DNA analysis can strengthen identification. Third, DNA analysis may have other applications, such as in archaeology— determining the source, local or imported, of cordage found at an excavation. Finally, with advancements in technology, DNA analysis could eventually provide a background for identifying individual samples of rope, in addition to the rope’s botanical origin.Human immunodeficiency virus infection is often accompanied by chronic fatigue and disrupted sleep patterns . A considerable number of people with HIV report sleep disturbance, with some studies estimating the prevalence of symptoms to be up to five times that of the general population . PWH face a variety of unique social , physical , and socioeconomic stressors , which may influence sleep disturbance . Prolonged poor sleep quality among PWH is associated with anxiety, depression, loss of productivity, interference with employment, physiologic stress, and poorer quality of life . Methamphetamine , a central nervous system stimulant, is among the most commonly used addictive drugs, with 35 million users per year worldwide . PWH and individuals at risk for HIV transmission, such as men who have sex with men, have a particularly high prevalence of MA use . A recent study on MA-dependent gay and bisexual men reported the prevlance of HIV infection to be 63% . Among PWH, MA is linked to accelerated viral replication, more rapid progression to AIDS, reduced effectiveness of antiretroviral therapy , and increased immune suppression . Global neuropsychological impairment and dependence on basic and instrumental activities of daily living are more common among PWH who also use MA than among those who do not, with an additive effect of HIV and MA on neuronal injury and glial activation . Despite these negative effects, perceived benefits, such as sexual enhancement and relief of negative psychosocial symptoms, continue to drive MA use among PWH . MA functions by stimulating monoamine release , and facilitates hyperactivity, euphoria, feelings of increased mental and physical capacity, and riskier sexual behavior . Among the general population, prolonged MA use can have detrimental effects on alertness, mood, cognition, and activity levels .

MA use also has been associated with poor sleep quality, increased sleep latency, and daytime sleepiness . Cessation of MA is often accompanied by withdrawal symptoms such as anxiety, depression, and craving that can further contribute to poor sleep quality. The adverse effects of MA also contribute to functional decline , such as unemployment , which also may exacerbate sleep disturbance. Among MA-using PWH, poorer adherence and missing ART doses after MA use have been reported, in part due to disrupted sleep-wake cycles . Taken together, acute and chronic MA use can have multiple direct and indirect effects on sleep quality.Few studies have examined the combined associations of MA use and HIV on sleep disturbance. This study evaluates effects of lifetime MA use on self-reported sleep quality among participants with or without HIV infection. The hypothesis was that lifetime MA use disorder would be associated with poorer sleep quality, particularly among PWH, and that this would relate to poor outcomes, including poorer cognition, reduced independence in activities of daily living, unemployment, and poorer life quality. Participants included 225 HIV-seropositive and 88 HIV-seronegative adults enrolled in NIH-funded research studies at the UC San Diego’s HIV Neurobehavioral Research Center . All participants completed a standard, selfreport evaluation of sleep quality as well as comprehensive neurobehavioral and neuromedical assessments. Exclusion criteria were: 1) sleep apnea or restless leg syndrome; 2) disruptions to sleep due to temporary circumstances ; 3) history of comorbid neurological illness or injury that would affect cognitive functioning ; 4) history of psychotic disorder; 5) alcohol dependence within a year; and 6) low premorbid verbal IQ as estimated by a Wide Range Achievement Test-4 score less than 80. The study protocol was approved by the UC San Diego Institutional Review Board and each participant provided written, informed consent. The Composite International Diagnostic Interview  was administered to diagnose participants for current and lifetime substance use and mood disorders , as defined by the Fourth edition of the Diagnostic and Statistical Manual of Mental Disorders . For the initial analyses, participants were stratified into four groups based on HIV status and lifetime MA use disorder diagnosis: HIV +/MA+ ; HIV+/MA− ; HIV−/MA+ ; and HIV−/MA− .

Current depressive symptoms were assessed using the Beck Depression Inventory, Second Edition . Item 16 on the BDI-II, which assesses change in sleep pattern in the last two weeks, was excluded from the BDI-II total score to avoid collinearity with our outcome of interest, perceived sleep quality. All participants completed the Pittsburgh Sleep Quality Index , a self-report questionnaire that assesses perceptions of average sleep quality and disturbances over the past 30 days . The PSQI is a widely used and well-validated measure of subjective sleep quality in adults . The PSQI has 19-items that assesses seven components of sleep, including quality, latency, duration, efficiency, disturbances,vertical grow lights use of medications to aid sleeping, and daytime sleepiness. Component scores range from 0 to 3 . Items were summed to generate a continuous global sleep score ranging from 0 to 21. Global scores > 5 indicate problematic sleep . For purposes of the present study, the continuous global PSQI score and dichotomous sleep quality classification were used as outcome variables.All participants underwent a standardized medical history interview, neuromedical examination, and blood and urine collection. HIV serological status was confirmed via ELISA and Western blot test, and HIV RNA levels were measured in plasma by rtPCR . Current CD4+ T-cell count was measured in blood by clinical flow cytometry. Additional HIV disease and treatment variables included nadir CD4+ T-cell count, AIDS diagnosis, estimated duration of HIV disease, and current ART regimen. MA use characteristics were self-reported. Comorbid medical conditions and current medication use were determined by self-report and medical chart review.All participants completed a comprehensive and validated neurocognitive assessment across seven neurocognitive domains commonly affected by HIV and MA use ; these include verbal fluency, executive functioning, speed of information processing, learning and memory , working memory/attention, and motor. Using established normative standards, test scores were adjusted for known influences on neurocognitive performance . Deficit scores were calculated for each domain and averaged across the test battery to derive a global deficit score ranging from 0 to 5 . Dependence in instrumental activities of daily living was determined using a revised version of the Lawton and Brody ADL questionnaire , in which participants rated current degree of independence as compared to prior best level of independence across 13 IADL domains. Participants were classified as IADL “dependent” if they endorsed requiring increased assistance in at least 2 IADL domains. Employment status and symptoms of cognitive difficulties in daily life were determined via the Patient’s Assessment of Own Functioning Inventory . The Karnofsky Performance Status Scale is a clinician administered assessment of disease-related functional impairment with a range from 0 to 100 with standard intervals of 10 . Self-reported physical and mental health quality of life were assessed using the Medical Outcomes Study Short-Form Survey . Physical and mental health composite scores were calculated via validated summary score formulas derived from an obliquely rotated factor solution . Group differences on demographics, neuropsychiatric and neuromedical characteristics, HIV disease and treatment parameters, MA use history, and global sleep outcomes were tested using analysis of variance , Kruskal-Wallis tests, Chi-square statistics, or Fisher’s Exact test . Two-tailed t-tests were used to compare groups on HIV disease and methamphetamine use characteristics. Follow-up pairwise comparisons were conducted using Tukey’s Honest Significant Difference or Wilcoxon tests for continuous outcomes, or Bonferroni-corrections for categorical outcomes.

Cohen’s d measured effect size for pairwise comparisons of means. Based on the pattern of univariable group differences in global sleep health and the small sample size of the HIV−/MA+ group, multiple linear regression examined global sleep scores as a function of MA status and clinical covariates specifically within PWH. Covariates included clinical variables from Table I with univariable associations with the primary independent variable [MA status ] as well as associations with the primary dependent variable with p values < 0.10. Variables sex and sexual orientation were included based on theoretical evidence . Additionally, HIV disease and treatment covariates were included to determine if HIVspecific factors attenuated the effects of MA status on global sleep in PWH. Stepwise regression models used backward selection based on Akaike Information Criterion to select the optimal model. To determine potential co-occuring neurobehavioral functional impairments associated with poor sleep quality within the dual-risk HIV+/MA+ group, additional nominal logistic regression models based on AIC were run to examine the association between problematic sleep membership and neurobehavioral outcomes . Covariates were selected based on univariable associations with global PSQI and did not include HIV or methamphetamine characteristics.Multiple regression analysis within PWH examined the independent contribution of MA status on Global PSQI scores while adjusting for clinical covariates and HIV-disease specific factors . Based on univariable associations with the primary independent variable [MA status ], the following were included as covariates in AIC-based regression: age, sex, education, BDI-II scores, lifetime alcohol use disorder, lifetime cocaine use disorder, lifetime cannabis use disorder, MA use in the last 30 days, and HCV. In addition, body mass index was added to the model based on its association with the primary dependent variable , along with sexual orientation and HIV-specific covariates and contained lifetime MA use disorder, having higher BDI-II scores, higher BMI, and detectable HIV RNA being associated with higher global PSQI scores. In considering the possible contribution of extraneous variables that may be common among participants who reported recent MA use, the regression model was rerun after excluding for those who endorsed MA use within the last 30 days . Using AIC selection criteria, lifetime MA use disorder continued to significantly contribute to the variance in sleep quality . Similarly, to focus on a clinically relevant subgroup, the regression model was rerun after excluding participants who were off ART or had HIV RNA levels above 200 copies/ml . In this virologically suppressed subgroup, lifetime MA dependence again remained associated with global sleep based on AIC selection . Rates of MA use are elevated among PWH and are associated with poorer sleep quality in the general population . The present study is the first to explore the relationships between past MA use disorder, HIV disease, and sleep quality. Our results demonstrate that PWH who have a history of prior MA use disorder had significantly poorer sleep quality and were more likely to be classified as problematic sleepers than those without a lifetime disorder. This relationship between lifetime MA use disorder among PWH is robust to MA group differences in biopsychosocial factors and is linked to sleep quality above and beyond the effects of HIV disease severity and other established risk factors for poor sleep.