Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving the predictive capability of benthic species distribution models by incorporating oceanographic data – Towards holistic ecological modelling of a submarine canyon

Submarine canyons are associated with increased biodiversity, including cold-water coral (CWC) colonies and reefs which are features of high conservation value that are under increasing anthropogenic pressure. Effective spatial management and conservation of these features requires accurate distribution maps and a deeper un- derstanding of the processes that generate the observed distribution patterns. Predictive distribution modelling offers a powerful tool in the deep sea, where surveys are constrained by cost and technological capabilities. To date, predictive distribution modelling in canyons has focussed on integrating groundtruthed acoustically acquired datasets as proxies for environmental variables thought to influence faunal patterns. Physical oceano- graphy is known to influence faunal patterns but has rarely been explicitly included in predictive distribution models of canyon fauna, thereby omitting key information required to adequately capture the species-en- vironment relationships that form the basis of predictive distribution modelling. In this study, acoustic, oceanographic and biological datasets were integrated to undertake high-resolution predictions of benthic mega- faunal diversity and CWC distribution within Whittard Canyon, North-East Atlantic. The main aim was to investigate which environmental variables best predict faunal patterns in canyons and to assess whether in- cluding oceanographic data improves predictive modelling. General additive models, random forests and boosted regression trees were used to build predictive maps for CWC occurrence, megafaunal abundance, species richness and biodiversity. To provide more robust predictions, ensemble techniques that summarise the variation in predictions and uncertainties between modelling approaches were applied to build final maps. Model per- formance improved with the inclusion of oceanographic data. Ensemble maps identified areas of elevated current speed that coincided with steep ridges and escarpment walls as the areas most likely to harbour CWCs and increased biodiversity, probably linked to local hydrodynamics interacting with topography to concentrate food resources. This study shows how incorporating oceanographic data into canyon models can broaden our un- derstanding of processes generating faunal patterns and improve the mapping of features of conservation, supporting effective procedures for spatial ecosystem management. species richness, 1/ D and abundance. To assess low terrain complexity (3). Model predictions beyond canyon branches (i.e. on the interfluves and the shelf) are less reliable because training datasets did not include these environments. excluded them from our interpretation.
A Literate Programming Approach for Hardware Description Language Instruction

the Department and Computer at Dr. investigates the use of digital systems to measure and support engineering education, speciﬁcally through learning analytics and the pedagogical uses of digital systems. She also investigates fundamental questions critical to improving undergraduate engineering degree pathways. Ph.D. Engineering a new engineering education researcher when she was ASEE Educational Research and Methods Division Apprentice
Ul Small Nuclear RNAs with Altered Specificity Can Be Stably Expressed in Mammalian Cells and Promote Permanent Changes in Pre-mRNA Splicing

Pre-mRNA 5' splice site activity depends, at least in part, on base complementarity to Ul small nuclear RNA. In transient coexpression assays, defective 5' splice sites can regain activity in the presence of Ul carrying compensatory changes, but it is unclear whether such mutant Ul RNAs can be permanently expressed in mammalian cells. We have explored this issue to determine whether Ul small nuclear RNAs with altered specificity may be of value to rescue targeted mutant genes or alter pre-mRNA processing profiles. This effort was initiated following our observation that Ul with specificity for a splice site associated with an alternative H-ras exon substantially reduced the synthesis of the potentially oncogenic p2lras protein in transient assays. We describe the development of a mammalian complementation system that selects for removal of a splicing-defective intron placed within a drug resistance gene. Complementation was observed in proportion to the degree of complementarity between transfected mutant Ul genes and different defective splice sites, and all cells selected in this manner were found to express mutant Ul RNA. In addition, these cells showed specific activation of defective splice sites presented by an unlinked reporter gene. We discuss the prospects of this approach to permanently alter the expression of targeted genes in mammalian cells.
PRE-PREGNANCY BODY MASS INDEX AND GESTATIONAL WEIGHT GAIN AS RISK FACTORS ON MATERNAL AND BIRTH OUTCOMES

Maternal pre-pregnancy body mass index (BMI) and gestational weight gain (GWG) have been reported to be associated with pregnancy outcomes. The aim of this study was to evaluate the effects of pre pregnancy BMI and gestational weight gain on maternal and birth outcomes. A prospective and a longitudinal cohort study was conducted among pregnant women who had attended antenatal centers in Constantine, Algeria, between 2013 and 2015. 200 pregnant women aged 19 to 41 years old were followed for 9 months of pregnancy. They underwent body weight measurement during routine examination at first, second and third trimester. Baby birth weight also measured after delivery. Data included age, parity and maternal outcomes. Results showed that mean BMI was 27.3 ± 4.7 kg/m2 and mean GWG was 8.9 ± 5.4 kg. Of all subjects, 33% were in a normal weight range, which left 41 and 26% classified as overweight and obese before pregnancy. Among these subjects, only 27.5% of women had gained the recommended amount of weight, with 48.5% gaining less than recommended, and 24% gaining more than recommended by the IOM. The average birth weight of infants born to inadequate GWG women was lower than that of those born to adequate GWG women (3232±564 g vs 3470±464 g, p=0.04). The risk of gestational hypertension (p=0.0006) and diabetes (p=0.04) increased steadily with pre-pregnancy BMI. Also, the risk of hypertension increased with excessive GWG (p<0.0001). Conclusion; the effects of gestational weight gain on pregnancy outcomes depend on the woman’s pre-pregnancy BMI.
Impact of Automatic Thoughts and Psychological Flexibility on Depressive Symptoms and on Relapse of Remitted Depressed Persons

wurde bei den Probanden beider Gruppen eine traurige Stim-mung induziert. Die remittiert depressiven Probanden wurden über eine 16-monatige Katamnesephase nach-untersucht. Ergebnisse: Nach der negativen Stimmungs-induktion riefen remittiert Depressive im Vergleich zu Gesunden weniger PAG ab. Zudem zeigten Frührückfällige während der Katamnesephase einen eingeschränkten Zugang zu PAG und eine niedrige PF. Weder PAG, NAG noch PF erwiesen sich als bedeutsame Prädiktoren eines depressiven Rückfalls. Schlussfolgerung: Remittiert Depressive und Frührückfällige zeigen einen eingeschränkten Zugang zu PAG. Die schwache Produktion von PAG stellt einen Risikofaktor für einen depressiven Rückfall depressed subjects who relapsed early in the follow-up phase differed from those who relapsed late or not at all, in terms of PF and AT. For this purpose, the remitted depressives were formed into 2 subgroups. The first subgroup (early relapse) consisted of the subjects who had already suffered a depressive relapse within the first 4 months. The second group (late relapse or no relapse) comprised subjects who had a depressive relapse later in the 16-month follow-up period, or no relapse at all. To study the association of an altered access to PAT and NAT after the negative mood induction as well as PF before the experiment, with the probability of occurrence of a depressive relapse during the follow-up phase, we used binary logistic hierarchical regression models. To determine the effect size, f according to Cohen was calculated and applied.
Simulation Model Composition for the Large-Scale Analysis of Smart Grid Control Mechanisms

For the intelligent future power system (Smart Grid) new control schemes have to be developed that analyze the status of all actors and schedule required actions among these to keep the power system stable. Modelling and simulation are considered appropriate means to virtually test these control schemes prior to deployment. The research objective is to develop a concept for building a simulative testbed for the evaluation of new Smart Grid control mechanisms by composing available simulation models. This is achieved by two metamodels. The semantic metamodel is used to formally specify simulator and simulation model semantics. Based on this, the scenario metamodel can be used to specify large-scale scenario models by capturing statistical data about the scenarios as well as additional constraints that govern the way in which the scenarios are built. Two case studies show that the approach is applicable to real-world research projects.
Effects of Dietary Enterococcus faecalis YFI-G720 on the Growth, Immunity, Serum Biochemical, Intestinal Morphology, Intestinal Microbiota, and Disease Resistance of Crucian Carp ( Carassius auratus )

: Diseases of crucian carp ( Carassius auratus ) are closely related to intestinal parameters. Enterococcus faecalis has strong colonization ability in the intestinal tract, and produces natural antibiotics, bacteriocin, and other bacteriostatic substances, which can effectively inhibit some pathogenic bacteria and improve the intestinal microenvironment. This study aimed to assess the effects of E. faecalis YFI-G720 which was isolated from the intestinal of crucian carp on the growth, immunity, intestinal health, and disease resistance of crucian carp. Fish (48.16 ± 0.55 g) were fed four diets, commercial diet or diet containing E. faecalis at 10 5 CFU/g (EF1), 10 6 CFU/g (EF2), or 10 7 CFU/g (EF3) for 28 days. The results showed that supplementation of E. faecalis signiﬁcantly improved the weight gain ratio (WGR) and the speciﬁc growth rate (SGR) compared with control group ( p < 0.05). Intestinal mucosal epithelial cells in EF2 were intact and normal, but there was obvious vacuolation in CG. Compared with CG, serum C3 and IgM in EF2 were signiﬁcantly increased at the end of the experiment ( p < 0.05), and serum alkaline phosphatase was signiﬁcantly higher in all experimental groups ( p < 0.05). Among studied immune-related genes, expression was detected by qPCR, C3, IgM, and IL-1 β were upregulated in all experimental groups to varying degrees from 14 days, with highest expression in EF2 at 28 days. Intestinal microbiota structure analyzed through high-throughput sequencing, and the results showed that the relative abundance of Aeromonas and Acinetobacter decreased while Cetobacterium increased in all experimental groups, with the greatest changes in EF2. Challenge tests showed that ﬁsh fed E. faecalis were more resistant to Aeromonas veronii ( p < 0.05). In conclusion, dietary E. faecalis YFI-G720 at 10 6 CFU/g can improve the health status, immune parameters, intestinal microbiota composition, and disease resistance of crucian carp.
Test of the "Healthy Migrant Hypothesis": A Longitudinal Analysis of Health Selectivity of Internal Migration in Indonesia

eScholarship provides open access, scholarly publishing services to the University of California and delivers a dynamic research platform to scholars worldwide. Previous studies have shown that immigrants are generally healthier than the native-born populations of receiving societies, a result generally attributed to the positive selection of migrants with respect to health. This hypothesis, however, has not been adequately evaluated due to data limitations. Using high-quality longitudinal data from Indonesia, I explicitly examine the health selectivity hypothesis, also referred to as the healthy migrant hypothesis, with respect to internal migration. Specifically, I study whether pre-migration health status affects the likelihood of migration by comparing those from the sending population who do and do not move. Results show that migrants in Indonesia do tend to be selected with respect to health and that this aspect of selection is robust to household unobserved heterogeneity. However, the strength and direction of the health-migration association vary by different types of migration and distinctive dimensions of health. Abstract Previous studies have shown that immigrants are generally healthier than the native-born populations of receiving societies, a result generally attributed to the positive selection of migrants with respect to health. This hypothesis, however, has not been adequately evaluated due to data limitations. Using high-quality longitudinal data from Indonesia, I explicitly examine the health selectivity hypothesis, also referred to as the healthy migrant hypothesis, with respect to internal migration. Specifically, I study whether pre-migration health status affects the likelihood of migration by comparing those from the sending population who do and do not move. Results show that migrants in Indonesia do tend to be selected with respect to health and that this aspect of selection is robust to household unobserved heterogeneity. However, the strength and direction of the health-migration association vary by different types of migration and distinctive dimensions of health.
Model experiments to support the design of large icebreaking tankers

important of the model and scaling of the important is the of the and its system. The two models are combined to predict the powering and manoeuvring performance for large tankers in a range of ice conditions including level first year ice, pack ice and rubble ice. The results of experiments on four hull designs, with single and twin-screw propulsion arrangements, are presented and discussed and some suggestions are made for refining the modelling techniques for future projects.
Testing of a Campylobacter N-glycan presenting Salmonella Typhimurium vaccine in broiler chickens

Campylobacteriosis is an emerging foodborne enteric disease in humans worldwide. Poultry meat is an important source of infection. One strategy in the combat against Campylobacter at production level is the vaccination of broiler chickens. In this study, a Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) strain was transformed with a vector to facilitate expression of a Nglycan from Campylobacter on its surface. The immunogenicity of this live vaccine was tested per os in commercial broilers. The vaccine was able to colonize broilers without causing disease. The chickens were shown to produce antibodies against the Campylobacter N-glycan upon infection with the Campylobacter jejuni challenge strain. However, following vaccination, no detectable humoral immune response and no reduction of colonization of C. jejuni in the caeca was observed. Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-56380 Dissertation Originally published at: Thommen, I N. Testing of a Campylobacter N-glycan presenting Salmonella Typhimurium vaccine in broiler chickens. 2011, University of Zurich, Vetsuisse Faculty. Institut für Veterinärbakteriologie Abteilung für Geflügelund Kaninchenkrankheiten der Vetsuisse-Fakultät Universität Zürich Direktor: Prof. Dr. Max M. Wittenbrink Arbeit unter Leitung von Prof. Dr. Richard K. Hoop Campylobacter N-glycan presenting Salmonella Typhimurium: a new vaccine for broiler chickens? Inaugural-Dissertation zur Erlangung der Doktorwürde der Vetsuisse-Fakultät Universität Zürich vorgelegt von Isabelle Nathalie Thommen Tierärztin von Arboldswil, BL und Vevey, VD genehmigt auf Antrag von Prof. Dr. med. vet. Richard K. Hoop, Referent Prof. Dr. med. vet. Roger Stephan, Korreferent
Comprehensive Analysis of Gene Expression Changes and Validation in Hepatocellular Carcinoma

Aim: This study aimed to analyze the involvement of hub genes in hepatocellular carcinoma. Methods: Four series were used in this study: GSE45267, GSE84402, and GSE101685 from GPL570 platform in the Gene Expression Omnibus and the other from The Cancer Genome Atlas. The gene audition was completed using R software and Venn diagrams. The outcome, Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes preliminary analyses of differentially expressed genes were performed using the R software. A string image was obtained using the Search Tool for the Retrieval of Interacting Genes. The protein– protein interaction network was examined using Cytoscape software. The corrplot package was used to analyze the correlation of genes. Human Protein Atlas was used to confirm the protein levels. Univariate Cox regression was used to analyze whether these genes were related to survival. UALCAN was used to confirm the effect of these genes on patient survival. Results: A total of 107 differentially expressed genes from 491 patients with hepatocellular carcinoma and 119 normal individuals were selected in this study. Cytoscape revealed 25 central nodes from the 107 genes. CCNB1, CDK1, CCNA2, PTTG1, and CDC20 were selected based on the cell cycle pathway. A significant correlation was found among the 6 DEGs. The transcription levels and protein levels of these genes were verified in cells and human tissue samples. The overall survival for these genes was analyzed using univariate Cox regression and UALCAN. Conclusion: CCNB1, CDK1, CDC20, PTTG1, CCNA2, and TTK were overexpressed and correlated in hepatocellular carcinoma cells and tumors. The results might help explore the prognosis and diagnostic markers of HCC.
Audience Size Effects in Field RNG Experiments: The Case of Japanese Professional Baseball Games

—This study examined the association between the outputs of a true random number generator (RNG) and audience size during Japanese professional baseball games. We regarded the RNG as a signal detector of fi eld consciousness and hypothesized that the number of signal sources may increase the ability of an RNG to detect signals. Experimenters and our assistants voluntarily obtained 76 samples from a total of 78 baseball games during the 2010–2011 baseball season. The eff ects of audience size at the stadium (M = 38970 ± 6058 SD, N = 78) and TV audience ratings (M = 7.07 ± 2.32 SD, N = 23) were examined in relation to the measurements of multiple Random Streamer and Psyleron RNG devices. RNGs set at remote locations ran simultaneously during the games. Our results showed a posi- tive correlation between accumulated chi-squared statistics by Random Streamer and audience size at the stadium. Unexpectedly, identical RNG devices showed strong negative correlations between diff erent machines, which suggested that their outputs canceled each other out. Finally, some future tasks are discussed.
RNA trafficking by acute myeloid leukemia exosomes

Extrinsic signaling cues in the microenvironment of acute myeloid leukemia (AML) contribute to disease progression and therapy resistance. Yet it remains unknown how the bone marrow niche where AML arises is subverted to support leukemic persistence at the expense of homeostatic function. Exosomes are cell membrane-derived vesicles carrying protein and RNA cargoes that have emerged as mediators of cell-cell communication. In this study, we examined the role of exosomes in developing the AML niche of the bone marrow microenvironment, investigating their biogenesis with a focus on RNA trafficking. We found that both primary AML and AML cell lines released exosome-sized vesicles that entered bystander cells. These exosomes were enriched for several coding- and non-coding RNAs relevant to AML pathogenesis. Further, their uptake by bone marrow stromal cells altered their secretion of growth factors. Proof-of-concept studies provided additional evidence for the canonical functions of the transferred RNA. Taken together, our findings revealed that AML exosome trafficking alters the proliferative, angiogenic, and migratory responses of co-cultured stromal and hematopoietic progenitor cell lines, helping explain how the microenvironmental niche becomes reprogrammed during invasion of the bone marrow by AML. The results presented here demonstrate the release of exosome-sized vesicles by AML cells and illustrate how vesicle trafficking alters gene expression, protein secretion, and behavior of bystander cells. We show that vesicles contain diverse RNA species, including mRNAs and miRNAs relevant to AML biology and with broad biomarker potential. In aggregate, our work indicates that trafficking of AML exosomes elicits broad functional changes in bystander cells. SDF-1 and VEGF secreted protein after vesicle without changes in its secretion. These results illustrate hat physiologic The diverse exosome cargo highlights the inherent challenge in assigning a specific functional outcome to the transfer of an individual exosomal protein or RNA transcript in the context of many others. The presence of prognostically relevant mRNA in AML-derived exosomes implies their potential development as a minimally-invasive AML biomarker platform. Here, it will be important to see the extent to which specific AML exosome content will track with diagnostic parameters and change during the course of treatment. Taken together, our results demonstrate that exosome trafficking by AML cells can alter the function of bystander cells. Our observations demonstrate the complexity of cell-cell communication and emphasize the potential impact of exosome trafficking on AML physiology. Coding and non-coding RNAs are key determinants of the cellular phenotype, and in vitro RNA transfer can produce experimental phenotype conversion (37, 41). The transfer of transcription factor- and micro-RNA from AML to bystander cells presents a compelling paradigm for cell-cell communication in the leukemic niche.
Human Immunodeﬁciency Virus Type 1 DNA Nuclear Import and Integration Are Mitosis Independent in Cycling Cells

An essential step in human immunodeﬁciency virus type 1 (HIV-1) replication is the movement of the viral preintegration complex from the cytoplasm into the nucleus. The pathway(s) and timing for HIV-1 DNA nuclear entry in cycling cells have not been established. Here, we show that if cycling cells are infected before S phase, viral DNA can be integrated prior to passage of the host DNA replication fork through the integration site, as indicated by stable inheritance in both daughter cells. We conclude that efﬁcient nuclear entry can occur independently of mitotic nuclear disassembly in cycling cells. it efﬁcient stable inheritance of the viral (the 8). Integration is catalyzed by the virus-encoded protein (IN), which is assembled with viral DNA in the “preintegration complex. ”