Biodiversity recovery of Neotropical secondary forests

Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of ve decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both oldgrowth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modied tropical landscapes

Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90815, doi:10.1371/journal.pone.0090815.Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.This work was supported by the National Science Foundation grant OCE-0430724, and the National Institute of Environmental Health Sciences grant P0ES012742 to the Woods Hole Center for Ocean and Human Health. E. Halliday was partially supported by WHOI Academic Programs and grants from the WHOI Ocean Ventures Fund and the WHOI Coastal Ocean Institute

Evidence-based sizing of non-inferiority trials using decision models

Abstract Background There are significant challenges to the successful conduct of non-inferiority trials because they require large numbers to demonstrate that an alternative intervention is “not too much worse” than the standard. In this paper, we present a novel strategy for designing non-inferiority trials using an approach for determining the appropriate non-inferiority margin (δ), which explicitly balances the benefits of interventions in the two arms of the study (e.g. lower recurrence rate or better survival) with the burden of interventions (e.g. toxicity, pain), and early and late-term morbidity. Methods We use a decision analytic approach to simulate a trial using a fixed value for the trial outcome of interest (e.g. cancer incidence or recurrence) under the standard intervention (pS) and systematically varying the incidence of the outcome in the alternative intervention (pA). The non-inferiority margin, pA – pS = δ, is reached when the lower event rate of the standard therapy counterbalances the higher event rate but improved morbidity burden of the alternative. We consider the appropriate non-inferiority margin as the tipping point at which the quality-adjusted life-years saved in the two arms are equal. Results Using the European Polyp Surveillance non-inferiority trial as an example, our decision analytic approach suggests an appropriate non-inferiority margin, defined here as the difference between the two study arms in the 10-year risk of being diagnosed with colorectal cancer, of 0.42% rather than the 0.50% used to design the trial. The size of the non-inferiority margin was smaller for higher assumed burden of colonoscopies. Conclusions The example demonstrates that applying our proposed method appears feasible in real-world settings and offers the benefits of more explicit and rigorous quantification of the various considerations relevant for determining a non-inferiority margin and associated trial sample size.https://deepblue.lib.umich.edu/bitstream/2027.42/146777/1/12874_2018_Article_643.pd

Complications of Decompressive Craniectomy

Introduction: Persistent elevation of intracranial pressure (ICP), if untreated, may lead to brain ischemia or lack of brain oxygen and even brain death.1-6,10 When standard treatments for elevated ICP are exhausted without any signs of improvement, decompressive craniectomy can be an effective alternative solution.7,19 Decompressive craniectomies (DC) have been used as a method of controlling intracranial pressure in patients with cerebral edema secondary to cerebral ischemia, subarachnoid hemorrhage (SAH), and traumatic brain injury (TBI), among others. 8-10 Several studies over the years have demonstrated the efficacy of this procedure.7-9,11,35,36 However, consensus is still lacking in the utility of DC as an effective first tier treatment for intractable intracranial pressure due to the rudimentary neurological outcome assessments, and the many complications associated with this procedure.11,12,59 There are a limited number of studies that have looked at complications secondary to the procedure itself.13-18 The majority of these studies only investigated the impact of this procedure in patients with traumatic brain injury. The purpose of this study is to investigate the rates of various complications associated with the decompressive craniectomy procedure in patients that did not suffer from traumatic brain injury, and to determine whether the same associations between preoperative parameters and development of complications can be made

The Effect of Including eHealth in Dietary Interventions for Patients with Type 2 Diabetes with Overweight or Obesity:A Systematic Review

eHealth has a growing impact on the delivery of healthcare, making health systems more efficient. This study examined the effect of dietary interventions using eHealth compared to face-to-face contact in patients with (pre-) type 2 diabetes (T2D) and who are overweight/obese. Literature databases were searched upon November 2022. Inclusion criteria: randomized controlled trial; duration ≥ 6 months; involving dietary interventions; performed in adults with (pre-) T2D and who are overweight/obese; using eHealth compared to face-to-face contact; and report outcomes on weight loss, glycemic regulation, and/or cost-effectiveness. Selection of articles was performed manually and using ASReviewLab. Fifteen studies were included for data extraction, investigating a wide variety of eHealth interventions. Seven studies reporting on weight loss showed a significant between-group difference (−1.18 to −5.5 kg); five studies showed a trend in favor of the eHealth programs. Eleven studies reported on HbA1c; three found a significant between-group difference (−0.23 to −0.70%) in favor of the eHealth programs and six studies showed non-significant improvements. Interaction with healthcare professionals led to better results of the dietary interventions. Two studies reported incomplete data on cost-effectiveness. In conclusion, eHealth shows better results of dietary interventions in (pre-) T2D patients compared to face-to-face, especially when combined with interaction with healthcare professionals.</p

A single genus in the gut microbiome reflects host preference and specificity

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 90–100, doi:10.1038/ismej.2014.97.Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns within members of this genus. In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping. Our analysis revealed 13 host-specific oligotypes that occurred exclusively in fecal samples of humans (three oligotypes), swine (six oligotypes), cows (one oligotype), deer (one oligotype), or chickens (two oligotypes). We identified an additional 171 oligotypes that exhibited differential abundance patterns among all the host species. Blautia oligotypes in the human population obtained from sewage and fecal samples displayed remarkable continuity. Oligotypes from only 10 Brazilian human fecal samples collected from individuals in a rural village encompassed 97% of all Blautia oligotypes found in a Brazilian sewage sample from a city of three million people. Further, 75% of the oligotypes in Brazilian human fecal samples matched those in US sewage samples, implying that a universal set of Blautia strains may be shared among culturally and geographically distinct human populations. Such strains can serve as universal markers to assess human fecal contamination in environmental samples. Our results indicate that host-specificity and host-preference patterns of organisms within this genus are driven by host physiology more than dietary habits.This study was funded by the NIH grant R01AI091829-01A1 to SLM

Sewage reflects the microbiomes of human populations

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 6 (2015): e02574-14, doi:10.1128/mBio.02574-14.Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome.Funding for this work was provided by the NIH grant R01AI091829-01A1 to S.L.M. and M.L.S

Function, Adjustment, Quality of Life and Symptoms (FAQS) in Allogeneic Hematopoietic Stem Cell Transplantation (HSCT) Survivors: A Study Protocol

<p>Abstract</p> <p>Background</p> <p>The population of survivors following allogeneic HSCT continues to increase, and yet their experiences of recovery and long-term survivorship have not been fully characterized. This paper presents a study protocol examining over time the functional status, psychosocial adjustment, health-related quality of life, and symptom experience of survivors who have undergone allogeneic transplantation. The aims of the study are to: 1) explore the patterns of change in these health outcomes during the survivorship phase; 2) characterize subgroups of survivors experiencing adverse outcomes; and 3) examine relationships among outcomes and demographic and clinical factors (such as age, graft-versus-host disease (GVHD), and disease relapse).</p> <p>Methods</p> <p>In this longitudinal observational study, adults who survive a minimum of 3 years from date of allogeneic transplantation complete a series of questionnaires annually. Demographic and clinical data are collected along with a series of patient-reported outcome measures, specifically: 1) Medical Outcomes Study SF- 36; 2) Functional Assessment of Chronic Illness Therapy (FACIT) - General, 3) FACIT-Fatigue; 4) FACIT- Spiritual; 5) Psychosocial Adjustment to Illness Scale; 6) Rotterdam Symptom Checklist-Revised; and 7) Pittsburgh Sleep Quality Index.</p> <p>Conclusions</p> <p>This study will provide multidimensional patient-reported outcomes data to expand the understanding of the survivorship experience across the trajectory of allogeneic transplantation recovery. There are a number of inherent challenges in recruiting and retaining a diverse and representative sample of long-term transplant survivors. Study results will contribute to an understanding of outcomes experienced by transplant survivors, including those with chronic GVHD, malignant disease relapse, and other late effects following allogeneic transplantation.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT00128960">NCT00128960</a></p

Potential influence of selection criteria on the demographic composition of students in an Australian medical school

<p>Abstract</p> <p>Background</p> <p>Prior to 1999 students entering our MBBS course were selected on academic performance alone. We have now evaluated the impact on the demographics of subsequent cohorts of our standard entry students (those entering directly from high school) of the addition to the selection process of an aptitude test (UMAT), a highly structured interview and a rural incentive program.</p> <p>Methods</p> <p>Students entering from 1985 to 1998, selected on academic performance alone (N = 1402), were compared to those from 1999 to 2011, selected on the basis of a combination of academic performance, interview score, and UMAT score together with the progressive introduction of a rural special entry pathway (N = 1437).</p> <p>Results</p> <p>Males decreased from 57% to 45% of the cohort, students of NE or SE Asian origin decreased from 30% to 13%, students born in Oceania increased from 52% to 69%, students of rural origin from 5% to 21% and those from independent high schools from 56% to 66%. The proportion of students from high schools with relative socio-educational disadvantage remained unchanged at approximately 10%. The changes reflect in part increasing numbers of female and independent high school applicants and the increasing rural quota. However, they were also associated with higher interview scores in females vs males and lower interview scores in those of NE and SE Asian origin compared to those born in Oceania or the UK. Total UMAT scores were unrelated to gender or region of origin.</p> <p>Conclusions</p> <p>The revised selection processes had no impact on student representation from schools with relative socio-educational disadvantage. However, the introduction of special entry quotas for students of rural origin and a structured interview, but not an aptitude test, were associated with a change in gender balance and ethnicity of students in an Australian undergraduate MBBS course.</p

Mutations in the EPHA2 gene are a major contributor to inherited cataracts in South-Eastern Australia.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Congenital cataract is the most common cause of treatable visual impairment in children worldwide. Mutations in many different genes lead to congenital cataract. Recently, mutations in the receptor tyrosine kinase gene, EPHA2, have been found to cause congenital cataract in six different families. Although these findings have established EPHA2 as a causative gene, the total contribution of mutations in this gene to congenital cataract is unknown. In this study, for the first time, a population-based approach was used to investigate the frequency of disease causing mutations in the EPHA2 gene in inherited cataract cases in South-Eastern Australia. A cohort of 84 familial congenital or juvenile cataract index cases was screened for mutations in the EPHA2 gene by direct sequencing. Novel changes were assessed for segregation with the disease within the family and in unrelated controls. Microsatellite marker analysis was performed to establish any relationship between families carrying the same mutation. We report a novel congenital cataract causing mutation c.1751C.T in the EPHA2 gene and the previously reported splice mutation c.2826-9G.A in two new families. Additionally, we report a rare variant rs139787163 potentially associated with increased susceptibility to cataract. Thus mutations in EPHA2 account for 4.7% of inherited cataract cases in South-Eastern Australia. Interestingly, the identified rare variant provides a link between congenital and age-related cataract