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Insights from biome-wide experiments can improve efficacy of landscape-scale ecological restoration projects. Such insights enable implementers to set temporal and geographical benchmarks and to identify key drivers of success during the often decades-long restoration trajectory. Here we report on a biome-wide experiment aimed at informing the ecological restoration of thousands of hectares of degraded subtropical thicket dominated by the succulent shrub, Portulacaria afra (spekboom). Restoration using spekboom truncheons has the potential to sequester, for a semi-arid region, large amounts of ecosystem carbon, while regenerating a host of associated ecosystem services. This study evaluates, after about three years post-propagation, the effects of spekboom truncheon size and treatment on survivorship in 40 fence-enclosed (0.25 ha) plots located in target habitat across the entire spekboom thicket biome. In each plot, locally harvested spekboom truncheons, comprising eight size/treatment combinations, were planted in replicated rows of between 24 and 49 individuals, depending on treatment. The experiment assessed the role of truncheon size, spacing, application of rooting hormone and watering at planting on survivorship percentage as an indicator of restoration success. All eight combinations recorded extreme minimum survivorship values of zero, while the range of extreme maximum values was 70-100%. Larger truncheons (>22.5 mm diameter) had almost double the survivorship (ca. 45%) than smaller truncheons (< 15 mm) (ca. 25%). Planting large, untreated truncheons at 1 m intervals—as opposed to 2 m intervals recommended in the current restoration protocol—resulted in no significant change in survivorship. The application of rooting hormone and water at planting had no significant effect on restoration success for both large and small truncheons. While our results do not provide an evidence base for changing the current spekboom planting protocol, we recommend research on the financial and economic costs and benefits of different propagation strategies in real-world contexts.

ABSTRACT Scatterplots of biological datasets often have no‐data zones, which suggest constraint or promotion of dependent variables. Although methods exist to estimate boundary lines—that is, to fit lines to the edges of scatters of data points—there are, to our knowledge, none available to assess the significance of the areal extents of no‐data zones. Accordingly, we propose a flexible boundary line definition paired with a permutation test of the magnitude of no‐data zones—rather than testing the shape or slope of the line as current methods do. Our proposed permutation test can be used with any method of defining a boundary line. We demonstrate our approach with empirical datasets, find no‐data zones that methods such as quantile regressions fail to detect, and discuss how our approach can quantify constraint and promotion relationships that are not always apparent with other statistics. Scatterplots of biological datasets often have no‐data zones, which suggest constraint or promotion of dependent variables by independent variables. We propose a flexible boundary line definition paired with a permutation test of the magnitude of areas without data—rather than testing the shape or slope of that line as previously developed methods do. Using empirical datasets, we demonstrate instances where—for example—quantile regressions fail to identify significant patterns.

Sealing of the soil surface during a rain event can, in many soils, have a large effect on infiltrability of water. Such sealing is usually temporary. Raindrop impact disperses clay particles which block the soil pores within the top millimetre of soil. This blockage can occur even in sandy soils with small amounts of dispersed clay. When the soil dries after a sealing event, whether in a clayey or sandy soil, the clay particles shrink, the thin seal breaks apart, and the seal is no longer easily discernible in the field. Sealing is usually ephemeral, occurring during rain events, as opposed to crusting which may be evident at the timescale of decades. Here, Mills and Medinski investigate the likelihood of the potentially negative effect of sealing being increased as a result of clay mining by termites and analyzed a range of physico-chemical properties of seven termite mounds, constructed by Macrotermes species, as well as adjacent topsoils and subsoils in northern Namibia.

Macrotermes termite mounds in the Kruger National Park occupy a significant part of the savanna landscapes, occurring at densities of up to 70 km−2 and often exceeding 10 m in width and 4 m in height. The mounds are usually devoid of trees, but have dense grass cover in wet years. As a result, these mounds form large patches of grassland amongst the wooded savanna. To our knowledge, it is not known why trees are largely excluded from the mounds. We analysed soil surface nutrient concentrations on and off mounds (0–2 cm deep, n = 80) to ascertain whether the availability of nutrients could be influencing competition between grasses and tree seedlings. The results showed that potential deficiencies in P, Ca, Cu, Zn and B in soils off the mounds are likely to be constraining plant growth. Notably, only B, with an average concentration of 0.19 mg kg−1, was likely to be limiting plant growth on the mounds. Notwithstanding likely interactions with herbivory and fire, we hypothesise that because grasses are far less susceptible to deficiencies of B than dicotyledonous trees, it is likely that grass competition with tree seedlings is considerably greater on mounds than off mounds. Many termite mounds in the Kruger National Park, South Africa, are devoid of trees amongst an otherwise wooded savanna, with no existing explanation for this vegetation pattern. We found potential deficiencies in multiple soil nutrients off the mounds that could constrain plant growth; of these nutrients, only boron was likely to be limiting on the mounds. We hypothesise that, because grasses are less susceptible to boron deficiency than dicotyledonous trees, grasses are likely to compete more with tree seedlings on than off termite mounds.

Background. Dolutegravir (DTG), a once-daily, human immunodeficiency virus type 1 (HIV-1) integrase inhibitor, was evaluated for distribution and antiviral activity in cerebrospinal fluid (CSF). Methods. ING116070 is an ongoing, single-arm, open-label, multicenter study in antiretroviral therapy–naive, HIV-1–infected adults. Subjects received DTG (50 mg) plus abacavir/lamivudine (600/300 mg) once daily. The CSF and plasma (total and unbound) DTG concentrations were measured at weeks 2 and 16. The HIV-1 RNA levels were measured in CSF at baseline and weeks 2 and 16 and in plasma at baseline and weeks 2, 4, 8, 12, and 16. Results. Thirteen white men enrolled in the study; 2 withdrew prematurely, 1 because of a non–drug-related serious adverse event (pharyngitis) and 1 because of lack of treatment efficacy. The median DTG concentrations in CSF were 18 ng/mL (range, 4–23 ng/mL) at week 2 and 13 ng/mL (4–18 ng/mL) at week 16. Ratios of DTG CSF to total plasma concentration were similar to the unbound fraction of DTG in plasma. Median changes from baseline in CSF (n = 11) and plasma (n = 12) HIV-1 RNA were -3.42 and -3.04 log10 copies/mL, respectively. Nine of 11 subjects (82%) had plasma and CSF HIV-1 RNA levels <50 copies/mL and 10 of 11 (91%) had CSF HIV-1 RNA levels <2 copies/mL at week 16. Conclusions. The DTG concentrations in CSF were similar to unbound plasma concentrations and exceeded the in vitro 50% inhibitory concentration for wild-type HIV (0.2 ng/mL), suggesting that DTG achieves therapeutic concentrations in the central nervous system. The HIV-1 RNA reductions were similar in CSF and plasma. Clinical Trials Registration. NCT01499199.

The causes of the worldwide problem of encroachment of woody plants into grassy vegetation are elusive. The effects of soil nutrients on competition between herbaceous and woody plants in various landscapes are particularly poorly understood. A long-term experiment of 60 plots in a South African savanna, comprising annual applications of ammonium sulphate (146-1166 kg ha-1 yr-1) and superphosphate (233-466 kg ha-1 yr-1) over three decades, and subsequent passive protection over another three decades, during which indigenous trees encroached on different plots to extremely variable degrees, provided an opportunity to investigate relationships between soil properties and woody encroachment. All topsoils were analysed for pH, acidity, EC, water-dispersible clay, Na, Mg, K, Ca, P, S, C, N, NH4, NO3, B, Mn, Cu and Zn. Applications of ammonium sulphate (AS), but not superphosphate (SP), greatly constrained tree abundance relative to control plots. Differences between control plots and plots that had received maximal AS application were particularly marked (16.3 ± 5.7 versus 1.2 ± 0.8 trees per plot). Soil properties most affected by AS applications included pH (H2O) (control to maximal AS application: 6.4 ± 0.1 to 5.1 ± 0.2), pH (KCl) (5.5 ± 0.2 to 4.0 ± 0.1), acidity (0.7 ± 0.1 to 2.6 ± 0.3 cmol kg-1), acid saturation (8 ± 2 to 40 ± 5%), Mg (386 ± 25 to 143 ± 15 mg kg-1), Ca (1022 ± 180 to 322 ± 14 mg kg-1), Mn (314 ± 11 to 118 ± 9 mg kg-1), Cu (3.6 ± 0.3 to 2.3 ± 0.2 mg kg-1) and Zn (6.6 ± 0.4 to 3.7 ± 0.4 mg kg-1). Magnesium, B, Mn and Cu were identified using principal component analysis, boundary line analysis and Kruskal-Wallis rank sum tests as the nutrients most likely to be affecting tree abundance. The ratio Mn/Cu was most related to tree abundance across the experiment, supporting the hypothesis that competition between herbaceous and woody plants depends on the availability of anabolic relative to catabolic nutrients. These findings, based on more than six decades of experimentation, may have global significance for the theoretical understanding of changes in vegetation structure and thus the practical control of invasive woody plants.

The integrase inhibitor elvitegravir (EVG) has been co-formulated with the CYP3A4 inhibitor cobicistat (COBI), emtricitabine (FTC), and tenofovir disoproxil fumarate (TDF) in a single tablet given once daily. We compared the efficacy and safety of EVG/COBI/FTC/TDF with standard of care—co-formulated efavirenz (EFV)/FTC/TDF—as initial treatment for HIV infection. In this phase 3 trial, treatment-naive patients from outpatient clinics in North America were randomly assigned by computer-generated allocation sequence with a block size of four in a 1:1 ratio to receive EVG/COBI/FTC/TDF or EFV/FTC/TDF, once daily, plus matching placebo. Patients and study staff involved in giving study treatment, assessing outcomes, and collecting and analysing data were masked to treatment allocation. Eligibility criteria included screening HIV RNA concentration of 5000 copies per mL or more, and susceptibility to efavirenz, emtricitabine, and tenofovir. The primary endpoint was HIV RNA concentration of fewer than 50 copies per mL at week 48. The study is registered with ClinicalTrials.gov, number NCT01095796. 700 patients were randomly assigned and treated (348 with EVG/COBI/FTC/TDF, 352 with EFV/FTC/TDF). EVG/COBI/FTC/TDF was non-inferior to EFV/FTC/TDF; 305/348 (87·6%) versus 296/352 (84·1%) of patients had HIV RNA concentrations of fewer than 50 copies per mL at week 48 (difference 3·6%, 95% CI −1·6% to 8·8%). Proportions of patients discontinuing drugs for adverse events did not differ substantially (13/348 in the EVG/COBI/FTC/TDF group vs 18/352 in the EFV/FTC/TDF group). Nausea was more common with EVG/COBI/FTC/TDF than with EFV/FTC/TDF (72/348 vs 48/352) and dizziness (23/348 vs 86/352), abnormal dreams (53/348 vs 95/352), insomnia (30/348 vs 49/352), and rash (22/348 vs 43/352) were less common. Serum creatinine concentration increased more by week 48 in the EVG/COBI/FTC/TDF group than in the EFV/FTC/TDF group (median 13 μmol/L, IQR 5 to 20 vs 1 μmol/L, −6 to 8; p<0·001). If regulatory approval is given, EVG/COBI/FTC/TDF would be the only single-tablet, once-daily, integrase-inhibitor-based regimen for initial treatment of HIV infection. Gilead Sciences.

Efavirenz with tenofovir-disoproxil-fumarate and emtricitabine is a preferred antiretroviral regimen for treatment-naive patients infected with HIV-1. Rilpivirine, a new non-nucleoside reverse transcriptase inhibitor, has shown similar antiviral efficacy to efavirenz in a phase 2b trial with two nucleoside/nucleotide reverse transcriptase inhibitors. We aimed to assess the efficacy, safety, and tolerability of rilpivirine versus efavirenz, each combined with tenofovir-disoproxil-fumarate and emtricitabine. We did a phase 3, randomised, double-blind, double-dummy, active-controlled trial, in patients infected with HIV-1 who were treatment-naive. The patients were aged 18 years or older with a plasma viral load at screening of 5000 copies per mL or greater, and viral sensitivity to all study drugs. Our trial was done at 112 sites across 21 countries. Patients were randomly assigned by a computer-generated interactive web response system to receive either once-daily 25 mg rilpivirine or once-daily 600 mg efavirenz, each with tenofovir-disoproxil-fumarate and emtricitabine. Our primary objective was to show non-inferiority (12% margin) of rilpivirine to efavirenz in terms of the percentage of patients with confirmed response (viral load <50 copies per mL intention-to-treat time-to-loss-of-virological-response [ITT-TLOVR] algorithm) at week 48. Our primary analysis was by intention-to-treat. We also used logistic regression to adjust for baseline viral load. This trial is registered with ClinicalTrials.gov, number NCT00540449. 346 patients were randomly assigned to receive rilpivirine and 344 to receive efavirenz and received at least one dose of study drug, with 287 (83%) and 285 (83%) in the respective groups having a confirmed response at week 48. The point estimate from a logistic regression model for the percentage difference in response was −0·4 (95% CI −5·9 to 5·2), confirming non-inferiority with a 12% margin (primary endpoint). The incidence of virological failures was 13% (rilpivirine) versus 6% (efavirenz; 11% vs 4% by ITT-TLOVR). Grade 2–4 adverse events (55 [16%] on rilpivirine vs 108 [31%] on efavirenz, p<0·0001), discontinuations due to adverse events (eight [2%] on rilpivirine vs 27 [8%] on efavirenz), rash, dizziness, and abnormal dreams or nightmares were more common with efavirenz. Increases in plasma lipids were significantly lower with rilpivirine. Rilpivirine showed non-inferior efficacy compared with efavirenz, with a higher virological-failure rate, but a more favourable safety and tolerability profile. Tibotec.

Antiretroviral regimens containing tenofovir disoproxil fumarate have been associated with renal toxicity and reduced bone mineral density. Tenofovir alafenamide is a novel tenofovir prodrug that reduces tenofovir plasma concentrations by 90%, thereby decreasing off-target side-effects. We aimed to assess whether efficacy, safety, and tolerability were non-inferior in patients switched to a regimen containing tenofovir alafenamide versus in those remaining on one containing tenofovir disoproxil fumarate. In this randomised, actively controlled, multicentre, open-label, non-inferiority trial, we recruited HIV-1-infected adults from Gilead clinical studies at 168 sites in 19 countries. Patients were virologically suppressed (HIV-1 RNA <50 copies per mL) with an estimated glomerular filtration rate of 50 mL per min or greater, and were taking one of four tenofovir disoproxil fumarate-containing regimens for at least 96 weeks before enrolment. With use of a third-party computer-generated sequence, patients were randomly assigned (2:1) to receive a once-a-day single-tablet containing elvitegravir 150 mg, cobicistat 150 mg, emtricitabine 200 mg, and tenofovir alafenamide 10 mg (tenofovir alafenamide group) or to carry on taking one of four previous tenofovir disoproxil fumarate-containing regimens (tenofovir disoproxil fumarate group) for 96 weeks. Randomisation was stratified by previous treatment regimen in blocks of six. Patients and treating physicians were not masked to the assigned study regimen; outcome assessors were masked until database lock. The primary endpoint was the proportion of patients who received at least one dose of study drug who had undetectable viral load (HIV-1 RNA <50 copies per mL) at week 48. The non-inferiority margin was 12%. This study was registered with ClinicalTrials.gov, number NCT01815736. Between April 12, 2013 and April 3, 2014, we enrolled 1443 patients. 959 patients were randomly assigned to the tenofovir alafenamide group and 477 to the tenofovir disoproxil fumarate group. Viral suppression at week 48 was noted in 932 (97%) patients assigned to the tenofovir alafenamide group and in 444 (93%) assigned to the tenofovir disoproxil fumarate group (adjusted difference 4·1%, 95% CI 1·6–6·7), with virological failure noted in ten and six patients, respectively. The number of adverse events was similar between the two groups, but study drug-related adverse events were more common in the tenofovir alafenamide group (204 patients [21%] vs 76 [16%]). Hip and spine bone mineral density and glomerular filtration were each significantly improved in patients in the tenofovir alafenamide group compared with those in the tenofovir disoproxil fumarate group. Switching to a tenofovir alafenamide-containing regimen from one containing tenofovir disoproxil fumarate was non-inferior for maintenance of viral suppression and led to improved bone mineral density and renal function. Longer term follow-up is needed to better understand the clinical impact of these changes. Gilead Sciences.

Following the achievement of deep molecular response on tyrosine kinase inhibitors (TKIs), approximately half of patients with chronic myeloid leukemia (CML) can discontinue TKI and remain in treatment-free remission (TFR). The ALLG CML8 study enrolled 40 imatinib-treated patients with undetectable BCR-ABL1 mRNA (approximately MR4.5). Molecular relapse was defined as detectable BCR-ABL1 on two consecutive tests or any single value >0.1%. With a median follow-up of 8.6 years (range 5.7–11.2 years), 18 patients remain in continuous TFR (45.0%; 95% confidence interval 31.9−63.4%). The latest relapse detected was 27 months after stopping imatinib. No patient progressed to advanced phase. Twenty-two patients met criteria for imatinib re-treatment and all regained undetectable molecular response. Nine patients in long-term TFR were monitored by highly sensitive individualized BCR-ABL1 DNA PCR in a sufficient number of samples to enable more precise quantification of residual leukemia. BCR-ABL1 DNA decreased from a median of MR5.0 in the first year of TFR to MR6.1 in the sixth year of TFR. Our results support the long-term safety and remarkable stability of response after imatinib discontinuation in appropriately selected CML patients. Serial high sensitivity testing provides a new and unexpected finding of gradually reducing CML cells in patients in long-term TFR.