Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling of Solar Radiation Interception and Biomass Production in an Intercropping System of Rubber with Banana and Pineapple

Simulation modelling is a powerful approach for studying complex intercropping systems in entirety and a complementary tool to conventional field experiments. This study aimed to: 1) construct a dynamic model to simulate the biological productivity of an immature rubber (R), banana (8) and pineapple (P) intercropping system based on the interception and utilisation of incident solar radiation (SR), 2) evaluate growth and yield of the intercrop components using the model, 3) compare production for various cropping scenarios and 4) investigate the likelihood and effects of water stress on crop growth using a simple water budget. A FORTRAN computer model, SURHIS (Sharing and Utilisation of Radiation intercepted in a Hedgerow-Intercropping System), was developed for simulating daily SR interception and growth of R-B-P intercropping system. SR interception was modelled using a modified Monsi-Saeki equation by including a clump factor to account for the loss in intercepted SR resulting from the wide row spacing between the crops. Crop growth was modelled based on the net biomass resulting from the difference between crop photosynthesis and respi ration. Simulation results showed that increments in the leaf area index (LAI) had a greater effect on SR interception by component crops compared to height increments. Changes in height affected only fractional interception, whereas LAI increments affected both fractional and total interception. The crop growth modules were suffiCiently accurate in estimating LAI and dry matter yield (OMY) but less precise for crop height. The girth of rubber was estimated with good accuracy. The general trend in overestimation for later part of the simulation period can be attributed to model assumptions for potential production conditions.
ksrates : positioning whole-genome duplications relative to speciation events using rate-adjusted mixed paralog–ortholog K S distributions

Summary: To position ancient whole-genome duplication (WGD) events with respect to speciation events in a phylogeny, the K S values of WGD paralog pairs in a species of interest are often compared with the K S values of ortholog pairs between this species and other species. However, if the lineages involved exhibit diﬀerent substitution rates, direct comparison of paralog and ortholog K S estimates can be misleading and result in phylogenetic misinterpretation of WGD signatures. Here we present ksrates , a user-friendly command-line tool to compare paralog and ortholog K S distributions derived from genomic or transcriptomic sequences. ksrates estimates differences in synonymous substitution rates among the lineages involved and generates an adjusted mixed plot of paralog and ortholog K S distributions that allows to assess the relative phylogenetic positioning of presumed WGD and speciation events. Availability and implementation: ksrates is open-source software implemented in Python 3 and as a Nextﬂow pipeline. The source code, Singularity and Docker containers, documentation and tutorial are available via https://github.com/VIB-PSB/ksrates.
ESTIMATING CORRIDOR TRAVEL TIME MEAN, VARIANCE, AND COVARIANCE WITH INTELLIGENT TRANSPORTATION SYSTEMS LINK TRAVEL TIME DATA

Accurate estimation of travel time mean and variance is valuable for a variety of real-time and off-line transportation applications. Travel time data can be estimated from a variety of intelligent transportation systems (ITS) data collection methods including inductance loop detectors, automatic vehicle identification (AVI), or more recently, the use of mobile cellular telephones. The ability to place confidence intervals around a travel time mean estimate along a link or corridor is dependent upon the ability to estimate the travel time variance. corridor travel time variance is often estimated from the summation of travel time variances of the links along the corridor by assuming independence of travel times between links. When independence is assumed, the covariance between the links can be treated as zero and the approach is straightforward. The impact of the independence assumption has been studied from a theoretical perspective. This paper uses empirical data to examine the validity of the independence assumption. In particular, procedures are described for investigating travel time variance estimates obtained from a naive method of assuming independence between links in comparison to a first- and second-order approximation obtained from a Taylor's Series
Controls of seismogenic zone width and subduction 1 velocity on interplate seismicity : insights from 2 analog and numerical models 3

FABIO CORBI, ROBERT HERRENDÖRFER, FRANCESCA FUNICIELLO, YLONA 4 VAN DINTHER 5 6 1 Géosciences Montpellier Laboratory, University of Montpellier, Montpellier, France. 7 2 Institute of Geophysics, ETH Zurich, Sonneggstrasse 5, CH-8092, Zurich, Switzerland. 8 3 Dipartimento di Scienze, University “Roma Tre”, L. S.L. Murialdo, 1, 00146, Rome, Italy. 9 *Correspondence to: fabio.corbi3@gmail.com 10
Changing access to forest resources in Tanzania.

This paper provides an empirical exploration of the dependence of villagers on non-timber forest products in the Morogoro region in Tanzania, the decision rules that villagers use concerning where and how much they collect, how their collection changes with degradation, and the implications of introducing more restrictive access rules of participatory forest management. Villagers’ responses to increased degradation vary by forest product: fuelwood collection tends to be displaced to other forests in response to degradation, fewer forest fruits and vegetables are collected, and collection times increase considerably for weaving and building materials.
Edinburgh Research Explorer Interrogation Theory

A variety of examples illustrates the generality of this method: an asset team investi-gating how best to exploit a subsurface reservoir, Monte Carlo sampling to estimate the Bayesian evidence for geophysical models, discriminating between different rock physics models of strain in laboratory deformation experiments, an organisation sequentially assessing the effectiveness of its methods to evaluate subsurface assets, assessing whether subsurface CO 2 storage should be promoted for climate change mitigation, and examples running through the text of seismic tomography, earthquake characterisation, and autonomous interplanetary robotic exploration.
Overcoming the Under- and Over-Estimation Problems in Adaptive Sliding Mode Control

Underand over-estimation problems are commonly observed in conventional adaptive sliding mode control (ASMC). These problems refer to the fact that the adaptive controller gain unnecessarily increases when the states are approaching the sliding surface (overestimation) or improperly decreases when the states are getting far from it (underestimation). In this work, we propose a novel ASMC strategy that overcomes such issues. In contrast to the state of the art, the proposed strategy is effective even when a priori constant bound on the uncertainty cannot be imposed. Comparative results using two-link manipulator demonstrate improved performance as compared to the conventional ASMC. Experimental results on a biped robot confirm the effectiveness and robustness of the proposed method under various practical uncertainties.
Supplementary Materials for “Understanding Deep Networks via Extremal Perturbations and Smooth Masks”

1 Area constraint . 2 2 Generating smooth masks . 2 3 Comparison with other visualization methods 4 4 Comparison with other visualization methods (more examples) . 5 5 Comparison with [2] . 6 6 Area growth (up to 5%). 7 7 Area growth (up to 10%). 7 8 Area growth (up to 20%). 8 9 Area growth (up to 40+%). 9 10 Cascading randomization sanity check (ours). 10 11 Independent randomization sanity check (ours). 11 12 Cascading randomization sanity check for “jungo’ (comparison). 12 13 Independent randomization sanity check for “jungo’ (comparison). 13 14 Pointing Examples from PASCAL . 14 15 Pointing Examples from COCO . 14
Should We Start Worrying ? Mass Higher Education , Skill Demand and the Increasingly Complex Landscape of Young Graduates ’ Employment DRAFT VERSION – NOT TO BE QUOTED

Recent decades have seen a massive expansion in the access to higher education, fuelled by high social and individual expectations about its potential economic benefits. The unprecedented speed and scale of expansion has raised concerns about the impact that such massification could have on the employability of more recent cohorts of graduates, as well as in the emergence of potential mismatches between their skills and the competences required by the job structure. In this paper we analyse some of the effects of mass higher education by looking at the transition to employment of a rapidly expanding cohort of graduates in Portugal during the 2000-2010 period. We explore the incidence of three inter-related but different aspects that aim at identifying problems in the transition of graduates to the labour market, namely overeducation, overskilling, and education-job mismatches. The paper concludes by discussing the implications of our findings regarding the policy and social expectations supporting mass higher education.
Education‐related inequity in healthcare with heterogeneous reporting of health

Summary. Reliance on self‐rated health to proxy medical need can bias estimation of education‐related inequity in healthcare utilization. We correct this bias both by instrumenting self‐rated health with objective health indicators and by purging self‐rated health of reporting heterogeneity that is identified from health vignettes. Using data on elderly Europeans, we find that instrumenting self‐rated health shifts the distribution of visits to a doctor in the direction of inequality favouring the better educated. There is a further, and typically larger, shift in the same direction when correction is made for the tendency of the better educated to rate their health more negatively.
Low sulfate seawater mitigates barite scale

Low-sulfate seawater (LSSW) technology provides operational and economic benefits for desulfating seawater to control barium sulfate (BaSO{sub 4}) and strontium sulfate (SrSO{sub 4}) scale. This concluding article in a three part series describes, from a scale control perspective, the membrane technology deployed in the North Sea Brae fields.
Effets du mode de travail du sol sur les microorganismes à l'échelle du profil cultural

RÉSUMÉ Le travail du sol modifie la répartition des résidus de culture et la structure du sol et affecte par conséquent les microorganismes du sol (nombre, structure génétique des populations) ainsi que les fonctions qu’ils assurent au premier rang desquelles la minéralisation de la matière organique. L’objectif est d’étudier l’effet de ces modifications engendrées par deux techniques contrastées de travail du sol : un labour traditionnel (LT) et un travail du sol réduit (TR). Les variables étudiées sont la biomasse microbienne du sol (BM), le potentiel de minéralisation du carbone (Cmin) et la structure des communautés bactériennes du sol évaluée par T-RFLP. Afin de prendre en compte l’effet simultané des modifications de la structure du sol et celles de la répartition des résidus de culture, une stratégie d’échantillonnage stratifiée au sein du profil cultural a été adoptée. Pour cela, les indicateurs microbiens ont été mesurés sur des mottes compactées et non-compactées (respectivement baptisées Δ et Γ ) prélevées
Governance in socio-economic pathways and its role for 1 future adaptive capacity

5 6 Weak governance is one of the key obstacles for sustainable development. Undoubtedly, improvement of 7 governance comes with a broad range of co-benefits including countries’ abilities to respond to pressing 8 global challenges such as climate change. However, beyond the qualitative acknowledgement of its 9 importance, quantifications of future pathways of governance are still lacking. This study provides 10 projections of future governance in line with the Shared Socio-economic Pathways (SSPs). We find that 11 under a “rocky road” scenario, 30% of the global population would still live in countries characterized by 12 weak governance in 2050, while under a “green road” scenario weak governance would almost be entirely 13 overcome over the same time frame. Based on pathways for governance, we estimate the adaptive capacity 14 of countries to climate change. Limits to adaptive capacity exist even under optimistic pathways beyond 15 mid-century. Our findings underscore the importance of accounting for governance in assessments of 16 climate change impacts. 17
DFT study of ligand binding in the β1 adrenergic receptor

Abstract The β2-adrenergic receptor, located in the prostate region, binds noradrenaline and can influence the growth of prostate tumors. The removal of Adrb2, the gene for this receptor, can halt tumor growth and thus can serve as an alternative to chemotherapy for cancer treatment. Inhibition of the receptor may have similar effects. Comparison of β2- (PDB ID: 5X7D) and β1-adrenergic receptor (PDB ID: 2Y04) structures showed a conserved binding region on Chain A offset by approximately eight amino acids between the two receptors. The structure of the β1-adrenergic receptor with the bound partial agonist salbutamol was used to create a model of the active site of the β2-adrenergic receptor. Potential inhibitors were optimized in the receptor binding site using M062X/6-31G with relaxed amino acid sidechains. Interaction energies between the ligands and the receptor were calculated using M062X/6-311+G*. Positively charged inhibitors show greater interaction energies as compared to negatively charged inhibitors.
The design of history mechanisms and their use in collaborative educational simulations

Reviewing past events has been useful in many domains. Videotapes and flight data recorders provide invaluable technological help to sports coaches or aviation engineers. Similarly, providing learners with a readable recording of their actions may help them monitor their behavior, reflect on their progress, and experiment with revisions of their experiences. It may also facilitate active collaboration among dispersed learning communities. Learning histories can help students and professionals make more effective use of digital library searching, word processing tasks, computer-assisted design tools, electronic performance support systems, and web navigation.This paper describes the design space and discusses the challenges of implementing learning histories. It presents guidelines for creating effective implementations, and the design tradeoffs between sparse and dense history records. The paper also presents a first implementation of learning histories for a simulation-based engineering learning environment called SimPLE (Simulated Processes in a Learning Environment) for the case of a semiconductor fabrication module, and reports on early user evaluation of learning histories implemented within SimPLE.
Effects of low molecular weight heparin, alone or combined with antithrombin III, on mortality, fibrin deposits and hemostatic parameters in endotoxin‐induced disseminated intravascular coagulation in rabbits

The effect of low molecular weight heparin (LMWH) with or without antithrombin III (AT III) has been studied in a rabbit model of disseminated intravascular coagulation (DIC) induced by continuous infusion of 100 μg/kg/hr of Escherichia coli endotoxin for 6 hr. LMWH (5 and 10 IU/kg/hr/6 hr), alone or in combination with AT III (20 U/kg/hr/6 hr), or saline were administered simultaneously with endotoxin. Hemostatic markers at 0, 2, and 6 hr as well as kidney fibrin deposits and the mortality rate at 24 hr were determined. Rabbits receiving only endotoxin showed an impairment in hemostasis, as well as high kidney fibrin deposits and a high mortality rate. LMWH alone did not exert any effect. The simultaneous infusion of LMWH and AT III exerted a beneficial effect on the hemostatic markers and reduced the kidney fibrin deposits as well as the mortality rate in a LMWH dose‐dependent manner. Fibrinogen and protein C consumption were significantly higher and renal fibrin deposits more intense in the rabbits that had died in the first 24 hr. There was also a significant positive correlation between kidney fibrin deposits and platelets, fibrinogen, and protein C consumption, taking the whole rabbit population. It is concluded that the simultaneous infusion of LMWH and AT III is useful in this DIC model and would make it possible to reduce significantly the AT III doses used when AT III is given alone. Am. J. Hematol. 60:6–11, 1999. © 1999 Wiley‐Liss, Inc.
Nutritional interventions for reducing the signs and symptoms of exercise-induced muscle damage and accelerate 1 recovery in athletes : current knowledge , practical application and future perspectives 2 3

Citation: Bongiovanni, Tindaro, Genovesi, Federico, Nemmer, Monika, Carling, Christopher, Alberti, Giampietro and Howatson, Glyn (2020) Nutritional interventions for reducing the signs and symptoms of exercise-induced muscle damage and accelerate recovery in athletes: current knowledge, practical application and future perspectives. European Journal of Applied Physiology, 120 (9). pp. 1965-1996. ISSN 1439-6319
First episode psychosis: a novel methodology reveals higher than expected incidence; a reality-based population profile in Northumberland, UK.

RATIONALE, AIMS AND OBJECTIVES To document the natural history/clinical course of an unselected population presenting with first episode psychosis across a Mental Health Trust. METHOD An observational database was set up covering all patients over 15 years of age. Data were collected at presentation and annual follow-up intervals. RESULTS A total of 227 patients presented during the 3 years initial study period with a first episode psychosis. The commonest diagnoses were psychotic depression 19%, paranoid schizophrenia 11%, persistent delusional disorder 7% and bipolar affective disorder 7.5% giving an annual incidence of 30.36 per 100 000 population. At presentation, half had been admitted to hospital, nearly half of whom were detained under the Mental Health Act, and only a quarter were currently employed. Twenty-six per cent had an episode of deliberate self-harm and 14% had harmed others. A recurring pattern emerged of over half the patients being no longer in contact with mental health services 1 year after presentation. Data collection is ongoing. CONCLUSIONS Clinical and managerial cooperation achieved a practical framework for data collection. This approach in an unselected population of patients yielded new insights into the course of first episode psychosis. The higher incidence than expected from the literature has implications for local strategic planning and provides a framework for detailed evaluation of a complex patient group.
Physical Activity and its Associations with other Lifestyle Elements in Polish Women

Physical Activity and its Associations with other Lifestyle Elements in Polish Women The aim of the study was to determine associations between physical activity and other elements of women's lifestyle (nutrition, being a nonsmoker, moderate alcohol consumption, medical check-ups). Between 1999 and 2004, 1361 women aged 20-75 were studied. They were inhabitants of cities located in the west of Poland and engaged in physical activity (purposeful selection). The subjects fell into four groups depending on the length of their physical exercise history: G I - those who had been exercising for 1 year; G II [1-4); G III [4-6); G IV [≥7). The diagnostic poll method was employed, (questionnaire and interview techniques). For the verification of the research hypotheses concerning the influence of socio-demographic factors on women's physical activity, the evaluation of changes in health-related behaviors resulting from long term physical activity, indication of associated behaviors, the independence χ2 test and multiple correspondence analysis were used. Women's physical activity was found to be related to maintenance of proper weight (BMI) (p≤0.05), moderate consumption of low-alcohol beverages (p≤0.05) and regular dental check-ups (p≤0.05). Despite more frequent attempts to take up smoking, the respondents gave up the habit two times as often as the whole population of women in Poland. These correlations were more apparent among women with longer exercise histories, who mostly had post-secondary education. Occurrence of associated behaviors affecting health positively and negatively was also shown, the latter concerning a smaller group of respondents. The noticed correlations between physical activity and health behaviors, which comprehensively influence lifestyle, may be of importance in gradual reduction of risk factors.
Prevalence of Systemic Lupus Erythematosus in the United States: Estimates From a Meta‐Analysis of the Centers for Disease Control and Prevention National Lupus Registries

Epidemiologic data on systemic lupus erythematosus (SLE) are limited, particularly for racial/ethnic subpopulations in the US. This meta‐analysis leveraged data from the Centers for Disease Control and Prevention (CDC) National Lupus Registry network of population‐based SLE registries to estimate the overall prevalence of SLE in the US.
Combinação dos métodos dos modos assumidos e matriz de transferência em dispositivos ópticos baseados em redes de Bragg sob deformação longitudinal

—This work presents an approach to simulate the temporal behavior of the Bragg grating reflected spectrum combining two numerical methods named assumed modes and transfer matrix. This approach consists in calculating the time-space variation of the displacement field and, consequently, the strain field inside the grating through the assumed modes method and apply this field as input in the transfer matrix in order to calculate the time-space behavior of the Bragg grating reflected spectrum. This approach is applied in an acousto-optic modulator based on FBG and results are compared to experimental data reported in the literature.
Alternative stable states, nonlinear behavior, and 1 predictability of microbiome dynamics 2

33 Microbiome dynamics are both crucial indicators and drivers of human health, agricultural 34 output, and industrial bio-applications. However, predicting microbiome dynamics is 35 notoriously difficult because communities often show abrupt structural changes, such as 36 “dysbiosis” in human microbiomes. We here integrate theoretical and empirical bases for 37 anticipating drastic shifts of microbial communities. We monitored 48 experimental 38 microbiomes for 110 days and observed that various community-level events, including 39 collapse and gradual compositional changes, occurred according to a defined set of 40 environmental conditions. We then confirmed that the abrupt community changes observed 41 through the time-series could be described as shifts between “alternative stable states“ or 42 dynamics around complex attractors. Furthermore, collapses of microbiome structure were 43 successfully anticipated by means of the diagnostic threshold defined with the energy 44 landscape analysis of statistical physics or that of a stability index of nonlinear mechanics. 45 These results indicate that abrupt microbiome events in complex microbial communities can 46 be forecasted by extending classic ecological concepts to the scale of species-rich microbial 47 systems. 48 49 51 , and plant-associated pest/pathogen agroecosystems the empirical and theoretical studies for predicting and controlling species-rich