency in USA, Uruguay and in southern Brazil, occurring in warmer months, as in the case reported. Evidence suggests that an ancient disease named “churrido” known for at least 100 years in southern Brazil and Uruguay is, in fact, equine neorickettsiosis and might have been introduced to North America from South America. Considering the epidemiological evidence and the worldwide distribution of NR, we suggest that EN is probably underdiagnosed in Brazil and that the etiology of equine enterocolitis should be more thoroughly investigated. Therefore, this report broadens the knowledge of EN in our region. In conclusion, considering the epidemiologic, pathologic, immunohistochemical and molecular evidence, and the specie-specificity of Neorickettsia spp., we report a putative case of EN in southern Brazil and the first report in Paraná state. IHC is a useful technique, less technically demanding and time consuming than bacterial culture and isolation, considered the gold standard; and can be used to diagnose EN when compatible pathologic evidence is present concomitantly.

Episodic memory in nonhuman animals?

Experimental psychologist Jonathan Crystal and evolutionary psychologist Thomas Suddendorf debate with nonhuman animals experience human-like episodic memory.

Object files and unconscious perception: a reply to Quilty-Dunn

Abstract A wealth of cases – most notably blindsight and priming under inattention or suppression – have convinced philosophers and scientists alike that perception occurs outside awareness. In recent work (Phillips 2016a, 2018; Phillips and Block 2017, Peters et al. 2017), I dispute this consensus, arguing that any putative case of unconscious perception faces a dilemma. The dilemma divides over how absence of awareness is established. If subjective reports are used, we face the problem of the criterion: the concern that such reports underestimate conscious experience (Eriksen 1960, Holender 1986, Peters and Lau 2015). If objective measures are used, we face the problem of attribution: the concern that the case does not involve genuine individual-level perception. Quilty-Dunn (2019) presents an apparently compelling example of unconscious perception due to Mitroff et al. (2005) which, he contends, evades this dilemma. The case is fascinating. However, as I here argue, it does not escape the dilemma’s clutches.

Dissimilar molecular and morphological patterns in an introgressed peripheral population of a sand dune species (Armeria pungens, Plumbaginaceae).

Introgression is a poorly understood evolutionary outcome of hybridisation because it may remain largely undetected whenever it involves the transfer of small parts of the genome from one species to another. Aiming to understand the early stages of this process, a putative case from the southernmost border of the Armeria pungens range from its congener A.macrophylla is revisited following the discovery of a subpopulation that does not show phenotypic signs of introgression and resembles typical A.pungens. We analysed morphometrics, nuclear ribosomal DNA ITS and plastid DNA (trnL-trnF) sequences, genome size, 45S and 5S rDNA loci-FISH data and nrDNA IGS sequences. Within the study site, most individuals match morphologies of either of the two hybridising species, particularly the new subpopulation, with intermediate phenotypes being scarce. This pattern does not fully fit molecular evidence revealing two ITS ribotypes co-occurring intragenomically in most plants from the study site and one single plastid haplotype. Genome size and structural features of the IGS sequences both indicate that A.pungens from the study site is genetically more similar to its sympatric congener than to the remainder of its conspecifics. Introgression of A.macrophylla into A.pungens and plastid capture explain all the evidence analysed. However, important features to understand the origin and fate of the introgressed population, such as the degree and direction of introgression, which are important for understanding early stages of hybridisation in plants with low reproductive barriers, should be addressed with new data.

The racing pigeon (Columba livia domestica) industry in Victoria, Australia, and epidemiology of a novel Group A rotavirus outbreak.

A novel Group A rotavirus, first identified clinically in racing, feral and fancy pigeons in Western Australia, had spread throughout Australia by March 2017. In December 2016, the putative index case of rotavirus in racing pigeons in the state of Victoria was confirmed at a regional bird sale, with rapid spread to peri-urban Melbourne, the capital city. A survey sent to approximately 400 Victorian pigeon fanciers identified eight (of 85 respondents) with a confirmed rotavirus infection in their loft(s). If a fancier had purchased live birds, either from the regional sale or from another source, there was a 13%-38% increased likelihood of the loft subsequently being confirmed rotavirus-positive. An increased loft-level risk of rotavirus was also positively associated with the number of neighbouring lofts within a 5-km radius of a home loft. It was concluded that rotavirus was primarily transmitted beyond the Victorian index case through the movement of live birds into a loft, either deliberately through bird purchase and/or inadvertently through the entry of pigeons from neighbouring lofts. As pigeon racing inherently requires consistent contact between birds from different lofts, vaccination is recommended as a primary method of rotavirus control in this unique industry.

Population genomics perspectives on convergent adaptation.

Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide an independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information owing to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew

BackgroundAs the genomes of more metazoan species are sequenced, reports of horizontal transposon transfers (HTT) have increased. Our understanding of the mechanisms of such events is at an early stage. The close physical relationship between a parasite and its host could facilitate horizontal transfer. To date, two studies have identified horizontal transfer of RTEs, a class of retrotransposable elements, involving parasites: ticks might act as vector for BovB between ruminants and squamates, and AviRTE was transferred between birds and parasitic nematodes.ResultsWe searched for RTEs shared between nematode and mammalian genomes. Given their physical proximity, it was necessary to detect and remove sequence contamination from the genome datasets, which would otherwise distort the signal of horizontal transfer. We developed an approach that is based on reads instead of genomic sequences to reliably detect contamination. From comparison of 43 RTEs across 197 genomes, we identified a single putative case of horizontal transfer: we detected RTE1_Sar from Sorex araneus, the common shrew, in parasitic nematodes. From the taxonomic distribution and evolutionary analysis, we show that RTE1_Sar was horizontally transferred.ConclusionWe identified a new horizontal RTE transfer in host-parasite interactions, which suggests that it is not uncommon. Further, we present and provide the workflow a read-based method to distinguish between contamination and horizontal transfer.

Varieties of Cognitive Integration

AbstractExtended cognition theorists argue that cognitive processes constitutively depend on resources that are neither organically composed, nor located inside the bodily boundaries of the agent, provided certain conditions on the integration of those processes into the agent's cognitive architecture are met. Epistemologists, however, worry that in so far as such cognitively integrated processes are epistemically relevant, agents could thus come to enjoy an untoward explosion of knowledge. This paper develops and defends an approach to cognitive integration—cluster‐model functionalism—which finds application in both domains of inquiry, and which meets the challenge posed by putative cases of cognitive or epistemic bloat.

TRUST Untruthfulness Framework in Forensic Contexts

This article introduces a comprehensive linguistic-ethical framework for analysing untruthfulness in situated discourse, as developed in much more depth in Heffer (in press). The TRUST (Trust-Related Untruthfulness in Situated Text) framework extends the analysis of insincerity beyond lying to misleading and withholding. More radically, it extends our conception of untruthfulness to include not only insincerity but also epistemic irresponsibility, or not taking care in establishing and conveying the evidence. The TRUST heuristic then provides a practical procedure for analysing putative cases of untruthfulness in situated discourse. This heuristic is then applied to two cases of putative untruthfulness in the legal process: the Bronston perjury case in the US and the Iraq Inquiry in the UK.

Branching Is Not a Bug; It’s a Feature: Personal Identity and Legal (and Moral) Responsibility

Prospective developments in computer and nanotechnology suggest that there is some possibility—perhaps as early as this century—that we will have the technological means to attempt to duplicate people. For example, it has been speculated that the psychology of individuals might be emulated on a computer platform to create a personality duplicate—an “upload.” Physical duplicates might be created by advanced nanobots tasked with creating molecule-for-molecule copies of individuals. Such possibilities are discussed in the philosophical literature as (putative) cases of “fission”: one person “splitting” into two. Many philosophers, perhaps most, reject the idea of fission, appealing to some form of a “no-branching” condition to rule out such possibilities. I argue, to the contrary, that there are good moral reasons to think that any account of personal identity that does not permit fission is deeply problematic, especially in connection with theorizing about criminal punishment. I discuss and reject David Lewis’ famous account of personal identity that invokes “multiple occupancy” to allow for branching. In contrast, I offer an account of personal identity that permits branching using the type/token distinction to help with such puzzling cases.

Lynch-like syndrome is as frequent as Lynch syndrome in early-onset nonfamilial nonpolyposis colorectal cancer.

Early-onset (<50 years-old) nonpolyposis nonfamilial colorectal cancer (EO NP NF CRC) is a common clinical challenge. Although Lynch syndrome (LS) is associated with EO CRC, the frequency of this syndrome in the EO NF cases remains unknown. Besides, mismatch repair deficient (MMRd) CRCs with negative MMR gene testing have recently been described in up to 60% of cases and termed "Lynch-like syndrome" (LLS). Management and counseling decisions of these patients are complicated because of unconfirmed suspicions of hereditary cancer. To define the prevalence of MMR deficient CRCs, LS and LLS in patients with EO NP NF CRC, we recruited 102 patients with a first diagnosis of NP NF CRC ≤ 50 years old during 2003-2009 who underwent genetic counseling at our institution in Argentina. Tumor immunohistochemical (IHC) MMR for protein expression and microsatellite instability (MSI) status were evaluated, and in those with loss of MLH1 expression by IHC, somatic BRAF V600E mutation and both somatic and germline MLH1 methylation levels were studied. Tumors characterized as MMRd without somatic BRAF mutation nor MLH1 methylation were sent for germline analysis. Twenty one (20.6%) tumors were MMRd. Fourteen of 16 putative LS cases underwent germline testing: 6 pathogenic mutations were identified and 8 cases had no identifiable pathogenic mutations. The prevalence of LS and LLS in this cohort was 5.8% (6/102) and 7.8% (8/102), respectively. As a conclusion we found that 20% of patients with EO NP NF CRC have MMRd tumors, and at least half of these are likely to have LLS.

Peripheral Odontogenic Myxoma: Report of Two New Cases with a Critical Review of the Literature

Introduction: Odontogenic myxoma is a benign mesenchymal odontogenic tumor that is more frequently found in the mandibular molar region. The extra-osseous counterpart, called Peripheral Odontogenic Myxoma (POM), is an exceedingly rare entity and with very low aggressive potential. Methods: Clinical and radiographic findings are not specific, and difficulties may exist in differentiating histological findings of POM from other tumors with myxoid features, such as fibromas and oral focal mucinosis. Due to the fact that the presence of odontogenic epithelium is not required for the diagnosis, a myxoid lesion without odontogenic nests that develops in extraosseous position can be misdiagnosed with a soft tissue myxoma. Case Reports: We thereby present two cases of POM and conduct an extensive and critical review of the English literature, taking into consideration both certain and putative cases of POM.

Why the evolution of vaccine resistance is less of a concern than the evolution of drug resistance

Vaccines and antimicrobial drugs both impose strong selection for resistance. Yet only drug resistance is a major challenge for 21st century medicine. Why is drug resistance ubiquitous and not vaccine resistance? Part of the answer is that vaccine resistance is far less likely to evolve than drug resistance. But what happens when vaccine resistance does evolve? We review six putative cases. We find that in contrast to drug resistance, vaccine resistance is harder to detect and harder to confirm and that the mechanistic basis is less well understood. Nevertheless, in the cases we examined, the pronounced health benefits associated with vaccination have largely been sustained. Thus, we contend that vaccine resistance is less of a concern than drug resistance because it is less likely to evolve and when it does, it is less harmful to human and animal health and well-being. Studies of pathogen strains that evolve the capacity to replicate and transmit from vaccinated hosts will enhance our ability to develop next-generation vaccines that minimize the risk of harmful pathogen evolution.

The performance of the European League Against Rheumatism/American College of Rheumatology idiopathic inflammatory myopathies classification criteria in an expert-defined 10 year incident cohort.

ObjectivesTo assess the performance of the EULAR/ACR idiopathic inflammatory myopathies (IIMs) classification criteria in a cohort of incident IIM cases and examine how criteria-assigned IIM subtype correlates with expert opinion.MethodsAdults with newly diagnosed IIM attending Salford Royal NHS Foundation Trust were identified over a 10 year period. A retrospective review of all putative cases was performed and those fulfilling a consensus expert opinion diagnosis of IIM were included. Clinical, serological and histological data were collected and each case was assigned a single IIM subtype. The EULAR/ACR classification criteria were then applied and sensitivity, specificity and positive and negative predictive values were calculated, presented with 95% CIs.ResultsA total of 1637 cases were screened, with 255 consensus expert opinion IIM cases ultimately identified. Applying the EULAR/ACR classification criteria, the sensitivity to diagnose an IIM was 99.6% (95% CI 97.2, 100) and 80.9% (95% CI 76.0, 85.8) for the criteria cut-points of probable and definite diagnoses, respectively. In 94/255 cases the IIM subtype differed between consensus expert opinion and classification criteria, most strikingly in the group subtyped as PM by the EULAR/ACR criteria, where there was discrepancy in the majority (i.e. in 87/161).ConclusionThe EULAR/ACR criteria performed with high sensitivity in identifying IIM in this external cohort of incident IIM. However, substantial disagreements arose between consensus expert opinion and the criteria regarding IIM subtype assignments, resulting in a large proportion of criteria-assigned cases of PM having heterogeneous features. These results may have important implications for future use of these criteria in subsequent research.

The Practical and Experiential Reality of Racism: Carter’s and Corlett’s Realism About Race and Racism

This paper examines the practical reality and experience of racism from the “internal point of view” of blacks who suffer racism and white racists. It uses this point of view to critically examine Carter’s and Corlett’s views regarding realism about race and racism. They suggest that theories must inquire about race and racism as categories for understanding the way-things-really-are. I argue that a plausible idea of racism, as a thick concept, must not be subservient to public policy. Rather, public policy must reflect experiential reality of racism. I argue that the views of Corlett and Carter, which tie racism to human agency, have heuristic value. However, they are too narrow; they have problematic implications, and do not sufficiently capture many putative cases and common usage of race and experience of racism.