How to fail at species delimitation Carstens, Bryan C.; Pelletier, Tara A.; Reid, Noah M. ...
Molecular ecology,
September 2013, Volume:
22, Issue:
17
Journal Article
Peer reviewed
Open access
Species delimitation is the act of identifying species‐level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting ...species. However, most recent investigations only utilize a handful (i.e. 2–3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Climate change induced by anthropogenic warming of the earth's atmosphere is a daunting problem. This review examines one of the consequences of climate change that has only recently attracted ...attention: namely, the effects of climate change on the environmental distribution and toxicity of chemical pollutants. A review was undertaken of the scientific literature (original research articles, reviews, government and intergovernmental reports) focusing on the interactions of toxicants with the environmental parameters, temperature, precipitation, and salinity, as altered by climate change. Three broad classes of chemical toxicants of global significance were the focus: air pollutants, persistent organic pollutants (POPs), including some organochlorine pesticides, and other classes of pesticides. Generally, increases in temperature will enhance the toxicity of contaminants and increase concentrations of tropospheric ozone regionally, but will also likely increase rates of chemical degradation. While further research is needed, climate change coupled with air pollutant exposures may have potentially serious adverse consequences for human health in urban and polluted regions. Climate change producing alterations in: food webs, lipid dynamics, ice and snow melt, and organic carbon cycling could result in increased POP levels in water, soil, and biota. There is also compelling evidence that increasing temperatures could be deleterious to pollutant-exposed wildlife. For example, elevated water temperatures may alter the biotransformation of contaminants to more bioactive metabolites and impair homeostasis. The complex interactions between climate change and pollutants may be particularly problematic for species living at the edge of their physiological tolerance range where acclimation capacity may be limited. In addition to temperature increases, regional precipitation patterns are projected to be altered with climate change. Regions subject to decreases in precipitation may experience enhanced volatilization of POPs and pesticides to the atmosphere. Reduced precipitation will also increase air pollution in urbanized regions resulting in negative health effects, which may be exacerbated by temperature increases. Regions subject to increased precipitation will have lower levels of air pollution, but will likely experience enhanced surface deposition of airborne POPs and increased run-off of pesticides. Moreover, increases in the intensity and frequency of storm events linked to climate change could lead to more severe episodes of chemical contamination of water bodies and surrounding watersheds. Changes in salinity may affect aquatic organisms as an independent stressor as well as by altering the bioavailability and in some instances increasing the toxicity of chemicals. A paramount issue will be to identify species and populations especially vulnerable to climate–pollutant interactions, in the context of the many other physical, chemical, and biological stressors that will be altered with climate change. Moreover, it will be important to predict tipping points that might trigger or accelerate synergistic interactions between climate change and contaminant exposures.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
We introduce the light-weight carbon fiber and aluminum gondola designed for the SPIDER balloon-borne telescope. SPIDER is designed to measure the polarization of the Cosmic Microwave Background ...radiation with unprecedented sensitivity and control of systematics in search of the imprint of inflation: a period of exponential expansion in the early Universe. The requirements of this balloon-borne instrument put tight constrains on the mass budget of the payload. The SPIDER gondola is designed to house the experiment and guarantee its operational and structural integrity during its balloon-borne flight, while using less than 10% of the total mass of the payload. We present a construction method for the gondola based on carbon fiber reinforced polymer tubes with aluminum inserts and aluminum multi-tube joints. We describe the validation of the model through Finite Element Analysis and mechanical tests.
Myocardial dysfunction after Fontan palliation for univentricular congenital heart disease is a challenging clinical problem. The medical treatment has a limited impact, with cardiac transplant being ...the ultimate management step. Cell-based therapies are evolving as a new treatment for heart failure. Phase 1 clinical trials using regenerative therapeutic strategies in congenital heart disease are ongoing. We report the first case of autologous bone marrow–derived mononuclear cell administration for ventricular dysfunction, 23 years after Fontan operation in a patient with hypoplastic left heart syndrome. The cells were delivered into the coronary circulation by cardiac catheterization. Ventricular size decreased and several parameters reflecting ventricular function improved, with maximum change noted 3 months after cell delivery. Such regenerative therapeutic options may help in delaying and preventing cardiac transplant.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract Background The association between early physical therapy (PT) and subsequent healthcare utilization following a new visit for low back pain is not clear, particularly in the setting of ...acute low back pain. Purpose To estimate the association between initiating early physical therapy following a new visit for an episode of low back pain and subsequent back-pain-specific health care utilization in older adults. Study Design/Setting Prospective cohort study. Data were collected at 3 integrated health care systems in the United States through the Back Pain Outcomes using Longitudinal Data (BOLD) registry. Patient Sample 4,723 adults, aged 65 and older, presenting to a primary care setting with a new episode of low back pain. Outcome Measures Primary outcome was total back-pain-specific relative value units (RVUs), from days 29-365. Secondary outcomes included overall RVUs for all healthcare and use of specific health care services including: imaging (x-ray and MRI or CT), Emergency Department visits, physician visits, physical therapy, spinal injections, spinal surgeries and opioid use. Methods We compared patients that had early PT (initiated within 28 days of the index visit) to those not initiating early PT using appropriate, generalized linear models to adjust for potential confounding variables. BOLD was funded by an Agency for Healthcare Research and Quality grant, R01 HS019222-01. The authors report no potential conflict of interest related to this study. Results Adjusted analysis found no statistically significant difference in total spine RVUs between the two groups (ratio of means 1.19, 95% CI of 0.72 to 1.96, p=0.49). For secondary outcomes, only the difference between total spine imaging RVUs and total PT RVUs was statistically significant. The early PT group had greater PT RVUs, the ratio of means was 2.56 (95% CI of 2.17-3.03, p<0.001.) The early PT group had greater imaging RVUs, the ratio of means was 1.37 (95% CI of 1.09-1.71, p=0.01.) Conclusions We found that, in a group of older adults presenting for a new episode of low back pain, the use of early PT is not associated with any statistically significant difference in subsequent back-pain-specific healthcare utilization compared to patients not receiving early PT.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Motivated by a Finnish case‐control study of early onset diabetes in which diabetic children are matched to sibling controls, we investigate ascertainment bias of the usual rate ratio estimator from ...case‐control data under simplex complete ascertainment of families during a fixed interval of time. Analytic results indicate that the assumptions necessary for valid estimation are that the disease is rare and the factors under study are exchangeable–essentially that the covariate distribution does not depend on calendar time or birth order. Further, we found that the rare disease assumption could be dropped by restricting to cases that were diagnosed during the enrollment period of the study or including all cases but eliminating the proband as a control for non‐enrollment‐period cases. An important consequence of this work is that standard family‐based case‐control studies are subject to ascertainment bias if exchangeability of the covariates under investigation does not hold.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, INZLJ, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZRSKP
Objective
This study aimed to examine the effectiveness of cognitive processing therapy (CPT) for posttraumatic stress disorder (PTSD) when administered on a daily basis during a 2‐week period of ...time.
Method
In an open‐label, prospective cohort pilot trial, 20 U.S. military personnel and veterans diagnosed with PTSD or subthreshold PTSD participated in 12 daily sessions of CPT. Primary outcomes included Clinician Administered PTSD Scale for DSM‐5 and PTSD Checklist for DSM‐5 scores. Secondary outcomes included Patient Health Questionnaire‐8 and Beck Scale for Suicide Ideation (BSSI) scores. Interviews and self‐report scales were completed at pretreatment, posttreatment, and 6 months after the treatment.
Results
Relative to baseline, PTSD symptom severity and rates of PTSD diagnosis were significantly reduced at posttreatment and 6‐month follow‐up. Depression symptom severity did not significantly improve, but suicide ideation significantly decreased at 6‐month follow‐up.
Conclusions
Daily administration of CPT is associated with significant reductions in PTSD and suicide ideation.
Full text
Available for:
BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
A full description of the human proteome relies on the challenging task of detecting mature and changing forms of protein molecules in the body. Large-scale proteome analysis has routinely involved ...digesting intact proteins followed by inferred protein identification using mass spectrometry. This 'bottom-up' process affords a high number of identifications (not always unique to a single gene). However, complications arise from incomplete or ambiguous characterization of alternative splice forms, diverse modifications (for example, acetylation and methylation) and endogenous protein cleavages, especially when combinations of these create complex patterns of intact protein isoforms and species. 'Top-down' interrogation of whole proteins can overcome these problems for individual proteins, but has not been achieved on a proteome scale owing to the lack of intact protein fractionation methods that are well integrated with tandem mass spectrometry. Here we show, using a new four-dimensional separation system, identification of 1,043 gene products from human cells that are dispersed into more than 3,000 protein species created by post-translational modification (PTM), RNA splicing and proteolysis. The overall system produced greater than 20-fold increases in both separation power and proteome coverage, enabling the identification of proteins up to 105 kDa and those with up to 11 transmembrane helices. Many previously undetected isoforms of endogenous human proteins were mapped, including changes in multiply modified species in response to accelerated cellular ageing (senescence) induced by DNA damage. Integrated with the latest version of the Swiss-Prot database, the data provide precise correlations to individual genes and proof-of-concept for large-scale interrogation of whole protein molecules. The technology promises to improve the link between proteomics data and complex phenotypes in basic biology and disease research.
Full text
Available for:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Advances in spectroscopic techniques have led to an increase in the use of optical properties (absorbance and fluorescence) to assess dissolved organic matter (DOM) composition and infer sources and ...processing. However, little information is available to assess the impact of biological and photolytic processing on the optical properties of original DOM source materials. Over a 3.5 month laboratory study, we measured changes in commonly used optical properties and indices in DOM leached from peat soil, plants, and algae following biological and photochemical degradation to determine whether they provide unique signatures that can be linked to original DOM source. Changes in individual optical parameters varied by source material and process, with biodegradation and photodegradation often causing values to shift in opposite directions. Although values for different source materials frequently overlapped, multivariate statistical analyses showed that unique optical signatures could be linked to original DOM source material, with 17 optical properties determined by discriminant analysis to be significant (p < 0.05) in distinguishing between DOM source and environmental processing. These results demonstrate that inferring source material from optical properties is possible when parameters are evaluated in combination even after extensive biological and photochemical alteration.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
PDF
