Regret Analysis for River Water Quality Management

The treatment of uncertainty inherent in water quality policy development and related modeling is a key issue. This is particularly true in the Central and Eastern European region which is characterized by high pollution levels, strong economic transition, lack of financial resources and scarce and imprecise data availability. Possibilities to account for uncertainties in policy development by a regret analysis approach were studied. The risks associated with regret in decision making were qualitatively and quantitatively defined. The design of a decision making procedure where these risks are accounted for was analyzed from a theoretical and practical viewpoint. A regret analysis procedure was implemented within an experimental decision support system (DSS) for water quality management of a river. This system was tested with a hypothetical situation where the best option of upgrading of a number of waste water treatment plants was to be selected from a small set of possible options. The main problem of analyses of this kind is the curse of dimensionality. The study shows that a modular approach, which uses already available software components and models, speeds up the building of a DSS

Impacts of Climate Change on Physical Characteristics of Lakes in Europe

One of the tasks of the EEWAI action is the assessment of the impacts of climate change on ecological water quality in order to support the implementation of the Water Framework Directive. This task requires development of comprehensive knowledge base, models, and databases to provide tools for the evaluation of the adaptation needs of the EU water resources management with respect of the anticipated changes in water quality due to climate change. In 2008, EEWAI initiated a service contract between Joint Research Centre and Helsinki University of Technology in order to develop further a Decision Support System elaborated within the EU project CLIME into a new tool called CLIME Maps. The aim was to extend the central lake database, to update the computational basis of lake physical parameters by applying the newest achievements in this field of science, and enable creating map views of the projected changes of physical parameters of basic lake types. Based on the model results, this report gives an overview of the impacts that climate change may have on physical properties of lakes and demonstrates further implications that these changes have on lake ecosystems. The technical report on CLIME Maps and the users¿ manual are included in annexes of the report.JRC.H.5-Rural, water and ecosystem resource

Proceedings of the 3rd Open Source Geospatial Research & Education Symposium OGRS 2014

The third Open Source Geospatial Research & Education Symposium (OGRS) was held in Helsinki, Finland, on 10 to 13 June 2014. The symposium was hosted and organized by the Department of Civil and Environmental Engineering, Aalto University School of Engineering, in partnership with the OGRS Community, on the Espoo campus of Aalto University. These proceedings contain the 20 papers presented at the symposium. OGRS is a meeting dedicated to exchanging ideas in and results from the development and use of open source geospatial software in both research and education.  The symposium offers several opportunities for discussing, learning, and presenting results, principles, methods and practices while supporting a primary theme: how to carry out research and educate academic students using, contributing to, and launching open source geospatial initiatives. Participating in open source initiatives can potentially boost innovation as a value creating process requiring joint collaborations between academia, foundations, associations, developer communities and industry. Additionally, open source software can improve the efficiency and impact of university education by introducing open and freely usable tools and research results to students, and encouraging them to get involved in projects. This may eventually lead to new community projects and businesses. The symposium contributes to the validation of the open source model in research and education in geoinformatics

Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

Transcription factors (TFs) achieve DNA-binding specificity through contacts with functional groups of bases (base readout) and readout of structural properties of the double helix (shape readout). Currently, it remains unclear whether DNA shape readout is utilized by only a few selected TF families, or whether this mechanism is used extensively by most TF families. We resequenced data from previously published HT-SELEX experiments, the most extensive mammalian TF–DNA binding data available to date. Using these data, we demonstrated the contributions of DNA shape readout across diverse TF families and its importance in core motif-flanking regions. Statistical machine-learning models combined with feature-selection techniques helped to reveal the nucleotide position-dependent DNA shape readout in TF-binding sites and the TF family-specific position dependence. Based on these results, we proposed novel DNA shape logos to visualize the DNA shape preferences of TFs. Overall, this work suggests a way of obtaining mechanistic insights into TF–DNA binding without relying on experimentally solved all-atom structures

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

Most transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (Delta G). To determine the molecular mechanism behind this effect, we solved the structures of human HOXB13 and CDX2 bound to their two optimal DNA sequences, CAATAAA and TCGTAAA. Thermodynamic analyses by isothermal titration calorimetry revealed that both sites were bound with similar Delta G. However, the interaction with the CAA sequence was driven by change in enthalpy (Delta H), whereas the TCG site was bound with similar affinity due to smaller loss of entropy (Delta S). This thermodynamic mechanism that leads to at least two local optima likely affects many macromolecular interactions, as Delta G depends on two partially independent variables Delta H and Delta S according to the central equation of thermodynamics, Delta G = Delta H - T Delta S.Peer reviewe

Children, Adolescents, and Young Adults with Borderline Intellectual Functioning: Etiological, Neurophysiological, and Mri Findings in a Cohort of 651 Patients

This retrospective chart review study explored the etiology, use, and yield of the etiological investigations of 651 children and adolescents diagnosed with borderline intellectual functioning (BIF). Neurological, neurodevelopmental, or neuropsychiatric comorbidities were frequent, and in 23%, the BIF diagnosis evolved into an intellectual disability (ID) by the time of discharge. A primary etiological cause was found in 37.6%, the most prevalent causes being pre- or perinatal conditions, genetic syndromes/chromosomal abnormalities, fetal exposure to maternal substance use, cerebral dysgenesis, and neurological diseases. In total, 79.1% of patients went through one or more investigations during their follow-up. The best etiologic yield leading to a diagnosis in this study population was with exome sequencing, a specific gene panel, microarrays, electroneuromyography, and brain magnetic resonance imaging (MRI). Etiological investigations were performed more frequently among those children receiving an ID diagnosis. Yet, there was no statistically significant difference in the proportion of abnormal findings between the BIF and ID groups. This may mean that the current strategy for determining the need for etiological investigations or current means to gain an etiology is still indecisive. Considering that BIF is defined to include individuals performing between normal cognitive functioning and mild ID, this implies that the prevalence would be anywhere between 7 and 14%. Thus, it could be argued whether in-depth etiological investigations may be justified in cases other than ID in this age group of children over five. With these children and adolescents, the clinicians have to discern between those with a normal variation and those having major difficulties in adaptive behavior affecting everyday life in order to specify and prescribe the rehabilitation or other measures needed. We advocate for a targeted etiological search after careful history-taking and neurological examination. National guidelines that take into account the severity of developmental delay are warranted

Rates of Water Loss and Absorption in Stick Insect Eggs

The thorny devil stick insect (Eurycantha calcarata) of New Guinea has eggs that take four months or more to develop—incredibly long for an insect. Long development times can be a challenge for eggs because of their finite resources, including nutrients, energy to support development, and water. I investigated the physiological mechanisms underlying long development times in stick insect eggs. The first experiment examined rates of water loss and survival of eggs held in different experimental humidities (0, 75, or 100% RH). Eggs dried quickly in the 0% humidity “dry” container; and more slowly in the 75% humidity “intermediate” container. The eggs did not dry out in the 100% “saturated” container and maintained their original mass throughout the experiment. While none of the dry treatment eggs hatched, one of the intermediate treatment eggs did, and nearly all of the saturated eggs hatched. To see if the eggs could reabsorb water, they were dried until they reached 90% of their original mass. Then they were transferred into a 100% humidity or wet cotton treatment. In both cases, the eggs gained some mass, but never returned to their original mass. These experiments show that the eggs require a high humidity to survive, and that they cannot absorb water from their environment. For these eggs, water is a finite resource. Finally, using flow-through respirometry, I measured metabolic rates of eggs during four months of development. Eggs were held in high humidity (100% RH) and their metabolic rates measured every 3 – 4 weeks. Metabolic rates were extraordinarily low early in development but increased near hatching. These data suggest that eggs delay much of their metabolism until late in development. I speculate that this delay in development is a way to keep the eggshell’s conductance to gases low, allowing the eggs to better conserve water

Rates of Water Loss and Metabolism in the Eggs of Stick Insect Eurycantha calcarata

The thorny devil stick insect (Eurycantha calcarata) of New Guinea has eggs that take four months or more to develop—incredibly long for an insect. Long development times can be a challenge for eggs because of their finite resources, including nutrients, energy to support development, and water. I investigated the physiological mechanisms underlying long development times in stick insect eggs. The first experiment examined rates of water loss and survival of eggs held in different experimental humidities (0, 75, or 100% RH). Eggs dried quickly in the 0% humidity “dry” container; and more slowly in the 75% humidity “intermediate” container. The eggs did not dry out in the 100% “saturated” container and maintained their original mass throughout the experiment. While none of the dry treatment eggs hatched, one of the intermediate treatment eggs did, and nearly all of the saturated eggs hatched. To see if the eggs could reabsorb water, they were dried until they reached 90% of their original mass. Then they were transferred into a 100% humidity or wet cotton treatment. In both cases, the eggs gained some mass, but never returned to their original mass. These experiments show that the eggs require a high humidity to survive, and that they cannot absorb water from their environment. For these eggs, water is a finite resource. Finally, using flow-through respirometry, I measured metabolic rates of eggs during four months of development. Eggs were held in high humidity (100% RH) and their metabolic rates measured every 3 – 4 weeks. Metabolic rates were extraordinarily low early in development but increased near hatching. These data suggest that eggs delay much of their metabolism until late in development. I speculate that this delay in development is a way to keep the eggshell’s conductance to gases low, allowing the eggs to better conserve water

Challenges and Neuropsychological Functioning in Children and Adolescents with Borderline Intellectual Functioning

This retrospective chart review study sought to explore neuropsychological profiles, neuropsychiatric and psychiatric comorbidity, changes in diagnoses, support at daycare and school, medication use, psychiatric referrals, and progression into further education in a cohort of participants with borderline intellectual functioning (BIF). Additionally, developmental factors connected to BIF were studied. Delays in language and gross motor development were the initial reasons for the parents to seek health care. Comorbid neuropsychiatric and psychiatric diagnoses were frequent, a total of 41% of participants were referred to psychiatric services, and 45% used medication. Educational support was needed by 92% of the study participants. The majority of those graduating elementary school continued their studies at ordinary or special vocational schools. The risk of dropping out during secondary studies appeared to increase. The results in most of the neuropsychological subdomains declined over time, and 23% of the participants were later diagnosed with an intellectual disability (ID). The early developmental signs pointing towards BIF and the need for prompt support were a delay in language and motor development, difficulties in executive function, a delay in learning the activities of daily living among children under school age, and difficulties in reading and arithmetic skills and abstract reasoning at school age. It is important to follow up and support individuals with BIF as their risk for being left behind in the society is increased. Also, it would be important to repeat the neuropsychological testing of cognitive and adaptive functions before graduating elementary school as to capture those who meet the ID criteria

Glial Cells Missing 1 Regulates Equine Chorionic Gonadotrophin Beta Subunit via Binding to the Proximal Promoter

Equine chorionic gonadotrophin (eCG) is a placental glycoprotein critical for early equine pregnancy and used therapeutically in a number of species to support reproductive activity. The factors in trophoblast that transcriptionally regulate eCGβ-subunit (LHB), the gene which confers the hormones specificity for the receptor, are not known. The aim of this study was to determine if glial cells missing 1 regulates LHB promoter activity. Here, studies of the LHB proximal promoter identified four binding sites for glial cells missing 1 (GCM1) and western blot analysis confirmed GCM1 was expressed in equine chorionic girdle (ChG) and surrounding tissues. Luciferase assays demonstrated endogenous activity of the LHB promoter in BeWo choriocarcinoma cells with greatest activity by a proximal 335 bp promoter fragment. Transactivation studies in COS7 cells using an equine GCM1 expression vector showed GCM1 could transactivate the proximal 335 bp LHB promoter. Chromatin immunoprecipitation using primary ChG trophoblast cells showed GCM1 to preferentially bind to the most proximal GCM1-binding site over site 2. Mutation of site 1 but not site 2 resulted in a loss of endogenous promoter activity in BeWo cells and failure of GCM1 to transactivate the promoter in COS-7 cells. Together, these data show that GCM1 binds to site 1 in the LHB promoter but also requires the upstream segment of the LHB promoter between −119 bp and −335 bp of the translation start codon for activity. GCM1 binding partners, ETV1, ETV7, HOXA13, and PITX1, were found to be differentially expressed in the ChG between days 27 and 34 and are excellent candidates for this role. In conclusion, GCM1 was demonstrated to drive the LHB promoter, through direct binding to a predicted GCM1-binding site, with requirement for another factor(s) to bind the proximal promoter to exert this function. Based on these findings, we hypothesize that ETV7 and HOXA13 act in concert with GCM1 to initiate LHB transcription between days 30 and 31, with ETV1 partnering with GCM1 to maintain transcription