Miracle-dz/UniFAR-FTUs huggingface dataset:
Markov Chain-Based Sampling for Exploring RNA Secondary Structure under the Nearest Neighbor Thermodynamic Model and Extended Applications

Ribonucleic acid (RNA) secondary structures and branching properties are important for determining functional ramifications in biology. While energy minimization of the Nearest Neighbor Thermodynamic Model (NNTM) is commonly used to identify such properties (number of hairpins, maximum ladder distance, etc.), it is difficult to know whether the resultant values fall within expected dispersion thresholds for a given energy function. The goal of this study was to construct a Markov chain capable of examining the dispersion of RNA secondary structures and branching properties obtained from NNTM energy function minimization independent of a specific nucleotide sequence. Plane trees are studied as a model for RNA secondary structure, with energy assigned to each tree based on the NNTM, and a corresponding Gibbs distribution is defined on the trees. Through a bijection between plane trees and 2-Motzkin paths, a Markov chain converging to the Gibbs distribution is constructed, and fast mixing time is established by estimating the spectral gap of the chain. The spectral gap estimate is obtained through a series of decompositions of the chain and also by building on known mixing time results for other chains on Dyck paths. The resulting algorithm can be used as a tool for exploring the branching structure of RNA, especially for long sequences, and to examine branching structure dependence on energy model parameters. Full exposition is provided for the mathematical techniques used with the expectation that these techniques will prove useful in bioinformatics, computational biology, and additional extended applications.
Evaluation of the U.S. Mothbean Collection for Seed Yield Potential in Virginia and Nutritional Composition of Freshly Harvested Seed

Even though mothbean (Vigna aconitifolia), a droughtand heattolerant crop,may have potential in the easternUnited States, information about its production in this region is not available. To characterize potential seed yields and preliminary nutritional quality, 54 accessions were grown near Petersburg, VA, during 2011, 2012, and 2013. The seed yields varied from 48 to 413 lb/acre. The mean concentrations of protein, calcium, iron, and zinc in mature mothbean seed were 21.9%, 0.17%, 64.8 ppm, and 37.5 ppm, respectively. These values compared well with those inmungbean (Vigna radiata) and tepary bean (Phaseolus acutifolius). The results demonstrated that mothbean has considerable potential as an alternative, new food legume crop in Virginia and eastern United States.
Obstacles to continued use of personal health records

ABSTRACT The purpose of this paper was to examine organisational change in a hospital setting. Specifically, the paper examines how patients responded to the introduction of personal health records (PHR). This research was an empirical investigation based on surveys completed by 136 patients in the United States. The paper draws on Lewin’s Force Field Analysis Model to explain patient responses to new PHR technology. The results indicate that affective and cognitive resistance factors exist, but the presence of change information can mitigate the resistance. While both resistance factors were relevant, the study found that reducing cognitive resistance had a stronger influence than reducing affective resistance. This research will contribute to the health care literature by offering insight into the factors associated with resistance and the continued use of PHR systems. The research also contributes to the individual IT literature by examining attitudes and beliefs that lead to continued use of IT systems.
Variability of head diameter in sunflower hybrids depending on planting date

Balalić I. , J. Crnobarac, S. Jocić, V. Miklič, V. Radić, N. Dušanić (2016): Variability of head diameter in sunflower hybrids depending on planting date. Genetika, Vol 48, No.3, 983 990. Head size contributes substantially to seed yield of sunflower because it influences both number of seeds per head, and seed size. The aim of this field study was to determine the variability of head diameter in sunflower hybrids depending on planting date across three cropping seasons. Three hybrids (Miro, Rimi, Pobednik) were sown at four planting dates (PD1 20 of March, PD2 10 of April, PD3 30 of April, PD4 20 of May). Head diameter was analysed in the stage of flowering and physiological maturity. The trial was arranged as Randomized Complete Block Design (RCBD) with four replications. Analysis of variance (ANOVA) showed that the effect of year, hybrid, planting date and most interactions were highly significant for head diameter in the flowering stage. In the stage of physiological maturity head diameter varied significantly depending only on the planting date. Also, all interactions, except year × hybrid (Y × H), were highly significant. Planting date had significant influence on head diameter in the stage of flowering and physiological maturity in sunflower. With later sowing head diameter increased, so that significantly highest head diameter across planting dates was found in PD4 (11.8 cm in flowering stage, and 22.6 cm at the stage of physiological maturity). Study results may be helpful in the recommendation for optimal planting date in sunflower.
Benthic Diatom Communities in Urban Streams and the Role of Riparian Buffers

Urbanization impacts stream ecosystems globally through degraded water quality, altered hydrology, and landscape disturbances at the catchment and riparian scales, causing biodiversity losses and altered system functioning. Addressing the “urban stream syndrome” requires multiple mitigation tools, and rehabilitation of riparian vegetation may help improve stream ecological status and provide key ecosystem services. However, the extent to which forested riparian buffers can help support stream biodiversity in the face of numerous environmental contingencies remains uncertain. We assessed how a key indicator of stream ecological status, benthic diatoms, respond to riparian habitat conditions using 10 urban site pairs (each comprising of one unbuffered and one buffered reach), and additional urban downstream and forest reference upstream sites in the Oslo Fjord basin. Diatom communities were structured by multiple drivers including spatial location, land use, water quality, and instream habitat. Among these, riparian habitat condition independently explained 16% of variation in community composition among site pairs. Changes in community structure and indicator taxa, along with a reduction in pollution-tolerant diatoms, suggested tangible benefits of forested riparian buffers for stream biodiversity in urban environments. Managing urban impacts requires multiple solutions, with forested riparian zones providing a potential tool to help improve biodiversity and ecosystem services.
Viability of Red (Ribes rubrum L.) and Black (Ribes nigrum L.) Currant Cuttings in Field Conditions after Cryopreservation in Vapors of Liquid Nitrogen

One of the prospective ways to safely preserve the genetic resources of red and black currant for breeding needs is the cryopreservation of cuttings with dormant buds. Vegetative cuttings of 12 varieties of red and 11 varieties of black currant were harvested in various regions of Russia: North, Northwest, and Central. Their viability after cryopreservation in nitrogen vapors (about −184 °C) under field conditions was studied. For red currant samples, it ranged from 61.2 ± 1.2% to 72.3 ± 3.0%, black currant—from 58.9 ± 1.1% to 73.5 ± 1.9%. In the group of red currant varieties, there were no significant differences in viability between varieties after cryopreservation. In the group of black currant varieties, “Chereshneva” and “Georgiy” had lower viability after storage in liquid nitrogen vapors than the others, 61.1% and 58.9%, respectively. On red currant, dry growing conditions of the experiment year significantly decreased the viability after cryopreservation. Neither black nor red currants revealed the influence of the place of harvesting on the survival of cuttings after cryopreservation. These results indicate the possibility of using cryopreservation to preserve cuttings of red and black currant with dormant buds collected in regions with different climatic environments.
The importance of recognising and conserving biological diversity: a reply to Dussex et al. (2018)

In their recent article, Dussex et al. (2018) draw attention to some current issues in New Zealand avian systematics, and particularly the difficulties that can potentially arise in cases where molecular and morphological data prove difficult to reconcile. These researchers call for integrative approaches to avian systematics, to overcome the limitations of singlemethod studies, and we wholeheartedly agree with this common-sense view. Additionally, while taxonomic studies at shallow phylogenetic levels may struggle to capture dynamic evolutionary processes, multiple forms of concordant data can provide a strong basis for recognising and conserving recently-evolved biological diversity. Given Dussex et al.’s (2018) plea for avian taxonomy to be grounded in multiple sources of non-conflicting data, we were surprised to read their criticism of a recent study that used precisely the type of integrative approach that these authors seem to advocate. Specifically, Dussex et al. (2018) take issue with Rawlence et al.’s (2017) recent recognition of
The Intellectual Legacy of Jaroslav Vanek: How the Twain Met

PurposeThis essay is a tribute to Jaroslav Vanek who spent 32 years at Cornell University where he founded the Program on Participation and Labor-Managed Systems (PPLMS) in 1970, which became the home for economic research on these issues in the US. It is a brief intellectual history of a multi-dimensional scholar.Design/methodology/approachVanek's seminal work in the American Economic Review in 1969 marked the culmination of a decade of work on labor management inspired by his brother Jan's work on Yugoslavia, considered then to be a worker-managed economic system. In two rapidly following tomes, Vanek laid out the landscape for the development of a new subfield in economics by providing precursors to many of the results to follow. In that previous decade, Vanek produced papers in traditional economic theory, e.g. international trade and economic growth.FindingsVanek's mindset persists in the interplay between the emerging theory of labor-managed firms and traditional economic literature that takes seriously the role of organizational form. This essay develops that cross-pollination and seeks to identify the remaining questions and issues for future work that the economics profession owes to Jaroslav Vanek.Originality/valueConnection of strands of literature in the economic theory with the literature on labor-managed firms and worker-managed economies tracing the evolution of the latter to the work of Jaroslav Vanek.
Entrepreneurial Strategies to Address Rural-Urban Climate-Induced Vulnerabilities: Assessing Adaptation and Innovation Measures in Dhaka, Bangladesh

Climate change amplifies social, political, economic, infrastructural and environmental challenges in many Global South cities, and perhaps no city is more vulnerable than Bangladesh’s capital of Dhaka. Climate-induced rural–urban migration is a profound concern, and Dhaka’s political leaders have embraced technology-based innovation as one solution pathway. This article explores the societal impact of Dhaka’s innovation environment strategies for climate change adaptation and mitigation. Employing a case study qualitative methodology, our three findings expand knowledge about innovation for urban climate adaptation and mitigation as understood by Dhaka-based entrepreneurs. First, the most effective innovations were not the most technologically advanced, but those with the highest degree of participant ownership. Second, gaps between recipient, corporate and governmental understandings of effective mitigation and adaptation harmed projects were driven by different definitions of risk and competing understandings of vulnerability. Third, even the most technical climate adaptation measures were inherently political in their application. We discuss how to better position urban climate innovation infrastructures in Bangladesh and beyond, including developing a better recognition of innovation lifecycles for urban climate adaptation and widening our definitions of “innovation” to better incorporate more effective and inclusive climate adaptation solutions.
Supramolecular Diversity of Oxabicyclo[2.2.2]octenes Formed between Substituted 2H-Pyran-2-ones and Vinyl-Moiety-Containing Dienophiles

In Diels–Alder reactions, 2H-pyran-2-ones as dienes can yield a large variety of cycloadducts with up to four contiguous carbon stereogenic centers. Some of the potentially most useful, however difficult to prepare due to their low thermal stability, are the primary CO2-containing oxabicyclo[2.2.2]octenes, which could be formed as eight distinctive isomers (two sets of regioisomers, each of these composed of four different stereoisomers). A high-pressure synthesis of such products was recently described in a few cases where vinyl-moiety-containing dienophiles were used as synthetic equivalents of acetylene. However, structures of the primary products have been so far only rarely investigated in detail. Herein, we present seven novel single-crystal X-ray diffraction structures of such cycloadducts of both stereoisomeric forms, i.e., endo and exo. Additionally, we present a single-crystal structure of a rare case of a cyclohexadiene system stable at room temperature, obtained as a secondary product upon the retro-hetero-Diels–Alder elimination of CO2 under thermal conditions (microwave irradiation), during this elimination the symmetry is increased and out of eight initially possible isomers of the reactant, this number in the product is decreased to four. In oxabicyclo[2.2.2]octene compounds, centrosymmetric hydrogen bonding was found to be the predominant motif and diverse supramolecular patterns were observed due to rich variety of C–H⋯O and C–H⋯π interactions.
Restoring Sage‐grouse nesting habitat through removal of early successional conifer

Conifer woodlands have expanded into sagebrush (Artemisia spp.) ecosystems and degrade habitat for sagebrush obligate species such as the Greater Sage‐grouse (Centrocercus urophasianus). Conifer management is increasing despite a lack of empirical evidence assessing outcomes to grouse and their habitat. Although assessments of vegetation recovery after conifer removal are common, comparisons of successional trends with habitat guidelines or actual data on habitat used by sage‐grouse is lacking. We assessed impacts of conifer encroachment on vegetation characteristics known to be important for sage‐grouse nesting. Using a controlled repeated measures design, we then evaluated vegetation changes for 3 years after conifer removal. We compared these results to data from 356 local sage‐grouse nests, rangewide nesting habitat estimates, and published habitat guidelines. We measured negative effects of conifer cover on many characteristics important for sage‐grouse nesting habitat including percent cover of forbs, grasses, and shrubs, and species richness of forbs and shrubs. In untreated habitat, herbaceous vegetation cover was slightly below the cover at local nest sites, while shrub cover and sagebrush cover were well below cover at the nest sites. Following conifer removal, we measured increases in herbaceous vegetation, primarily grasses, and sagebrush height. Our results indicate that conifer abundance can decrease habitat suitability for nesting sage‐grouse. Additionally, conifer removal can improve habitat suitability for nesting sage‐grouse within 3 years, and trajectories indicate that the habitat may continue to improve in the near future.
Modeling the Influence of Public Risk Perceptions on the Adoption of Green Stormwater Infrastructure: An Application of Bayesian Belief Networks Versus Logistic Regressions on a Statewide Survey of Households in Vermont

There is growing environmental psychology and behavior literature with mixed empirical evidence about the influence of public risk perceptions on the adoption of environmentally friendly “green behaviors”. Adoption of stormwater green infrastructure on residential properties, while costlier in the short term compared to conventional greywater infrastructure, plays an important role in the reduction of nutrient loading from non-point sources into freshwater rivers and lakes. In this study, we use Bayesian Belief Networks (BBNs) to analyze a 2015 survey dataset (sample size = 472 respondents) about the adoption of green infrastructure (GSI) in Vermont’s residential areas, most of which are located in either the Lake Champlain Basin or Connecticut River Basin. Eight categories of GSI were investigated: roof diversion, permeable pavement, infiltration trenches, green roofs, rain gardens, constructed wetlands, tree boxes, and others. Using both unsupervised and supervised machine learning algorithms, we used Bayesian Belief Networks to quantify the influence of public risk perceptions on GSI adoption while accounting for a range of demographic and spatial variables. We also compare the effectiveness of the Bayesian Belief Network approach and logistic regression in predicting the pro-environmental behaviors (adoption of GSI). The results show that influencing factors for current adoption differ by the type of GSI. Increased perception of risk from stormwater issues is associated with the adoption of rain gardens and infiltration trenches. Runoff issues are more likely to be considered the governments’ (town, state, and federal agencies) responsibility, whereas lawn erosion is more likely to be considered the residents’ responsibility. When using the same set of variables to predict pro-environmental behaviors (adoption of GSI), the BBN approach produces more accurate predictions compared to logistic regression. The results provide insights for further research on how to encourage residents to take measures for mitigating stormwater issues and stormwater management.
A gene therapy approach for Argininosuccinic aciduria

Argininosuccinate lyase (ASL) is central to two metabolic pathways: i) the liver-based urea cycle, which detoxifies ammonia, ii) the citrulline-nitric oxide cycle, which synthesises nitric oxide from L-arginine. Patients deficient in argininosuccinate lyase present with argininosuccinic aciduria characterised by hyperammonaemia and a multi-organ disease with a severe neurological phenotype. Compared to other urea cycle disorders, argininosuccinic aciduria presents a low frequency of hyperammonaemic crises but a high frequency of cognitive impairment. This paradox questions the causative role of hyperammonaemia in the neuropathology. An observational UK-wide study was designed to study the natural history. Data about clinical status, neuroimaging and hASL genotyping were collected from 56 patients. Six had molecular analysis performed in this work. A homogeneous neurological phenotype was observed in most patients. hASL sequencing was available in 19 patients and 20 mutations (1) were found. A genotype-phenotype correlation showed that the prognosis was more likely related to genotype rather than severity of hyperammonaemia. The hypomorph mouse model AslNeo/Neo mimicking the human disease was used to study the neuropathology in argininosuccinic aciduria and showed a neuronal disease with oxidative/nitrosative stress. To define the role of hyperammonaemia in this finding, a gene therapy approach using an adeno-associated viral vector (AAV) encoding the murine Asl gene was delivered in AslNeo/Neo mice. The long-term correction of both pathways was observed: i) the urea cycle after a single systemic injection in adult mice; ii) the citrulline-nitric oxide cycle in the brain after a single systemic injection at birth. The neuronal disease persisted if ammonaemia only was normalised but was dramatically reduced after correction of both ammonaemia and neuronal ASL activity. This demonstrated the key-role of a neuronal disease independent from hyperammonaemia in argininosuccinic aciduria. This work provides new insight in the neuropathology of argininosuccinic aciduria and a proof of concept of successful AAV-mediated gene therapy.
Actividad física realizada por escolares españoles según edad y género

espanolEstilos de vida poco saludables, asociados a casos de sedentarismo, obesidad y sobrepeso, constituyen un grave problema desalud de la poblacion infantil en Espana. A pesar de los esfuerzos de organismos como la Organizacion Mundial de la Salud (OMS) porpromover programas de promocion y educacion para la salud en los colegios, los indices de sobrepeso y obesidad siguen siendo muyelevados en nuestro pais. El objetivo de este estudio fue determinar el nivel de actividad fisica en escolares espanoles de 5o y 6o deeducacion primaria. Participaron 1009 estudiantes de 10 y 12 anos (Medad = 10.85, DE = 0.79), empleando como instrumento para larecogida de datos el Inventario de Actividad Fisica Habitual para Escolares (IAFHE). Los resultados muestran diferencias estadisticamentesignificativas respecto del genero y la practica deportiva fuera del colegio (NPFC) (p EnglishUnhealthy lifestyles, associated with cases of sedentary lifestyle, obesity and overweight, constitute a serious health problemfor children in Spain. Despite the efforts of organizations, such as the World Health Organization (WHO), to promote health promotionand education programs in schools, rates of overweight and obesity remain very high in our country. The objective of this study was todetermine the level of physical activity in Spanish students of 5th and 6th grade of primary education. A total of 1009 students of 10 and12 years old (Mage = 10.85, DE = 0.79), responded the Inventory of Habitual Physical Activity for Schoolchildren (IAFHE), used as theinstrument for data collection. The results show statistically significant differences by gender and out-of-school sports practice (NPOS)(p
Governance disclosure quality and market valuation of firms in
 UK
 and Germany

This study develops a ‘comply or explain’ index which captures compliance and quality of explanations given for non-compliance with the corporate governance codes in UK and Germany. In particular, we explain, how compliance and quality of explanations provided in non-compliance disclosures, and various other internal corporate governance mechanisms, affect the market valuation of firms in the two countries. A dynamic generalised method of moments (GMM) estimator is employed as the research technique for our analysis, which enabled us to control for the potential effects of endogeneity in our models. The findings of our content analysis suggest that firms exhibit significant differences in compliance, board independence and ownership structure in both countries. The ‘comply or explain’ index is positively associated with the market valuation of UK firms suggesting that compliance and quality governance disclosure is value relevant in the UK. Institutional blockholders’ ownership is however, negatively associated with the market value of firms, which raises questions about the monitoring role of institutional shareholders in both countries. We argue that both compliance and explanations given for non-compliance are equally important, as long as valid reasons and justifications for non-compliance are provided by the reporting companies. These findings thus imply that the ‘comply or explain’ principle is working well and that UK and German companies could benefit from the flexibility offered by this principle. With respect to the role of board size, board independence, ownership structure, and institutional ownership of firms, this study offers policy implications.