Rectilinear Link Diameter and Radius in a Rectilinear Polygonal Domain

We study the computation of the diameter and radius under the rectilinear link distance within a rectilinear polygonal domain of $n$ vertices and $h$ holes. We introduce a \emph{graph of oriented distances} to encode the distance between pairs of points of the domain. This helps us transform the problem so that we can search through the candidates more efficiently. Our algorithm computes both the diameter and the radius in $\min \{\,O(n^\omega), O(n^2 + nh \log h + \chi^2)\,\}$ time, where $\omega<2.373$ denotes the matrix multiplication exponent and $\chi\in \Omega(n)\cap O(n^2)$ is the number of edges of the graph of oriented distances. We also provide a faster algorithm for computing the diameter that runs in $O(n^2 \log n)$ time

Circularization of the HIV-1 RNA genome

Genomic RNA circularization has been proposed for several RNA viruses. In this study, we examined if the 5′ and 3′ ends of the 9-kb HIV-1 RNA genome can interact. In vitro assays demonstrated a specific interaction between transcripts encompassing the 5′ and 3′ terminal 1 kb, suggesting that the HIV-1 RNA genome can circularize. Truncation of the transcripts indicated that the 5′–3′ interaction is formed by 600–700 nt in the gag open reading frame and the terminal 123 nt of the genomic RNA. Detailed RNA structure probing indicates that sequences flanking the 3′ TAR hairpin interact with complementary sequences in the gag gene. Phylogenetic analysis indicates that all HIV-1 subtypes can form the 5′/3′ interaction despite considerable sequence divergence, suggesting an important role of RNA circularization in the HIV-1 replication cycle

HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome

HIV-1 replication can be efficiently inhibited by intracellular expression of an siRNA targeting the viral RNA. However, HIV-1 escape variants emerged after prolonged culturing. These RNAi-resistant viruses contain nucleotide substitutions or deletions in or near the targeted sequence. We observed an inverse correlation between the level of resistance and the stability of the siRNA/target-RNA duplex. However, two escape variants showed a higher level of resistance than expected based on the duplex stability. We demonstrate that these mutations induce alternative folding of the RNA such that the target sequence is occluded from binding to the siRNA, resulting in reduced RNAi efficiency. HIV-1 can thus escape from RNAi-mediated inhibition not only through nucleotide substitutions or deletions in the siRNA target sequence, but also through mutations that alter the local RNA secondary structure. The results highlight the enormous genetic flexibility of HIV-1 and provide detailed molecular insight into the sequence specificity of RNAi and the impact of target RNA secondary structure

APOBEC3G Polymorphism as a Selective Barrier to Cross-Species Transmission and Emergence of Pathogenic SIV and AIDS in a Primate Host

Cellular restriction factors, which render cells intrinsically resistant to viruses, potentially impose genetic barriers to cross-species transmission and emergence of viral pathogens in nature. One such factor is APOBEC3G. To overcome APOBEC3G-mediated restriction, many lentiviruses encode Vif, a protein that targets APOBEC3G for degradation. As with many restriction factor genes, primate APOBEC3G displays strong signatures of positive selection. This is interpreted as evidence that the primate APOBEC3G locus reflects a long-term evolutionary “arms-race” between retroviruses and their primate hosts. Here, we provide direct evidence that APOBEC3G has functioned as a barrier to cross-species transmission, selecting for viral resistance during emergence of the AIDS-causing pathogen SIVmac in captive colonies of Asian macaques in the 1970s. Specifically, we found that rhesus macaques have multiple, functionally distinct APOBEC3G alleles, and that emergence of SIVmac and simian AIDS required adaptation of the virus to evade APOBEC3G-mediated restriction. Our evidence includes the first comparative analysis of APOBEC3G polymorphism and function in both a reservoir and recipient host species (sooty mangabeys and rhesus macaques, respectively), and identification of adaptations unique to Vif proteins of the SIVmac lineage that specifically antagonize rhesus APOBEC3G alleles. By demonstrating that interspecies variation in a known restriction factor selected for viral counter-adaptations in the context of a documented case of cross-species transmission, our results lend strong support to the evolutionary “arms-race” hypothesis. Importantly, our study confirms that APOBEC3G divergence can be a critical determinant of interspecies transmission and emergence of primate lentiviruses, including viruses with the potential to infect and spread in human populations

Functional characterization of Vif proteins from HIV-1 infected patients with different APOBEC3G haplotypes.

CAPRISA, 2016.Abstract available in PDF file

Optimization of the doxycycline-dependent simian immunodeficiency virus through in vitro evolution

<p>Abstract</p> <p>Background</p> <p>Vaccination of macaques with live attenuated simian immunodeficiency virus (SIV) provides significant protection against the wild-type virus. The use of a live attenuated human immunodeficiency virus (HIV) as AIDS vaccine in humans is however considered unsafe because of the risk that the attenuated virus may accumulate genetic changes during persistence and evolve to a pathogenic variant. We earlier presented a conditionally live HIV-1 variant that replicates exclusively in the presence of doxycycline (dox). Replication of this vaccine strain can be limited to the time that is needed to provide full protection through transient dox administration. Since the effectiveness and safety of such a conditionally live virus vaccine should be tested in macaques, we constructed a similar dox-dependent SIV variant. The Tat-TAR transcription control mechanism in this virus was inactivated through mutation and functionally replaced by the dox-inducible Tet-On regulatory system. This SIV-rtTA variant replicated in a dox-dependent manner in T cell lines, but not as efficiently as the parental SIVmac239 strain. Since macaque studies will likely require an efficiently replicating variant, we set out to optimize SIV-rtTA through in vitro viral evolution.</p> <p>Results</p> <p>Upon long-term culturing of SIV-rtTA, additional nucleotide substitutions were observed in TAR that affect the structure of this RNA element but that do not restore Tat binding. We demonstrate that the bulge and loop mutations that we had introduced in the TAR element of SIV-rtTA to inactivate the Tat-TAR mechanism, shifted the equilibrium between two alternative conformations of TAR. The additional TAR mutations observed in the evolved variants partially or completely restored this equilibrium, which suggests that the balance between the two TAR conformations is important for efficient viral replication. Moreover, SIV-rtTA acquired mutations in the U3 promoter region. We demonstrate that these TAR and U3 changes improve viral replication in T-cell lines and macaque peripheral blood mononuclear cells (PBMC) but do not affect dox-control.</p> <p>Conclusion</p> <p>The dox-dependent SIV-rtTA variant was optimized by viral evolution, yielding variants that can be used to test the conditionally live virus vaccine approach and as a tool in SIV biology studies and vaccine research.</p

Origin of the HIV-1 group O epidemic in western lowland gorillas

HIV-1, the cause of AIDS, is composed of four phylogenetic lineages, groups M, N, O, and P, each of which resulted from an independent cross-species transmission event of simian immunodeficiency viruses (SIVs) infecting African apes. Although groups M and N have been traced to geographically distinct chimpanzee communities in southern Cameroon, the reservoirs of groups O and P remain unknown. Here, we screened fecal samples fromwestern lowland (n = 2,611), eastern lowland (n = 103), and mountain (n = 218) gorillas for gorilla SIV (SIVgor) antibodies and nucleic acids. Despite testing wild troops throughout southern Cameroon (n = 14), northern Gabon (n = 16), the Democratic Republic of Congo (n = 2), and Uganda (n = 1), SIVgor was identified at only four sites in southern Cameroon, with prevalences ranging from 0.8-22%. Amplification of partial and full-length SIVgor sequences revealed extensive genetic diversity, but all SIVgor strains were derived from a single lineage within the chimpanzee SIV (SIVcpz) radiation. Two fully sequenced gorilla viruses from southwestern Cameroon were very closely related to, and likely represent the source population of, HIV-1 group P. Most of the genome of a third SIVgor strain, from central Cameroon, was very closely related to HIV-1 group O, again pointing to gorillas as the immediate source. Functional analyses identified the cytidine deaminase APOBEC3G as a barrier for chimpanzee-to-gorilla, but not gorilla-to-human, virus transmission. These data indicate that HIV-1 group O, which spreads epidemically in west central Africa and is estimated to have infected around 100,000 people, originated by cross-species transmission from western lowland gorillas

Impact of Valvulo-Arterial Impedance on Long-Term Quality of Life and Exercise Performance After Transcatheter Aortic Valve Replacement

BACKGROUND: In aortic stenosis, valvulo-arterial impedance (Zva) estimates the overall left ventricular afterload (valve and arterial component). We investigated the association of Zva (≥5 versus <5 mm Hg mL-1 m-2) on quality of life (QOL) and exercise performance (EP) ≥1 year after transcatheter aortic valve replacement (TAVR). METHODS: The study population consists of 250 TAVR patients in whom baseline Zva and follow-up QOL was prospectively assessed using EuroQOL-5-dimensions instruments; EP was assessed in 192 patients who survived ≥1 year after TAVR using questionnaires related to daily activities. In 124 patients, Zva at 1-year was also available and was used to study the change in Zva (baseline to 1 year) on QOL/EP. RESULTS: Elevated baseline Zva was present in 125 patients (50%). At a median of 28 (IQR, 17-40) months, patients with elevated baseline Zva were more limited in mobility (88% versus 71%; P=0.004), self-care (40% versus 25%; P=0.019), and independent daily activities (taking a shower: 53% versus 38%, P=0.030; walking 100 meter: 76% versus 54%, P=0.001; and walking stairs: 74% versus 54%, P=0.011). By multivariable analysis, elevated Zva predicted unfavorable QOL (lower EuroQOL-5-dimensions-Utility Index, odds ratio, 1.98; CI, 1.15-3.41) and unfavorable EP (any limitation in ≥3 daily activities, odds ratio, 2.55; CI, 1.41-4.62). After TAVR, the proportion of patients with elevated Zva fell from 50% to 21% and remained 21% at 1 year and was found to be associated with more limitations in mobility, self-care, and daily activities compared with patients with Zva <5 mm Hg mL-1 m-2. CONCLUSIONS: Elevated Zva was seen in half of patients and predicted unfavorable long-term QOL and EP. At 1 year after TAVR, the prevalence of elevated Zva was 21% but remained associated with poor QOL/EP

Measurement of overall quality of life in nursing homes through self-report: the role of cognitive impairment

Measuring quality of life is a necessity for adequate interventions. This paper concerns the usefulness of six self-report measures for overall quality of life for nursing home residents with various levels of cognitive impairment. It was investigated which proportion of residents from four cognition groups could complete a scale, and internal consistency and construct validity of the scales were studied. Data collection took place in ten Dutch nursing homes (N = 227). The proportion of residents that could complete each scale varied. The Depression List could be administered most often to the cognitively most impaired group (43%; Mini Mental State Examination-scores 0–4). In the three cognition groups with MMSE-score >5, internal consistency of the Depression List, Geriatric Depression Scale and Negative Affect Scale was adequate in all three groups (alpha ≥.68). Intercorrelation was highest for the Philadelphia Geriatric Center Morale Scale, the Depression List, and the Geriatric Depression Scale (rho ≥.65). Nonetheless, self-report scales were not strongly correlated with two observational scales for depression, especially in cognitively severely impaired residents (rho ≤.30). In conclusion, it may not be possible to measure overall quality of life through self-report, and possibly also through observation, in many nursing home residents

Students' perceptions of online-learning quality given comfort, motivation, satisfaction, and experience

Understanding factors in successful online course experiences can provide suggestions for instructors and students to promote improved learning experiences. A survey of 700 students regarding perceptions of online-learning quality was analyzed with a structural equation model. For students with online-learning experience, comfort with technology and motivation to learn technology skills were related to satisfaction with online courses, which was related to perceived quality. For students with hybrid-learning experience, comfort was related to motivation and perceived quality, motivation was related to satisfaction, and satisfaction was related to perceived quality. For students with no online-learning experiences, comfort was related to motivation to learn technology skills, but neither of these factors was related to perceived quality of online courses