The Safety of Adult Male Circumcision in HIV-Infected and Uninfected Men in Rakai, Uganda

Ron Gray and colleagues report on complications of circumcision in HIV-infected and HIV-uninfected men from two related trials in Uganda, finding increased risk with intercourse before wound healing

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

Background International and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda. Methods We did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15–49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population. Findings Between Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4–7·3) of transmissions occurred within lakeside areas, 89·2% (86·0–91·8) within inland areas, 1·3% (0·6–2·6) from lakeside to inland areas, and 3·7% (2·3–5·8) from inland to lakeside areas. Interpretation Cross-community HIV transmissions between Lake Victoria hotspots and surrounding inland populations are infrequent and when they occur, virus more commonly flows into rather than out of hotspots. This result suggests that targeted interventions to these hotspots will not alone control the epidemic in inland populations, where most transmissions occur. Thus, geographical targeting of high prevalence areas might not be effective for broader epidemic control depending on underlying epidemic dynamics. Funding The Bill & Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, the National Institute of Mental Health, the National Institute of Child Health and Development, the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases, the World Bank, the Doris Duke Charitable Foundation, the Johns Hopkins University Center for AIDS Research, and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8–28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa

Using te reo Māori and ta re Moriori in taxonomy

AUHEKE Ko ngā ingoa Linnaean ka noho hei pou mō te pārongo e pā ana ki ngā momo koiora. He mea nui rawa kia mārama, kia ahurei hoki ngā ingoa pūnaha whakarōpū. Me pēnei kia taea ai te whakawhitiwhiti kōrero ā-pūtaiao nei. Nā tēnā kua āta whakatakotohia ētahi ture, tohu ārahi hoki hei whakahaere i ngā whakamārama pūnaha whakarōpū. Kua whakamanahia ēnei kia noho hei tikanga mō te ao pūnaha whakarōpū. Heoi, arā noa atu ngā hua o te tukanga waihanga ingoa Linnaean mō ngā momo koiora i tua atu i te tautohu noa i ngā momo koiora. Ko tētahi o aua hua ko te whakarau: (1) i te mātauranga o ngā iwi takatake, (2) i te kōrero rānei mai i te iwi o te rohe, (3) i ngā kōrero pūrākau rānei mō te wāhi whenua. Kei te piki haere tēnei āhua whakamahinga hei āwhina kia whakamanahia ngā iwi taketake i roto i te mahi pūnaha whakarōpū. Nā tēnā ka whakamanawahia te iwi i runga i tōna mōhio he hoa-rangapū ia i roto i te mahi whiriwhiri ingoa kōrero pūrākau. Kua roa noa atu a Aotearoa e whakamahi ana i te reo taketake o Aotearoa / Rēkohu rānei i roto i te mahi whakamārama pūnaha whakarōpū. Engari ahakoa tērā, kāore i te pērā rawa te kaha o te ao pūnaha whakarōpū ki te whakapiri mai ki ngā iwi taketake i roto i tēnei tukanga. Kei roto i te rangahau nei i arotakengia ngā tau ki muri, me te aha, ko tōna kitenga e pēnei na: mai i tau 1830, neke atu i te 1,288 ngā wā kua whakamahia te reo Māori, te reo Moriori rānei i roto i te pūnaha whakarōpū. Kei te piki haere hoki tēnei tatauranga. Ko tētahi kitenga o te arotake nei, ko te tohu atu i ētahi āhuatanga whakamahi i te reo Māori, reo Moriori hoki. Hei tauira: (1) ngā momo whakarerekētanga whakamahi o ngā kupu “Māori, Moriori” rānei hei tohu atu tērā i ahu mai tēnā momo koiora mai i Aotearoa. (2) ngā ingoa kōrero pūrākau Māori / Moriori mō ngā momo koiora; (3) ngā ingoa whenua Māori / Moriori hoki e whai hononga ana ki ngā momo koiora (4) ētahi ingoa whakamārama i hangaia mai i ngā kupu Māori / Moriori hoki me (5) ētahi ingoa hou kua whakaarahia e te iwi e mahi ngātahi nei ki te taha o ngā kaipūnaha whakarōpū. Ko tā mātou nei, he arotahi he tautoko hoki i te tuarima o ēnei āhuatanga. He pūnaha mahi ngātahi tēnei hei whakamārama i ngā momo koiora. Ka pēnei mā te āta titiro ki ētahi tauira. Ko ēnei tauira ka whakamiramira i ngā huanga me ngā uauatanga o tēnei pūnaha mahi ngātahi hei whakamārama i ngā momo koiora. Ka tuku āwhina hoki mātou hei ārahi i ngā kaipūnaha whakarōpū kia pai ake te whakapiri atu ki te iwi mō te whakamārama momo koiora. Ka mātua matapakihia ngā take e pā ana ki te “whakarōmahanga” o ētahi kupu Māori, te whakamahinga o te tohutō, me te hiranga hoki kia whakapiri atu ki te iwi mā te roanga atu o te tukanga whakaingoa. Ko tā mātou hoki e tohutohu nei kia kohia katoatia ngā ingoa reo Māori, reo Moriori hoki kia noho hei rārangi tohutoro mō te wā anamata hei ārahi i te whakamahinga, hei hanga pātengi raraunga hoki mō Aotearoa. Ko tēnei pātengi raraunga me māmā te tomo atu, me wātea hoki hei rauemi whakamahi mā te kaiarangahau. ABSTRACT Linnaean names are an anchor for biological information about a species, and having clear, unique, taxonomic names is vital for scientific communication. Accordingly, there are specific rules and guidelines enshrined in codes that govern nomenclature and taxonomic description. The process of creating Linnean names for species can however provide multiple functions beyond identification, including the incorporation of cultural knowledge, vernacular and place names as epithets. Increasingly this usage helps engage and empower Indigenous cultures in taxonomic work through a shared sense of ownership over the species and the choice of epithet. Aotearoa New Zealand has a long history of using both the indigenous Maori language – te reo, and the Indigenous language of Rekohu (the Chatham Islands) – ta re Moriori, in taxonomic description, but not necessarily one of engaging Maori and Moriori in this process. Here we review this history, finding that since its first use in 1830, te reo and ta re have been incorporated over 1288 times within taxonomic nomenclature, and that this usage is increasing. We identify five central ways in which te reo and ta re have been incorporated, including the use of (1) variations of the words “Maori” and “Moriori” to designate Aotearoa New Zealand origins, (2) Maori / Moriori vernacular names for species, (3) Maori / Moriori place names associated with species, (4) novel descriptive names created from Māori and Moriori words, (5) novel names suggested by Maori in collaboration with taxonomists. We focus on and promote this last, collaborative system for species description through case studies that highlighting the advantages and the potential challenges of this process, and we provide guidance for taxonomists to better engage with iwi / imi in species description. Specifically, we discuss issues relating to the Latinisation of Maori words, the use of macrons, and the need for engagement of iwi / imi throughout the naming process. We also recommend creation of a central depository to log te reo and ta re names to act as a reference for future usage and provide a readily accessible electronic database for Aotearoa New Zealand people and researchers to use

Toward quantum optics with free electrons

The weak coupling between free electrons and light remains the limiting factor that has prevented access to versatile electron–photon physics, such as the entanglement of individual photons and electrons. This year, we demonstrated that photonic cavities can increase the coupling strength of electrons and light by more than an order of magnitude