Why genes overlap in viruses

The genomes of most virus species have overlapping genes\u2014two or more proteins coded for by the same nucleotide sequence. Several explanations have been proposed for the evolution of this phenomenon, and we test these by comparing the amount of gene overlap in all known virus species. We conclude that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length. However, we do find a negative relationship between overlap proportion and genome length among viruses with icosahedral capsids, but not among those with other capsid types that we consider easier to enlarge in size. Our interpretation is that a physical constraint on genome length by the capsid has led to gene overlap evolving as a mechanism for producing more proteins from the same genome length. We consider that these patterns cannot be explained by other factors, namely the possible roles of overlap in transcription regulation, generating more divergent proteins and the relationship between gene length and genome length

Does Culture affect Consumer Behaviour, when shopping On-Line?

Abstract. On-line retailers have to decide whether to standardize or adapt their marketing strategy to the foreign consumer markets. The objective of this article is not only to locate differences in on-line shopping behavior between English, Italian, and Chinese consumers, but also to explain these differences, through cultural dimensions. A discriminant analysis was conducted on English, Italian and Chinese consumers, based on eighteen behavioral variables, to illustrate the effect that a change of culture would have on a consumer’s on-line shopping behavior. The behavioral variables were classified in a descending lexicographic order of their discriminating power, between these cultures. After running the discriminant analysis, a factorial analysis of the eighteen behavioral describers was also run, to organize the latter into a smaller number of factors that are mutually exclusive, and very exhaustive. Factorial analysis identified five distinct factors that point out differences between the three countries, underlining that on-line retailers cannot duplicate abroad their home marketing strategy, because the needs e-shoppers wish to fulfill diverge between these markets

The relation between the minor chlorophyll spectral forms and fluorescence quenching in aggregated light harvesting chlorophyll a b complex II

The hypothesis that fluorescence quenching in aggregated light harvesting chlorophyll a/b protein complex II is associated with the formation of minor spectral forms absorbing near 655 nm and between 680 nm-690 nm is examined. Using an homogeneous LHCII preparation, steady-state absorption changes measured at room temperature are quantitatively compared with the associated steady state fluorescence changes by means of the Stepanov relation. It is demonstrated that upon LHCII aggregation, the relative fluorescence yield is constant for chlorophyll forms absorbing between 650 nm and 690 nm. This indicates that the minor chlorophyll forms formed upon LHCII aggregation are not quenching species

Legal geographies of irregular migration : An outlook on immigration detention

In this article, I discuss legal geographies of irregular migration, drawing on a case study on immigration detention in Finland. Based on analysis of detention records, four different types of legal geographies are identified, relating to south–north movement of third‐country nationals inside Europe, criminalised Eastern European EU citizens, irregularity during the asylum process (in particular, related to the Dublin Regulation) and irregularly residing foreign nationals, including deportable long‐term residents. The analysis focuses on the relations between space, law and persons during detainees' irregular migration trajectories, paying attention to their varying entry routes, residence times, legal grounds for removal and detention and removal countries. I argue for the need for empirically contextualised analysis that addresses the complex relations between law and geography beyond a particular national context, in order to better understand the dynamics of irregular migration in all its variety.In this article, I discuss legal geographies of irregular migration, drawing on a case study on immigration detention in Finland. Based on analysis of detention records, four different types of legal geographies are identified, relating to south–north movement of third‐country nationals inside Europe, criminalised Eastern European EU citizens, irregularity during the asylum process (in particular, related to the Dublin Regulation) and irregularly residing foreign nationals, including deportable long‐term residents. The analysis focuses on the relations between space, law and persons during detainees' irregular migration trajectories, paying attention to their varying entry routes, residence times, legal grounds for removal and detention and removal countries. I argue for the need for empirically contextualised analysis that addresses the complex relations between law and geography beyond a particular national context, in order to better understand the dynamics of irregular migration in all its variety.Peer reviewe

Moss survival through in situ cryptobiosis after six centuries of glacier burial

Cryptobiosis is a reversible ametabolic state of life characterized by the ceasing of all metabolic processes, allowing survival of periods of intense adverse conditions. Here we show that 1) entire moss individuals, dated by 14C, survived through cryptobiosis during six centuries of cold-based glacier burial in Antarctica, 2) after re-exposure due to glacier retreat, instead of dying (due to high rates of respiration supporting repair processes), at least some of these mosses were able to return to a metabolically active state and remain alive. Moss survival was assessed through growth experiments and, for the first time, through vitality measurements. Future investigations on the genetic pathways involved in cryptobiosis and the subsequent recovery mechanisms will provide key information on their applicability to other systematic groups, with implications for fields as divergent as medicine, biodiversity conservation, agriculture and space exploration

Ruxolitinib discontinuation syndrome: incidence, risk factors, and management in 251 patients with myelofibrosis

none36Ruxolitinib discontinuation syndrome: incidence, risk factors, and management in 251 patients with myelofibrosisopenPalandri F.; Palumbo G.A.; Elli E.M.; Polverelli N.; Benevolo G.; Martino B.; Abruzzese E.; Tiribelli M.; Tieghi A.; Latagliata R.; Cavazzini F.; Bergamaschi M.; Binotto G.; Crugnola M.; Isidori A.; Caocci G.; Heidel F.; Pugliese N.; Bosi C.; Bartoletti D.; Auteri G.; Cattaneo D.; Scaffidi L.; Trawinska M.M.; Stella R.; Ciantia F.; Pane F.; Cuneo A.; Krampera M.; Semenzato G.; Lemoli R.M.; Iurlo A.; Vianelli N.; Cavo M.; Breccia M.; Bonifacio M.Palandri, F.; Palumbo, G. A.; Elli, E. M.; Polverelli, N.; Benevolo, G.; Martino, B.; Abruzzese, E.; Tiribelli, M.; Tieghi, A.; Latagliata, R.; Cavazzini, F.; Bergamaschi, M.; Binotto, G.; Crugnola, M.; Isidori, A.; Caocci, G.; Heidel, F.; Pugliese, N.; Bosi, C.; Bartoletti, D.; Auteri, G.; Cattaneo, D.; Scaffidi, L.; Trawinska, M. M.; Stella, R.; Ciantia, F.; Pane, F.; Cuneo, A.; Krampera, M.; Semenzato, G.; Lemoli, R. M.; Iurlo, A.; Vianelli, N.; Cavo, M.; Breccia, M.; Bonifacio, M

Life after ruxolitinib: Reasons for discontinuation, impact of disease phase, and outcomes in 218 patients with myelofibrosis

Background: After discontinuing ruxolitinib, the outcome of patients with myelofibrosis reportedly has been poor. The authors investigated whether disease characteristics before the receipt of ruxolitinib may predict drug discontinuation in patients with myelofibrosis and whether reasons for drug discontinuation, disease phase at discontinuation, and salvage therapies may influence the outcome. Methods: A centralized electronic clinical database was created in 20 European hematology centers, including clinical and laboratory data for 524 patients who received ruxolitinib for myelofibrosis. Results: At 3\ua0years, 40.8% of patients had stopped ruxolitinib. Baseline predictors of drug discontinuation were: intermediate-2\u2013risk/high-risk category (Dynamic International Prognostic Score System), a platelet count <100 7109 per liter, transfusion dependency, and unfavorable karyotype. At last contact, 268 patients (51.1%) had discontinued therapy, and the median drug exposure was 17.5\ua0months. Fifty patients (18.7%) died while taking ruxolitinib. The reasons for discontinuation in the remaining 218 patients were the lack (22.9%) or loss (11.9%) of a spleen response, ruxolitinib-related adverse events (27.5%), progression to blast phase (23.4%), ruxolitinib-unrelated adverse events (9.2%), and allogeneic transplantation during response (5.1%). The median survival after ruxolitinib was 13.2\ua0months and was significantly better in the 167 patients who discontinued ruxolitinib in chronic phase (27.5 vs 3.9\ua0months for those who discontinued in blast phase; P\ua0<.001). No survival differences were observed among patients who discontinued ruxolitinib in chronic phase because of lack of response, loss of response, or ruxolitinib-related adverse events. The use of investigational agents and/or ruxolitinib rechallenge were associated with improved outcome. Conclusions: The survival of patients with myelofibrosis after discontinuation of ruxolitinib is poor, particularly for those who discontinue in blast phase. Salvage therapies can improve outcome, emphasizing the need for novel therapies

Ruxolitinib in cytopenic myelofibrosis: Response, toxicity, drug discontinuation, and outcome

BackgroundPatients with cytopenic myelofibrosis (MF) have more limited therapeutic options and poorer prognoses compared with patients with the myeloproliferative phenotype. Aims and MethodsPrognostic correlates of cytopenic phenotype were explored in 886 ruxolitinib-treated patients with primary/secondary MF (PMF/SMF) included in the RUX-MF retrospective study. Cytopenia was defined as: leukocyte count &lt;4 x 10(9)/L and/or hemoglobin &lt;11/&lt;10 g/dL (males/females) and/or platelets Overall, 407 (45.9%) patients had a cytopenic MF, including 249 (52.4%) with PMF. In multivariable analysis, high molecular risk mutations (p = .04), intermediate 2/high Dynamic International Prognostic Score System (p &lt; .001) and intermediate 2/high Myelofibrosis Secondary to Polycythemia Vera and Essential Thrombocythemia Prognostic Model (p &lt; .001) remained associated with cytopenic MF in the overall cohort, PMF, and SMF, respectively. Patients with cytopenia received lower average ruxolitinib at the starting (25.2 mg/day vs. 30.2 mg/day, p &lt; .001) and overall doses (23.6 mg/day vs. 26.8 mg/day, p &lt; .001) and achieved lower rates of spleen (26.5% vs. 34.1%, p = .04) and symptom (59.8% vs. 68.8%, p = .008) responses at 6 months compared with patients with the proliferative phenotype. Patients with cytopenia also had higher rates of thrombocytopenia at 3 months (31.1% vs. 18.8%, p &lt; .001) but lower rates of anemia (65.6% vs. 57.7%, p = .02 at 3 months and 56.6% vs. 23.9% at 6 months, p &lt; .001). After competing risk analysis, the cumulative incidence of ruxolitinib discontinuation at 5 years was 57% and 38% in patients with cytopenia and the proliferative phenotype (p &lt; .001), whereas cumulative incidence of leukemic transformation was similar (p = .06). In Cox regression analysis adjusted for Dynamic International Prognostic Score System score, survival was significantly shorter in patients with cytopenia (p &lt; .001). ConclusionsCytopenic MF has a lower probability of therapeutic success with ruxolitinib as monotherapy and worse outcome. These patients should be considered for alternative therapeutic strategies

A Prognostic Model to Predict Ruxolitinib Discontinuation and Death in Patients with Myelofibrosis

Most patients with myelofibrosis (MF) discontinue ruxolitinib (JAK1/JAK2 inhibitor) in the first 5 years of therapy due to therapy failure. As the therapeutic possibilities of MF are expanding, it is critical to identify patients predisposed to early ruxolitinib monotherapy failure and worse outcomes. We investigated predictors of early ruxolitinib discontinuation and death on therapy in 889 patients included in the "RUX-MF" retrospective study. Overall, 172 patients were alive on ruxolitinib after ≥5 years (long-term ruxolitinib, LTR), 115 patients were alive but off ruxolitinib after ≥5 yrs (short-term RUX, STR), and 123 patients died while on ruxolitinib after &lt;5 yrs (early death on ruxolitinib, EDR). The cumulative incidence of the blast phase was similar in LTR and STR patients (p = 0.08). Overall survival (OS) was significantly longer in LTR pts (p = 0.002). In multivariate analysis, PLT &lt; 100 × 109/L, Hb &lt; 10 g/dL, primary MF, absence of spleen response at 3 months and ruxolitinib starting dose &lt;10 mg BID were associated with higher probability of STR. Assigning one point to each significant variable, a prognostic model for STR (STR-PM) was built, and three groups were identified: low (score 0-1), intermediate (score 2), and high risk (score ≥ 3). The STR-PM may identify patients at higher risk of failure with ruxolitinib monotherapy who should be considered for alternative frontline strategies