Miracle-dz/UniFAR-FTUs huggingface dataset:
The influence of seasonal forcing on the population dynamics of ecological systems

Seasonal forcing represents a pervasive source of environmental variability and it has been shown to be important in generating the cycles observed in many ecological and epidemiological systems. We use a combination of bifurcation analysis and simulation to understand the impact of seasonality on population dynamics, with a focus on predator-prey and host-macroparasite systems. Multi-year cycles with a wide range of periods, quasi-periodicity and chaos are found. We consider the importance of the unforced dynamics in a predator-prey system by contrasting the effect of seasonality when the underlying behaviour is oscillatory decay to the equilibrium or limit cycles. The limit cycles case shows a wider range of dynamics and multiple solutions. The effect of variations in the seasonal forcing term are analysed in a predator-prey model by changing the breeding season length, using the vole system in Fennoscandia as a case study. It is found that the period of the multi-year cycles increases as the breeding season length decreases. By studying a general host-macroparasite system, in which the effect of seasonality has not previously been explored in detail, we find a larger potential for multiple solution behaviour compared to predator-prey systems. Overall, we show the critical role that seasonality can play in ecological systems.
AKADEMIN FÖR HÄLSA OCH ARBETSLIV

The aim of this study was to investigate how common the use of performanceenhancing substances is among gym users and to identify the different purposes of using performance-enhancing substances. A self-completion questionnaire was handed to 246 gym users at seven different gyms in Södertälje municipality, Sweden. Connell’s masculinity theory and Gidden’s self-identity theory were used to interpret and analyze the results. The result showed that is not common among gym users to use doping substances (Anabolic Androgen Steroids, AAS): 4 percent had occasionally used AAS. On the other hand, it was common to use dietary supplements among gym users; 79 percent used some type of dietary supplement. A positive correlation between exercising at the gym a couple of times week and the use of dietary supplements was shown. The two most common purposes for using performance-enhancing substances were to increase physical appearance and get bigger muscles. This study also discussed the risks and effects of using performance-enhancing substances that are related to social problems.
On the Consistency Rule in Causal Inference: Axiom, Definition, Assumption, or Theorem?

In 2 recent communications, Cole and Frangakis (Epidemiology. 2009;20:3–5) and VanderWeele (Epidemiology. 2009;20:880–883) conclude that the consistency rule used in causal inference is an assumption that precludes any side-effects of treatment/exposure on the outcomes of interest. They further develop auxiliary notation to make this assumption formal and explicit. I argue that the consistency rule is a theorem in the logic of counterfactuals and need not be altered. Instead, warnings of potential side-effects should be embodied in standard modeling practices that make causal assumptions explicit and transparent.
A Single Ancient Origin for Prototypical Serine/Arginine-Rich Splicing Factors1[W][OA]

Eukaryotic precursor mRNA splicing is a process involving a very complex RNA-protein edifice. Serine/arginine-rich (SR) proteins play essential roles in precursor mRNA constitutive and alternative splicing and have been suggested to be crucial in plant-specific forms of developmental regulation and environmental adaptation. Despite their functional importance, little is known about their origin and evolutionary history. SR splicing factors have a modular organization featuring at least one RNA recognition motif (RRM) domain and a carboxyl-terminal region enriched in serine/arginine dipeptides. To investigate the evolution of SR proteins, we infer phylogenies for more than 12,000 RRM domains representing more than 200 broadly sampled organisms. Our analyses reveal that the RRM domain is not restricted to eukaryotes and that all prototypical SR proteins share a single ancient origin, including the plant-specific SR45 protein. Based on these findings, we propose a scenario for their diversification into four natural families, each corresponding to a main SR architecture, and a dozen subfamilies, of which we profile both sequence conservation and composition. Finally, using operational criteria for computational discovery and classification, we catalog SR proteins in 20 model organisms, with a focus on green algae and land plants. Altogether, our study confirms the homogeneity and antiquity of SR splicing factors while establishing robust phylogenetic relationships between animal and plant proteins, which should enable functional analyses of lesser characterized SR family members, especially in green plants.
Leaf Nutrient Concentrations in Oil Palm as Affected by Genotypes, Irrigation and Terrain

Four clonal oil palm materials namely AVROS, Yangambi, La Me and NIFOR and two DxP hybrid Yangambi, grown on terraced and unterraced fields were subjected to irrigated and non-irrigated conditions. There were significant differences in all leaf nutrient concentrations for all the planting materials for both terrain and irrigation conditions. For non-irrigated palms, most of the leaf nutrients were higher than the irrigated palms, especially K and Mg concentrations. Most of the leaf nutrient concentrations in palms grown on undulating area were also high, especially for leaf Mg and K concentrations. Leaf K concentration for DxP hybrid Yangambi-DQ8 was consistently lower than AVROS-A122 by almost 15-20% in all the growing conditions. In contrast, the leaf K contents for Yangambi-DQ8 and Yangambi-Y103 were comparable to that of AVROS-A122 and these three planting materials produced the highest oil yields. In view of future high current fertilizer cost, selecting oil palm genotypes that are able to produce good oil yields on low fertilizer inputs and giving consistent leaf nutrition need to be given consideration.
Trends of mean temperatures and warm extremes in northern tropical Africa (1961–2014) from observed and PPCA‐reconstructed time series

Trends in daily maximum (TX) and minimum (TN) temperatures and indices of warm extremes are studied in tropical North Africa, west of the eastern African highlands, from 1961 to 2014. The analysis is based on the concatenation and cross‐checking of two observed databases. Due to the large number of missing entries (~25%), a statistical infilling using probabilistic principal component analysis was applied. Averaged over 90 stations, the linear trends of annual mean TX and TN equal respectively +0.021 °C/yr and +0.028 °C/yr. The frequency of very hot days (TX > 35°C) and tropical nights (TN > 20°C), as well as the frequency of daily TX and TN above the 90th percentile (p90) (“warm days” and “warm nights”), roughly follows the variations of mean TX and TN, respectively. Heat spells of TX or TN > p90 are often short (usually <2–3 days), and the interannual variation of their mean duration is noisier than for the other indices. Nevertheless, heat spells tend to last longer, with almost constantly positive anomalies since the mid‐1990s. The trends in March–June, the warmest season across the Sahelian and Sudanian belts, show similar variations as annual means. Overall, the local‐scale warming in annual temperatures, and in March–June, may be viewed merely as a simple shift of the probability distribution function of daily TX and TN. The correlations between the thermal indices and the 2 m temperatures suggest that the low‐frequency (>8 years) variations may be viewed as a regional‐scale fingerprint of the global warming, with largest correlations in the tropical Atlantic and Indian basins, while the high‐frequency (<8 years) variations should be mostly viewed as a delayed remote impact of El Niño–Southern Oscillation (ENSO) events over the region, with warm (cold) anomalies tending to follow warm (cold) ENSO events.
Characterization of the basal hydraulic system of a surge-type glacier : Trapridge Glacier, 1989-92

Subglacial hydrology is a critical issue in understanding glacier and ice-sheet dynamics. This is especially true for surge-type glaciers, which are distinguished by their regular, quasi-periodic alternation between slow and fast flow regimes (Meier and Post, 1969); the fast flow during a surge is thought to be caused by rapid sliding brought about by sustained high basal water pressure. How sustained high pressures develop and how the subglacial distribution of water influences glacier sliding are fundamental unsolved questions. We describe an investigation of the water drainage system beneath Trapridge Glacier, a surge-type glacier in Yukon Territory, Canada. We take two different approaches to characterizing the basal hydraulic system of the glacier. The first approach is borehole response testing, which involves changing the basal water pressure in the vicinity of a borehole and simultaneously observing the drainage system's response. We develop a theoretical model that describes the movement of water, induced by response tests, in a coupled borehole—subglacial flow layer. The model encompasses a broad range of flow regimes, from laminar Darcian flow in a thick permeable unit to turbulent sheet flow in a very thin layer. Important terms in the model are highlighted by a dimensional analysis. We show how the model can be used in numerical simulations to generate predicted data, which can be compared with field observations. We use our model as the basis for a formal inversion scheme that is aimed at objectively quantifying model parameters associated with subglacial water flow. Response test data from Trapridge Glacier are inverted to obtain estimates of hydraulic properties of the basal drainage system. The second approach that we have taken involves direct measurement of the properties of subglacial water. Year-round measurements of subglacial water pressure, turbidity, and electrical conductivity were made at intervals ranging from 2-20 minutes for three consecutive years. Turbidity and conductivity were measured using new subglacial sensors that we designed and constructed. The data in this study are unique and important because they were obtained directly at the glacier bed and because they span multiple summer and winter seasons. Spontaneous changes in the subglacial drainage system have been recorded and are sometimes accompanied by a release of stored basal water. In general, a single, stable drainage configuration cannot be identified. Instead, we infer a seasonal progression of drainage structures from the data. The complex behavior of the drainage system points to a dynamic subglacial environment, one in which the basal hydrology is governed by the combined influences of the glacier thermal regime, meltwater input, sediment movement, and mechanical interactions with
Comparative evaluation of antimicrobial activity of human granulysin, bovine and porcine NK-lysins against Shiga toxin-producing Escherichia coli O157:H7

Shiga toxin-producing Escherichia coli (STEC) O157:H7 (O157) is a foodborne pathogen causing human disease ranging from hemorrhagic colitis and hemolytic uremic syndrome to kidney failure, while remaining harmless to cattle, its primary reservoir. The severity of the human disease associated mainly with Shiga toxin production and a global emergence of antibiotic resistant STEC highlights the need for effective non-antibiotic, pre-harvest strategies to reduce O157 in cattle, the principal source of human infection. Towards this goal three synthetic antimicrobial peptides (AMPs): human granulysin (hGRNL), bovine NK-lysin (bNK2A), and porcine NK-lysin (pNKL), were tested in vitro against O157 isolates. As expected, circular dichroism spectroscopy findings were consistent with a predominantly α-helical conformation for all three AMPs in an environment mimicking bacterial outer surface or liposaccharides. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations of hGRNL (200 μM), bNK2A (12.5 μM against strain 86–24 and 25 μM against EDL933), and pNKL (6.25 μM) were determined using the Clinical and Laboratory Standards Institute broth microdilution method in Müeller-Hinton broth (cation-adjusted). The bNK2A and pNKL AMPs did not induce Shiga toxin expression in O157 at MIC, as there was a significant decrease or no change in toxin expression following 4- or 20 h incubation with the AMPs; bNK2A p <0.0001 (4 h) and p = 0.4831 (20 h); pNKL p <0.0001 (4 h) and p = 0.0001 (20 h). Propidium iodide uptake assay revealed faster O157 membrane damage or killing kinetics with bNK2A and pNKL compared to hGRNL. Nonetheless, transmission electron microscopy demonstrated that all three AMPs mediated damage to O157 membranes. In contrast, the three AMPs showed minimal cytotoxicity (<2%) against cattle red blood cells at tested concentrations (0.39–50 μM). Overall, our results demonstrate the potential for bNK2A and pNKL to be further developed into novel non-antibiotic agents to reduce O157 shedding in cattle.
The sequential cueing effect in children's speech production

This article investigated the development of phonological encoding in speech production by examining the production of reiterant two-word sequences varying in phonological similarity. Two groups of typically developing children and a group of college-aged adults participated. Both groups of children produced target words with longer durations when they were preceded by words sharing initial consonant–vowel (CV) sequences than when preceded by phonologically unrelated words or words sharing vowel–consonant (VC) sequences. For adults, the duration of target words was shorter when they were preceded by words sharing final VC sequences than in the other conditions. The developmental decrease in the influence of CV-related prime words on target-word duration may be related to changes in the level of activation of lexical items during speech production. Developmental changes in the influence of VC-related prime words are less clear, but may be due to age-group specific behavior in the production of identical sequences of words.
TO ISRAEL CARMI ( 2002 ) : “ ARE THE 14 C DATES OF THE DEAD SEA SCROLLS AFFECTED BY CASTOR OIL CONTAMINATION ? ”

Carmi (2002) is a response to our study published in Radiocarbon 43(1) by Rasmussen et al. (2001). We noted widespread possible exposure to castor oil of the Dead Sea Scrolls (DSS) in the Rockefeller Museum in the 1950s and reported experiments showing that the AAA pretreatment used in the first 2 series of radiocarbon datings of the DSS (Bonani et al. [1992] and Jull et al. [1995]), “cannot be guaranteed to have removed all of the modern carbon in any samples if they had been contaminated with castor oil and hence could have produced some 14C dates that were younger than the texts’ true ages. ” Carmi, a coauthor of the Bonani et al. (1992) study, criticizes our analysis on 4 grounds:
Taking Charge: A Proposed Psychological Intervention to Improve Pulmonary Rehabilitation Outcomes for People with COPD

: Pulmonary rehabilitation (PR) is an important, evidence-based treatment that improves outcomes for people with COPD. Individualized exercise programmes aim to improve exercise capacity; self-management education and psychological support are also provided. Translating increased exercise capacity into sustained behavioural change of increased physical activity is difficult. Other unresolved problems with PR programmes include improving uptake, completion, response and sustaining long-term benefit. We offer a different perspective drawn from clinical experience of PR, quantitative and qualitative studies of singing groups for people with COPD, and stroke rehabilitation research that gives psychological factors a more central role in determining outcomes after PR. We discuss Take Charge; a simple but effective psychological intervention promoting self-management––that could be used as part of a PR programme or in situations where PR was declined or unavailable. This may be particularly relevant now when traditional face-to-face group programmes have been disrupted by COVID-19 precautions.
Understanding the travel behavior of the elderly on Oahu

Because Hawaii is expected to experience mpid growth in its population segment of people aged 65 and older, their trovel needs and understanding their trovel behavior is of increasing importance. A literature review of studies that focused on the trovel behavior of older people suggested that the following factors affect trovel behavior: age, gender, medical condition, ability to drive, cost of a trip, residentia1location (suburb vs. city), trip purpose, day of the week, time of day, income, and availability of a private vehicle. This thesis estimated two multinomia1logit models of mode choice using data from the 1995 Household Interview Survey (HIS) which was conducted by the Oahu Metropolitan Planning Organization (OMPO). These models suggest being elderly has a negative effect toward drive, passenger and walk as compared with tmnsit In addition, being retired has a negative effect toward drive, passenger, walk and bike as compared
Under Consideration for Publication in Theory and Practice of Logic Programming Diagnostic Reasoning with A-prolog *

In this paper we suggest an architecture for a software agent which operates a physical device and is capable of making observations and of testing and repairing the device's components. We present simplified definitions of the notions of symptom, candidate diagnosis , and diagnosis which are based on the theory of action language AL. The definitions allow one to give a simple account of the agent's behavior in which many of the agent's tasks are reduced to computing stable models of logic programs.
Under Consideration for Publication in Theory and Practice of Logic Programming an Event Calculus Production Rule System for Reasoning in Dynamic and Uncertain Domains

Action languages have emerged as an important field of Knowledge Representation for reasoning about change and causality in dynamic domains. This article presents Cerbere, a production system designed to perform online causal, temporal and epistemic reasoning based on the Event Calculus. The framework implements the declarative semantics of the underlying logic theories in a forward-chaining rule-based reasoning system, coupling the high expressiveness of its formalisms with the efficiency of rule-based systems. To illustrate its applicability, we present both the modeling of benchmark problems in the field, as well as its utilization in the challenging domain of smart spaces. A hybrid framework that combines logic-based with probabilistic reasoning has been developed, that aims to accommodate activity recognition and monitoring tasks in smart spaces.
Factor structure and psychometric properties of an Arabic version of the Internet Gaming Disorder Scale, short form (IGDS-SF9)

Background In its most recent edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM), the American Psychological Association recognized that internet gaming disorder is a psychological condition and provides nine criteria for its diagnosis, and the Internet Gaming Disorder Scale, short form (IGDS-SF9) was developed to assess individuals. Aim To develop and investigate the psychometric properties of an Arabic version of IGDS-SF9. Method A five-stage translation and verification process produced an Arabic version of IGDS-SF9, and a study was conducted using a sample of 410 respondents (45.6% females, mean age = 17.6, SD = 1.56) to assess its psychometric properties. Respondents completed the Arabic version, the Smartphone Addiction Scale, the Smartphone Application-Based Addiction Scale, the Hospital Anxiety and Depression Scale, as well as a demographic survey. Exploratory and confirmatory factor analyses, measurement invariance, item response theory, convergent, concurrent, criterion validity, and internal consistency reliability and test–retest reliability were employed to validate the scale. Results The exploratory factor analysis suggested the scale’s unidimensional structure; the confirmatory factor analysis exhibited good model fit and factor loadings. Measurement invariance, and concurrent, convergent, and criterion validity were established, resulting in good internal consistency and test–retest reliability for the scale. Conclusion The Arabic version of IGDS-SF9 is a valid and reliable measure for research and diagnosis in Arabic-speaking countries.
Demography , Urbanization and Development : Rural Push , Urban Pull and . . . Urban Push ? ∗

Developing countries have urbanized rapidly since 1950. To explain urbanization, standard models emphasize rural-urban migration, focusing on rural push factors (agricultural modernization and rural poverty) and urban pull factors (industrialization and urban-biased policies). Using new historical data on urban birth and death rates for 7 countries from Industrial Europe (1800-1910) and 35 developing countries (1960-2010), we argue that a non-negligible part of developing countries’ rapid urban growth and urbanization may also be linked to demographic factors, i.e. rapid internal urban population growth, or an urban push. High urban natural increase in today’s developing countries follows from lower urban mortality, relative to Industrial Europe, where higher urban deaths offset urban births. This compounds the effects of migration and displays strong associations with urban congestion, providing additional insight into the phenomenon of urbanization without growth.
FOLIA POMERANAE UNIVERSITATIS TECHNOLOGIAE STETINENSIS

The formation of adventitious roots is an essential step in vegetative propagation. Well-developed root system allows for easier and faster adaptation of plants to ex vitro conditions. The aim of this study was to determine the effect of exogenous auxin on Celosia 46 M. Krupa-Małkiewicz and O. Mgłosiek argentea var.cristata (L.) Kuntze rooting under in vitro conditions and on ex vitro adaptation of those plants. MS rooting media were supplemented with IBA, IAA and NAA at subsequent concentrations 0.5, 1.0, 1.5, and 2.0 mg · dm. The results showed, that subsequent hormones had a positive effect on root development and morphology. The longest and thickest roots were formed in the presence of IBA at the concentration of 1.0 mg · dm. The highest percent of ex vitro survived plants was obtained after application of IBA and NAA (1.0 mg · dm). Plants survival ex vitro decreased (12.5–62.5%), when culture treated with IBA and NAA (1.5 and 2.0 mg · dm).