Miracle-dz/UniFAR-FTUs huggingface dataset:
Likelihood-Based Parameter Estimation for High-Dimensional Phylogenetic Comparative Models: Overcoming the Limitations of "Distance-Based" Methods.

Recently, a suite of distance-based multivariate phylogenetic comparative methods has been proposed for studying the evolution of high-dimensional traits, such as morphometric coordinates, gene expression data, and function-valued traits. These methods allow for the statistical comparison of evolutionary rates, assessment of phylogenetic signal, and tests of correlated high-dimensional trait evolution. Simulations reveal that distance-based comparative methods exhibit low statistical power and high Type I error under various evolutionary scenarios. Distance-based methods are also limited to relatively simple model specification (e.g., Brownian motion evolution) due to the lack of a likelihood function for parameter estimation. Here I propose an alternative method for studying high-dimensional trait evolution which overcomes some of the statistical limitations associated with distance-based methods. This framework, based on parametric bootstrapping and maximum pseudolikelihood parameter estimation, opens up the ability to estimate alternative evolutionary models, combine multiple evolutionary hypotheses, and potentially allow missing data and within-species variation. Simulations reveal that pairwise composite likelihood methods demonstrate appropriate Type I error and high statistical power, thus providing a robust framework for studying high-dimensional trait evolution. These methods are implemented in the R package phylocurve [Covariance; distance; evolutionary rate; function-valued trait; high-dimensional; morphometric; multivariate; pairwise composite likelihood; phylogenetic comparative method; phylogenetic generalized least squares; phylogenetic signal. ].
The Role of the Midfoot in Drop Landings

Purpose The midfoot is instrumental to foot function; however, quantifying its roles in human movement has been difficult. A forceful dynamic activity like landing may help elucidate the midfoot’s contribution to foot energetics and function. The main purpose of this study was to measure midtarsal joint kinematics and kinetics during a barefoot single-leg landing task. A secondary aim of this study was to explore the relationship between static foot posture and dynamic midfoot function. Methods In a cross-sectional study design, 48 females (age = 20.4 ± 1.8 yr, body mass index = 21.6 ± 1.7 kg·m−1) performed drop landings from a height of 0.4 m onto split force platforms. Subjects hung from wooden rings and landed on their dominant leg. Midtarsal joint kinematic and kinetic data were recorded using a 14-camera optical motion capture system in conjunction with two in-ground force platforms and a custom kinetic three-segment foot model. Foot structure was measuring using the arch height index (AHI) and the static midtarsal joint angle from motion capture. Results Kinematic data revealed an average sagittal plane midtarsal joint range of motion of 27° through the landing phase. Kinetic data showed that between 7% and 22% of the total lower extremity joint, work during the landing was performed by the midtarsal joint. Both standing AHI and static midtarsal joint angle (static MA) were correlated with sagittal plane midtarsal joint range of motion (standing AHI: r = −0.320, P = 0.026; static MA: r = 0.483, P < 0.001) and with midtarsal joint work (standing AHI: r = 0.332, P = 0.021; static MA: r = −0.323, P = 0.025). Conclusion The midfoot contributes substantially to landing mechanics during a barefoot single-leg landing task. Static foot posture measures have limited value in predicting midfoot kinematics and kinetics during sportlike landings.
Rapidity of Correction of Hyponatremia Due to Syndrome of Inappropriate Secretion of Antidiuretic Hormone Following Tolvaptan.

BACKGROUND Tolvaptan effectively corrects hyponatremia due to the syndrome of inappropriate secretion of antidiuretic hormone (SIADH), but undesired overcorrection can occur. We hypothesized that pretherapy parameters can predict the rapidity of response to tolvaptan in SIADH. STUDY DESIGN Multicenter historical cohort study. SETTING & PARTICIPANTS Adults with SIADH or congestive heart failure (CHF) treated with tolvaptan for a serum sodium concentration ≤ 130 mEq/L at 5 US hospitals. PREDICTORS Demographic and laboratory parameters. OUTCOMES Rate of change in serum sodium concentration. MEASUREMENTS Spearman correlations, analysis of variance, and multivariable linear mixed-effects models. RESULTS 28 patients with SIADH and 39 patients with CHF treated with tolvaptan (mean baseline serum sodium, 120.6 and 122.4 mEq/L, respectively) were studied. Correction of serum sodium concentration > 12 mEq/L/d occurred in 25% of patients with SIADH compared to 3% of those with CHF (P<0.001). Among patients with SIADH, the increase in serum sodium over 24 hours was correlated with baseline serum sodium concentration (r=-0.78; P<0.001), serum urea nitrogen concentration (SUN; r=-0.76; P<0.001), and estimated glomerular filtration rate (r=0.58; P=0.01). Baseline serum sodium and SUN concentrations were identified as independent predictors of change in serum sodium concentration in multivariable analyses. When patients were grouped into 4 categories according to baseline serum sodium and SUN median values, those with both low baseline serum sodium (≤121 mEq/L) and low baseline SUN concentrations (≤10mg/dL) exhibited a significantly greater rate of increase in serum sodium concentration (mean 24-hour increase of 15.4 mEq/L) than the other 3 categories (P<0.05). Among patients with CHF, only baseline SUN concentration was identified as an independent predictor of change in serum sodium concentration over time. LIMITATIONS Lack of uniformity in serial serum sodium concentration determinations and documentation of water intake. CONCLUSIONS Baseline serum sodium and SUN values are predictive of the rapidity of hyponatremia correction following tolvaptan use in SIADH. We advise caution when dosing tolvaptan in patients with both low serum sodium and SUN concentrations.
Environmental Exposures and the Risk of Central Venous Catheter Complications and Readmissions in Home Infusion Therapy Patients

BACKGROUND Patients are frequently discharged with central venous catheters (CVCs) for home infusion therapy. OBJECTIVE To study a prospective cohort of patients receiving home infusion therapy to identify environmental and other risk factors for complications. DESIGN Prospective cohort study between March and December 2015. SETTING Home infusion therapy after discharge from academic medical centers. PARTICIPANTS Of 368 eligible patients discharged from 2 academic hospitals to home with peripherally inserted central catheters and tunneled CVCs, 222 consented. Patients remained in the study until 30 days after CVC removal. METHODS Patients underwent chart abstraction and monthly telephone surveys while the CVC was in place, focusing on complications and environmental exposures. Multivariable analyses estimated adjusted odds ratios and adjusted incident rate ratios between clinical, demographic, and environmental risk factors and 30-day readmissions or CVC complications. RESULTS Of 222 patients, total parenteral nutrition was associated with increased 30-day readmissions (adjusted odds ratio, 4.80 [95% CI, 1.51–15.21) and CVC complications (adjusted odds ratio, 2.41 [95% CI, 1.09–5.33]). Exposure to soil through gardening or yard work was associated with a decreased likelihood of readmissions (adjusted odds ratio, 0.09 [95% CI, 0.01–0.74]). Other environmental exposures were not associated with CVC complications. CONCLUSIONS complications and readmissions were common and associated with the use of total parenteral nutrition. Common environmental exposures (well water, cooking with raw meat, or pets) did not increase the rate of CVC complications, whereas soil exposures were associated with decreased readmissions. Interventions to decrease home CVC complications should focus on total parenteral nutrition patients. Infect Control Hosp Epidemiol 2016;1–8
Impact of molecular profiling on overall survival of patients with advanced ovarian cancer

Objective Patients with recurrent epithelial ovarian cancer (EOC) have limited treatment options. Studies have reported that biomarker profiling may help predict patient response to available treatments. This study sought to determine the value of biomarker profiling in recurrent EOC. Results Patients in the Matched cohort had a median OS of 36 months compared to 27 months for patients in the Unmatched cohort (HR 0.62, 95% CI 0.41-0.96; p < 0.03). Individual biomarkers were analyzed, with TUBB3, and PGP prognostic for survival. Biomarker analysis also identified a molecular subtype (positive for at least two of the following markers: ERCC1, RRM1, TUBB3, PGP) with particularly poor overall survival. Methods 224 patients from a commercial registry (NCT02678754) with stage IIIC/IV EOC at diagnosis, or restaged to IIIC/IV EOC at the time of molecular profiling, were retrospectively divided into two cohorts based on whether or not the drugs they received matched their profile recommendations. The Matched cohort received no drugs predicted to be lack-of-benefit while the Unmatched cohort received at least one drug predicted to be lack-of-benefit. Profile biomarker/drug associations were based on multiple test platforms including immunohistochemistry, fluorescent in situ hybridization and DNA sequencing. Conclusions This report demonstrates the ability of multi-platform molecular profiling to identify EOC patients at risk of inferior survival. It also suggests a potential beneficial role of avoidance of lack-of-benefit therapies which, when administered, resulted in decreased survival relative to patients who received only therapies predicted to be of benefit.
Ectomycorrhization of Tricholoma matsutake with Quercus aquifolioides affects the endophytic microbial community of host plant

Tricholoma matsutake (S. Ito et Imai) is an ectomycorrhizal basidiomycete associated with Pinaceae and Fagaceae trees in the Northern Hemisphere. It is still unknown whether the symbiotic relationship with this ectomycorrhiza could affect the host plant's endophytic microbial community. In this study, we used high throughput sequencing to analyze the endophytic microbial communities of different Quercus aquifolioides tissues with or without T. matsutake partner. About 35,000 clean reads were obtained per sample, representing 34 bacterial phyla and 7 fungal phyla. We observed 3980 operational taxonomic units (OTUs) of bacteria and 457 OTUs of fungi at a 97% similarity level. Three bacterial phyla, Proteobacteria, Cyanobacteria, and Bacteroidetes, and the fungal phylum Ascomycota were dominant in all tissues. The relative abundance of these taxa differed significantly between Q. aquifolioides tissues with and without T. matsutake partner (p < 0.05). The bacterial genus Pseudomonas and the fungal genus Cryptosporiopsis were more abundant in mycorrhized roots than in control roots. This study showed that the community structure and dominant species of endophytic microbial communities in Q. aquifolioides tissues might be altered by colonization with T. matsutake. This work provides a new insight into the interactions between ectomycorrhizal fungus and host plant.
A method for the quantification of biased signalling at constitutively active receptors

Biased agonism, the ability of an agonist to differentially activate one of several signal transduction pathways when acting at a given receptor, is an increasingly recognized phenomenon at many receptors. The Black and Leff operational model lacks a way to describe constitutive receptor activity and hence inverse agonism. Thus, it is impossible to analyse the biased signalling of inverse agonists using this model. In this theoretical work, we develop and illustrate methods for the analysis of biased inverse agonism.
Brief Mindfulness Meditation Training Reduces Mind Wandering: The Critical Role of Acceptance

Mindfulness meditation programs, which train individuals to monitor their present-moment experience in an open or accepting way, have been shown to reduce mind wandering on standardized tasks in several studies. Here we test 2 competing accounts for how mindfulness training reduces mind wandering, evaluating whether the attention-monitoring component of mindfulness training alone reduces mind wandering or whether the acceptance training component is necessary for reducing mind wandering. Healthy young adults (N = 147) were randomized to either a 3-day brief mindfulness training condition incorporating instruction in both attention monitoring and acceptance, a mindfulness training condition incorporating attention monitoring instruction only, a relaxation training condition, or an active reading-control condition. Participants completed measures of dispositional mindfulness and treatment expectancies before the training session on Day 1 and then completed a 6-min Sustained Attention to Response Task (SART) measuring mind wandering after the training session on Day 3. Acceptance training was important for reducing mind wandering, such that the attention-monitoring plus acceptance mindfulness training condition had the lowest mind wandering relative to the other conditions, including significantly lower mind wandering than the attention-monitoring only mindfulness training condition. In one of the first experimental mindfulness training dismantling studies to-date, we show that training in acceptance is a critical driver of mindfulness-training reductions in mind wandering. This effect suggests that acceptance skills may facilitate emotion regulation on boring and frustrating sustained attention tasks that foster mind wandering, such as the SART.
Brown Marmorated Stink Bug (Hemiptera: Pentatomidae) Infestations in Tree Borders and Subsequent Patterns of Abundance in Soybean Fields

Abstract The invasive brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), is an important pest of soybean (Glycine max L. Merr.) in the Mid-Atlantic United States. In order to assess the influence of nonmanaged wooded borders on H. halys infestation patterns in soybean, 12 soybean fields in Orange and Madison Counties, VA, were sampled each week from July to October in 2013 or 2014 for H. halys. At each location, five 2-min visual counts of H. halys life stages were made on tree of heaven (Ailanthus altissima Mill.) and other favorable host trees along a wooded border, on the adjacent soybean edge, 15 m into the soybean field, and 30 m into the field. Seasonal data showed a clear trend at all locations of H. halys densities building up on A. altissima-dominated wooded borders in July, then, gradually moving into adjacent soybean field edges later in the summer. Halyomorpha halys did not move far from the invading field edge, with approximately half as many bugs being present at 15 m into the field and very few being detected 30 m into the field. These results have implications for continued monitoring and management using field border sprays, particularly on edges adjacent to woods.
The potential impact of recent insights into proteomic changes associated with glaucoma

ABSTRACT Introduction: Glaucoma, a major ocular neuropathy, is still far from being understood on a molecular scale. Proteomic workflows revealed glaucoma associated alterations in different eye components. By using state-of-the-art mass spectrometric (MS) based discovery approaches large proteome datasets providing important information about glaucoma related proteins and pathways could be generated. Corresponding proteomic information could be retrieved from various ocular sample species derived from glaucoma experimental models or from original human material (e.g. optic nerve head or aqueous humor). However, particular eye tissues with the potential for understanding the disease’s molecular pathomechanism remains underrepresented. Areas covered: The present review provides an overview of the analysis depth achieved for the glaucomatous eye proteome. With respect to different eye regions and biofluids, proteomics related literature was found using PubMed, Scholar and UniProtKB. Thereby, the review explores the potential of clinical proteomics for glaucoma research. Expert commentary: Proteomics will provide important contributions to understanding the molecular processes associated with glaucoma. Sensitive discovery and targeted MS approaches will assist understanding of the molecular interplay of different eye components and biofluids in glaucoma. Proteomic results will drive the comprehension of glaucoma, allowing a more stringent disease hypothesis within the coming years.
Role of Exercise in the Management of Diabetes Mellitus: the Global Scenario

Background Exercise training programs have emerged as a useful therapeutic regimen for the management of type 2 diabetes mellitus (T2DM). Majority of the Western studies highlighted the effective role of exercise in T2DM. Therefore, the main aim was to focus on the extent, type of exercise and its clinical significance in T2DM in order to educate the clinicians from developing countries, especially in Asians. Methods Pubmed, Science Direct, Scopus, ISI Web of Knowledge and Google scholar were searched using the terms “type 2 diabetes mellitus,” “type 2 DM,” “exercise,” and/or “physical activity,” and “type 2 diabetes mellitus with exercise. ” Only clinical or human studies published in English language between 2000 and 2012 were included. Certain criteria were assigned to achieve appropriate results. Results Twenty five studies met the selected criteria. The majority of the studies were randomized controlled trial study design (65%). Most of the aerobic exercise based studies showed a beneficial effect in T2DM. Resistance exercise also proved to have positive effect on T2DM patients. Minimal studies related to other types of exercises such as yoga classes, joba riding and endurance-type exercise were found. On the other hand, United States of America (USA) showed strong interest of exercise management towards T2DM. Conclusion Aerobic exercise is more common in clinical practice compared to resistance exercise in managing T2DM. Treatment of T2DM with exercise training showed promising role in USA. A large number of researches are mandatory in the developing countries for incorporating exercise in the effective management of T2DM.
De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis

Next‐generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory‐controlled setting and in two different water types, a native and a non‐native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi‐Seq 2000 achieving 365 M 50‐nt reads. High‐quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.
Quantification and comparison of 4D‐flow MRI‐derived wall shear stress and MRE‐derived wall stiffness of the abdominal aorta

Aortic wall shear stress (WSSFlow) alters endothelial function, which in‐turn changes aortic wall stiffness leading to remodeling in different disease states. Therefore, the aims of this study are to determine normal physiologic correlations between: (1) Magnetic Resonance Elastography (MRE)‐derived aortic wall stiffness (WSMRE) and WSSFlow; (2) WSMRE and mean velocity; (3) WSMRE and pulse wave velocity (PWV);( 4) WSMRE and mean peak flow; and (5) WSMRE, WSSFlow and age using MRE and 4D‐flow MRI in the abdominal aorta in healthy human subjects.
Attitudes and Practices Related to Clinical Alarms: A Follow‐up Survey

&NA; Background Alarm fatigue is a widely acknowledged patient safety concern in hospitals. In 2013, The Joint Commission issued a National Patient Safety Goal on Alarm Management, making addressing alarm management a priority. To capture changes in attitudes and practices related to alarms, the Healthcare Technology Foundation conducted and reported findings from national online surveys in 2006 and 2011 and completed a third survey in 2016. Objectives The goal of the 2016 survey was to identify how hospital practices and clinicians' perceptions of alarms have changed since 2006. Methods The online survey was distributed via national health care organizations during a 2‐month period. Results of the 2016 survey (N = 1241) were compared with results of the 2006 and 2011 surveys by using &khgr;2 and Kruskal‐Wallis analyses. Results Responses were significantly different for almost all items across the 3 surveys. Respondents in 2016 were more likely to agree that nuisance alarms occur frequently and disrupt patient care and were less likely to agree that clinical staff responds quickly to alarms. Compared with respondents in 2011, those in 2016 were almost twice as likely to report that their hospitals had experienced adverse events related to alarms in the past 2 years. However, in 2016 a much higher proportion of respondents indicated that their hospitals had implemented alarm improvement initiatives. Conclusions Although survey findings show disappointing trends in the past 10 years, including worsening perceptions of nuisance alarms and more alarm‐related adverse events, the increase in alarm improvement initiatives is encouraging.