The role of causes in action explanations: Two competing approaches.

The thesis deals with the question of whether causation can play a (relevant) part in the explanation of action; it approaches it through the critical assessment of two paradigmatic theories of action, one of each side of the debate. In the first part D. Davidson's Causal Theory of Action is presented (as a development of the Causal Nomological Theory), and criticised on the grounds that it cannot provide adequate singular causal explanations of actions. The argument questions Davidson's model by challenging the way in which Davidson could justify the causal relevance of reasons. It concludes that the causal condition adds no additional explanatory force on non-causal rationalisations. In the second part, the nature of action explanations is examined through von Wright's non-causal approach. After presentation of his theory, his version of the Logical Connection Argument is considered in the light of various criticisms that have been directed against it. Although his argument is found to be inconclusive with respect to the impossibility of a Causal Theory of Action, it is argued that, the implications that follow from von Wright's discussion of it, render the causal claim irrelevant to the explanation of action. Finally von Wright's possible response to two types of criticism, is considered: The justification Vs explanation argument and the problem of congruence. The conclusion is that his theory deals in a satisfactory way with the first one, but fails to meet the challenge of the second one

Utjecaj vrste na kakvoću komercijalnih fileta puževa

Research background. This study fulfils a need for investigation of a quality profile of snail fillets. Edible snails are a famous food product consumed worldwide and treated as delicacy. Nutritional value, colour and textural properties, such as hardness, are critical factors that impact consumer acceptance of the product. Hardness of snail meat is affected by its native original microstructure. Experimental approach. Fresh snails of the farmed species Cornu aspersum maximum, wild and farmed Cornu aspersum aspersum and wild Helix lucorum were used in order to investigate the qualitative profile of snail meat. Proximate composition, hardness and colour measurements were conducted on fillets of all species. The histological structure of the fillets of Cornu aspersum maximum was examined. Results and conclusions. Quality parameters of snail fillets were studied. A novel method of hardness analysis was proposed where the cylindrical part of snail fillets from the mid-posterior region with specific geometry 6 mm diameter and 6 mm height was used. The suitability of the mid-posterior region was enhanced by the uniform structure confirmed by the histological analysis. Helix lucorum snail fillet had the highest energy content and the highest hardness but the lowest carbohydrate content. The species Cornu aspersum maximum was evaluated with the highest values of a* (redness), b* (yellowness) and C* (chroma) compared to other species. Parameter L* (lightness) of wild snail fillets was lower than of the farmed ones due to age, diet, farming or environmental conditions, but it could also be related to snail carbohydrate content. Novelty and scientific contribution. This study yielded notable results on qualitative characteristics of snail fillets as food and important information is given on its meat properties. Furthermore, a novel methodology of hardness is provided in order to minimize natural, breeding and environmental influences. Finally, the research outcomes could lead to proper handling methods for further fabrication of snail meat.Pozadina istraživanja. Ovaj rad dopunjava istraživanje o kakvoći fileta puževa. Jestivi su puževi poznati prehrambeni proizvod širom svijeta i smatraju se delikatesom. Hranjiva vrijednost, boja i teksturalna svojstva, poput tvrdoće, bitni su čimbenici koji utječu na prihvatljivost proizvoda. Prirodna mikrostruktura utječe na čvrstoću mesa puževa. Eksperimentalni pristup. Za ispitivanje kakvoće mesa korišteni su svježi uzorci uzgojene vrste puža Cornu aspersum maximum, divlje i uzgojene vrste Cornu aspersum aspersum i divlje vrste Helix lucorum. Ispitani su kemijski sastav, tvrdoća i boja svih uzoraka puževa, te struktura tkiva fileta vrste Cornu aspersum maximum. Rezultati i zaključci. Ispitana je kakvoća fileta puževa i predložena nova metoda analize tvrdoće na cilindričnim uzorcima izrezanim iz sredine stražnjeg dijela fileta, promjera 6 mm i visine 6 mm. Histološka je analiza potvrdila da je taj dio fileta najprikladniji za analizu zbog svoje ujednačene strukture. Fileti vrste Helix lucorum imali su najveću energetsku vrijednost i tvrdoću, a najmanji udjel ugljikohidrata. Uzorci vrste Cornu aspersum maximum imali su najveće vrijednosti boje a* (crvena komponenta), b* (žuta komponenta) i C* (intenzitet obojenja). Vrijednost svjetloće L* uzoraka fileta divljih puževa bila je manja od one uzgojenih zbog starosti, prehrane te uvjeta uzgoja i okoliša, ali vjerojatno i zbog manjeg udjela ugljikohidrata. Novina i znanstveni doprinos. U ovom su radu izneseni važni rezultati ispitivanja kakvoće fileta puževa i dane bitne informacije o svojstvima mesa. Osim toga, prikazana je nova metoda analize tvrdoće, koja smanjuje utjecaj uzgoja i okoliša na rezultate ispitivanja. Rezultati istraživanja mogu pridonijeti pravilnom rukovanju pri uzgoju puževa

Porcine endogenous retroviruses PERV A and A/C recombinant are insensitive to a range of divergent mammalian TRIM5 proteins including human TRIM5

The potential risk of cross-species transmission of porcine endogenous retroviruses (PERV) to humans has slowed the development of xenotransplantation, using pigs as organ donors. Here, we show that PERVs are insensitive to restriction by divergent TRIM5{alpha} molecules despite the fact that they strongly restrict a variety of divergent lentiviruses. We also show that the human PERV A/C recombinant clone 14/220 reverse transcribes with increased efficiency in human cells, leading to significantly higher infectivity. We conclude that xenotransplantation studies should consider the danger of highly infectious TRIM5{alpha}-insensitive human-tropic PERV recombinants

Assisted evolution enables HIV-1 to overcome a high trim5α-imposed genetic barrier to rhesus macaque tropism

Diversification of antiretroviral factors during host evolution has erected formidable barriers to cross-species retrovirus transmission. This phenomenon likely protects humans from infection by many modern retroviruses, but it has also impaired the development of primate models of HIV-1 infection. Indeed, rhesus macaques are resistant to HIV-1, in part due to restriction imposed by the TRIM5α protein (rhTRIM5α). Initially, we attempted to derive rhTRIM5α-resistant HIV-1 strains using two strategies. First, HIV-1 was passaged in engineered human cells expressing rhTRIM5α. Second, a library of randomly mutagenized capsid protein (CA) sequences was screened for mutations that reduced rhTRIM5α sensitivity. Both approaches identified several individual mutations in CA that reduced rhTRIM5α sensitivity. However, neither approach yielded mutants that were fully resistant, perhaps because the locations of the mutations suggested that TRIM5α recognizes multiple determinants on the capsid surface. Moreover, even though additive effects of various CA mutations on HIV-1 resistance to rhTRIM5α were observed, combinations that gave full resistance were highly detrimental to fitness. Therefore, we employed an 'assisted evolution' approach in which individual CA mutations that reduced rhTRIM5α sensitivity without fitness penalties were randomly assorted in a library of viral clones containing synthetic CA sequences. Subsequent passage of the viral library in rhTRIM5α-expressing cells resulted in the selection of individual viral species that were fully fit and resistant to rhTRIM5α. These viruses encoded combinations of five mutations in CA that conferred complete or near complete resistance to the disruptive effects of rhTRIM5α on incoming viral cores, by abolishing recognition of the viral capsid. Importantly, HIV-1 variants encoding these CA substitutions and SIVmac239 Vif replicated efficiently in primary rhesus macaque lymphocytes. These findings demonstrate that rhTRIM5α is difficult to but not impossible to evade, and doing so should facilitate the development of primate models of HIV-1 infection

Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies [preprint]

Antibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on the properties of SARS-CoV-2 spike receptor-binding domain (RBD)-specific antibodies, we analyzed six independent antibody lineages. As well as increased neutralization potency, antibody evolution changed pathways for acquisition of resistance and, in some cases, restricted the range of neutralization escape options. For some antibodies, maturation apparently imposed a requirement for multiple spike mutations to enable escape. For certain antibody lineages, maturation enabled neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses

A facile quantitative assay for viral particle genesis reveals cooperativity in virion assembly and saturation of an antiviral protein

Conventional assays of viral particle assembly and release are time consuming and laborious. We have developed an enzymatic virus-like particle (VLP) genesis assay that rapid and quantitative and is also versatile and applicable to diverse viruses including HIV-1 and Ebola virus. Using this assay, which has a dynamic range of several orders of magnitude, we show that the efficiency of VLP assembly and release, i.e., the fraction of the expressed protein that is assembled into extracellular particles, is dependent on the absolute level of expression of either HIV-1 Gag or Ebola virus VP40. We also demonstrate that the activity of the antiviral factor tetherin is dependent on the level of HIV-1 Gag expression and the numbers of VLPs generated, and appears to become saturated as these parameters are increased

Species-Specific Activity of HIV-1 Vpu and Positive Selection of Tetherin Transmembrane Domain Variants

Tetherin/BST-2/CD317 is a recently identified antiviral protein that blocks the release of nascent retrovirus, and other virus, particles from infected cells. An HIV-1 accessory protein, Vpu, acts as an antagonist of tetherin. Here, we show that positive selection is evident in primate tetherin sequences and that HIV-1 Vpu appears to have specifically adapted to antagonize variants of tetherin found in humans and chimpanzees. Tetherin variants found in rhesus macaques (rh), African green monkeys (agm) and mice were able to inhibit HIV-1 particle release, but were resistant to antagonism by HIV-1 Vpu. Notably, reciprocal exchange of transmembrane domains between human and monkey tetherins conferred sensitivity and resistance to Vpu, identifying this protein domain as a critical determinant of Vpu function. Indeed, differences between hu-tetherin and rh-tetherin at several positions in the transmembrane domain affected sensitivity to antagonism by Vpu. Two alterations in the hu-tetherin transmembrane domain, that correspond to differences found in rh- and agm-tetherin proteins, were sufficient to render hu-tetherin completely resistant to HIV-1 Vpu. Interestingly, transmembrane and cytoplasmic domain sequences in primate tetherins exhibit variation at numerous codons that is likely the result of positive selection, and some of these changes coincide with determinants of HIV-1 Vpu sensitivity. Overall, these data indicate that tetherin could impose a barrier to viral zoonosis as a consequence of positive selection that has been driven by ancient viral antagonists, and that the HIV-1 Vpu protein has specialized to target the transmembrane domains found in human/chimpanzee tetherin proteins

Evaluation of SARS-CoV-2 antibody point of care devices in the laboratory and clinical setting

SARS-CoV-2 antibody tests have been marketed to diagnose previous SARS-CoV-2 infection and as a test of immune status. There is a lack of evidence on the performance and clinical utility of these tests. We aimed to carry out an evaluation of 14 point of care (POC) SARS-CoV-2 antibody tests. Serum from participants with previous RT-PCR (real-time polymerase chain reaction) confirmed SARS-CoV-2 infection and pre-pandemic serum controls were used to determine specificity and sensitivity of each POC device. Changes in sensitivity with increasing time from infection were determined on a cohort of study participants. Corresponding neutralising antibody status was measured to establish whether the detection of antibodies by the POC device correlated with immune status. Paired capillary and serum samples were collected to ascertain whether POC devices performed comparably on capillary samples. Sensitivity and specificity varied between the POC devices and in general did not meet the manufacturers’ reported performance characteristics, which signifies the importance of independent evaluation of these tests. The sensitivity peaked at ≥20 days following onset of symptoms, however sensitivity of 3 of the POC devices evaluated at extended time points showed that sensitivity declined with time. This was particularly marked at >140 days post infection. This is relevant if the tests are to be used for sero-prevalence studies. Neutralising antibody data showed that positive antibody results on POC devices did not necessarily confer high neutralising antibody titres, and that these POC devices cannot be used to determine immune status to the SARS-CoV-2 virus. Comparison of paired serum and capillary results showed that there was a decline in sensitivity using capillary blood. This has implications in the utility of the tests as they are designed to be used on capillary blood by the general population

Comparison of SARS-CoV-2 serological assays for use in epidemiological surveillance in Scotland

Background: Sero-surveillance of SARS-CoV-2 is crucial to monitoring levels of population exposure and informing public health responses, but may be influenced by variability in performance between available assays. Methods: Five commercial immunoassays and a neutralising activity assay were used to detect antibodies to SARS-CoV-2 in routine primary care and paediatric samples collected during the first wave of the pandemic in NHS Lothian, Scotland as part of ongoing surveillance efforts. For each assay, sensitivity and specificity was calculated relative to consensus results (majority of immunoassays positive = overall positive) and neutralising activity. Quantitative correlation was performed between serological and neutralising titres. Results: Seroprevalence ranged from 3.4–7.3 % in primary care patients and 3–5.9 % in paediatric patients according to different immunoassays. Neutralising activity was detectable in 2.8 % and 1.3 % respectively. Relative assay performance changed depending on comparison to immunoassay consensus versus neutralising activity and qualititative versus quantitative agreement. Cross-reactivity with endemic seasonal coronaviruses was confirmed by neutralising assay in false positives for one immunoassay. Presence of false positives for another assay was found specifically in paediatric but not adult samples. Conclusions: Five serological assays show variable accuracy when applied to the general population, impacting seroprevalence estimates. Assay performance may also vary in detection of protective neutralising antibody levels. These aspects should be considered in assay selection and interpretation in epidemiological studies