Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-Level Determinants of Parasitic Fly Infection in Forest Passerines

The study of myiasis is important because they may cause problems to the livestock industry, public health, or wildlife conservation. The ecology of parasitic dipterans that cause myiasis is singular, as they actively seek their hosts over relatively long distances. However, studies that address the determinants of myiasis dynamics are very scarce. The genus Philornis include species that may be excellent models to study myiasis ecology, as they exclusively parasitize bird nestlings, which stay in their nests until they are fully fledged, and larvae remain at the point of entry until the parasitic stage is over, thus allowing the collection of sequential individual-level infection data from virtually all the hosts present at a particular area. Here we offer a stratified multi-level analysis of longitudinal data of Philornis torquans parasitism in replicated forest bird communities of central Argentina. Using Generalized Linear Models and Generalized Linear Mixed Models and an information theory approach for model selection, we conducted four groups of analyses, each with a different study unit, the individual, the brood, the community at a given week, and the community at a given year. The response variable was larval abundance per nestling or mean abundance per nestling. At each level, models included the variables of interest of that particular level, and also potential confounders and effect modifiers of higher levels. We found associations of large magnitude at all levels, but only few variables truly governed the dynamics of this parasite. At the individual level, the infection was determined by the species and the age of the host. The main driver of parasite abundance at the microhabitat level was the average height of the forest, and at the community level, the density of hosts and prior rainfall. This multi-level approach contributed to a better understanding of the ecology of myiasis.
Advances in Cryptococcus genomics: insights into the evolution of pathogenesis

Cryptococcus species are the causative agents of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals. Initial work on the molecular epidemiology of this fungal pathogen utilized genotyping approaches to describe the genetic diversity and biogeography of two species, Cryptococcus neoformans and Cryptococcus gattii. Whole genome sequencing of representatives of both species resulted in reference assemblies enabling a wide array of downstream studies and genomic resources. With the increasing availability of whole genome sequencing, both species have now had hundreds of individual isolates sequenced, providing fine-scale insight into the evolution and diversification of Cryptococcus and allowing for the first genome-wide association studies to identify genetic variants associated with human virulence. Sequencing has also begun to examine the microevolution of isolates during prolonged infection and to identify variants specific to outbreak lineages, highlighting the potential role of hyper-mutation in evolving within short time scales. We can anticipate that further advances in sequencing technology and sequencing microbial genomes at scale, including metagenomics approaches, will continue to refine our view of how the evolution of Cryptococcus drives its success as a pathogen.
Iterative Development and Evaluation of a Pharmacogenomic-Guided Clinical Decision Support System for Warfarin Dosing

Summary Objective Pharmacogenomic-guided dosing has the potential to improve patient outcomes but its implementation has been met with clinical challenges. Our objective was to develop and evaluate a clinical decision support system (CDSS) for pharmacogenomic-guided warfarin dosing designed for physicians and pharmacists. Methods Twelve physicians and pharmacists completed 6 prescribing tasks using simulated patient scenarios in two iterations (development and validation phases) of a newly developed pharmacogenomic-driven CDSS prototype. For each scenario, usability was measured via efficiency, recorded as time to task completion, and participants’ perceived satisfaction which were compared using Kruskal-Wallis and Mann Whitney U tests, respectively. Debrief interviews were conducted and qualitatively analyzed. Usability findings from the first (i.e. development) iteration were incorporated into the CDSS design for the second (i.e. validation) iteration. Results During the CDSS validation iteration, participants took more time to complete tasks with a median (IQR) of 183 (124–247) seconds versus 101 (73.5–197) seconds in the development iteration (p=0.01). This increase in time on task was due to the increase in time spent in the CDSS corresponding to several design changes. Efficiency differences that were observed between pharmacists and physicians in the development iteration were eliminated in the validation iteration. The increased use of the CDSS corresponded to a greater acceptance of CDSS recommended doses in the validation iteration (4% in the first iteration vs. 37.5% in the second iteration, p<0.001). Overall satisfaction did not change statistically between the iterations but the qualitative analysis revealed greater trust in the second prototype. Conclusions A pharmacogenomic-guided CDSS has been developed using warfarin as the test drug. The final CDSS prototype was trusted by prescribers and significantly increased the time using the tool and acceptance of the recommended doses. This study is an important step toward incorporating pharmacogenomics into CDSS design for clinical testing. Citation: Melton BL, Zillich AJ, Saleem JJ, Russ AL, Tisdale JE, Overholser BR. Iterative development and evaluation of a pharmacogenomic-guided clinical decision support system for warfarin dosing.
Electron Crescent Distributions as a Manifestation of Diamagnetic Drift in an Electron‐Scale Current Sheet: Magnetospheric Multiscale Observations Using New 7.5 ms Fast Plasma Investigation Moments

We report Magnetospheric Multiscale observations of electron pressure gradient electric fields near a magnetic reconnection diffusion region using a new technique for extracting 7.5 ms electron moments from the Fast Plasma Investigation. We find that the deviation of the perpendicular electron bulk velocity from E × B drift in the interval where the out‐of‐plane current density is increasing can be explained by the diamagnetic drift. In the interval where the out‐of‐plane current is transitioning to in‐plane current, the electron momentum equation is not satisfied at 7.5 ms resolution.
Gene Flow and Maintenance of Genetic Diversity in Invasive Mosquitofish (Gambusia holbrooki)

Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki) that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations.
Prevalence, Risk Factors, and Outcomes of Financial Stress in Survivors of Critical Illness

Objectives: Little is known about the experience of financial stress for patients who survive critical illness or their families. Our objective was to describe the prevalence of financial stress among critically ill patients and their families, identify clinical and demographic characteristics associated with this stress, and explore associations between financial stress and psychologic distress. Design: Secondary analysis of a randomized trial comparing a coping skills training program and an education program for patients surviving acute respiratory failure and their families. Setting: Five geographically diverse hospitals. Participants: Patients (n = 175) and their family members (n = 85) completed surveys within 2 weeks of arrival home and 3 and 6 months after randomization. Measurements and Main Results: We used regression analyses to assess associations between patient and family characteristics at baseline and financial stress at 3 and 6 months. We used path models and mediation analyses to explore relationships between financial stress, symptoms of anxiety and depression, and global mental health. Serious financial stress was high at both time points and was highest at 6 months (42.5%) among patients and at 3 months (48.5%) among family members. Factors associated with financial stress included female sex, young children at home, and baseline financial discomfort. Experiencing financial stress had direct effects on symptoms of anxiety (&bgr; = 0.260; p < 0.001) and depression (&bgr; = 0.048; p = 0.048). Conclusions: Financial stress after critical illness is common and associated with symptoms of anxiety and depression. Our findings provide direction for potential interventions to reduce this stress and improve psychologic outcomes for patients and their families.
Comparison of warm fluid and cold fluid resuscitation during uncontrolled hemorrhagic shock model in rats.

BACKGROUND This study was designed to compare the effects of resuscitation with cold and warm fluid on survival time, rate and volume of hemorrhage, hemodynamics, hypothermia, coagulopathy, acid-base balance, hematocrit, lactate, and base deficit during uncontrolled hemorrhagic shock (HS) model in rats. METHODS HS model was created with splenic vascular and parenchymal injury in 29 rats under ketamine and xylazine anesthesia. Thirty minutes after the hemorrhage, the rats were randomized to receive 14.5 mL/kg 0.9% sodium chloride solution at either 24ºC (Group 1; n=9) or 4ºC (Group 2; n=10) for 20 minutes. Groups 1 and 2 were compared with group that did not receive fluid (Group 3; n=10). Statistical data were represented as mean±SD. SPSS for Windows, Version 15.0 (SPSS, Inc., Chicago, IL, USA) software, Bonferroni-adjusted Mann-Whitney U test and Kaplan-Meier procedure were used to perform statistical data analysis. P value of ≤0.05 was considered statistically significant. RESULTS Cold fluid resuscitation decreased survival time due to increased rate and volume of hemorrhage, acidosis, hypothermia, lactate, and base deficit and decreased blood pressure and hematocrit. CONCLUSION There is a great need for further experimental and clinical trials on fluid resuscitation in trauma in order to define which fluid should be administered, temperature of the fluid, quantity to be delivered, and duration.
Motor development evaluated by Test of Infant Motor Performance: comparison between preterm and full-term infants.

OBJECTIVES To compare the motor development of preterm infants whose gestational age had been corrected to 38-40 weeks with full term newborns using the Test of Infant Motor Performance (TIMP). METHODS The cross-sectional study compared preterm infants (PT group), with a gestational age at birth of 28-33 weeks, at an equivalent age to full term newborns (FT group), who were assessed up to 48 hours after birth. The assessments were performed between December 2008 and April 2009 in a hospital nationally recognized for premature infant care in the city of Recife, PE, Brazil. The sample consisted of 92 infants, 46 in each group. The test was administered at age 38-40 weeks (or equivalent age in the PT group). RESULTS In the 46 preterm infants studied, 26.1% were classified as atypical, while in the FT group 100% were classified as typical (p<0.001). Moreover, there was a significant difference in average raw TIMP score between the two groups, with the PT group being lower (p<0.001). CONCLUSION According to TIMP performance, prematurity seems to be associated with impaired motor development.
Joint Trajectories of Spousal Social Support and Depressive Symptoms in Older Age

Objective: We describe changes in depressive symptoms and positive and negative social support from the spouse/partner in a representative sample of older people in England. Method: Men and women aged 50+ (N = 7,171) from the English Longitudinal Study of Ageing reported social support and depressive symptoms (Center for Epidemiologic Studies Depression Scale) on up to five occasions between 2002-2003 and 2010-2011. Parallel process latent growth models estimated their bidirectional associations, adjusted for gender, wealth, education, and limiting illness. Results: In age- and gender-adjusted models, positive spousal support decreased and negative support increased over time, especially among women. Greater increases over time in depressive symptoms were seen in those with lower positive support or higher negative support at baseline. More baseline depressive symptoms predicted greater declines in positive support and greater increases in negative support from the spouse. Discussion: Improving older couple’s relationship quality may help reduce depressive symptoms.
Effects of problem-based learning in Chinese radiology education

Background: In recent years, the problem-based learning (PBL) teaching method has been extensively applied as an experimental educational method in Chinese radiology education. However, the results of individual studies were inconsistent and inconclusive. A meta-analysis was performed to evaluate the effects of PBL on radiology education in China. Methods: Databases of Chinese and English languages were searched from inception up to November 2017. The standard mean difference (SMD) with its 95% confidence interval (95% CI) was used to determine the over effects of PBL compared with the traditional teaching method. Results: Seventeen studies involving 1487 participants were included in this meta-analysis. Of them, 16 studies provided sufficient data for the pooled analysis and showed that PBL teaching method had a positive effect on achieving higher theoretical scores compared with the traditional teaching method (SMD = 1.20, 95% CI [0.68, 1.71]). Thirteen studies provided sufficient data on skill scores, and a significant difference in favor of PBL was also observed (SMD = 2.10, 95% CI [1.38, 2.83]). Questionnaire surveys were applied in most of the included studies and indicated positive effects of PBL on students’ learning interest, scope of knowledge, team spirit, and oral expression. Conclusion: The result shows that PBL appears to be more effective on radiology education than traditional teaching method in China. However, the heterogeneity of the included studies cannot be neglected. Further well-designed studies about this topic are needed to confirm the above findings.
Association of Proteinuria Threshold in Pre-Eclampsia with Maternal and Perinatal Outcomes: A Nested Case Control Cohort of High Risk Women

Objectives To evaluate occurrence of adverse maternal and perinatal outcomes with different thresholds of proteinuria (300-499mg and ≥500mg/24 hours) in pre-eclamptic women, comparing outcomes against women with chronic and gestational hypertension. Design Secondary analysis of the Vitamins in Pre-Eclampsia Trial. Setting 25 UK hospitals in ten geographical areas. Population 946 women with pre-existing risk factors for pre-eclampsia. Methods Women with pre-eclampsia and proteinuria 300-499mg/24h (PE300, referent group, n=60) or proteinuria ≥500 mg/24h (PE500, n=161) were compared with two groups of non-proteinuric women with chronic hypertension (CHT, n=615) or gestational hypertension (GH, n=110). Main Outcome Measures Maternal: progression to severe hypertension. Perinatal: small for gestational age (SGA) <5th centile, gestation at delivery. Results Severe hypertension occurred more frequently in PE500 (35%) and PE300 (27%) than CHT (5.9%; P≤0.01) and GH (10%; p≤0.001). Gestation at delivery was earlier in PE500 (33.2w) than PE300 (37.3w; P≤0.001), and later in CHT (38.3w; P≤0.05) and GH (39.1w; P≤0.001). SGA infants were more frequent in PE300 (32%) than in CHT (13.3%; P≤0.001) and GH (16.5%; P≤0.05). Women in PE500 were more likely to have a caesarean section than PE300 (78% vs. 48%; P≤0.001), and to receive magnesium sulphate (17% vs. 1.7%, P≤0.05). Conclusion Women with PE300 have complication rates above those of women managed as out-patients (GH and CHT), meriting closer surveillance and confirming 300 mg/d as an appropriate threshold for determining in-patient management. Adverse perinatal outcomes are higher still in women with PE500.
Cellular differentiation state modulates the mRNA export activity of SR proteins

SR proteins function in nuclear pre-mRNA processing, mRNA export, and translation. To investigate their cellular dynamics, we developed a quantitative assay, which detects differences in nucleocytoplasmic shuttling among seven canonical SR protein family members. As expected, SRSF2 and SRSF5 shuttle poorly in HeLa cells but surprisingly display considerable shuttling in pluripotent murine P19 cells. Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein–protein and protein–RNA interactions. Moreover, SRSF5 is bound to pluripotency-specific transcripts such as Lin28a and Pou5f1/Oct4 in the cytoplasm. SRSF5 depletion reduces and overexpression increases their cytoplasmic mRNA levels, suggesting that enhanced mRNA export by SRSF5 is required for the expression of pluripotency factors. Remarkably, neural differentiation of P19 cells leads to dramatically reduced SRSF5 shuttling. Our findings indicate that posttranslational modification of SR proteins underlies the regulation of their mRNA export activities and distinguishes pluripotent from differentiated cells.
Nocturnal Cramps in Patients with Lumbar Spinal Canal Stenosis Treated Conservatively: A Prospective Study

Study Design Prospective cohort study with questionnaire. Purpose To compare the treatment outcome of nocturnal leg cramps in lumbar spinal canal stenosis (LSCS) patients on conservative treatment with historical surgical cohorts and to determine the sensitivity and specificity as well as positive predictive value and negative predictive value of knee flexion test suggested for LSCS patient. Overview of Literature True prevalence of nocturnal leg cramps in LSCS patients as well as the clinical outcome of its surgical treatment have been reported. Methods A questionnaire suggested from previous study with minor modifications was used in this study. Clinical data was collected. Knee flexion test was performed in two groups. Results The prevalence of nocturnal leg cramp was higher in the LSCS group compared to the control group (second group). In LSCS patients, 38 (88%) had improved leg cramps after the conservative treatment, 3 (6.97%) remained unchanged, and 2 (4.6%) had worsened leg cramps. Of the 43 patients, 21 (48.8%) had no disturbance to their activities of daily living. In the LSCS group, the sensitivity and specificity of the knee flexion test was 53.5% and 33.3%, respectively. The knee flexion test in the LSCS group had a positive predictive value and a negative predictive value of 65.71% and 23.1%, respectively. Conclusions Our study demonstrated that nocturnal leg cramps were significantly more frequent in LSCS patients than in the control group.
Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks

Abstract Herbaria worldwide are housing a treasure of hundreds of millions of herbarium specimens, which are increasingly being digitized and thereby more accessible to the scientific community. At the same time, deep-learning algorithms are rapidly improving pattern recognition from images and these techniques are more and more being applied to biological objects. In this study, we are using digital images of herbarium specimens in order to identify taxa and traits of these collection objects by applying convolutional neural networks (CNN). Images of the 1000 species most frequently documented by herbarium specimens on GBIF have been downloaded and combined with morphological trait data, preprocessed and divided into training and test datasets for species and trait recognition. Good performance in both domains suggests substantial potential of this approach for supporting taxonomy and natural history collection management. Trait recognition is also promising for applications in functional ecology.
Lysophosphatidylcholine and Carotid Intima-Media Thickness in Young Smokers: A Role for Oxidized LDL-Induced Expression of PBMC Lipoprotein-Associated Phospholipase A2?

Background Although cigarette smoking has been associated with carotid intima-media thickness (CIMT) the mechanisms are yet not completely known. Lysophosphatidylcholine (lysoPC), a main product of lipoprotein-associated phospholipase A2 (Lp-PLA2) activity, appears to be a major determinant of the pro-atherogenic properties of oxidized LDL (oxLDL) and to induce proteoglycan synthesis, a main player in intimal thickening. In this study we assessed whether cigarette smoking-induced oxidative stress may influence plasma Lp-PLA2 and lysoPC and Lp-PLA2 expression in peripheral blood mononuclear cells (PBMC), as well as the relationship between lysoPC and CIMT. Methods/Results 45 healthy smokers and 45 age and sex-matched subjects participated in this study. Smokers, compared to non-smokers, showed increased plasma concentrations of oxLDL, Lp-PLA2 and lysoPC together with up-regulation of Lp-PLA2 (mRNA and protein) expression in PBMC (P<0.001). Plasma Lp-PLA2 positively correlated with both lysoPC (r=0.639, P<0.001) and PBMC mRNA Lp-PLA2 (r=0.484, P<0.001) in all subjects. Moreover CIMT that was higher in smokers (P<0.001), positively correlated with lysoPC (r=0.55, P<0.001). Then in in vitro study we demonstrated that both oxLDL (at concentrations similar to those found in smoker’s serum) and oxidized phospholipids contained in oxLDL, were able to up-regulate mRNA Lp-PLA2 in PBMC. This effect was likely due, at least in part, to the enrichment in oxidized phospholipids found in PBMC after exposure to oxLDL. Our results also showed that in human aortic smooth muscle cells lysoPC, at concentrations similar to those found in smokers, increased the expression of biglycan and versican, two main proteoglycans. Conclusions In smokers a further effect of raised oxidative stress is the up-regulation of Lp-PLA2 expression in PBMC with subsequent increase of plasma Lp-PLA2 and lysoPC. Moreover the correlation between lysoPC and CIMT together with the finding that lysoPC up-regulates proteoglycan synthesis suggests that lysoPC may be a link between smoking and intimal thickening.