An inference model gives insights into innate immune adaptation and repertoire diversity.

The innate immune system is the body's first line of defense against infection. Natural killer (NK) cells, a vital part of the innate immune system, help to control infection and eliminate cancer. Studies have identified a vast array of receptors that NK cells use to discriminate between healthy and unhealthy cells. However, at present, it is difficult to explain how NK cells will respond to novel stimuli in different environments. In addition, the expression of different receptors on individual NK cells is highly stochastic, but the reason for these variegated expression patterns is unclear. Here, we studied the recognition of unhealthy target cells as an inference problem, where NK cells must distinguish between healthy targets with normal variability in ligand expression and ones that are clear "outliers." Our mathematical model fits well with experimental data, including NK cells' adaptation to changing environments and responses to different target cells. Furthermore, we find that stochastic, "sparse" receptor expression profiles are best able to detect a variety of possible threats, in agreement with experimental studies of the NK cell repertoire. While our study was specifically motivated by NK cells, our model is general and could also apply more broadly to explain principles of target recognition for other immune cell types.

Correlated Allele Frequency Changes Reveal Clonal Structure and Selection in Temporal Genetic Data.

In evolving populations where the rate of beneficial mutations is large, subpopulations of individuals with competing beneficial mutations can be maintained over long times. Evolution with this kind of clonal structure is commonly observed in a wide range of microbial and viral populations. However, it can be difficult to completely resolve clonal dynamics in data. This is due to limited read lengths in high-throughput sequencing methods, which are often insufficient to directly measure linkage disequilibrium or determine clonal structure. Here, we develop a method to infer clonal structure using correlated allele frequency changes in time-series sequence data. Simulations show that our method recovers true, underlying clonal structures when they are known and accurately estimate linkage disequilibrium. This information can then be combined with other inference methods to improve estimates of the fitness effects of individual mutations. Applications to data suggest novel clonal structures in an E. coli long-term evolution experiment, and yield improved predictions of the effects of mutations on bacterial fitness and antibiotic resistance. Moreover, our method is computationally efficient, requiring orders of magnitude less run time for large data sets than existing methods. Overall, our method provides a powerful tool to infer clonal structures from data sets where only allele frequencies are available, which can also improve downstream analyses.

Association between wrist-worn free-living accelerometry and hand grip strength in middle-aged and older adults.

INTRODUCTION: Wrist-worn activity monitors have seen widespread adoption in recent times, particularly in young and sport-oriented cohorts, while their usage among older adults has remained relatively low. The main limitations are in regards to the lack of medical insights that current mainstream activity trackers can provide to older subjects. One of the most important research areas under investigation currently is the possibility of extrapolating clinical information from these wearable devices. METHODS: The research question of this study is understanding whether accelerometry data collected for 7-days in free-living environments using a consumer-based wristband device, in conjunction with data-driven machine learning algorithms, is able to predict hand grip strength and possible conditions categorized by hand grip strength in a general population consisting of middle-aged and older adults. RESULTS: The results of the regression analysis reveal that the performance of the developed models is notably superior to a simple mean-predicting dummy regressor. While the improvement in absolute terms may appear modest, the mean absolute error (6.32 kg for males and 4.53 kg for females) falls within the range considered sufficiently accurate for grip strength estimation. The classification models, instead, excel in categorizing individuals as frail/pre-frail, or healthy, depending on the T-score levels applied for frailty/pre-frailty definition. While cut-off values for frailty vary, the results suggest that the models can moderately detect characteristics associated with frailty (AUC-ROC: 0.70 for males, and 0.76 for females) and viably detect characteristics associated with frailty/pre-frailty (AUC-ROC: 0.86 for males, and 0.87 for females). CONCLUSIONS: The results of this study can enable the adoption of wearable devices as an efficient tool for clinical assessment in older adults with multimorbidities, improving and advancing integrated care, diagnosis and early screening of a number of widespread diseases.

Adenovirus-vectored vaccine containing multidimensionally conserved parts of the HIV proteome is immunogenic in rhesus macaques.

An effective vaccine that can protect against HIV infection does not exist. A major reason why a vaccine is not available is the high mutability of the virus, which enables it to evolve mutations that can evade human immune responses. This challenge is exacerbated by the ability of the virus to evolve compensatory mutations that can partially restore the fitness cost of immune-evading mutations. Based on the fitness landscapes of HIV proteins that account for the effects of coupled mutations, we designed a single long peptide immunogen comprising parts of the HIV proteome wherein mutations are likely to be deleterious regardless of the sequence of the rest of the viral protein. This immunogen was then stably expressed in adenovirus vectors that are currently in clinical development. Macaques immunized with these vaccine constructs exhibited T-cell responses that were comparable in magnitude to animals immunized with adenovirus vectors with whole HIV protein inserts. Moreover, the T-cell responses in immunized macaques strongly targeted regions contained in our immunogen. These results suggest that further studies aimed toward using our vaccine construct for HIV prophylaxis and cure are warranted.

Inferring Epistasis from Genetic Time-series Data.

Epistasis refers to fitness or functional effects of mutations that depend on the sequence background in which these mutations arise. Epistasis is prevalent in nature, including populations of viruses, bacteria, and cancers, and can contribute to the evolution of drug resistance and immune escape. However, it is difficult to directly estimate epistatic effects from sampled observations of a population. At present, there are very few methods that can disentangle the effects of selection (including epistasis), mutation, recombination, genetic drift, and genetic linkage in evolving populations. Here we develop a method to infer epistasis, along with the fitness effects of individual mutations, from observed evolutionary histories. Simulations show that we can accurately infer pairwise epistatic interactions provided that there is sufficient genetic diversity in the data. Our method also allows us to identify which fitness parameters can be reliably inferred from a particular data set and which ones are unidentifiable. Our approach therefore allows for the inference of more complex models of selection from time-series genetic data, while also quantifying uncertainty in the inferred parameters.

Gestational hypertension and "severe" disease: time for a change.

Our understanding and management of gestational hypertension and its variants are substantially hindered by a reliance on antiquated terminology and on practice recommendations based largely on tradition rather than outcomes-based evidence. Unsurprisingly, gestational hypertension remains a major contributor to maternal and neonatal morbidity and mortality rates, with little improvement seen over the past half century except as it relates to better newborn care. Reliance on a binary classification of vastly disparate types and degrees of organ dysfunction (severe or not severe) and the use of nonphysiological and largely arbitrary gestational age cutoffs are particularly problematic. If this situation is to improve, it will be necessary to abandon current misleading terminology and non-evidence-based traditional practice patterns and start again, building on management approaches validated by outcomes-based data.

Care plan for individuals at risk for preeclampsia: shared approach to education, strategies for prevention, surveillance, and follow-up.

Preeclampsia is a multisystemic disorder of pregnancy that affects 250,000 pregnant individuals in the United States and approximately 10 million worldwide per annum. Preeclampsia is associated with substantial immediate morbidity and mortality but also long-term morbidity for both mother and offspring. It is now clearly established that a low dose of aspirin given daily, beginning early in pregnancy modestly reduces the occurrence of preeclampsia. Low-dose aspirin seems safe, but because there is a paucity of information about long-term effects on the infant, it is not recommended for all pregnant individuals. Thus, several expert groups have identified clinical factors that indicate sufficient risk to recommend low-dose aspirin preventive therapy. These risk factors may be complemented by biochemical and/or biophysical tests that either indicate increased probability of preeclampsia in individuals with clinical risk factors, or more importantly, identify increased likelihood in those without other evident risk. In addition, the opportunity exists to provide this population with additional care that may prevent or mitigate the short- and long-term effects of preeclampsia. Patient and provider education, increased surveillance, behavioral modification, and other approaches to improve outcomes in these individuals can improve the chance of a healthy outcome. We assembled a group with diverse, relevant expertise (clinicians, investigators, advocates, and public and private stakeholders) to develop a care plan in which providers and pregnant individuals at risk can work together to reduce the risk of preeclampsia and associated morbidities. The plan is for care of individuals at moderate to high risk for developing preeclampsia, sufficient to receive low-dose aspirin therapy, as identified by clinical and/or laboratory findings. The recommendations are presented using the GRADE methodology with the quality of evidence upon which each is based. In addition, printable appendices with concise summaries of the care plan's recommendations for patients and healthcare providers are provided. We believe that this shared approach to care will facilitate prevention of preeclampsia and its attendant short- and long-term morbidity in patients identified as at risk for development of this disorder.

Characterizing Spatial Information Loss for Wastewater Surveillance Using crAssphage: Effect of Decay, Temperature, and Population Mobility.

Populations contribute information about their health status to wastewater. Characterizing how that information degrades in transit to wastewater sampling locations (e.g., wastewater treatment plants and pumping stations) is critical to interpret wastewater responses. In this work, we statistically estimate the loss of information about fecal contributions to wastewater from spatially distributed populations at the census block group resolution. This was accomplished with a hydrologically and hydraulically influenced spatial statistical approach applied to crAssphage (Carjivirus communis) load measured from the influent of four wastewater treatment plants in Hamilton County, Ohio. We find that we would expect to observe a 90% loss of information about fecal contributions from a given census block group over a travel time of 10.3 h. This work demonstrates that a challenge to interpreting wastewater responses (e.g., during wastewater surveillance) is distinguishing between a distal but large cluster of contributions and a near but small contribution. This work demonstrates new modeling approaches to improve measurement interpretation depending on sewer network and wastewater characteristics (e.g., geospatial layout, temperature variability, population distribution, and mobility). This modeling can be integrated into standard wastewater surveillance methods and help to optimize sewer sampling locations to ensure that different populations (e.g., vulnerable and susceptible) are appropriately represented.

Optical and physical properties of annealed amorphous niobium oxide thin films.

The physical and optical properties of coatings deposited using physical vapor deposition techniques exhibit changes during post deposition annealing. Optical properties including the index of refraction and spectral transmission vary when coatings are annealed. Physical and mechanical properties such as thickness, density, and stress are also impacted by annealing. In this paper, we study the source of these changes by examining the impact of 150-500°C annealing on N b 2 O 5 films deposited using thermal evaporation and reactive magnetron sputtering. Models based on the Lorentz-Lorenz equation and potential energy considerations explain the data, and rationalize conflicts between previously reported results.

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease.

Drug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance.

Maternal Sepsis: A Review of National and International Guidelines.

Sepsis is a life-threatening syndrome caused by the body's response to infection. The Global Maternal Sepsis Study (GLOSS) suggests sepsis plays a larger role in maternal morbidity and mortality than previously thought. We therefore sought to compare national and international guidelines for maternal sepsis to determine their consistency with each other and the Third International Consensus for Sepsis and Septic Shock (SEPSIS-3). Using Cochrane Database of Systematic Reviews, PubMed, Google Scholar, and organization Web sites, we identified seven guidelines on maternal sepsis in the English language-The American College of Obstetricians and Gynecologists, Society for Maternal-Fetal Medicine, Royal Australian and New Zealand College of Obstetricians and Gynaecologists, Society of Obstetric Medicine of Australia and New Zealand, Royal College of Obstetricians and Gynaecologists, Royal College of Physicians of Ireland Institute of Obstetricians and Gynaecologists, and World Health Organization. Guidelines were reviewed to ascertain the commonality and variation, if any, in definitions of maternal sepsis, tools and criteria utilized for diagnosis, obstetric warning systems used, as well as evaluation and management of maternal sepsis. These variables were also compared with SEPSIS-3. All guidelines provided definitions consistent with a version of the SEPSIS, although the specific version utilized were varied. Clinical variables and tools employed for diagnosis of maternal sepsis were also varied. Evaluation and management of maternal sepsis and septic shock were similar. In conclusion, national and international maternal sepsis guidelines were incongruent with each other and SEPSIS-3 in diagnostic criteria and tools but similar in evaluation and management recommendations. KEY POINTS: · Definitions for maternal sepsis and septic shock are varied.. · Maternal sepsis guidelines differ in proposed criteria and tools.. · Maternal sepsis guidelines have similar management recommendations..

Development of the Sepsis-Associated Adverse Outcomes in Pregnancy Score.

OBJECTIVE: This study aimed to develop and evaluate a scoring system-called the Sepsis-Associated Adverse Outcomes in Pregnancy (SAAP) Score-to identify individuals with maternal infection that have composite maternal adverse outcomes (CMAO). STUDY DESIGN: Using the International Classification of Disease codes, we identified pregnant and postpartum (up to 6 weeks after birth) individuals admitted at our center with a primary diagnosis of infection. The primary outcome was CMAO which included any of the following: maternal intensive care unit admission, surgical intervention, vasopressor use, acute respiratory distress syndrome, pulmonary edema, mechanical ventilation, high-flow nasal cannula, disseminated intravascular coagulation, dialysis, organ failure, venous thromboembolism, or maternal death. Regularized logistic regression was used to identify variables that best discriminate CMAO status. Variables were chosen for inclusion following evaluation of statistical and clinical significance. Model performance was evaluated using area under the curve (AUC) with 95% confidence intervals (CIs), sensitivity, specificity, and predictive values. RESULTS: Of the 23,235 deliveries during the study period, 227 (0.9%) individuals met inclusion criteria and among them CMAO occurred in 39.2% (95% CI: 33.1-45.7%). The SAAP score consisted of six variables (white blood cell count, systolic blood pressure, respiratory rate, heart rate, lactic acid, and abnormal diagnostic imaging) with scores ranging from 0 to 11 and a score of ≥7 being abnormal. An abnormal SAAP score had an AUC of 0.80 (95% CI: 0.74-0.86) for CMAO. The sensitivity and specificity of the SAAP score for CMAO was 0.71 (95% CI: 0.60-0.80) and 0.73 (95% CI: 0.64-0.80), respectively. The positive predictive value was 0.62 (95% CI: 0.52-0.72) and negative predictive value was 0.79 (95% CI: 0.71-0.86). CONCLUSION: Pending external validation, the sixth variable SAAP score may permit early recognition of pregnant and postpartum individuals with infection who are likely to develop adverse maternal outcomes. KEY POINTS: · Sepsis is a leading cause of maternal morbidity and mortality.. · Early recognition improves maternal sepsis outcomes.. · The SAAP score may permit early recognition of maternal adverse outcomes due to infection..

Reloadable Stapler Use during Peripartum Hysterectomy for Placenta Accreta Spectrum: A Novel Surgical Technique and Case Series.

OBJECTIVE: This study aimed to describe a novel surgical technique for the management of antenatally suspected placenta accreta spectrum (PAS). STUDY DESIGN: This is a retrospective, case series of patients with suspected PAS undergoing peripartum hysterectomy with a reloadable articulating stapler at a tertiary care center. RESULTS: Eighteen patients with antenatally suspected PAS were identified and underwent peripartum hysterectomy with the aid of a reloadable stapler. Mean gestational age at delivery was 344/7 ± 11/7 weeks. Mean total operative time (skin-to-skin) was 117.3 ± 39.3 minutes, and 79.8 ± 19.8 minutes for the hysterectomy. Mean blood loss for the entire case was 1,809 ± 868 mL. Mean blood loss for the hysterectomy was 431 ± 421 mL. Mean units of intraoperative red blood cells transfused was 3 ± 1 units. Mean units of postoperative red blood cells transfused was 1 ± 0.5 units. Five cases were complicated by urological injury (two intentional cystotomies). Four patients were admitted to the intensive care unit (ICU) for a mean of ≤24 hours. Mean postoperative LOS was 4.11 ± 1.45 days. Three patients had final pathology that did not demonstrate PAS while four were consistent with accreta, six increta, and five percreta. CONCLUSION: Use of a reloadable articulating stapler device as part of the surgical management of antenatally suspected PAS results in a shorter operative time (117 ± 39 minutes vs. 140-254 minutes previously reported), lower average blood loss (1,809 ± 868 mL vs. 2,500-5,000 mL previously reported) and shorter LOS (4.11 ± 1.45 days vs. 9.8 ± 13.5 days previously reported) compared with traditional cesarean hysterectomy. The reloadable stapling device offers an advantage of more rapidly achieving hemostasis in the surgical management of PAS. KEY POINTS: · PAS is associated with severe maternal morbidity.. · Decreased operative time and blood loss have many clinical benefits.. · Reloadable stapler use for PAS decreases operative time.. · Reloadable stapler use for PAS decreases operative blood loss..

State-of-the-Art Sensors Research in Ireland.

This Special Issue captures a significant portion of the current sensors research excellence in Ireland [...].

MPF-BML: a standalone GUI-based package for maximum entropy model inference.

SUMMARY: Learning underlying correlation patterns in data is a central problem across scientific fields. Maximum entropy models present an important class of statistical approaches for addressing this problem. However, accurately and efficiently inferring model parameters are a major challenge, particularly for modern high-dimensional applications such as in biology, for which the number of parameters is enormous. Previously, we developed a statistical method, minimum probability flow-Boltzmann Machine Learning (MPF-BML), for performing fast and accurate inference of maximum entropy model parameters, which was applied to genetic sequence data to estimate the fitness landscape for the surface proteins of human immunodeficiency virus and hepatitis C virus. To facilitate seamless use of MPF-BML and encourage more widespread application to data in diverse fields, we present a standalone cross-platform package of MPF-BML which features an easy-to-use graphical user interface. The package only requires the input data (protein sequence data or data of multiple configurations of a complex system with large number of variables) and returns the maximum entropy model parameters. AVAILABILITY AND IMPLEMENTATION: The MPF-BML software is publicly available under the MIT License at https://github.com/ahmedaq/MPF-BML-GUI. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies.

HIV is a highly mutable virus, and over 30 years after its discovery, a vaccine or cure is still not available. The isolation of broadly neutralizing antibodies (bnAbs) from HIV-infected patients has led to renewed hope for a prophylactic vaccine capable of combating the scourge of HIV. A major challenge is the design of immunogens and vaccination protocols that can elicit bnAbs that target regions of the virus's spike proteins where the likelihood of mutational escape is low due to the high fitness cost of mutations. Related challenges include the choice of combinations of bnAbs for therapy. An accurate representation of viral fitness as a function of its protein sequences (a fitness landscape), with explicit accounting of the effects of coupling between mutations, could help address these challenges. We describe a computational approach that has allowed us to infer a fitness landscape for gp160, the HIV polyprotein that comprises the viral spike that is targeted by antibodies. We validate the inferred landscape through comparisons with experimental fitness measurements, and various other metrics. We show that an effective antibody that prevents immune escape must selectively bind to high escape cost residues that are surrounded by those where mutations incur a low fitness cost, motivating future applications of our landscape for immunogen design.

Relationship between intact HIV-1 proviruses in circulating CD4+ T cells and rebound viruses emerging during treatment interruption.

Combination antiretroviral therapy controls but does not cure HIV-1 infection because a small fraction of cells harbor latent viruses that can produce rebound viremia when therapy is interrupted. The circulating latent virus reservoir has been documented by a variety of methods, most prominently by viral outgrowth assays (VOAs) in which CD4+ T cells are activated to produce virus in vitro, or more recently by amplifying proviral near full-length (NFL) sequences from DNA. Analysis of samples obtained in clinical studies in which individuals underwent analytical treatment interruption (ATI), showed little if any overlap between circulating latent viruses obtained from outgrowth cultures and rebound viruses from plasma. To determine whether intact proviruses amplified from DNA are more closely related to rebound viruses than those obtained from VOAs, we assayed 12 individuals who underwent ATI after infusion of a combination of two monoclonal anti-HIV-1 antibodies. A total of 435 intact proviruses obtained by NFL sequencing were compared with 650 latent viruses from VOAs and 246 plasma rebound viruses. Although, intact NFL and outgrowth culture sequences showed similar levels of stability and diversity with 39% overlap, the size of the reservoir estimated from NFL sequencing was larger than and did not correlate with VOAs. Finally, intact proviruses documented by NFL sequencing showed no sequence overlap with rebound viruses; however, they appear to contribute to recombinant viruses found in plasma during rebound.

A Smart Archive Box for Museum Artifact Monitoring Using Battery-Less Temperature and Humidity Sensing.

For the first time, this paper reports a smart museum archive box that features a fully integrated wireless powered temperature and humidity sensor. The smart archive box has been specifically developed for microclimate environmental monitoring of stored museum artifacts in cultural heritage applications. The developed sensor does not require a battery and is wirelessly powered using Near Field Communications (NFC). The proposed solution enables a convenient means for wireless sensing with the operator by simply placing a standard smartphone in close proximity to the cardboard archive box. Wireless sensing capability has the advantage of enabling long-term environmental monitoring of the contents of the archive box without having to move and open the box for reading or battery replacement. This contributes to a sustainable preventive conservation strategy and avoids the risk of exposing the contents to the external environment, which may result in degradation of the stored artifacts. In this work, a low-cost and fully integrated NFC sensor has been successfully developed and demonstrated. The developed sensor is capable of wirelessly measuring temperature and relative humidity with a mean error of 0.37 °C and ±0.35%, respectively. The design has also been optimized for low power operation with a measured peak DC power consumption of 900 µW while yielding a 4.5 cm wireless communication range. The power consumption of the NFC sensor is one of the lowest found in the literature. To the author's knowledge, the NFC sensor proposed in this paper is the first reporting of a smart archive box that is wirelessly powered and uniquely integrated within a cardboard archive box.

Feasibility of Sensor Technology for Balance Assessment in Home Rehabilitation Settings.

The increased use of sensor technology has been crucial in releasing the potential for remote rehabilitation. However, it is vital that human factors, that have potential to affect real-world use, are fully considered before sensors are adopted into remote rehabilitation practice. The smart sensor devices for rehabilitation and connected health (SENDoc) project assesses the human factors associated with sensors for remote rehabilitation of elders in the Northern Periphery of Europe. This article conducts a literature review of human factors and puts forward an objective scoring system to evaluate the feasibility of balance assessment technology for adaption into remote rehabilitation settings. The main factors that must be considered are: Deployment constraints, usability, comfort and accuracy. This article shows that improving accuracy, reliability and validity is the main goal of research focusing on developing novel balance assessment technology. However, other aspects of usability related to human factors such as practicality, comfort and ease of use need further consideration by researchers to help advance the technology to a state where it can be applied in remote rehabilitation settings.

Characterization of Intact Proviruses in Blood and Lymph Node from HIV-Infected Individuals Undergoing Analytical Treatment Interruption.

The role of lymphoid tissue as a potential source of HIV-1 rebound following interruption of antiretroviral therapy (ART) is uncertain. To address this issue, we compared the latent viruses obtained from CD4+ T cells in peripheral blood and lymph nodes to viruses emerging during treatment interruption. Latent viruses were characterized by sequencing near-full-length (NFL) proviral DNA and env from viral outgrowth assays (VOAs). Five HIV-1-infected individuals on ART were studied, four of whom participated in a clinical trial of a TLR9 agonist that included an analytical treatment interruption. We found that 98% of intact or replication-competent clonal sequences overlapped between blood and lymph node. In contrast, there was no overlap between 205 latent reservoir and 125 rebound sequences in the four individuals who underwent treatment interruption. However, rebound viruses could be accounted for by recombination. The data suggest that CD4+ T cells carrying latent viruses circulate between blood and lymphoid tissues in individuals on ART and support the idea that recombination may play a role in the emergence of rebound viremia.IMPORTANCE HIV-1 persists as a latent infection in CD4+ T cells that can be found in lymphoid tissues in infected individuals during ART. However, the importance of this tissue reservoir and its contribution to viral rebound upon ART interruption are not clear. In this study, we sought to compare latent HIV-1 from blood and lymph node CD4+ T cells from five HIV-1-infected individuals. Further, we analyzed the contribution of lymph node viruses to viral rebound. We observed that the frequencies of intact proviruses were the same in blood and lymph node. Moreover, expanded clones of T cells bearing identical proviruses were found in blood and lymph node. These latent reservoir sequences did not appear to be the direct origin of rebound virus. Instead, latent proviruses were found to contribute to the rebound compartment by recombination.