Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase II trial of conformal radiation therapy for pediatric low-grade glioma.

PURPOSE The use of radiotherapy in pediatric low-grade glioma (LGG) is controversial, especially for young patients. We conducted a phase II trial of conformal radiation therapy (CRT) to estimate disease control by using a 10-mm clinical target volume (CTV) margin. MATERIALS AND METHODS Between August 1997 and August 2006, 78 pediatric patients with LGG and a median age of 8.9 years (range, 2.2 to 19.8 years) received 54 Gy CRT by using a 10-mm CTV and by targeting with systematic magnetic resonance imaging (MRI) registration. Tumor locations were diencephalon (n = 58), cerebral hemisphere (n = 3), and cerebellum (n = 17). Sixty-seven patients had documented or presumed WHO grade 1 tumors, 25 patients had prior chemotherapy, and 13 patients had neurofibromatosis type 1. RESULTS During a median follow-up of 89 months, 13 patients experienced disease progression. One patient experienced marginal treatment failure, eight experienced local failures, and four experienced metastatic failure. The mean and standard error 5- and 10-year event-free (87.4% +/- 4.4% and 74.3% +/- 15.4%, respectively) and overall (98.5% +/- 1.6% and 95.9% +/- 5.8%, respectively) survival rates were determined. The mean and standard error cumulative incidences of local failure at 5 and 10 years were 8.7% +/- 3.5% and 16.4% +/- 5.4%, respectively. The mean and standard error cumulative incidence of vasculopathy was 4.79% +/- 2.73% at 6 years, and it was higher for those younger than 5 years of age (P = .0105) at the time of CRT. CONCLUSION This large, prospective series of irradiated children with LGG demonstrates that CRT with a 10-mm CTV does not compromise disease control. The results suggest that CRT should be delayed in young patients to reduce the risk of vasculopathy.
Experimental context classification: incentives and experience of subjects

There is a need to identify factors that affect the result of empirical studies in software engineering research. It is still the case that seemingly identical replications of controlled experiments result in different conclusions due to the fact that all factors describing the experiment context are not clearly defined and hence controlled. In this article, a scheme for describing the participants of controlled experiments is proposed and evaluated. It consists of two main factors, the incentives for participants in the experiment and the experience of the participants. The scheme has been evaluated by classifying a set of previously conducted experiments from literature. It can be concluded that the scheme was easy to use and understand. It is also found that experiments that are classified in the same way to a large extent point at the same results, which indicates that the scheme addresses relevant factors.
Marine mammal population decline linked to obscured by-catch

Significance Declines of marine megafauna such as turtles, pinnipeds, and whales are often related to mortality caused by capture or entanglement in fisheries gear. To help recovery of these species, trawl fisheries have implemented exclusion devices that release nontarget species. Despite decades of use, there has been no empirical evaluation of whether or not exclusion devices aid recovery of affected species. Long-term data on the endangered New Zealand sea lion and a trawl fishery in the Southern Ocean indicate that exclusion devices have paradoxically contributed to ongoing decline rather than recovery. Exclusion devices obscure the postrelease impact of elevated mortality or reproductive failure; meanwhile, reduced levels of reported by-catch may mislead management that continued decline is not associated with fisheries. Declines of marine megafauna due to fisheries by-catch are thought to be mitigated by exclusion devices that release nontarget species. However, exclusion devices may instead conceal negative effects associated with by-catch caused by fisheries (i.e., unobserved or discarded by-catch with low postrelease survival or reproduction). We show that the decline of the endangered New Zealand (NZ) sea lion (Phocarctos hookeri) is linked to latent levels of by-catch occurring in sub-Antarctic trawl fisheries. Exclusion devices have been used since 2001 but have not slowed or reversed population decline. However, 35% of the variability in NZ sea lion pup production is explained by latent by-catch, and the population would increase without this factor. Our results indicate that exclusion devices can obscure rather than alleviate fishery impacts on marine megafauna.
Genetic differentiation in two widespread, open-forest bird species of Southeast Asia (Copsychus saularis and Megalaima haemacephala): Insights from ecological niche modeling

Ecological niche modeling has emerged as an useful tool in the investigation of the phylogeographic histories of spe- cies or communities in a region. The high biodiversity (oftentimes cryptic), and complex geography and geological history of Southeast Asia particularly call for multipronged approaches in phylogeographic investigations. Past studies have focused on taxa that are associated with lowland rainforests, which is the dominant natural vegetation type. Here, we combine published phylo- genetic data, ecological niche modeling and paleo-climate models to reveal potential drivers of divergence in two open-forest bird species, the oriental magpie-robin Copsychus saularis and Coppersmith barbet Megalaima haemacephala. In spite of broad overlap in current distributions, there are subtle differences in their climatic niches, which result in different responses to past climatic changes. For C. saularis, both Last Glacial Maximum climate models indicated that the entire Sundaland was climati- cally suitable, while phylogenetic analyses found divergent eastern and western Sundaland lineages. We thus postulate that this genetic divergence was a result of past separations of coastal habitats into eastern and western portions due to the emergence of Sunda shelf as sea-level fell. The current separation of morphological subspecies in Borneo is maintained by low climatic suita- bility (high annual rainfall) in certain regions. The extirpation of M. haemacephala from Borneo and southern Malay Peninsula might have been driven by unsuitable conditions (high temperature seasonality) in central Sundaland and/or the lack of open woodlands. Our study shows that ecological niche modeling adds a powerful dimension to our attempt to understand lineage evolution in space (Current Zoology 61 (5): 922-934, 2015).
Dependability Issues in a Robot Control Architecture

This paper presents the LAAS architecture for autonomous mobile robots and some recent developments to improve the dependability of the system. In particular, this paper focuses on the role of the Execution Control level of this architecture. This level has a fault protection (safety bag) role with respect to the commands issued to the functional level which is connected to the physical devices. These commands come either from the decisional level, or from the functional level itself. We introduce a new approach and a new tool inspired from the model checking domain. We present a new language to specify the model of acceptable and required states of the system (valid contexts for requests to functional module and resources usage). This language is compiled in an OBDD (Ordered Binary Decision Diagram) like structure which is then used online to check the specified constraints in realtime. Such a model checking approach could be extended to check off line more complex temporal properties of the system.
Zero-Shot Relation Extraction via Reading Comprehension

We show that relation extraction can be reduced to answering simple reading comprehension questions, by associating one or more natural-language questions with each relation slot. This reduction has several advantages: we can (1) learn relation-extraction models by extending recent neural reading-comprehension techniques, (2) build very large training sets for those models by combining relation-specific crowd-sourced questions with distant supervision, and even (3) do zero-shot learning by extracting new relation types that are only specified at test-time, for which we have no labeled training examples. Experiments on a Wikipedia slot-filling task demonstrate that the approach can generalize to new questions for known relation types with high accuracy, and that zero-shot generalization to unseen relation types is possible, at lower accuracy levels, setting the bar for future work on this task.
Bayesian Information Criterion for Censored Survival Models

Summary. We investigate the Bayesian Information Criterion (BIG) for variable selection in models for censored survival data. Kass and Wasserman (1995, Journal of the American Statistical Association90, 928–934) showed that BIG provides a close approximation to the Bayes factor when a unit‐information prior on the parameter space is used. We propose a revision of the penalty term in BIG so that it is defined in terms of the number of uncensored events instead of the number of observations. For a simple censored data model, this revision results in a better approximation to the exact Bayes factor based on a conjugate unit‐information prior. In the Cox proportional hazards regression model, we propose defining BIG in terms of the maximized partial likelihood. Using the number of deaths rather than the number of individuals in the BIC penalty term corresponds to a more realistic prior on the parameter space and is shown to improve predictive performance for assessing stroke risk in the Cardiovascular Health Study.
Mapping the narratives of natural disasters and their domino effects. The case study of floods impacting railways

ABSTRACT Studying past at-risk phenomena is useful to prepare against future risks. Thanks to maps, it is possible to locate historical events in their spatial context. Animation and interactivity support the analysis of the dynamics of events. This paper deals with a visual method to represent narratives of past natural risk events in a map. It is based on the case study of past floods, which impacted the railway network. Map visualizations were developed with experts of the railway system, to overcome two main challenges: to visualize punctual events which have occurred at the same place over time and to display causality relationships between events in order to show domino effects. Proposals were evaluated during a user study. It showed that the combination between an animated map and a synthesis map helped users to carry out different tasks. It also showed that the combination between a map and a timeline, in a geovisualization interface, increased the efficiency of the exploration of flood narratives.
Oleosome-Associated Protein of the Oleaginous Diatom Fistulifera solaris Contains an Endoplasmic Reticulum-Targeting Signal Sequence

Microalgae tend to accumulate lipids as an energy storage material in the specific organelle, oleosomes. Current studies have demonstrated that lipids derived from microalgal oleosomes are a promising source of biofuels, while the oleosome formation mechanism has not been fully elucidated. Oleosome-associated proteins have been identified from several microalgae to elucidate the fundamental mechanisms of oleosome formation, although understanding their functions is still in infancy. Recently, we discovered a diatom-oleosome-associated-protein 1 (DOAP1) from the oleaginous diatom, Fistulifera solaris JPCC DA0580. The DOAP1 sequence implied that this protein might be transported into the endoplasmic reticulum (ER) due to the signal sequence. To ensure this, we fused the signal sequence to green fluorescence protein. The fusion protein distributed around the chloroplast as like a meshwork membrane structure, indicating the ER localization. This result suggests that DOAP1 could firstly localize at the ER, then move to the oleosomes. This study also demonstrated that the DOAP1 signal sequence allowed recombinant proteins to be specifically expressed in the ER of the oleaginous diatom. It would be a useful technique for engineering the lipid synthesis pathways existing in the ER, and finally controlling the biofuel quality.
Monocyte Subsets and Related Chemokines in Carotid Artery Stenosis and Ischemic Stroke

Carotid stenosis (CS) is an important cause of ischemic stroke. However, reliable markers for the purpose of identification of high-risk, so-called vulnerable carotid plaques, are still lacking. Monocyte subsets are crucial players in atherosclerosis and might also contribute to plaque rupture. In this study we, therefore, aimed to investigate the potential role of monocyte subsets and associated chemokines as clinical biomarkers for vulnerability of CS. Patients with symptomatic and asymptomatic CS (n = 21), patients with cardioembolic ischemic strokes (n = 11), and controls without any cardiovascular disorder (n = 11) were examined. Cardiovascular risk was quantified using the Essen Stroke Risk Score (ESRS). Monocyte subsets in peripheral blood were measured by quantitative flow cytometry. Plaque specimens were histologically analyzed. Furthermore, plasma levels of monocyte chemotactic protein 1 (MCP-1) and fractalkine were measured. Intermediate monocytes (Mon2) were significantly elevated in symptomatic and asymptomatic CS-patients compared to controls. Mon2 counts positively correlated with the ESRS. Moreover, stroke patients showed an elevation of Mon2 compared to controls, independent of the ESRS. MCP-1 levels were significantly higher in patients with symptomatic than in those with asymptomatic CS. Several histological criteria significantly differed between symptomatic and asymptomatic plaques. However, there was no association of monocyte subsets or chemokines with histological features of plaque vulnerability. Due to the multifactorial influence on monocyte subsets, the usability as clinical markers for plaque vulnerability seems to be limited. However, monocyte subsets may be critically involved in the pathology of CS.
Disaggregating the Effect of Drought and Heat Stress During Flowering on Spikelet Fertility in Rice

Due to rice’s wide geographic distribution, extending from 50°N to 35°S, rice is forecasted to be the most vulnerable crop to warming global climates. Previous studies have predicted lower rice yields and increasing rice yield variability due to higher frequencies of heat stress events, and a higher variability in precipitation patterns due to global warming. As such, understanding the effects of drought and heat stress intensity and frequency on rice yields is of upmost importance to feeding the growing global population. Given that drought and high-temperature stress often occur together, it is essential to disaggregate the two individual stressors and examine possible interactions by modeling them simultaneously. A reliable and robust temperature and drought threshold inducing rice spikelet sterility under field conditions involving cultivars with highly varying phenology has been a major limitation for devising adaptation strategies for rice breeders and to estimate heat stress and drought impacts by the climate and crop modeling communities. It is in this spirit that this study was designed. This study examines and quantifies the individual marginal effects of drought and heat stress occurring simultaneously under field conditions by means of a regression analysis. Moreover, a cardinal threshold is found for drought as well as for heat in relation to spikelet fertility. This study utilizes canopy temperature threshold instead of the more commonly found ambient temperature thresholds in the literature. The canopy temperature threshold is more precise since canopy temperature has a more direct connection to spikelet temperature and therefore spikelet fertility than ambient temperature. Another contribution of this thesis is from modeling the relationship between ambient temperature, drought and canopy temperature as a recursive system which will allow future research to estimate the effects of changes in global ambient temperature to spikelet fertility. The results of this study found that exposure to a canopy temperature over a threshold of 33°C causes a severe increase in rice spikelet sterility. An estimated drought threshold of 12 kPa (kilopascal) was found to be the most detrimental to spikelet fertility. This is important given two of the largest pressures facing future rice production are heat and drought stress. Another related finding is that in the presence of heat stress the availability of adequate water during flowering can decrease sterility by 14.16 %. The results of this study, which are variety specific, can allow for understanding the properties of combined heat and drought stress, which can provide information to rice breeders on how to promote reproductive-stage drought tolerance through improved germplasm and attempt to help mitigate the effects of a global climate change.
Techno-Economic and Life Cycle Assessment of Hydrothermal Processing of Microalgae for Biofuels and Co-Product Generation

TECHNO-ECONOMIC AND LIFE CYCLE ASSESSMENT OF HYDROTHERMAL PROCESSING OF MICROALGAE FOR BIOFUELS AND CO-PRODUCT GENERATION Andrew P. Bessette Old Dominion University, 2018 Director: Dr. Sandeep Kumar Traditional processing methods of algae to biofuels require dewatering after harvesting of the algae before the lipids can be extracted. This is typically the most energy intensive and therefore the most expensive step. Old Dominion University (ODU) has successfully utilized a flash hydrolysis (a kind of hydrothermal) process where proteins are solubilized into the liquid phase of product and the remainder lipid-rich, low nitrogen product is separated into a solid phase. The solid phase (lipid-rich) is then an ideal candidate for biofuel feedstock and the liquid phase, or hydrolysate, can be used for coproducts such as a source of nutrients for new batches of algal cultivation or fertilizer production. The importance of this research lies within the energy conservation associated with the flash hydrolysis process, the quality of the co-products that are generated during the flash hydrolysis process, and the subsequent processing methods utilized to recover the nutrients not directly used for biofuel products. Processes which complement each other in the processing of microalgae to biofuel must be utilized for improving life cycle assessment (LCA) and technoeconomic analysis (TEA) results. These LCA and TEA data are critical for investors in both the public and private sectors. A valuable return on investment must be quantified in order for investors to move forward with advanced biofuels production. A combination of resources are utilized in this dissertation to quantify the LCA and TEA of the hydrothermal processes that are utilized in the ODU Biomass Research Laboratory (BRL) which include Argonne National Laboratory GREET, SuperPro Designer, Aspen Plus, and SimaPro’s Ecoinvent databases. This dissertation evaluates the novel processes researched in the BRLfrom the microscopic flash hydrolysis process level to a community level macroscopic evaluation. The clarity of how the flash hydrolysis compares with other hydrothermal processes is studied by conducting a LCA comparison. The flash hydrolysis process is then modeled utilizing two different microalgae species with varying cultivation and nutrient extraction properties. The alternate downstream processing methods for recovering preserved nutrients is then modeled for LCA and TEA results in order to quantify how coproduct generation offsets energy costs associated with algae biofuel processing. The final chapter of this dissertation utilizes the LCA and TEA results captured within the preceding assessments to develop a sustainable community model with algae cultivation and downstream processing at the focus of the sustainable community and an ultimate goal of zero net energy and zero waste system boundaries for the community.
Genetic structure of three marine fishes from the Gulf of Pagasitikos (Greece) based on allozymes, RAPD, and mtDNA RFLP markers

In the present work we used three molecular techniques (allozymes, RAPDs and mtDNA RFLPs) in order to study the genetic structure of three commercial marine species (Mullus surmuletus, Mullus barbatus, and Pagellus erythrinus). Each species was sampled from three locations within the Gulf of Pagasitikos, Greece and from two neighbouring locations outside the Gulf (Trikeri and Alonissos). Values of genetic heterozygosity and nucleotide diversity for all populations studied were similar or above the mean values observed in marine fishes. None of the three types of molecular markers used revealed diagnostic patterns, which could allow the allocation of individuals to one of the populations. The analyses revealed that the three populations within Pagasitikos were homogenous representing thus a panmictic stock. However, there were evidences of genetic population subdivision between localities from inside and outside of the Pagasitikos Gulf. The results provide essential information for the design of a sustainable management plan of the Gulf of Pagasitikos and its demersal fish resources.
The use of brief post‐surgical low frequency electrical stimulation to enhance nerve regeneration in clinical practice

Despite efforts to enhance peripheral nerve regeneration, there has been little progress in improving clinical outcomes. Recently, a method of brief post‐surgical low frequency electrical stimulation of surgically repaired nerves has been developed. It was shown to accelerate axon outgrowth across the repair site and it hastened target reinnervation. In this brief review, we describe the mechanistic insights and functional impacts of the post‐surgical electrical stimulation that have been gained through animal studies. Brain‐derived neurotrophic factor, cyclic AMP and regeneration‐associated genes play a vital role in expediting the outgrowth of axons across the injury site. The method of stimulation has also been shown to be effective in patients with severe compressive neuropathy as well as those with digital nerve laceration. Its clinical feasibility and positive impact open the door of further clinical translation in other peripheral nerve injuries.
Current sheets at three-dimensional magnetic nulls: Effect of compressibility

The nature of current sheet formation in the vicinity of three-dimensional (3D) magnetic null points is investigated. The particular focus is upon the effect of the compressibility of the plasma on the qualitative and quantitative properties of the current sheet. An initially potential 3D null is subjected to shearing perturbations, as in a previous paper [Pontin et al., Phys. Plasmas 14, 052106 (2007)]. It is found that as the incompressible limit is approached, the collapse of the null point is suppressed and an approximately planar current sheet aligned to the fan plane is present instead. This is the case regardless of whether the spine or fan of the null is sheared. Both the peak current and peak reconnection rate are reduced. The results have a bearing on previous analytical solutions for steady-state reconnection in incompressible plasmas, implying that fan current sheet solutions are dynamically accessible, while spine current sheet solutions are not.
Dependence Potential of Tramadol: Behavioral Pharmacology in Rodents

Tramadol is an opioid analgesic agent that has been the subject of a series of case reports suggesting potential for misuse or abuse. However, it is not a controlled substance and is not generally considered addictive in Korea. In this study, we examined the dependence potential and abuse liability of tramadol as well as its effect on the dopaminergic and serotonergic systems in rodents. In animal behavioral tests, tramadol did not show any positive effects on the experimental animals in climbing, jumping, and head twitch tests. However, in the conditioned place preference and self-administration tests, the experimental animals showed significant positive responses. Taken together, tramadol affected the neurological systems related to abuse liability and has the potential to lead psychological dependence.