Miracle-dz/UniFAR-FTUs huggingface dataset:
Cumulative Burden of Chronic Health Conditions in Adult Survivors of Osteosarcoma and Ewing Sarcoma: A Report from the St. Jude Lifetime Cohort Study

Background: Adult survivors of childhood osteosarcoma and Ewing sarcoma are at risk of developing therapy-related chronic health conditions. We characterized the cumulative burden of chronic conditions and health status of survivors of childhood bone sarcomas. Methods: Survivors (n = 207) treated between 1964 and 2002 underwent comprehensive clinical assessments (history/physical examination, laboratory analysis, and physical and neurocognitive testing) and were compared with community controls (n = 272). Health conditions were defined and graded according to a modified version of the NCI's Common Terminology Criteria for Adverse Events and the cumulative burden estimated. Results: Osteosarcoma and Ewing sarcoma survivors [median age 13.6 years at diagnosis (range 1.7–24.8); age at evaluation 36.6 years (20.7–66.4)] demonstrated an increased prevalence of cardiomyopathy (14.5%; P < 0.005) compared with controls. Nearly 30% of osteosarcoma survivors had evidence of hypertension. By age 35 years, osteosarcoma and Ewing sarcoma survivors had, on average, 12.0 (95% confidence interval, 10.2–14.2) and 10.6 (8.9–12.6) grade 1–4 conditions and 4.0 (3.2–5.1) and 3.5 (2.7–4.5) grade 3–4 conditions, respectively, compared with controls [3.3 (2.9–3.7) grade 1–4 and 0.9 (0.7–1.0) grade 3–4]. Both survivor cohorts exhibited impaired 6-minute walk test, walking efficiency, mobility, strength, and endurance (P < 0.0001). Accumulation of ≥4 grade 3–4 chronic conditions was associated with deficits in executive function [RR: osteosarcoma 1.6 (1.0–2.4), P = 0.049; Ewing sarcoma 2.0 (1.2–3.3), P = 0.01] and attention [RR: osteosarcoma 2.3 (1.2–4.2); P = 0.008]. Conclusions: Survivors of osteosarcoma and Ewing sarcoma experience a high cumulative burden of chronic health conditions, with impairments of physical function and neurocognition. Impact: Early intervention strategies may ameliorate the risk of comorbidities in bone sarcoma survivors.
Genomic insights into the early peopling of the Caribbean

A complex dispersal into the Caribbean The settlement of the Caribbean and genetic relationships among pre-European Caribbean people remain a mystery. After examining 93 ancient genomes dating to a range from about 3200 to 400 years ago, Nägele et al. suggest that at least three separate colonization events, including a previously unknown wave, were connected to radiation events in North America. The two more ancient lineages coexisted in Cuba but were fully separate genetically, with later movement into the region from a third group from South America. The study not only informs on the settlement of the Caribbean but also lends insights into the broader-scale intercontinental radiation of humans across the American landscape, including across substantial water boundaries. Science, this issue p. 456 Genome-wide data for 93 ancient Caribbean islanders reveals evidence of at least three separate dispersals into the region. The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.
Effect of dicyandiamide applied in a granular form on nitrous oxide emissions from a grazed dairy pasture in Southland, New Zealand

Abstract The trial reported here investigated the effect of applying dicyandiamide (DCD) in a granular form on N2O emissions in a grazed pasture system over 2 years. In 2004, treatments of urea or urea + zeolite‐DCD were applied randomly to pairs of plots following grazing in late autumn. Both treatments received urea at a rate of 50 kg N ha‐1, while the latter treatment also included an application of granular zeolite/DCD at 42 kg ha‐1 (DCn™: 10 kg ha‐1 DCD). In 2005, the same treatments were applied following grazing in early and late autumn and early spring. Measurements of N2O emissions were made at frequent intervals following treatment application using a standardised soil cover technique. Large variability in N2O emissions and soil mineral N levels were measured, due to the variable nature of urine N return by grazing animals. Nevertheless, the results clearly showed that the granular zeolite/DCD significantly reduced N2O emissions from grazed pasture from 1.0 to 0.3 kg N ha‐1, 3.7 to 0.7 kg N ha‐1 and 2.9 to 0.3 kg N ha‐1 for the three measurement periods. This equates to reductions of between 75 and 90% over a 2‐ to 3‐month measurement period. Based on these results, and the assumption that 40–50% of annual N2O emissions occur during the times when nitrification inhibitor application is recommended, granular zeolite/DCD reduced annual N2O emission from grazed pastures by 30–45%.
Effects of supplemental xylanase on health of the small intestine in nursery pigs fed diets with corn distillers' dried grains with solubles.

Forty pigs (10.7 ± 1.2 kg initial BW at 6 wk of age) were used in a 21-d study to evaluate the effects of supplemental xylanase (Hostazym X 100, Huvepharma, Inc., Peachtree City, GA) in nursery diets on digesta viscosity, nutrient digestibility, health of the small intestine, and growth performance when supplemented with corn distillers' dried grains with solubles (DDGS). Pigs were individually housed and randomly allotted to 4 treatments in a 2 × 2 factorial arrangement (n = 20/factor, 0 or 30% DDGS and 0 or 1,500 EPU/kg xylanase as 2 factors) based on sex and initial BW. Feed intake and BW were recorded weekly. On d 15 of the study, TiO2 in diets (0.3%) was used as an indigestible marker to calculate apparent ileal digestibility (AID). Plasma samples were collected on d 19 to measure tumor necrosis factor-alpha (TNF-α), malondialdehyde and peptide YY. On d 21, all pigs were euthanized to collect tissues from duodenum, jejunum, and colon to measure morphology, TNF-α, and MDA concentrations. Distal jejunal digesta were collected to measure viscosity. Ileum digesta were collected to measure AID of nutrients. During the entire period, supplemental xylanase increased (P < 0.05) ADG (616 to 660 g/d) of nursery pigs whereas DDGS (0 or 30%) did not affect ADG. On wk 3, ADFI was increased (P < 0.05) when fed DDGS (1,141 to 1,267 g/d) and there was an interaction (P < 0.05) between 2 factors indicating that supplemental xylanase decreased ADFI when DDGS was used in a diet. Use of DDGS increased (P < 0.05) viscosity (1.86 to 2.38 cP), whereas supplemental xylanase reduced (P < 0.05) viscosity (2.27 to 1.96 cP) of jejunal digesta. The AID of DM and GE were improved (P < 0.05) by supplemental xylanase. Plasma TNF-α was decreased (P < 0.05, 108.5 to 69.9 pg/mL) by supplemental xylanase. Use of DDGS reduced (P < 0.05) villus height:crypt depth (1.46 to 1.27) whereas supplemental xylanase increased (P < 0.05) the crypt depth (360 to 404 µm) in duodenum. In conclusion, feeding a diet with 30% DDGS to nursery pigs for 3 wk had no negative effect on growth performance, whereas reduced AID of DM and GE, increased TNF-α level in colon tissue, and reduced the ratio of villus height to crypt depth. Dietary supplementation of xylanase reduced digesta viscosity improving AID of nutrients, reduced inflammatory response, and altered intestinal morphology, collectively improving ADG of nursery pigs regardless of the use of DDGS in a diet.
Annual Reproductive Cycle of the Common Snook: Endocrine Correlates of Maturation

Abstract Wild common snook Centropomus undecimalis were captured off the Gulf coast of Florida over a 2-year period and sampled for serum and gonad tissue to characterize their annual reproductive cycle. During the summer months, levels of the sex steroid hormones estradiol-17β (E2) and testosterone (T) in females were significantly elevated above basal winter values. Mean gonadosomatic index (GSI) was also significantly elevated in females during summer. In addition, fish whose ovaries contained oocytes in vitellogenic and final maturation stages had elevated levels of alkali-labile protein phosphorus (ALPP), an indirect measure of the egg yolk precursor, vitellogenin. Peak levels of E2, T, and ALPP were measured in females during the spawning season (late summer) when GSI was also maximal. Circulating levels of T and 11-ketotestosterone (11-KT) in males were also higher in the summer months than at any other time of the year. Males showed an increase in GSI over basal winter values during the summer mon.
Human interleukin-4–treated regulatory macrophages promote epithelial wound healing and reduce colitis in a mouse model

Human IL-4 macrophages promote epithelial wound recovery and suppress colitis, supporting their use as a cell therapy for IBD. Murine alternatively activated macrophages can exert anti-inflammatory effects. We sought to determine if IL-4–treated human macrophages [i.e., hM(IL4)] would promote epithelial wound repair and can serve as a cell transfer treatment for inflammatory bowel disease (IBD). Blood monocytes from healthy volunteers and patients with active and inactive IBD were converted to hM(IL4)s. IL-4 treatment of blood-derived macrophages from healthy volunteers and patients with inactive IBD resulted in a characteristic CD206+CCL18+CD14low/− phenotype (RNA-seq revealed IL-4 affected expression of 996 genes). Conditioned media from freshly generated or cryopreserved hM(IL4)s promoted epithelial wound healing in part by TGF, and reduced cytokine-driven loss of epithelial barrier function in vitro. Systemic delivery of hM(IL4) to dinitrobenzene sulphonic acid (DNBS)–treated Rag1−/− mice significantly reduced disease. These findings from in vitro and in vivo analyses provide proof-of-concept support for the development of autologous M(IL4) transfer as a cellular immunotherapy for IBD.
Ranking of Feeding Positions by Drift-Feeding Arctic Grayling (Thymallus arcticus) in Dominance Hierarchies

Field experiments in the pools of a mountain stream demonstrate that Arctic grayling (Thymallus arcticus) rank feeding positions according to desirability and that competition sorts fish so that the dominance rank of each individual matches the rank desirability of its position. Groups containing the same number of fish always occupied the same set of positions, and positions were added (in reverse order of desirability) as group size was increased; these results show that fish ranked positions. There was an almost perfect correlation between the dominance rank (measured as fish length) of each fish and the rank desirability of its position, suggesting that competition sorts fish among positions. This conclusion was strengthened by the results of sequential removal experiments in which the dominant fish was removed at the end of each day. After each removal the remaining fish almost always moved into the positions previously occupied by fish immediately above them in the dominance hierarchy.
Componentes Reprodutivos e Produtivos no Rebanho de Corte da Embrapa Cerrados

The objective of this work was to analyze the various factors which influence calving interval (CI), true fertility (TF), ratio of birth (RBW) and weaning weight (RWW) of the calf to the calving weight of the cow, using the crossbred herd of EMBRAPA Cerrados as a model. The data, from 4469 calvings, collected between 1976 and 1999, was analyzed using the GLM, CORR and PRINCOMP procedures of SAS. The reproductive parameters investigated include ratio of calf birth weight/calving weight of cow (RBW), calf weaning weight / calving weight of cow (RWW) and TF as well as body condition scores (BC) and weights. The correlations between the traits were, generally, low, and sometimes negative with RBW and RWW while with TF they were higher. BC at calving did not affect mortality nor calf birth weight but did affect the following calving interval. The FR increased with increased calving BC as did calving interval. A lower calving interval and higher true fertility was observed with higher weaning BC score. The genetic group of the bull did not influence any of the traits analyzed, which group of the cow influenced birth weight. The environment (month, year and number of parturition) and genetics (sex) significantly influenced birth and weaning weights. The first two principal components explain 56% of the total variation between the traits examined.
Punicalagin Protects Human Retinal Pigment Epithelium Cells from Ultraviolet Radiation-Induced Oxidative Damage by Activating Nrf2/HO-1 Signaling Pathway and Reducing Apoptosis

The oxidative damage of the retinal pigment epithelium (RPE) is the early event that underlies the pathogenesis of maculopathies. Numerous studies have shown that punicalagin (PUN), a polyphenol present in pomegranate, can protect several cell types from oxidative stress. Our study aims to establish if PUN protects RPE from UV radiation-induced oxidative damage. We used an experimental model which involves the use of a human-RPE cell line (ARPE-19) exposed to UV-A radiation for 1, 3, and 5 h. ARPE-19 cells were pre-treated with PUN (24 h) followed by UV-A irradiation; controls were treated identically, except for UV-A. Effects of pre-treatment with PUN on cell viability, intracellular reactive oxygen species ROS levels, modulation of Nrf2 and its antioxidant target genes, and finally apoptosis were examined. We found that pre-treatment with PUN: (1) antagonized the decrease in cell viability and reduced high levels of ROS associated with UV-A-induced oxidative stress; (2) activated Nrf2 signaling pathway by promoting Nrf2 nuclear translocation and upregulating its downstream antioxidant target genes (HO-1 and NQO1); (3) induced an anti-apoptotic effect by decreasing Bax/Bcl-2 ratio. These findings provide the first evidence that PUN can prevent UV-A-induced oxidative damage in RPE, offering itself as a possible antioxidant agent capable of contrasting degenerative eye diseases.
Annual microplankton cycles in Villefranche Bay, Ligurian Sea, NW Mediterranean

Abundance and composition of microplankton were studied over a period of 2 years at two depths in Villefranche Bay (Ligurian Sea, NW Meditrranean Sea). Diatoms dominated the microplankton in late spring and autumn, whereas dinoflagellates composed the major part of the microplankton in summer. The silicoflagellate Dictyocha, fibula and the diatom Thalassionema frauenfeldii dominated in winter. Ciliates showed low variability throughout the year with the lowest abundance in February and an increase which coincided with the diatom maxima during autumn in both years. In 1998, the spring bloom (in May) was mainly composed of dinoflagellates near the surface and of diatoms in deeper layers. Subsurface diatom maxima were observed in August-September and November. In 1999, diatoms peaked in May both at the surface and at the depth of 50 m. They showed a strong maximum in October. Dinoflagellates and tintinnids showed maxima in early November. Comparisons with previous studies reveal that (i) changes in species composition have not been significant, (ii) the silicoflagellate's abundance is lower during the present study, (iii) the sequential spring bloom is composed of a pico-nanoplankton bloom in March and microphytoplankton in May, whereas in other western Mediterranean areas the spring microphytoplankton bloom is reported in February and March, (iv) high water transport through the Corsica channel coinciding with low or negative winter values of North Atlantic Oscillation (NAO) index are associated with the anomalous strong development of the spring diatom blooms in the Bay of Villefranche, whereas the usual trend is the lack of or weak development of the spring diatom bloom. This feature may determine the nature and the fate of primary production and the interannual variability in the relative importance of the microbial food web versus the microbial loop.
Effect of Olive Oil-Fried Sardine Consumption on Liver Lipid Composition and Fatty Acid Cholesterol Esterification in Hypercholesterolemic Rats

PUFA n-3 diets have hypolipemic and cardiovascular protection properties, however their effects on liver lipids are not well established. This work aimed to find out the acceptability and effects of diets containing olive oil-fried sardines on serum cholesterol, liver lipid and fatty acids profile in hypercholesterolemic growing Wistar rats. Hypercholesterolemia was induced for three weeks by a casein plus DL-methionine, olive oil and cholesterol plus bovine bileas cholesterol-raising agent. Rats were later transferred for three weeks to semisynthetic diets containing casein plus DL-methionine and olive oil (CO), casein plus DLmethionine, olive oil and the cholesterol-raising agent (COC), sardines fried in olive oil (S), and sardines friedin olive oil and the cholesterol-raising agent (SC). SC or S diets were well accepted by the rats. The SC-diet markedly blocked and reversed the hypercholesterolemic induction of the cholesterol-raising agent. The cholesterol withdrawal decreased serum cholesterol in CO and S dietsby decreasing the serum non-HDL-cholesterol content but the S-diet totally normalised the serum cholesterol. Fried sardines did not change the triacylglycerol, free, esterified and total cholesterol contents of liver. Although long PUFA n-6 and PUFA n-3 were decreased by the dietary cholesterol, olive oil-fried sardine consumption maintained the docosahexaenoic acid and thedocosahexaenoic acid/linolenic acid ratio in liver and cholesterol ester fraction at a high level. Olive oil fried sardines blocked the hypercholesterolemic effect of the diet containing cholesterol and help normalising lipoprotein profile in a rather short period. The oleic acid esterification of cholesterol was kept high in all experimental diets as a mechanism to maintain the liver cholesterol ester/free cholesterol ratio as high as possible. The fat in the oliveoil-fried sardines was used similarly to the oleic acid by the liver of hypercholesterolemic rats but increased its PUFA n-3 content in the total liver and its cholesterol ester fraction.
Variability of ammonia and methane emissions from animal feeding operations in northeastern Colorado.

Concentrated animal feeding operations (CAFOs) are major emitters of both ammonia (NH3) and methane (CH4), however, current emission inventories have limited temporal resolution and use data derived from a small subset of farms. To this end, we deployed three mobile laboratories during the DISCOVER-AQ campaign in summer 2014 with a focus on northeastern Colorado. Observations of NH3 and CH4 plumes downwind of 43 CAFOs were used to investigate the diurnal and site-to-site variability of emissions with an inverse area plume modeling approach. Ammonia emissions scaled to all permitted animals in Weld, Morgan, and Larimer counties were estimated at 1.9 Gg month-1, 50% greater than the U.S. NEI 2014 and 360% greater than EDGAR for the month of August. Methane emissions were likewise estimated at 10.6 Gg month-1, consistent with the U.S. GHGI but 99% greater than EDGAR. Significant differences between individual CAFOs with repeat observations were also observed for both CH4 and NH3 emissions. The large sub-farm, site-to-site, and diurnal variabilities observed show the importance of measurements taken across these scales in order to derive representative emission factors.
Application of Deep Learning to Predict Standardized Uptake Value Ratio and Amyloid Status on 18F-Florbetapir PET Using ADNI Data

Using the Alzheimer's Disease Neuroimaging Initiative dataset, the authors identified 2582 18F-florbetapir PET scans, which were separated into positive and negative cases by using a standardized uptake value ratio threshold of 1.1. They trained convolutional neural networks to predict standardized uptake value ratio and classify amyloid status. The best performance was seen for ResNet-50 by using regression before classification, 3 input PET slices, and pretraining, with a standardized uptake value ratio root-mean-squared error of 0.054, corresponding to 95.1% correct amyloid status prediction. The best trained network was more accurate than humans (96% versus a mean of 88%, respectively). They conclude that deep learning algorithms can estimate standardized uptake value ratio and use this to classify 18F-florbetapir PET scans and have promise to automate this laborious calculation. BACKGROUND AND PURPOSE: Cortical amyloid quantification on PET by using the standardized uptake value ratio is valuable for research studies and clinical trials in Alzheimer disease. However, it is resource intensive, requiring co-registered MR imaging data and specialized segmentation software. We investigated the use of deep learning to automatically quantify standardized uptake value ratio and used this for classification. MATERIALS AND METHODS: Using the Alzheimer’s Disease Neuroimaging Initiative dataset, we identified 2582 18F-florbetapir PET scans, which were separated into positive and negative cases by using a standardized uptake value ratio threshold of 1.1. We trained convolutional neural networks (ResNet-50 and ResNet-152) to predict standardized uptake value ratio and classify amyloid status. We assessed performance based on network depth, number of PET input slices, and use of ImageNet pretraining. We also assessed human performance with 3 readers in a subset of 100 randomly selected cases. RESULTS: We have found that 48% of cases were amyloid positive. The best performance was seen for ResNet-50 by using regression before classification, 3 input PET slices, and pretraining, with a standardized uptake value ratio root-mean-square error of 0.054, corresponding to 95.1% correct amyloid status prediction. Using more than 3 slices did not improve performance, but ImageNet initialization did. The best trained network was more accurate than humans (96% versus a mean of 88%, respectively). CONCLUSIONS: Deep learning algorithms can estimate standardized uptake value ratio and use this to classify 18F-florbetapir PET scans. Such methods have promise to automate this laborious calculation, enabling quantitative measurements rapidly and in settings without extensive image processing manpower and expertise.
MEK or ERK inhibition effectively abrogates emergence of acquired osimertinib resistance in the treatment of epidermal growth factor receptor–mutant lung cancers

The majority of patients with non–small cell lung cancer (NSCLC) harboring activating epidermal growth factor receptor (EGFR) mutations respond well to osimertinib (AZD9291), a third‐generation, mutation‐selective EGFR inhibitor. The current study focuses on determining whether targeting MEK/ERK signaling prevents or delays the development of acquired resistance to osimertinib.