Miracle-dz/UniFAR-FTUs huggingface dataset:
Urban ponds as an aquatic biodiversity resource in modified landscapes

Urbanization is a global process contributing to the loss and fragmentation of natural habitats. Many studies have focused on the biological response of terrestrial taxa and habitats to urbanization. However, little is known regarding the consequences of urbanization on freshwater habitats, especially small lentic systems. In this study, we examined aquatic macro‐invertebrate diversity (family and species level) and variation in community composition between 240 urban and 782 nonurban ponds distributed across the United Kingdom. Contrary to predictions, urban ponds supported similar numbers of invertebrate species and families compared to nonurban ponds. Similar gamma diversity was found between the two groups at both family and species taxonomic levels. The biological communities of urban ponds were markedly different to those of nonurban ponds, and the variability in urban pond community composition was greater than that in nonurban ponds, contrary to previous work showing homogenization of communities in urban areas. Positive spatial autocorrelation was recorded for urban and nonurban ponds at 0–50 km (distance between pond study sites) and negative spatial autocorrelation was observed at 100–150 km and was stronger in urban ponds in both cases. Ponds do not follow the same ecological patterns as terrestrial and lotic habitats (reduced taxonomic richness) in urban environments; in contrast, they support high taxonomic richness and contribute significantly to regional faunal diversity. Individual cities are complex structural mosaics which evolve over long periods of time and are managed in diverse ways. This facilitates the development of a wide range of environmental conditions and habitat niches in urban ponds which can promote greater heterogeneity between pond communities at larger scales. Ponds provide an opportunity for managers and environmental regulators to conserve and enhance freshwater biodiversity in urbanized landscapes whilst also facilitating key ecosystem services including storm water storage and water treatment.
Potential for adaptation to climate change in a coral reef fish

Predicting the impacts of climate change requires knowledge of the potential to adapt to rising temperatures, which is unknown for most species. Adaptive potential may be especially important in tropical species that have narrow thermal ranges and live close to their thermal optimum. We used the animal model to estimate heritability, genotype by environment interactions and nongenetic maternal components of phenotypic variation in fitness‐related traits in the coral reef damselfish, Acanthochromis polyacanthus. Offspring of wild‐caught breeding pairs were reared for two generations at current‐day and two elevated temperature treatments (+1.5 and +3.0 °C) consistent with climate change projections. Length, weight, body condition and metabolic traits (resting and maximum metabolic rate and net aerobic scope) were measured at four stages of juvenile development. Additive genetic variation was low for length and weight at 0 and 15 days posthatching (dph), but increased significantly at 30 dph. By contrast, nongenetic maternal effects on length, weight and body condition were high at 0 and 15 dph and became weaker at 30 dph. Metabolic traits, including net aerobic scope, exhibited high heritability at 90 dph. Furthermore, significant genotype x environment interactions indicated potential for adaptation of maximum metabolic rate and net aerobic scope at higher temperatures. Net aerobic scope was negatively correlated with weight, indicating that any adaptation of metabolic traits at higher temperatures could be accompanied by a reduction in body size. Finally, estimated breeding values for metabolic traits in F2 offspring were significantly affected by the parental rearing environment. Breeding values at higher temperatures were highest for transgenerationally acclimated fish, suggesting a possible role for epigenetic mechanisms in adaptive responses of metabolic traits. These results indicate a high potential for adaptation of aerobic scope to higher temperatures, which could enable reef fish populations to maintain their performance as ocean temperatures rise.
Respiratory infections in young children with cystic fibrosis: A community-based longitudinal study

Viral infections in early childhood might play a role in causing lung damage in cystic fibrosis(CF). Aim: To study the respiratory viral burden during symptomatic and asymptomatic states of children with CF under 3 years in a community setting over one year. Methods: A longitudinal multi centric pilot study is being done in 3 tertiary care hospitals of Australia with CF Units.Parents of eligible children are enrolled and taught how to collect, mail the nasal swabs and record symptoms with validated methodology (Lambert, S.B. et al. Vaccine 2008; 26(15):1826-3). They were asked to collect one swab every fortnight and one during symptoms. Swabs were mailed to the laboratory in a viral transport tube. Samples were analyzed with PCR for a range of common respiratory viruses. Results: A total of 78 children were recruited. 946 nasal swabs were collected during 530 child months. Mean ARI rate was 0.4 episodes per child month. 913 swabs have been analyzed to date. 45.1% of parent reported symptom swabs and 19.5% of asymptomatic swabs were virus positive. The pattern of viruses isolated is as below. Conclusions: ARI rate, viral isolation in asymptomatic swabs, pattern of viruses is similar to previous studies. Isolation in symptom swabs(45.1%) is less than expected. Acute respiratory infections, viral isolation and virus carriage in children with CF is similar to that reported in children without lung conditions.Acknowledgements: Australian Cystic fibrosis Rsearch Trust & Telethon Foundation.
Stream network geomorphology mediates predicted vulnerability of anadromous fish habitat to hydrologic change in southeast Alaska

In rivers supporting Pacific salmon in southeast Alaska, USA, regional trends toward a warmer, wetter climate are predicted to increase mid‐ and late‐21st‐century mean annual flood size by 17% and 28%, respectively. Increased flood size could alter stream habitats used by Pacific salmon for reproduction, with negative consequences for the substantial economic, cultural, and ecosystem services these fish provide. We combined field measurements and model simulations to estimate the potential influence of future flood disturbance on geomorphic processes controlling the quality and extent of coho, chum, and pink salmon spawning habitat in over 800 southeast Alaska watersheds. Spawning habitat responses varied widely across watersheds and among salmon species. Little variation among watersheds in potential spawning habitat change was explained by predicted increases in mean annual flood size. Watershed response diversity was mediated primarily by topographic controls on stream channel confinement, reach‐scale geomorphic associations with spawning habitat preferences, and complexity in the pace and mode of geomorphic channel responses to altered flood size. Potential spawning habitat loss was highest for coho salmon, which spawn over a wide range of geomorphic settings, including steeper, confined stream reaches that are more susceptible to streambed scour during high flows. We estimated that 9–10% and 13–16% of the spawning habitat for coho salmon could be lost by the 2040s and 2080s, respectively, with losses occurring primarily in confined, higher‐gradient streams that provide only moderate‐quality habitat. Estimated effects were lower for pink and chum salmon, which primarily spawn in unconfined floodplain streams. Our results illustrate the importance of accounting for valley and reach‐scale geomorphic features in watershed assessments of climate vulnerability, especially in topographically complex regions. Failure to consider the geomorphic context of stream networks will hamper efforts to understand and mitigate the vulnerability of anadromous fish habitat to climate‐induced hydrologic change.
A meta‐analysis of fertilizer‐induced soil NO and combined NO+N2O emissions

Soils are among the important sources of atmospheric nitric oxide (NO) and nitrous oxide (N2O), acting as a critical role in atmospheric chemistry. Updated data derived from 114 peer‐reviewed publications with 520 field measurements were synthesized using meta‐analysis procedure to examine the N fertilizer‐induced soil NO and the combined NO+N2O emissions across global soils. Besides factors identified in earlier reviews, additional factors responsible for NO fluxes were fertilizer type, soil C/N ratio, crop residue incorporation, tillage, atmospheric carbon dioxide concentration, drought and biomass burning. When averaged across all measurements, soil NO‐N fluxes were estimated to be 4.06 kg ha−1 yr−1, with the greatest (9.75 kg ha−1 yr−1) in vegetable croplands and the lowest (0.11 kg ha−1 yr−1) in rice paddies. Soil NO emissions were more enhanced by synthetic N fertilizer (+38%), relative to organic (+20%) or mixed N (+18%) sources. Compared with synthetic N fertilizer alone, synthetic N fertilizer combined with nitrification inhibitors substantially reduced soil NO emissions by 81%. The global mean direct emission factors of N fertilizer for NO (EFNO) and combined NO+N2O (EFc) were estimated to be 1.16% and 2.58%, with 95% confidence intervals of 0.71–1.61% and 1.81–3.35%, respectively. Forests had the greatest EFNO (2.39%). Within the croplands, the EFNO (1.71%) and EFc (4.13%) were the greatest in vegetable cropping fields. Among different chemical N fertilizer varieties, ammonium nitrate had the greatest EFNO (2.93%) and EFc (5.97%). Some options such as organic instead of synthetic N fertilizer, decreasing N fertilizer input rate, nitrification inhibitor and low irrigation frequency could be adopted to mitigate soil NO emissions. More field measurements over multiyears are highly needed to minimize the estimate uncertainties and mitigate soil NO emissions, particularly in forests and vegetable croplands.
Association Between Baseline Corticothalamic-Mediated Inhibitory Control and Smoking Relapse Vulnerability

Importance Tobacco use disorder is associated with dysregulated neurocognitive function in the right inferior frontal gyrus (IFG)—one node in a corticothalamic inhibitory control (IC) network. Objective To examine associations between IC neural circuitry structure and function and lapse/relapse vulnerability in 2 independent studies of adult smokers. Design, Setting, and Participants In study 1, treatment-seeking smokers (n = 81) completed an IC task during functional magnetic resonance imaging (fMRI) before making a quit attempt and then were followed up for 10 weeks after their quit date. In study 2, a separate group of smokers (n = 26) performed the same IC task during fMRI, followed by completing a laboratory-based smoking relapse analog task. Study 1 was performed at Duke University Medical Center between 2008 and 2012; study 2 was conducted at the Medical University of South Carolina between 2013 and 2016. Main Outcomes and Measures Associations between corticothalamic-mediated IC, gray-matter volume, and smoking lapse/relapse. Results Of the 81 study participants in study 1 (cessation study), 45 were women (56%), with mean (SD) age, 38.4 (10.2) years. In study 1, smoking relapse was associated with less gray-matter volume (F1,74 = 28.32; familywise error P threshold = 0.03), greater IC task-related blood oxygenation level–dependent (BOLD) response in the right IFG (F1,78 = 14.87) and thalamus (F1,78 = 14.97) (P < .05), and weaker corticothalamic task-based functional connectivity (tbFC) (F1,77 = 5.87; P = .02). Of the 26 participants in study 2 (laboratory study), 15 were women (58%), with mean (SD) age, 34.9 (10.3). Similar to study 1, in study 2, greater IC-BOLD response in the right IFG (t23 = −2.49; &bgr; = −0.47; P = .02), and weaker corticothalamic tbFC (t22 = 5.62; &bgr; = 0.79; P < .001) were associated with smoking sooner during the smoking relapse-analog task. In both studies, corticothalamic tbFC mediated the association between IC performance and smoking outcomes. Conclusions and Relevance In these 2 studies, baseline differences in corticothalamic circuitry function were associated with mediated IC and smoking relapse vulnerability. These findings warrant further examination of interventions for augmenting corticothalamic neurotransmission and enhancing IC during the course of tobacco use disorder treatment.
Development, implementation and evaluation of a patient handoff tool to improve safety in orthopaedic surgery.

OBJECTIVE To develop, implement and test the effect of a handoff tool for orthopaedic trauma residents that reduces adverse events associated with the omission of critical information and the transfer of erroneous information. DESIGN Components of this project included a literature review, resident surveys and observations, checklist development and refinement, implementation and evaluation of impact on adverse events through a chart review of a prospective cohort compared with a historical control group. SETTING Large teaching hospital. PARTICIPANTS Findings of a literature review were presented to orthopaedic residents, epidemiologists, orthopaedic surgeons and patient safety experts in face-to-face meetings, during which we developed and refined the contents of a resident handoff tool. The tool was tested in an orthopaedic trauma service and its impact on adverse events was evaluated through a chart review. The handoff tool was developed and refined during the face-to-face meetings and a pilot implementation. Adverse event data were collected on 127 patients (n = 67 baseline period; n = 60 test period). INTERVENTION A handoff tool for use by orthopaedic residents. MAIN OUTCOME MEASUREMENTS Adverse events in patients handed off by orthopaedic trauma residents. RESULTS After controlling for age, gender and comorbidities, testing resulted in fewer events per person (25-27% reduction; P < 0.10). CONCLUSIONS Preliminary evidence suggests that our resident handoff tool may contribute to a decrease in adverse events in orthopaedic patients.
Comparing Public Safety Outcomes for Traditional Probation vs Specialty Mental Health Probation

Importance Probation is a cornerstone of efforts to reduce mass incarceration. Although it is understudied, specialty probation could improve outcomes for the overrepresented group of people with mental illness. Objective To test whether specialty probation yields better public safety outcomes than traditional probation. Design, Setting, and Participants A longitudinal observational study with group matching on age, sex, race/ethnicity, probation time, and offense at 2 urban agencies that exemplify specialty and traditional probation. Enrollment began October 19, 2005; follow-up data were complete January 26, 2013. Participants were 359 diverse probationers with serious mental health problems and functional impairment. Probationers and officers were assessed 3 times (for probationers, 6-month retention, 315 of 359 [88%]; 12-month retention 304 of 359 [85%]) and follow-up records were obtained. Machine learning algorithms were combined with a targeted maximum likelihood estimation, a double robust estimator that accounts for associations between confounders and both treatment assignment and outcomes. Statistical analysis was conducted from January 1, 2016 to May 5, 2017. Interventions Specialty probationers were assigned to small, homogeneous caseloads supervised by experts. Prior data indicate that specialty officers had better relationships with probationers, participated more in probationers’ treatment, and relied more on positive compliance strategies than traditional officers. Main Outcomes and Measures Violence during 1 year, determined by probationer report, officer report, and records, and rearrest during a period of 2 to 5 years, according to Federal Bureau of Investigation records. Results Participants were 183 specialty (73.8% of 248 eligible) and 176 traditional (56.6% of 311 eligible) probationers (205 men and 154 women; mean [SD] age, 36.9 [10.6]). Although specialty probation had no significant effect on violence (odds ratio, 0.97; 95% CI, 0.69-1.36), the odds of rearrest were 2.68 times higher for traditional probationers than for specialty probationers (95% CI, 1.86-3.84; P < .001). At 2 years, estimated probabilities of rearrest were 28.6% for specialty probationers and 51.8% for traditional probationers. Survival analyses indicate that arrest effects endured up to 5 years. Conclusions and Relevance Although it did not specifically reduce violence, well-implemented specialty probation appears to be effective in reducing general recidivism. Reform efforts for people with mental illness could leverage probation—a ubiquitous and revitalized node of the justice system.
Placebo Response and Practice Effects in Schizophrenia Cognition Trials

Importance Patients’ previous experience with performance-based cognitive tests in clinical trials for cognitive impairment associated with schizophrenia can create practice-related improvements. Placebo-controlled trials for cognitive impairment associated with schizophrenia are at risk for these practice effects, which can be difficult to distinguish from placebo effects. Objectives To conduct a systematic evaluation of the magnitude of practice effects on the Measurement and Treatment Research to Improve Cognition in Schizophrenia Consensus Cognitive Battery (MCCB) in cognitive impairment associated with schizophrenia and to examine which demographic, clinical, and cognitive characteristics were associated with improvement in placebo conditions. Design, Setting, and Participants A blinded review was conducted of data from 813 patients with schizophrenia who were treated with placebo in 12 randomized placebo-controlled clinical trials conducted mostly in outpatient clinics in North America, Europe, Asia, and Latin America from February 22, 2007, to March 1, 2014. A total of 779 patients provided data for the primary outcome measure at baseline and at least 1 follow-up. Seven trials had prebaseline assessments wherein the patients knew that they were not receiving treatment, allowing a comparison of practice and placebo effects in the same patients. Interventions Placebo compared with various experimental drug treatments. Main Outcomes and Measures Composite score on the MCCB. Results Of the 813 patients in the study (260 women and 553 men; mean [SD] age, 41.2 [11.5] years), the mean MCCB composite score at baseline was 22.8 points below the normative mean, and the mean (SEM) total change in the MCCB during receipt of placebo was 1.8 (0.2) T-score points (95% CI, 1.40-2.18), equivalent to a change of 0.18 SD. Practice effects in the 7 studies in which there was a prebaseline assessment were essentially identical to the postbaseline placebo changes. Baseline factors associated with greater improvements in the MCCB during receipt of placebo included more depression/anxiety (F1,438 = 5.41; P = .02), more motivation (F1,272 = 4.63; P = .03), and less improvement from screening to baseline (F1,421 = 59.32; P < .001). Conclusions and Relevance Placebo effects were minimal and associated with the number of postbaseline assessments and several patient characteristics. Given that the patients performed 2.28 SDs below normative standards on average at baseline, a mean placebo-associated improvement of less than 0.2 SD provides evidence that ceiling effects do not occur in these trials. These minimal changes in the MCCB could not be responsible for effective active treatments failing to separate from placebo.
A randomized comparison between league tables and funnel plots to inform health care decision-making.

Objective Comparison of provider performance is commonly used to inform health care decision-making. Little attention has been paid to how data presentations influence decisions. This study analyzes differences in suggested actions by decision-makers informed by league tables or funnel plots. Design Decision-makers were invited to a survey and randomized to compare hospital performance using either league tables or funnel plots for four different measures within the area of cancer care. For each measure, decision-makers were asked to suggest actions towards 12-16 hospitals (no action, ask for more information, intervene) and provide feedback related to whether the information provided had been useful. Setting Swedish health care. Participants Two hundred and twenty-one decision-makers at administrative and clinical levels. Intervention Data presentations in the form of league tables or funnel plots. Main outcome measures Number of actions suggested by participants. Proportion of appropriate actions. Results For all four measures, decision-makers tended to suggest more actions based on the information provided in league tables compared to funnel plots (44% vs. 21%, P < 0.001). Actions were on average more appropriate for funnel plots. However, when using funnel plots, decision-makers more often missed to react even when appropriate. Conclusions The form of data presentation had an influence on decision-making. With league tables, decision-makers tended to suggest more actions compared to funnel plots. A difference in sensitivity and specificity conditioned by the form of presentation could also be identified, with different implications depending on the purpose of comparisons. Explanations and visualization aids are needed to support appropriate actions.