Miracle-dz/UniFAR-FTUs huggingface dataset:
Global metaanalysis of the nonlinear response of soil nitrous oxide (N2O) emissions to fertilizer nitrogen

Significance We clarify the response of the greenhouse gas nitrous oxide (N2O) to nitrogen (N) fertilizer additions, a topic of considerable debate. Previous analyses have used single N-rate experiments to define a linear response to N additions across climate, management, and soil conditions globally. Here, we provide a first quantitative comparison of N2O emissions for all available studies that have used multiple N rates. Results show that a nonlinear emission factor better represents global emission patterns with lower uncertainty, offering more power for balancing the global N2O budget and for designing effective mitigation strategies. Nitrous oxide (N2O) is a potent greenhouse gas (GHG) that also depletes stratospheric ozone. Nitrogen (N) fertilizer rate is the best single predictor of N2O emissions from agricultural soils, which are responsible for ∼50% of the total global anthropogenic flux, but it is a relatively imprecise estimator. Accumulating evidence suggests that the emission response to increasing N input is exponential rather than linear, as assumed by Intergovernmental Panel on Climate Change methodologies. We performed a metaanalysis to test the generalizability of this pattern. From 78 published studies (233 site-years) with at least three N-input levels, we calculated N2O emission factors (EFs) for each nonzero input level as a percentage of N input converted to N2O emissions. We found that the N2O response to N inputs grew significantly faster than linear for synthetic fertilizers and for most crop types. N-fixing crops had a higher rate of change in EF (ΔEF) than others. A higher ΔEF was also evident in soils with carbon >1.5% and soils with pH <7, and where fertilizer was applied only once annually. Our results suggest a general trend of exponentially increasing N2O emissions as N inputs increase to exceed crop needs. Use of this knowledge in GHG inventories should improve assessments of fertilizer-derived N2O emissions, help address disparities in the global N2O budget, and refine the accuracy of N2O mitigation protocols. In low-input systems typical of sub-Saharan Africa, for example, modest N additions will have little impact on estimated N2O emissions, whereas equivalent additions (or reductions) in excessively fertilized systems will have a disproportionately major impact.
Diagnosis of autosomal dominant retinitis pigmentosa by linkage-based exclusion screening with multiple locus-specific microsatellite markers.

PURPOSE To describe a hierarchical approach for efficient genetic diagnosis of autosomal dominant retinitis pigmentosa (adRP). METHODS Forty di-, tri-, or tetra-nucleotide repeats tightly linked to 10 genes known to be responsible for adRP were identified from the human genome sequence and used as markers in multiplex amplification and genotyping, followed by linkage analysis. Discordance of cosegregation of markers and the disease excluded the majority of the examined genes as candidates, and mutation screening for the remaining genes was performed. RESULTS With this strategy, examination of an adRP-affected family indicated that 3 of 10 candidate genes segregated concordantly with the disease. Further searches for mutations revealed a novel insertion and deletion in the last exon of a splicing factor gene, PRPF8. CONCLUSIONS This systematic approach facilitates the molecular diagnosis of adRP, which is known to have a highly heterogeneous genetic background.
Ga-PSMA-PET in prostrate cancer Delineating biochemical failure with 68 Ga-PSMA-PET following definitive external beam radiation treatment for prostate cancer

Background and purpose: We investigated the role of Ga-PSMA-PET (PSMA) to determine the location of disease recurrence in those with a rising PSA following definitive external beam radiation treatment (EBRT). Materials and methods: 538 men were treated with image guided EBRT to a dose of 78 or 82 Gy between 2007 and 2014. Patients at least 24 months post EBRT with biochemical failure (nadir + 2) underwent PSMA scanning. Local recurrence (LR) was defined as increased uptake within the prostate or seminal vesicles. Distant disease included lymph node (LN), bone or visceral metastases. Results: 419 men formed the study cohort. Median follow-up was 50 months, 70 patients (17%) had biochemical failure (BF), 13 of whom have died. Of the 57 survivors, 5 had metastases detected on conventional scans; 2 were lost to follow up. 48 men (of 50 candidates) underwent PSMA; in all cases, the PSMA was unequivocally positive. Of the 48 positive scans, 25 patients (52%) failed beyond the prostate – 5 in bones, 16 LN, 3 in both, and 1 in the lungs. Fifteen men (31%) failed within the gland and in either LN (11), bones (3), or both (1). Eight (17%) had an isolated LR, which represents 2% of patients managed with definitive EBRT and followed for at least 2 years. Conclusions: PSMA was positive in all patients with BF. Site of failure following dose-escalated EBRT was generally distant. Isolated LR (on PSMA) occurred in only 8 of 419 patients post-EBRT. Crown Copyright 2016 Published by Elsevier Ireland Ltd. All rights reserved. Radiotherapy and Oncology 122 (2017) 99–102 The source of a rising PSA following definitive EBRT may be local, distant or both. This has important implications with respect to salvage versus systemic management options. In this situation, and with a PSA < 10, conventional imaging with CT and bone scan is unhelpful [1]. PSMA has a higher detection rate with a higher specificity than choline-PET [2,3], and is able to evaluate distant metastatic disease in contrast to multi-parametric MRI (mp-MRI). Since 2015, our high risk prostate cancers have been routinely staged with PSMA; and we use PSMA to identify sites of recurrence in men post-prostatectomy, with a rising PSA above 0.2 ng/mL [4]. We have also performed PSMA in those who fail EBRT to determine sites of failure and identify those who may benefit from focal or targeted radiation treatment versus those who are best managed with observation or systemic treatment. In this analysis, we set out to determine whether PSMA was positive in men with BF; if so, to then investigate its role to delineate sites of failure in patients who received definitive image guided and dose-escalated EBRT and who subsequently met the Phoenix definition [5] of BF (nadir + 2). Our hypothesis was that those with LR alone may have had radio-resistant disease based on bulky or hypoxic tumours predicted by factors such as PSA, T stage, dose, and higher core positivity. Methods and materials
Clinical and pathologic factors predicting reclassification in active surveillance cohorts

ABSTRACT The incidence of small, lower risk well-differentiated prostate cancer is increasing and almost half of the patients with this diagnosis are candidates for initial conservative management in an attempt to avoid overtreatment and morbidity associated with surgery or radiation. A proportion of patients labeled as low risk, candidates for Active Surveillance (AS), harbor aggressive disease and would benefit from definitive treatment. The focus of this review is to identify clinicopathologic features that may help identify these less optimal AS candidates. A systematic Medline/PubMed Review was performed in January 2017 according to PRISMA guidelines; 83 articles were selected for full text review according to their relevance and after applying limits described. For patients meeting AS criteria including Gleason Score 6, several factors can assist in predicting those patients that are at higher risk for reclassification including higher PSA density, bilateral cancer, African American race, small prostate volume and low testosterone. Nomograms combining these features improve risk stratification. Clinical and pathologic features provide a significant amount of information for risk stratification (>70%) for patients considering active surveillance. Higher risk patient subgroups can benefit from further evaluation or consideration of treatment. Recommendations will continue to evolve as data from longer term AS cohorts matures.
The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)

We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf (limnetic) and normal (benthic) whitefish. We observed a sex bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between the sexes. Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed. We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development on the basis of colocalization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations. Eighty-eight percent of eQTL-phenotypic QTL colocalization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs. Hotspots colocalized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc-finger protein in one case, control gene expression directly related to adaptive phenotypic divergence. We observed little evidence of colocalization of brain eQTL with behavioral QTL, which provides insight into the genes identified by behavioral QTL studies. These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological, differences appear to play a key role in this divergence.
Use of serum retinol-binding protein for prediction of vitamin A deficiency: effects of HIV-1 infection, protein malnutrition, and the acute phase response.

BACKGROUND Serum retinol is the most commonly used indicator of vitamin A status. Retinol is transported in a 1-to-1 complex with retinol-binding protein (RBP). RBP is easy and inexpensive to measure, and studies have shown a high correlation between concentrations of RBP and concentrations of retinol. The performance of RBP in the context of infection or protein malnutrition, however, has not been evaluated. OBJECTIVE Our aim was to determine whether RBP is a good surrogate measure for retinol in the context of HIV-1 infection, protein malnutrition, and the acute phase response. DESIGN The relation between RBP and retinol was examined in a cross-sectional study of 600 Kenyan women. RESULTS There was a high correlation between concentrations of RBP and those of retinol (r = 0.88). When equimolar cutoffs were used, RBP predicted marginal vitamin A status (retinol < 1.05 micro mol/L) with 93% sensitivity and 75% specificity and vitamin A deficiency (retinol < 0.70 micro mol/L) with 91% sensitivity and 94% specificity. Similarly high sensitivities and specificities were found among subgroups with HIV-1 infection, a positive acute phase response, and protein malnutrition. Protein malnutrition and a positive acute phase response were common, especially among HIV-1-infected women, and were independently and synergistically associated with lower RBP concentrations. CONCLUSIONS Equimolar RBP cutoffs predict vitamin A deficiency with high sensitivity and specificity, even in the context of infection and protein malnutrition. Like retinol, RBP may not accurately identify true vitamin A status under all conditions, because the acute phase response and protein malnutrition depress RBP concentrations. However, RBP may be a simple, inexpensive tool for assessment of vitamin A deficiency in population studies.
Distributed Constraint Optimization Problems and Applications: A Survey

The field of Multi-Agent System (MAS) is an active area of research within Artificial Intelligence, with an increasingly important impact in industrial and other real-world applications. Within a MAS, autonomous agents interact to pursue personal interests and/or to achieve common objectives. Distributed Constraint Optimization Problems (DCOPs) have emerged as one of the prominent agent architectures to govern the agents' autonomous behavior, where both algorithms and communication models are driven by the structure of the specific problem. During the last decade, several extensions to the DCOP model have enabled them to support MAS in complex, real-time, and uncertain environments. This survey aims at providing an overview of the DCOP model, giving a classification of its multiple extensions and addressing both resolution methods and applications that find a natural mapping within each class of DCOPs. The proposed classification suggests several future perspectives for DCOP extensions, and identifies challenges in the design of efficient resolution algorithms, possibly through the adaptation of strategies from different areas.
Chemical Contaminants in Raw and Pasteurized Human Milk

Background: Environmental contaminants ranging from legacy chemicals like p,p’-dichlorodiphenyltrichloroethane (DDT) to emerging chemicals like phthalates are ubiquitous. Research aims/questions: This research aims to examine the presence and co-occurrence of contaminants in human milk and effects of pasteurization on human milk chemical contaminants. Methods: We analyzed human milk donated by 21 women to a milk bank for 23 chemicals, including the persistent organic pollutants (POPs) polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), dichlorodiphenyltrichloroethane (DDT), and dichlorodiphenyldichloroethylene (DDE) isomers that are known to sequester in adipose tissue, along with the current-use and nonpersistent pesticides chlorpyrifos and permethrin, phthalates, and bisphenol A (BPA). Human milk was analyzed raw and pasteurized for these chemicals using gas chromatography–tandem mass spectrometry for the POPs and high-performance liquid chromatography–tandem mass spectrometry for non-POPs. Results: Within the different chemical classes, PBDE47, PCB153, ppDDE, and MEHHP (phthalate metabolite) had the highest median concentrations and were observed in all samples. We also observed chlorpyrifos and BPA in all samples and permethrin in 90% of the samples tested. Only two chemicals, chlorpyrifos and permethrin, were susceptible to substantial degradation from pasteurization, a standard method for processing donated human milk. Conclusion: We detected 19 of 23 chemicals in all of our prepasteurized milk and 18 of 23 chemicals in all of our pasteurized milk. Pasteurization did not affect the presence of most of the chemicals. Future research should continue to explore human milk for potential chemical contamination and as a means to surveil exposures among women and children.
The Pre-Surgical Planning of Brain Neoplasms: From Diffusion Tensor Imaging to More Advanced Approaches

©2015 Arrigo A. This is an open access article distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Volume 1 : Issue 1 Article Ref. #: 1000ROJ1e001 The Pre-Surgical Planning of Brain Neoplasms: From Diffusion Tensor Imaging to More Advanced Approaches
Quantifying training intensity distribution in elite endurance athletes: is there evidence for an “optimal” distribution?

This study was designed to quantify the daily distribution of training intensity in a group of well‐trained junior cross‐country skiers and compare the results of three different methods of training intensity quantification. Eleven male athletes performed treadmill tests to exhaustion to determine heart rate and VO2 corresponding to ventilatory thresholds (VT1, VT2), maximal oxygen consumption (VO2max), and maximal heart rate. VT1 and VT2 were used to delineate three intensity zones. During the same time period, all training sessions (N=384, 37 strength training, 347 endurance) performed over 32 consecutive days were quantified using continuous heart rate registration and session Rating of Perceived Exertion (RPE). In addition, a subset of 60 consecutive training sessions was quantified using blood lactate measurements. Intensity distribution across endurance training sessions (n=318) was similar when based on heart rate analysis (75±3%, zone 1; 8±3%, zone 2; 17±4%, zone 3) or session RPE (76±4%, zone 1; 6±5%, zone 2; 18±7%, zone 3). Similarly, from measurements of 60 consecutive sessions, 71% were performed with ≤2.0 mM blood lactate, 7% between 2 and 4 mM, and 22% with over 4 mM (mean=9.5±2.8 mM). In this group of nationally competitive junior skiers, training was organized after a polarized pattern, with most sessions performed clearly below (about 75%) or with substantial periods above (15–20%) the lactate accommodation zone, which is bounded by VT1 and VT2. The pattern quantified here is similar to that reported in observational studies of elite endurance athletes across several sports. It appears that elite endurance athletes train surprisingly little at the lactate threshold intensity.
Constrained Energy Minimization for Matching-Based Image Recognition

We propose to use energy minimization in MRFs for matching-based image recognition tasks. To this end, the Tree-Reweighted Message Passing algorithm is modified by geometric constraints and efficiently used by exploiting the guaranteed monotonicity of the lower bound within a nearest-neighbor based classification framework. The constraints allow for a speedup linear to the dimensionality of the reference image, and the lower bound allows to optimally prune the nearest-neighbor search without loosing accuracy, effectively allowing to increase the number of optimization iterations without an effect on runtime. We evaluate our approach on well-known OCR and face recognition tasks and on the latter outperform current state-of-the-art.
The morphological plastic response to water current velocity varies with age and sexual state in juvenile Atlantic salmon, Salmo salar

SUMMARY 1. Salmonids, like many other fish species, exhibit morphological plasticity to variations in water current velocity. However, little is known about how this response varies with age and alternative sexual tactics that usually coexist in the same area. We therefore sampled immature 1- and 2-year-old and sexually mature Salmo salar parr to determine how the morphological response to slow and rapid water currents varies across these groups. 2. Both 1- and 2-year-old immature parr in rapid habitats can be distinguished from individuals in slow habitats using a combination of fin measurements. In contrast, body shape measurements were useful only to distinguish 2-year-old individuals in the different habitat types. We also showed that mature parr are notably robust, irrespective of habitat type. For these individuals, only their body length differed between slow and rapid water currents, being bigger in slow water currents. 3. Our results imply that fins are the first structures to respond to water current velocity, followed by changes in body shape as individuals grow bigger. The robust phenotype observed for mature parr is likely to pose extra limitations on movement due to an increase in drag forces, thus contributing to their smaller size in rapid water currents.
Consumption of cocoa flavanols results in acute improvements in mood and cognitive performance during sustained mental effort

Cocoa flavanols (CF) positively influence physiological processes in ways that suggest their consumption may improve aspects of cognitive function. This study investigated the acute cognitive and subjective effects of CF consumption during sustained mental demand. In this randomized, controlled, double-blinded, balanced, three period crossover trial 30 healthy adults consumed drinks containing 520 mg, 994 mg CF and a matched control, with a three-day washout between drinks. Assessments included the state anxiety inventory and repeated 10-min cycles of a Cognitive Demand Battery comprising of two serial subtraction tasks (Serial Threes and Serial Sevens), a Rapid Visual Information Processing (RVIP) task and a ‘mental fatigue’ scale, over the course of 1 h. Consumption of both 520 mg and 994 mg CF significantly improved Serial Threes performance. The 994 mg CF beverage significantly speeded RVIP responses but also resulted in more errors during Serial Sevens. Increases in self-reported ‘mental fatigue’ were significantly attenuated by the consumption of the 520 mg CF beverage only. This is the first report of acute cognitive improvements following CF consumption in healthy adults. While the mechanisms underlying the effects are unknown they may be related to known effects of CF on endothelial function and blood flow.
Insulin secretion kinetics from single islets reveals distinct subpopulations

Type II diabetes progresses with inadequate insulin secretion and prolonged elevated circulating glucose levels. Also, pancreatic islets isolated for transplantation or tissue engineering can be exposed to glucose over extended timeframe. We hypothesized that isolated pancreatic islets can secrete insulin over a prolonged period of time when incubated in glucose solution and that not all islets release insulin in unison. Insulin secretion kinetics was examined and modeled from single mouse islets in response to chronic glucose exposure (2.8‐20 mM). Results with single islets were compared to those from pools of islets. Kinetic analysis of 58 single islets over 72 h in response to elevated glucose revealed distinct insulin secretion profiles: slow‐, fast‐, and constant‐rate secretors, with slow‐secretors being most prominent (ca., 50%). Variations in the temporal response to glucose therefore exist. During short‐term (<4 h) exposure to elevated glucose few islets are responding with sustained insulin release. The model allowed studying the influence of islet size, revealing no clear effect. At high‐glucose concentrations, when secretion is normalized to islet volume, the tendency is that smaller islets secrete more insulin. At high‐glucose concentrations, insulin secretion from single islets is representative of islet populations, while under low‐glucose conditions pooled islets did not behave as single ones. The characterization of insulin secretion over prolonged periods complements studies on insulin secretion performed over short timeframe. Further investigation of these differences in secretion profiles may resolve open‐ended questions on pre‐diabetic conditions and transplanted islets performance. This study deliberates the importance of size of islets in insulin secretion. © 2018 American Institute of Chemical Engineers Biotechnol. Prog. , 34:1059–1068, 2018