Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach

Accurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and timeeffective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates

Effects of the Histone Deacetylase Inhibitor Valproic Acid on Human Pericytes In Vitro

Microvascular pericytes are of key importance in neoformation of blood vessels, in stabilization of newly formed vessels as well as maintenance of angiostasis in resting tissues. Furthermore, pericytes are capable of differentiating into pro-fibrotic collagen type I producing fibroblasts. The present study investigates the effects of the histone deacetylase (HDAC) inhibitor valproic acid (VPA) on pericyte proliferation, cell viability, migration and differentiation. The results show that HDAC inhibition through exposure of pericytes to VPA in vitro causes the inhibition of pericyte proliferation and migration with no effect on cell viability. Pericyte exposure to the potent HDAC inhibitor Trichostatin A caused similar effects on pericyte proliferation, migration and cell viability. HDAC inhibition also inhibited pericyte differentiation into collagen type I producing fibroblasts. Given the importance of pericytes in blood vessel biology a qPCR array focusing on the expression of mRNAs coding for proteins that regulate angiogenesis was performed. The results showed that HDAC inhibition promoted transcription of genes involved in vessel stabilization/maturation in human microvascular pericytes. The present in vitro study demonstrates that VPA influences several aspects of microvascular pericyte biology and suggests an alternative mechanism by which HDAC inhibition affects blood vessels. The results raise the possibility that HDAC inhibition inhibits angiogenesis partly through promoting a pericyte phenotype associated with stabilization/maturation of blood vessels

Properties of the Binary Black Hole Merger GW150914

On September 14, 2015, the Laser Interferometer Gravitational-Wave Observatory (LIGO) detected a gravitational-wave transient (GW150914); we characterize the properties of the source and its parameters. The data around the time of the event were analyzed coherently across the LIGO network using a suite of accurate waveform models that describe gravitational waves from a compact binary system in general relativity. GW150914 was produced by a nearly equal mass binary black hole of masses 36+5−4M⊙ and 29+4−4M⊙; for each parameter we report the median value and the range of the 90% credible interval. The dimensionless spin magnitude of the more massive black hole is bound to be <0.7 (at 90% probability). The luminosity distance to the source is 410+160−180  Mpc, corresponding to a redshift 0.09+0.03−0.04 assuming standard cosmology. The source location is constrained to an annulus section of 610  deg2, primarily in the southern hemisphere. The binary merges into a black hole of mass 62+4−4M⊙ and spin 0.67+0.05−0.07. This black hole is significantly more massive than any other inferred from electromagnetic observations in the stellar-mass regime

Axial MRI biomarkers of spinal cord damage to predict future walking and motor function: a retrospective study

Study design: Retrospective. Objectives: Primary: to assess if axial damage ratios are predictors of future walking after spinal cord injury (SCI), and if they add any predictive value if initial neurological impairment grades are available. Secondary: to determine if lateral spinal cord regions are predictors of future lower extremity motor scores (LEMS). Setting: University/hospital. Methods: Axial T2-weighted MRIs were used. Axial damage ratios and non-damaged lateral cord volumes were calculated. Each participant answered at 1 year after SCI, “Are you able to walk for 150 feet? (45.72 meters)” For the secondary aim, right and left LEMS were used. Results: In total, 145 participants were selected. Individuals that could walk had smaller ratios than those that were unable. Walking and axial damage ratios were negatively correlated. A 0.374 ratio cut-off showed optimal sensitivity/specificity. When initial neurological grades were used, axial damage ratios did not add predictive value. Forty-two participants had LEMS available and were included for the secondary aim. Right cord regions and right LEMS were positively correlated and left regions and left LEMS, but these variables were also correlated with each other. Conclusions: Axial damage ratios were significant predictors of walking ability 1 year after SCI. However, this measure did not add predictive value over initial neurological grades. Lateral cord regions correlated with same-side LEMS, but the opposite was also found, calling this biomarker’s specificity into question. Axial damage ratios may be useful in predicting walking after SCI if initial neurological grades are unavailable. Sponsorship: This research was funded by a National Institutes of Health award, National Institute of Child Health and Development—NIH R03HD094577

The influence of conventional T2 MRI indices in predicting who will walk outside one year after spinal cord injury

Context/Objective: Magnetic resonance imaging (MRI) indices of spinal cord damage are predictive of future motor function after spinal cord injury (SCI): hyperintensity length, midsagittal tissue bridges, and Brain and Spinal Injury Center (BASIC) scores. Whether these indices are predictive of outdoor walking after SCI is unknown. The primary purpose was to see if these MRI indices predict the ability to walk outdoors one-year after SCI. The secondary purpose was to determine if MRI indices provide additional predictive value if initial lower extremity motor scores are available. Design: Retrospective. Clinical T2-weighted MRIs were used to quantify spinal cord damage. Three MRI indices were calculated: midsagittal ventral tissue bridges, hyperintensity length, BASIC scores. Setting: Academic hospital. Participants: 129 participants with cervical SCI. Interventions: Inpatient rehabilitation. Outcomes Measures: One year after SCI, participants self-reported their outdoor walking ability. Results: Midsagittal ventral tissue bridges, hyperintensity length, and BASIC scores significantly correlated with outdoor walking ability (R = 0.34, P \u3c 0.001; R = −0.25, P \u3c 0.01; Rs = −0.35, P \u3c 001, respectively). Using midsagittal ventral tissue bridges and hyperintensity length, the final adjusted R 2 for model 1 = 0.19. For model 2, the adjusted R 2 using motor scores alone = 0.81 and MRI variables were non-significant. All five participants with observable intramedullary hemorrhage reported they were unable to walk one block outdoors. Conclusions: The MRI indices were significant predictors of outdoor walking ability, but when motor scores were available, this was the strongest predictor and neither midsagittal tissue bridges nor hyperintensity length contributed additional value. MRI indices may be a quick and convenient supplement to physical examination when motor testing is unavailable

An Evaluation of Neurocognitive Status and Markers of Immune Activation as Predictors of Time to Death in Advanced HIV Infection

Background: Several markers of immune activation have been identified as potential prognostic markers for human immunodeficiency virus (HIV)–associated morbidity and mortality, but the results from studies are conflicting. Objective: To evaluate whether neurocognitive status and baseline levels of plasma and cerebrospinal fluid tumor necrosis factor α (TNF-α), macrophage chemoattractant protein 1 (MCP-1), matrix metalloproteinase 2 (MMP-2), or macrophage colony-stimulating factor (M-CSF) are associated with time to death in a cohort with advanced HIV infection. Design: Cohort study. Setting: Enrollees in the Northeast AIDS Dementia Study. Participants: Three hundred twenty-nine subjects who were positive for HIV-1 and had a CD4 cell count of less than 200/μL (or <300/μL but with cognitive impairment at baseline) were assessed for CD4 cell count, neurocognitive status, pertinent demographic and clinical variables, and plasma and cerebrospinal fluid HIV RNA, TNF-α, MCP-1, MMP-2, and M-CSF levels. Main Outcome Measures: Cox proportional hazards regression models were used to examine the associations between the variables of interest (using time-dependent covariates, where applicable) and time to death, adjusting for possible confounders. Results: There were 50 deaths in the cohort after a median of 25.2 months of follow-up. The cumulative incidences of death were 7% at 1 year and 16% at 2 years. In Cox proportional hazards regression analyses adjusting for demographic, clinical, and immunological variables, HIV-associated dementia (hazard rate, 6.10; P = .001) was significantly associated with time to death; (log) plasma MCP-1 level (hazard rate, 3.38; P = .08) trended toward significance. Conclusion: In patients with advanced HIV infection, HIV-associated dementia is an independent predictor of time to death. Before the widespread use of highly active antiretroviral therapy (HAART), plasma human immunodeficiency virus (HIV) RNA level and CD4 cell count were considered the best biological prognostic markers of morbidity and survival for patients with HIV infection.1 The use of HAART has resulted in a significant and sustained decrease in HIV-associated morbidity and mortality, 2 presumably mediated through superior virological control enabling a more robust and durable immune reconstitution. Consequently, the predictive value of plasma HIV RNA level seems to have been attenuated by the potency of the new antiretroviral (ARV) therapies.3 Several other markers of immune activation, including neopterin,4 β2-microglobulin,5 and plasma tumor necrosis factor α (TNF-α),6 have been identified as potential prognostic markers for HIV-associated morbidity and mortality, but the results from these studies are conflicting. Possible associations were recently reported between plasma TNF-α and cerebrospinal fluid macrophage chemoattractant protein 1 (MCP-1) levels and the development of HIV-associated dementia (HIVD) in a HAART-experienced cohort with advanced HIV infection.7 Clinical and demographic criteria have been correlated with HIV-associated morbidity and mortality. Pre–HAART era studies8-11 identified cognitive impairment and psychomotor slowing as predictors of mortality. These publications did not describe the relationship between the syndromic diagnosis of HIVD and mortality, but another pre–HAART era study12 failed to find a significant association between onset of dementia and mortality. The objective of this study was to determine whether neurocognitive status and baseline levels of plasma and cerebrospinal fluid TNF-α, MCP-1, matrix metalloproteinase 2 (MMP-2), or macrophage colony-stimulating factor (M-CSF) are associated with time to death in a well-characterized cohort of HAART-experienced subjects with advanced HIV. Methods: Participants in this study were enrolled in the Northeast AIDS Dementia Study cohort.7 From April 14, 1998, through July 22, 2002, we recruited ambulatory subjects who were seropositive for HIV and had a CD4+ cell count of less than 200/μL (or <300/μL but with cognitive impairment) at Columbia University, New York, NY; University of Rochester, Rochester, NY; The Johns Hopkins University, Baltimore, Md; and (beginning in 1999) Northwestern University, Chicago, Ill. Subjects with concurrent or past schizophrenia, severe affective disorder, central nervous system infection, or other chronic neurological disorders were excluded; subjects were not evaluated if they were under the influence of alcohol or illicit drugs, as judged by the examining physician. Subjects underwent semiannual evaluations. Institutional review board and ethics committee approval was obtained at each institution, and informed consent was obtained from each participant. Clinical and demographic assessments: The clinical and demographic data collected included the following: age, sex, race/ethnicity, years of education, use of illicit drugs, date of HIV diagnosis, history of AIDS-defining illness (clinical category C), and type of ARV use. The type of ARV use was classified as none, 1 to 2 ARVs, or 3 ARVs or more (HAART). Age, years of education, and duration of HIV were treated as continuous variables and sex, race/ethnicity, use of illicit drugs, history of AIDS-defining illness, and type of ARV use were treated as categorical variables in the analyses. Neurocognitive assessments: The clinical evaluations focused on the signs and symptoms associated with HIVD and included a neurological examination, neuropsychological battery, functional assessment, and psychiatric assessment, as previously described.7 The neuropsychological battery included 8 tests covering the following 6 cognitive domains: verbal memory (Rey Auditory Verbal Learning Test), visual memory (Rey-Osterrieth Complex Figure Delayed Recall Test), construction (Rey-Osterrieth Complex Figure Copy), psychomotor (Digit Symbol Test), motor speed (Grooved Pegboard and Timed Gait), and frontal systems (Verbal Fluency and Odd-Man-Out Test).7 Performance on each test was referenced to age- and education-appropriate norms where available.13,14 Based on the results from these clinical assessments, subjects were categorized as nonimpaired, as having minor cognitive and motor disorder (MCMD), or as demented (having HIVD) using the American Academy of Neurology criteria.15 Neurocognitive status was treated as a categorical variable in the analyses. For purposes of enrollment, cognitive impairment was defined as performing at least 1 SD below the mean on 2 separate neuropsychological tests (or 2 SDs below the mean on 1 test). However, if Timed Gait was the only test for which a score was 2 SDs below the mean, then criteria for cognitive impairment were not met. Laboratory assessments: Baseline assessments of CD4 cell count, hemoglobin level, and levels of HIV RNA, MCP-1, TNF-α, M-CSF, and MMP-2 in plasma and cerebrospinal fluid were performed. In addition, CD4 cell count, hemoglobin level, and plasma and cerebrospinal fluid HIV RNA levels were measured at follow-up visits (cerebrospinal fluid was measured only annually). The HIV RNA levels were determined using the NucliSens QT assay (logarithm of odds, 80 copies/mL; bioMerieux, Inc, Durham, NC); the TNF-α, MCP-1, M-CSF, and MMP-2 levels were determined using Quantikine ELISA kits (R&D Systems, Minneapolis, Minn). Values were log-transformed in base 10, except for CD4 cell count, for which the natural logarithm (ln) was used. All biological markers were treated as continuous variables in the analyses. Data analyses: The primary outcome for this study was time from study enrollment to death. Only subjects with at least 1 follow-up were included in the analyses. A subject was classified as deceased based on information from a friend, family member, medical record, or death certificate. Subjects not completing the study were classified as withdrawals. For subjects who withdrew or survived until the end of scheduled follow-up, follow-up time was censored at the last available visit. Baseline variables were compared among the deceased, those who completed follow-up, and those who withdrew from the study using t and χ2 tests. A Kaplan-Meier curve was constructed to estimate the cumulative incidence of death for subjects with at least 1 follow-up assessment. Associations between the independent variables and time to death were examined using Cox proportional hazards regression models. Independent variables with values that could change over time were treated as time-dependent covariates, except for plasma and cerebrospinal fluid immune markers, for which only baseline values were examined. Univariate analyses were performed on the independent variables. Next, Cox proportional hazards regression models were created to examine whether (in separate analyses) CD4 cell count, neurocognitive status (MCMD or HIVD), and plasma and cerebrospinal fluid levels of HIV RNA, MCP-1, TNF-α, MMP-2, and M-CSF were independent predictors of time to death, adjusting for the following core group of variables considered to be potential confounders: age, sex, hemoglobin level, HAART use (yes or no), race/ethnicity (nonwhite vs white), history of HIV-related illness, and National Adult Reading Test score (a measure of IQ). Finally, Cox proportional hazards regression models containing the core variables and various combinations of the immune markers, CD4 cell count, and neurocognitive status (nonimpaired, MCMD, or HIVD) were examined. All of the Cox regression models included site of enrollment as a stratification factor. Results: Of 396 subjects enrolled into the study, 329 (83%) had at least 1 follow-up visit. The median total duration of follow-up for the cohort was 25.2 months (interquartile range, 14.3-41.7 months). One hundred seventy-four subjects (53%) completed all scheduled follow-up visits, 50 subjects (15%) died, and 105 subjects (32%) withdrew prematurely. The chief reason (90%) for withdrawal was loss to follow-up (eg, unavailability or chose not to continue among other reasons). Those who withdrew had a shorter median total duration of follow-up (19.5 months [interquartile range, 12.0-29.5 months]). The baseline characteristics of the cohort, overall and stratified by follow-up status (completed, died, or withdrew), are summarized in Table 1. The estimated cumulative incidences of death were 7% at 1 year and 16% at 2 years (Figure). Compared with subjects who completed follow-up, those who died were more likely at baseline to have had an AIDS-defining illness, a lower hemoglobin level, a lower (ln) CD4 cell count, an abnormal neurocognitive status (MCMD or HIVD), a higher (log) plasma HIV RNA level, and higher (log) plasma and cerebrospinal fluid MCP-1 levels. In univariate analyses, significant associations were found between time to death and HAART use, HIVD, hemoglobin level, (ln) CD4 cell count, history of AIDS-defining illness, (log) plasma MCP-1 level, (log) plasma HIV RNA level, and (log) cerebrospinal fluid MCP-1 level. These results are summarized in Table 2. In the Cox proportional hazards regression analyses adjusting for the 7 core variables, the following were significantly associated with time to death: HIVD (Table 3, model A), (log) plasma MCP-1 level (Table 4, model A), and (ln) CD4 cell count (hazard rate [HR], 0.64; 95% confidence interval [CI], 0.51-0.81; P<.001). Not significant were MCMD (Table 3, model A), (log) cerebrospinal fluid MCP-1 level (Table 4, model A), (log) plasma HIV RNA level (HR, 1.17; 95% CI, 0.92-1.48; P = .19), and (log) cerebrospinal fluid HIV RNA level (HR, 0.89; 95% CI, 0.60-1.33; P = .58). In models adjusting for the 7 core variables and (ln) CD4 cell count, HIVD (Table 3, model B) was significantly associated with time to death. Not significant were MCMD (Table 3, model B), (log) plasma MCP-1 level (Table 4, model B), and (log) cerebrospinal fluid MCP-1 level (Table 4, model B). In a model containing the 7 core variables, neurocognitive status (MCMD or HIVD), (1n) CD4 cell count, and (log) MCP-1 (plasma or CSF), the following were significantly associated with time to death: HIVD (Table 3A, model C) and (1n) CD4 (HR, 0.73; 95% CI, 0.56-0.96; P = .02). Not significant were MCMD (Table 3, model C), (log) plasma MCP-1 (Table 4, model D), and (log) CSF MCP-1 (Table 4, model D). Of the 1517 subject-visits that occurred, there were 427 subject-visits (28%) by 196 subjects (60%) at which the subject met criteria for HIVD. The most common neuropsychological test abnormalities found in subjects with HIVD at these visits were in the domains of verbal memory (Rey Auditory Verbal Learning Test: 72% ≥1 SD below age- and education-appropriate norms and 38% ≥2 SDs below norms), construction (Rey-Osterrieth Complex Figure Copy: 66% ≥1 SD below norms and 48% ≥2 SDs below norms), and motor speed (Grooved Pegboard: 63% ≥1 SD below norms and 38% ≥2 SDs below norms; Timed Gait: 59% ≥1.5 SDs below norms and 41% ≥2.5 SDs below norms)