Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive modelling of brain disorders with magnetic resonance imaging: A systematic review of modelling practices, transparency, and interpretability in the use of convolutional neural networks

Brain disorders comprise several psychiatric and neurological disorders which can be characterized by impaired cognition, mood alteration, psychosis, depressive episodes, and neurodegeneration. Clinical diagnoses primarily rely on a combination of life history information and questionnaires, with a distinct lack of discriminative biomarkers in use for psychiatric disorders. Symptoms across brain conditions are associated with functional alterations of cognitive and emotional processes, which can correlate with anatomical variation; structural magnetic resonance imaging (MRI) data of the brain are therefore an important focus of research, particularly for predictive modelling. With the advent of large MRI data consortia (such as the Alzheimer's Disease Neuroimaging Initiative) facilitating a greater number of MRI‐based classification studies, convolutional neural networks (CNNs)—deep learning models well suited to image processing tasks—have become increasingly popular for research into brain conditions. This has resulted in a myriad of studies reporting impressive predictive performances, demonstrating the potential clinical value of deep learning systems. However, methodologies can vary widely across studies, making them difficult to compare and/or reproduce, potentially limiting their clinical application. Here, we conduct a qualitative systematic literature review of 55 studies carrying out CNN‐based predictive modelling of brain disorders using MRI data and evaluate them based on three principles—modelling practices, transparency, and interpretability. We propose several recommendations to enhance the potential for the integration of CNNs into clinical care.
Performance evaluation of security-aware routing protocols for clustered mobile ad hoc networks

Secure routing is vital to the acceptance of ad hoc networks for several applications. This paper explores the efficacy of security aware routing protocols to support real-time multimedia data transmission over clustered mobile ad hoc networks. Two state-of-the-art secure routing protocols, SEAD and ARIADNE, are tested on a simulated environment and their performance is compared under various traffic conditions and network topologies. For this operational scenario SEAD has exhibited overall better performance, but still it fails to accommodate fully real-time traffic at data rates that can support audio/visual multimedia communications.
Combination of Clinical Factors and Radiomics Can Predict Local Recurrence and Metastasis After Stereotactic Body Radiotherapy for Non-small Cell Lung Cancer

Background/Aim: Radiomics, which links radiological image features with patient prognoses, is expected to be applied for the prediction of the clinical outcomes of radiotherapy. We investigated the clinical and radiomic factors associated with recurrence patterns after stereotactic body radiotherapy (SBRT) for non-small cell lung cancer (NSCLC). Patients and Methods: We retrospectively analyzed 125 patients with histologically confirmed NSCLC who underwent SBRT between April 2003 and June 2017 at our institution. A radiomic score was calculated from five radiomics features (histogram and texture features) selected using the LASSO Cox regression model. These features were extracted from the gross tumor volume (GTV) in three-dimensional wavelet decomposition CT images. We used univariate and multivariate analyses to determine the associations between local control (LC) time and metastasis-free survival (MFS), clinical factors (age, sex, performance status, operability, smoking, histology, and tumor diameter), and the radiomic score. Results: With a median follow-up of 37 months, the following 3-year rates were observed: overall survival, 80.9%; progression-free survival, 61.7%; LC, 75.1%, and MFS; 74.5%. In multivariate analysis, histology (squamous cell carcinoma vs. non-squamous cell carcinoma, p=0.0045), tumor diameter (>3 cm vs. ≤3 cm, p=0.039); and radiomic score (>0.043 vs. ≤0.043, p=0.042) were significantly associated with LC, and the radiomic score (>0.304 vs. ≤0.304, p<0.001) was significantly associated with MFS. Conclusion: Histology, tumor diameter, and radiomic score could be significant factors for predicting NSCLC recurrence patterns after SBRT.
Can earlier biomarker measurements explain a treatment effect on diabetes incidence? A robust comparison of five surrogate markers

Introduction We measured and compared five individual surrogate markers—change from baseline to 1 year after randomization in hemoglobin A1c (HbA1c), fasting glucose, 2-hour postchallenge glucose, triglyceride–glucose index (TyG) index, and homeostatic model assessment of insulin resistance (HOMA-IR)—in terms of their ability to explain a treatment effect on reducing the risk of type 2 diabetes mellitus at 2, 3, and 4 years after treatment initiation. Research design and methods Study participants were from the Diabetes Prevention Program study, randomly assigned to either a lifestyle intervention (n=1023) or placebo (n=1030). The surrogate markers were measured at baseline and 1 year, and diabetes incidence was examined at 2, 3, and 4 years postrandomization. Surrogacy was evaluated using a robust model-free estimate of the proportion of treatment effect explained (PTE) by the surrogate marker. Results Across all time points, change in fasting glucose and HOMA-IR explained higher proportions of the treatment effect than 2-hour glucose, TyG index, or HbA1c. For example, at 2 years, glucose explained the highest (80.1%) proportion of the treatment effect, followed by HOMA-IR (77.7%), 2-hour glucose (76.2%), and HbA1c (74.6%); the TyG index explained the smallest (70.3%) proportion. Conclusions These data suggest that, of the five examined surrogate markers, glucose and HOMA-IR were the superior surrogate markers in terms of PTE, compared with 2-hour glucose, HbA1c, and TyG index.
Why Maintaining Tropical Forests is Essential and Urgent for a Stable Climate

Tropical forests have the highest carbon density and cover more land area than forests in any other biome. They also serve a vital role as a natural buffer to climate change ― capturing 2.2–2.7 Gt of carbon per year. Unfortunately, tropical forests, mangroves, and peatlands are also subjected to the highest levels of deforestation and account for nearly all net emissions from Forestry and Other Land Use (FOLU) (1.1–1.4 Gt C/year). Net emissions from FOLU accounted for only 11% of total anthropogenic greenhouse gas emissions or 14% of total carbon emissions in 2010, though these figures are somewhat misleading and do not reflect the full potential of tropical forests to mitigate climate change. First, net FOLU emissions have reduced only slightly while emissions from all other sectors have skyrocketed. Secondly, the FOLU net flux is made up of two larger fluxes — deforestation emissions (2.6–2.8 Gt C/year) minus sequestration from forest regrowth (1.2–1.7 Gt C/year). Additionally, intact tropical forests also appear to be capturing at least 1.0 Gt C/year. Gross deforestation, therefore, accounts for over a quarter of all carbon emissions, and tropical forests have removed 22–26% of all anthropogenic carbon emissions in the 2000s. If deforestation were halted entirely, forests were allowed to regrow, and mature forests were left undisturbed, tropical forests alone could have captured 25–35% of all other anthropogenic carbon emissions. On the other hand, if climate change continues unabated, forests could turn from net sinks to net sources of carbon. Forestrelated activities are among the most economically feasible and cost-effective mitigation strategies, which are important for both short- and long-term mitigation strategies. Action is needed immediately to utilize these natural mitigation solutions, and we need coordinated and comprehensive forest-related policies for mitigation. An international mechanism such as REDD+ is essential to realize the great natural potential for tropical forests to stabilize the climate.
Adaptation and habitat preference in a hybrid zone between Bombina bombina and Bombina variegata in Croatia

This thesis describes a hybrid zone between two taxa of toads, Bombina bombina and Bombina variegata in north eastern Croatia. The two taxa can be distinguished at four diagnostic enzyme loci. Clines at these loci are highly concordant; there is strong disequilibrium and substantial heterozygote deficit. Both the linkage disequilibrium and heterozygote deficit are asymmetric, being greater on the bombina side than on the variegata side. Different habitats are identified across the zone and a strong association with the genotype of the populations sampled from them is found. This relationship is consistent across the hybrid zone. The dine is best described by a model which incorporates both a difference in gene frequency between habitats and a width which varies from place to place. Mark recapture studies show extensive movement, which implies that the association between habitat and genotype is due to a habitat preference. Translocation experiments suggest that there is adaptation to the habitats. A habitat preference combined with mixing between habitats will inflate linkage disequilibrium over and above that expected from dispersal alone. Non-random mating and selection in relation to the environment will also contribute to the disequilibrium. As a result, inferences made using traditional dine models, where disequilibrium is mainly generated by dispersal, no longer apply. These results are very different from those made from a previous analysis of the Bombina hybrid zone in Poland. There the dine showed a smoother transition of genotypes and a sharper step in gene frequency at the centre of the dine. The differences to the transect described here can be accounted for by a habitat
Tortuosity: a guide through the maze

Abstract Despite its widespread use in petrophysics, tortuosity remains a poorly understood concept. Tortuosity can have various meanings when used by physicists, engineers or geologists to describe different transport processes taking place in a porous material. Values for geometrical, electrical, diffusional and hydraulic tortuosity are in general different from one another. Electrical tortuosity is defined in terms of conductivity whereas hydraulic tortuosity is usually defined geometrically, and diffusional tortuosity is typically computed from temporal changes in concentration. A better approach may be to define tortuosity in terms of the underlying flux of material or electrical current with respect to the forces which drive this flow. Unsteady transport processes, including diffusion, can be described only by a population of tortuosities corresponding to the different flow paths taken by particles traversing the medium. In measurements of steady flow (e.g., those normally used to obtain resistivity or permeability), information about particle travel times is lost, and so the multiple values of tortuosity are homogenised. It can be shown that the maximum amount of information about pore structure is embedded in transport processes that combine advective and diffusive elements. Most existing formulations of tortuosity are model-dependent, and cannot be correlated with independently measurable pore-structure properties. Nevertheless, tortuosity underpins the rigorous relationships between transport processes in rocks, and ties them with the underlying geometry and topology of their pore spaces. Tortuosity can be redefined in terms of the energetic efficiency of a flow process. The efficiency is related to the rate of entropy dissipation (or isothermally, energy dissipation) with respect to a simple, non-tortuous model medium using the postulates of non-equilibrium thermodynamics. Through Onsager’s reciprocity relation for coupled flows it is possible to inter-relate efficiency for pairs of transport processes, and so go some way towards unifying tortuosity measures. In this way we can approach the goal of predicting the value of one transport parameter from measurements of another.
Intermittent Nicotine Access is as Effective as Continuous Access in Promoting Nicotine Seeking and Taking in Rats

Nicotine is a principal psychoactive agent in tobacco, contributing to tobacco’s addictive potential. Preclinical studies on the effects of voluntary nicotine intake typically use self-administration procedures that provide continuous nicotine access during each self-administration session. However, many smokers consume cigarettes intermittently rather than continuously throughout each day. For drugs including cocaine and opioids, research in laboratory rats shows that intermittent intake can be more effective than continuous intake in producing patterns of drug use relevant to addiction. We asked, therefore, how intermittent versus continuous nicotine self-administration influences nicotine seeking and taking behaviours. Female and male rats had continuous (i.e., Long Access; LgA, 6 h/day) or intermittent (IntA; 12 min ON, 60 min OFF, for 6 h/day) access to intravenous nicotine (15 µg/kg/infusion), for 12 daily sessions. We then assessed intake, responding for nicotine under a progressive ratio schedule of drug reinforcement and cue- and nicotine-induced reinstatement of drug seeking. We also estimated nicotine pharmacokinetic parameters during LgA and IntA self-administration. Overall, LgA rats took twice more nicotine than did IntA rats, yielding more sustained increases in estimated brain concentrations of the drug. However, the two groups showed similar motivation to seek and take nicotine, as measured using reinstatement and progressive ratio procedures, respectively. Thus, intermittent nicotine use is just as effective as continuous use in producing addiction-relevant behaviours, despite significantly less nicotine exposure. This has implications for modeling nicotine self-administration patterns in human smokers and resulting effects on brain and behaviour.
Geochemical evidence for iron‐mediated anaerobic oxidation of methane

Anaerobic oxidation of methane (AOM) by sulfate has been recognized as a critical process to maintain this greenhouse gas stability by limiting methane flux to the atmosphere. We show geochemical evidence for AOM in deep lake sediments and demonstrate that AOM is likely driven by iron (Fe) reduction. Pore‐water profiles from Lake Kinneret (Sea of Galilee, Israel) show that this sink for methane is located below the 20‐cm depth in the sediment, which is well below the depths at which nitrate and sulfate are completely exhausted, as well as below the zone of methanogenesis. Iron‐dependant AOM was verified by Fe(III)‐amended mesocosm studies using intact sediment cores, and native iron oxides were detectable throughout the sediments. Because anaerobic Fe(III) respiration is thermodynamically more favorable than both sulfate‐dependent methanotrophy and methanogenesis, its occurrence below the zone of methane production supports the idea that reduction of sedimentary iron oxides is kinetically or biologically limited. Similar conditions are likely to prevail in other incompletely pyritized aquatic sediments, indicating that AOM with Fe(III) is an important global sink for methane.
Visualization and Modeling of Smoke Transport Over Landscape Scales

Computational tools have been developed at the National Institute of Stan- dards and Technology (NIST) for modeling fire spread and smoke transport. These tools have been adapted to address fire scenarios that occur in the wildland urban interface (WUI) over kilometer-scale distances. These models include the smoke plume transport model ALOFT (A Large Open Fire plume Trajectory model) and WFDS (Wildland- urban interface Fire Dynamics Simulator) for fire spread and smoke transport in the wildland-urban interface. The visualization tool is called Smokeview. In this paper, an overview of the physical basis of the fire spread and smoke transport models will be discussed briefly along with the visualization of characteristic results using Smokeview. A technique will be described for visualizing smoke realistically, and indications will be given how Smokeview can be applied to other fire models.
NeoHeadHunter: an algorithm for the detection, ranking and probabilistic classification of neoepitope candidates

Background The manufacturing of personalized cancer vaccine requires the accurate identification of neoepitopes, abnormal peptides presented by cancer cells and recognized by the host immune system of the cancer patient. Results We designed and developed NeoHeadHunter, a computational algorithm and pipeline to detect and rank neoepitope candidates. Unlike other algorithms, NeoHeadHunter can estimate the probability that each predicted neoepitope candidate is true positive. To evaluate NeoHeadHunter, we used the Tumor neoantigEn SeLection Alliance (TESLA) data-set derived from the sequencing of nine patients and characterized by 44 experimentally validated positive neoepitopes, a data-set derived from the sequencing of three cancer patients and characterized by eight experimentally validated positive neoepitopes and a manually curated data-set consisting of 64 experimentally validated positive neoepitopes. Our evaluation shows that NeoHeadHunter performs the best compared with other algorithms for both detecting and ranking neoepitope candidates and that NeoHeadHunter can accurately predict such probabilities. Conclusions NeoHeadHunter can increase the effectiveness of personalized cancer vaccine by sensitively detect, accurately rank and probabilistically classify neoepitope candidates. NeoHeadHunter is released under the APACHE-II license at https://github.com/XuegongLab/neoheadhunter for academic use.
An Assessment of the Topographic Effects on Sar Image Tone

RESUMELes variations topographiques influencent les relations angulaires entre la cible et le capteur. comme la retrodiffusion des microondes par une cible donnee est fonction de ces relations angulaires, des cibles similaires observees suivant des geometries angulaires differentes produiront une retrodiffusion differente et, par consequent, presenteront des niveaux de gris differents sur les images radar. Dans le cas de terrains plats, ces variations sont introduites uniquement par les geometries de visee obliques du capteur. Dans le cas de terrains plus complexes, des cibles observees suivant le meme angle de depression seront quand meme observees suivant des angles d'incidence locaux differents en raison des differences topographiques locales. Dans le cas de regions vallonnees, on a constate que ces effets representaient entre 15 % et 50 % de la variance des niveaux de gris de l'image. Les effets topographiques sont egalement fonction de la longueur d'onde, avec des tendances differentes pour les bande.
Above-soil and in-soil degradation of oxo- and bio-degradable mulches: a qualitative approach

Degradable materials have been suggested to overcome accumulation in the field of persistent plastic residues associated with the increasing use of polyethylene mulches. New degradable materials have been proven successful for increasing crop productivity; however, their degradation in the field has been hardly addressed. A qualitative scale was used in the present study to assess the above-soil and in-soil degradation of degradable mulches during the cropping season. Degradation was determined in three biodegradable plastic mulches (Biofilm, BF; Mater-Bi, MB; Bioflex, BFx), two paper sheet mulches (Saikraft, PSA; MimGreen, PMG) and one oxo-degradable plastic mulch (Enviroplast, EvP). Polyethylene (PE) mulch was used as control. Mulches were tested in five Spanish locations (Castilla-La Mancha, La Rioja, Navarra, Aragon and Catalunya), with three crop seasons of processing tomato. Biodegradable plastic mulches BF and MB degraded more and faster above-soil than paper mulches; among biodegradable mulches BF degraded more than MB, and MB more than BFx. The above-soil degradation of the oxo-degradable mulch EvP was highly dependent on location and crop season, and it degraded more than PE. Main environmental factors triggering above-soil degradation were radiation, rainfall and crop cover. In-soil, paper mulches and BF degraded more and faster than MB, whereas BFx and EvP barely degraded. Environmental factors triggering in-soil degradation during the crop season were rainfall and irrigation water. The effect of soil parameters (organic matter, nutrient availability) on degradation during the cropping season was not evidenced. The qualitative scale used proved convenient for determining mulch field degradation. A visual scale for supporting the qualitative evaluation is provided. In order to standardise parameters and criteria for future studies on field mulching degradation evaluation, a unified degradation qualitative scale is suggested.
Internet Addiction and its Relation to Psychosocial Adaptation among Jordanian High Basic Stage Students

The study aimed at identifying the level of internet addiction among high basic stage students (8 th , 9 th and 10 th grades) in Jordan. It also aimed at predicting the effect of psychosocial adaptation and other variables related to internet use on internet addiction. To achieve the objectives of the study, the internet addiction scale and the psychosocial adaptation scale were used and administered to a sample of (600) male and female students. The results of the study showed that the rate of internet addicts reached (8.5 %) for the total sample. The results revealed that the following dimensions of the psychosocial adaptation scale (attention problems, physical problems, anxiety and depression, and social problems), and the number of hours spent on the internet, checking the e-mail, visiting social sites, and years of internet usage contributed in predicting internet addiction. The results also showed that the psychosocial adaptation among non-addicted students was higher than that of the addicted students.
Exploring the effect of lithium on pegmatitic textures: An experimental study

Abstract The effect of lithium (Li) on the development of pegmatitic textures was evaluated experimentally at H2O-saturated and H2O-undersaturated conditions at 500 MPa pressure and temperatures ranging from 400 to 800 °C. The addition of ~3700 ppm Li to a starting material of common granitic composition (Lake County obsidian) reduces the crystallization and melting temperatures by approximately 50-70 and 200 °C, respectively, and promotes the formation of quartz-feldspar graphic and granophyric intergrowths. The presence of Li in the hydrous granitic system lowers significantly the degree of undercooling needed for the development of graphic and granophyric intergrowths to 85-110 °C in comparison with the Li-free systems where approximately 200 °C of undercooling is necessary. The feldspar crystals developed in Li-bearing samples can incorporate from 150 to 250 ppm Li, assume skeletal and spherulitic morphologies, and exhibit one order of magnitude faster growth rates than crystals in Li-free samples. The results of this study attest to the effectiveness of Li as a fluxing agent and highlight the crucial role it plays in the development of pegmatitic textures, leading to important implications for the conditions of formation of Li-bearing granitic pegmatites.