Adjusting mortality for loss to follow-up: analysis of five ART programmes in sub-Saharan Africa

Background

Evaluation of antiretroviral treatment (ART) programmes in sub-Saharan Africa is difficult because many patients are lost to follow-up. Outcomes in these patients are generally unknown but studies tracing patients have shown mortality to be high. We adjusted programme-level mortality in the first year of antiretroviral treatment (ART) for excess mortality in patients lost to follow-up.

Methods and Findings

Treatment-naïve patients starting combination ART in five programmes in Côte d''Ivoire, Kenya, Malawi and South Africa were eligible. Patients whose last visit was at least nine months before the closure of the database were considered lost to follow-up. We filled missing survival times in these patients by multiple imputation, using estimates of mortality from studies that traced patients lost to follow-up. Data were analyzed using Weibull models, adjusting for age, sex, ART regimen, CD4 cell count, clinical stage and treatment programme. A total of 15,915 HIV-infected patients (median CD4 cell count 110 cells/µL, median age 35 years, 68% female) were included; 1,001 (6.3%) were known to have died and 1,285 (14.3%) were lost to follow-up in the first year of ART. Crude estimates of mortality at one year ranged from 5.7% (95% CI 4.9–6.5%) to 10.9% (9.6–12.4%) across the five programmes. Estimated mortality hazard ratios comparing patients lost to follow-up with those remaining in care ranged from 6 to 23. Adjusted estimates based on these hazard ratios ranged from 10.2% (8.9–11.6%) to 16.9% (15.0–19.1%), with relative increases in mortality ranging from 27% to 73% across programmes.

Conclusions

Naïve survival analysis ignoring excess mortality in patients lost to follow-up may greatly underestimate overall mortality, and bias ART programme evaluations. Adjusted mortality estimates can be obtained based on excess mortality rates in patients lost to follow-up.     

Localization and irregular distribution of Na,K-ATPase in myelin sheath from rat sciatic nerve

Sodium, potassium adenosine triphosphatase (Na,K-ATPase) is a membrane-bound enzyme that maintains the Na(+) and K(+) gradients used in the nervous system for generation and transmission of bioelectricity. Recently, its activity has also been demonstrated during nerve regeneration. The present study was undertaken to investigate the ultrastructural localization and distribution of Na,K-ATPase in peripheral nerve fibers. Small blocks of the sciatic nerves of male Wistar rats weighing 250-300g were excised, divided into two groups, and incubated with and without substrate, the para-nitrophenyl phosphate (pNPP). The material was processed for transmission electron microscopy, and the ultra-thin sections were examined in a Philips CM 100 electron microscope. The deposits of reaction product were localized mainly on the axolemma, on axoplasmic profiles, and irregularly dispersed on the myelin sheath, but not in the unmyelinated axons. In the axonal membrane, the precipitates were regularly distributed on the cytoplasmic side. These results together with published data warrant further studies for the diagnosis and treatment of neuropathies with compromised Na,K-ATPase activity.     

A novel potassium channel in lymphocyte mitochondria

The margatoxin-sensitive Kv1.3 is the major potassium channel in the plasma membrane of T lymphocytes. Electron microscopy, patch clamp, and immunological studies identified the potassium channel Kv1.3, thought to be localized exclusively in the cell membrane, in the inner mitochondrial membrane of T lymphocytes. Patch clamp of mitoplasts and mitochondrial membrane potential measurements disclose the functional expression of a mitochondrial margatoxin-sensitive potassium channel. To identify unambiguously the mitochondrial localization of Kv1.3, we employed a genetic model and stably transfected CTLL-2 cells, which are genetically deficient for this channel, with Kv1.3. Mitochondria isolated from Kv1.3-reconstituted CTLL-2 expressed the channel protein and displayed an activity, which was identical to that observed in Jurkat mitochondria, whereas mitochondria of mock-transfected cells lacked a channel with the characteristics of Kv1.3. Our data provide the first molecular identification of a mitochondrial potassium conductance.     

Glyphosate affects photosynthesis in first and second generation of glyphosate-resistant soybeans

The crop area planted to conventional soybeans has decreased annually while that planted to glyphosate-resistant (RR) soybean has drastically increased mainly due to the wide adoption of glyphosate in current weed management systems. With the extensive use of glyphosate, many farmers have noted visual plant injury in RR soybean varieties after glyphosate application. A new generation designated as “second generation—RR2” has been recently developed and these RR2 cultivars already are commercially available for farmers and promoted as higher yielding relative to the previous RR cultivars. However, little information is currently available about the performance of RR2 soybean beyond commercial and farmer testimonial data. Thus, an evaluation of different glyphosate rates applied in different growth stages of the first and second generation of RR soybeans, revealed a significant decrease in photosynthesis. In general, increased glyphosate rate and late applications (V6) pronounced decrease photosynthetic parameters and consequently decreased in leaf area and shoot biomass production. In contrast, low rate and early applications were less damage for the RR soybean plants, suggesting that with early applications (V2), plants probably have more time to recover from glyphosate or its metabolites effects regarding late applications.     

Effect of Carbon Source on Enzymes and Metabolites of Arginine Metabolism in Neurospora

The levels of enzymes and metabolites of arginine metabolism were determined in exponential cultures of Neurospora crassa grown on various carbon sources. The carbon sources decreased in effectiveness (as determined by generation times) in the following order: sucrose, acetate, glycerol, and ethanol. The basal and induced levels of the catabolic enzymes, arginase (EC 3.5.3.1) and ornithine transaminase (EC 2.6.1.13), were lower in mycelia grown on poor carbon sources. Arginase was more sensitive to variations in carbon source than was ornithine transaminase. Induction of both enzymes was sensitive to nitrogen metabolite control, but this sensitivity was reduced in mycelia grown on glycerol or ethanol. The pools of arginine and ornithine were reduced in mycelia grown in unsupplemented medium containing poor carbon sources, but the biosynthetic enzyme ornithine transcarbamylase (EC 2.1.3.3) was not derepressed. The arginine pools were similar, regardless of carbon source, in mycelia grown in arginine-supplemented medium. The ornithine pool was reduced by growth on poor carbon sources. The rate of arginine degradation was proportional to the level of arginase in both sucrose- and glycerol-grown mycelia. The distribution of arginine between cytosol and vesicles was only slightly altered by growth on glycerol instead of sucrose. The slightly smaller cytosolic arginine concentration did not appear to be sufficient to account for the alterations in basal and induced enzyme levels. The results suggest a possible carbon metabolite effect on the expression or turnover of a variety of genes for enzymes of arginine metabolism in Neurospora.     

Modular inverse reinforcement learning for visuomotor behavior

In a large variety of situations one would like to have an expressive and accurate model of observed animal or human behavior. While general purpose mathematical models may capture successfully properties of observed behavior, it is desirable to root models in biological facts. Because of ample empirical evidence for reward-based learning in visuomotor tasks, we use a computational model based on the assumption that the observed agent is balancing the costs and benefits of its behavior to meet its goals. This leads to using the framework of reinforcement learning, which additionally provides well-established algorithms for learning of visuomotor task solutions. To quantify the agent’s goals as rewards implicit in the observed behavior, we propose to use inverse reinforcement learning, which quantifies the agent’s goals as rewards implicit in the observed behavior. Based on the assumption of a modular cognitive architecture, we introduce a modular inverse reinforcement learning algorithm that estimates the relative reward contributions of the component tasks in navigation, consisting of following a path while avoiding obstacles and approaching targets. It is shown how to recover the component reward weights for individual tasks and that variability in observed trajectories can be explained succinctly through behavioral goals. It is demonstrated through simulations that good estimates can be obtained already with modest amounts of observation data, which in turn allows the prediction of behavior in novel configurations.     

Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics

Productive cis folding by the chaperonin GroEL is triggered by the binding of ATP but not ADP, along with cochaperonin GroES, to the same ring as non-native polypeptide, ejecting polypeptide into an encapsulated hydrophilic chamber. We examined the specific contribution of the gamma-phosphate of ATP to this activation process using complexes of ADP and aluminium or beryllium fluoride. These ATP analogues supported productive cis folding of the substrate protein, rhodanese, even when added to already-formed, folding-inactive cis ADP ternary complexes, essentially introducing the gamma-phosphate of ATP in an independent step. Aluminium fluoride was observed to stabilize the association of GroES with GroEL, with a substantial release of free energy (-46 kcal/mol). To understand the basis of such activation and stabilization, a crystal structure of GroEL-GroES-ADP.AlF3 was determined at 2.8 A. A trigonal AlF3 metal complex was observed in the gamma-phosphate position of the nucleotide pocket of the cis ring. Surprisingly, when this structure was compared with that of the previously determined GroEL-GroES-ADP complex, no other differences were observed. We discuss the likely basis of the ability of gamma-phosphate binding to convert preformed GroEL-GroES-ADP-polypeptide complexes into the folding-active state.     

Structure, Dynamics and Thermodynamics of the Human Centrin 2/hSfi1 Complex

Centrin, an EF-hand calcium-binding protein, has been shown to be involved in the duplication of centrosomes, and Sfi1 (Suppressor of fermentation-induced loss of stress resistance protein 1) is one of its centrosomal targets. There are three isoforms of human centrin, but here we only considered centrin 2 (HsCen2). This protein has the ability to bind to any of the ∼ 25 repeats of human Sfi1 (hSfi1) with more or less affinity. In this study, we mainly focused on the 17th repeat (R17-hSfi1-20), which presents the highest level of similarity with a well-studied 17-residue peptide (P17-XPC) from human xeroderma pigmentosum complementation group C protein, another centrin target for DNA repair. The only known structure of HsCen2 was resolved in complex with P17-XPC. The 20-residue peptide R17-hSfi1-20 exhibits the motif L8L4W1, which is the reverse of the XPC motif, W1L4L8. Consequently, the dipole of the helix formed by this motif has a reverse orientation. We wished to ascertain the impact of this reversal on the structure, dynamics and affinity of centrin. To address this question, we determined the structure of C-HsCen2 [the C-terminal domain of HsCen2 (T94-Y172)] in complex with R17-hSfi1-20 and monitored its dynamics by NMR, after having verified that the N-terminal domain of HsCen2 does not interact with the peptide. The structure shows that the binding mode is similar to that of P17-XPC. However, we observed a 2 -Å translation of the R17-hSfi1-20 helix along its axis, inducing less anchorage in the protein and the disruption of a hydrogen bond between a tryptophan residue in the peptide and a well-conserved nearby glutamate in C-HsCen2. NMR dynamic studies of the complex strongly suggested the existence of an unusual calcium secondary binding mode in calcium-binding loop III, made possible by the uncommon residue composition of this loop. The secondary metal site is only populated at high calcium concentration and depends on the type of bound ligand.     

Nine-year experience with extended use of the commissure-based buccal musculomucosal flap

This study reports on the extended use of the commissure-based buccal musculomucosal (CBMM) flap. Large lip defects and medium-size intraoral defects have the general problem of being too large for primary closure to avoid a major functional and aesthetic impairment. Elaborate free flaps, such as axial flaps, although excellent in large defects, may not provide mucosa-equivalent sensitivity, motility, volume, and texture to replace lost tissue with a similar kind of tissue. A total of 60 flap procedures were performed with bilateral and unilateral flaps up to 7.5 x 4 cm in size. The partial and total upper and lower vermilion, gingivobuccal sulcus, floor of the mouth, lateral tongue margin, oropharynx, and hard and soft palates were reconstructed. Partial necrosis was seen in four flaps; all patients recovered with good oral function in speech and swallowing, good aesthetics, and prosthetic rehabilitation if necessary. The donor site could be closed primarily. In flaps with dorsal advancement, the mucosal excess above and below was closed, creating two small dog-ears. Facial expression and mouth opening returned to normal after less than 2 months. The parotid duct had to be marsupialized in large flap preparations, but this did never provoke stasis or infection. The two-point sensitivity of the flaps was, on average, equal to that of the nonoperated mucosa in intraindividual correlation, and the flaps lost, on average, 15 percent of their original size. In the authors' estimation, the results indicate a reliable and technically easy option for intraoral, medium-size defect reconstruction that yields sensitivity and facilitates the rehabilitation of oral function in speaking and ingestion.     

FUN26 (Function Unknown Now 26) Protein from Saccharomyces cerevisiae Is a Broad Selectivity,High Affinity,Nucleoside and Nucleobase Transporter

Equilibrative nucleoside transporters (ENTs) are polytopic integral membrane proteins that transport nucleosides and, to a lesser extent, nucleobases across cell membranes. ENTs modulate efficacy for a range of human therapeutics and function in a diffusion-controlled bidirectional manner. A detailed understanding of ENT function at the molecular level has remained elusive. FUN26 (function unknown now 26) is a putative ENT homolog from S. cerevisiae that is expressed in vacuole membranes. In the present system, proteoliposome studies of purified FUN26 demonstrate robust nucleoside and nucleobase uptake into the luminal volume for a broad range of substrates. This transport activity is sensitive to nucleoside modifications in the C(2′)- and C(5′)-positions on the ribose sugar and is not stimulated by a membrane pH differential. [³H]Adenine nucleobase transport efficiency is increased ∼4-fold relative to nucleosides tested with no observed [³H]adenosine or [³H]UTP transport. FUN26 mutational studies identified residues that disrupt (G463A or G216A) or modulate (F249I or L390A) transporter function. These results demonstrate that FUN26 has a unique substrate transport profile relative to known ENT family members and that a purified ENT can be reconstituted in proteoliposomes for functional characterization in a defined system.