Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing Transgenic Aspen Plants with bar Gene for Herbicide Resistance under Semi-natural Conditions

Obtaining herbicide resistant plants is an important task in the genetic engineering of forest trees. Transgenic European aspen plants (Populus tremula L.) expressing the bar gene for phosphinothricin resistance have been produced using Agrobacterium tumefaciens-mediated transformation. Successful genetic transformation was confirmed by PCR analysis for thirteen lines derived from two elite genotypes. In 2014–2015, six lines were evaluated for resistance to herbicide treatment under semi-natural conditions. All selected transgenic lines were resistant to the herbicide Basta at doses equivalent to 10 l/ha (twofold normal field dosage) whereas the control plants died at 2.5 l/ha. Foliar NH4-N concentrations in transgenic plants did not change after treatment. Extremely low temperatures in the third ten-day period of October 2014 revealed differences in freeze tolerance between the lines obtained from Pt of f2 aspen genotypes. Stable expression of the bar gene after overwintering outdoors was confirmed by RT-PCR. On the basis of the tests, four transgenic aspen lines were selected. The bar gene could be used for retransformation of transgenic forest trees expressing valuable traits, such as increased productivity.
Journal of Reproduction and Development

This study aimed to determine if lactation can be induced by exogenous hormonal treatment in non-pregnant sows. In experiment 1, pseudopregnant animals were divided into four groups and given: 1) 5 mg of estradiol dipropionate (EDP) 5 days before (n = 4), 2) 5 mg of EDP 10 days before (n = 3), 3) 10 mg of EDP 5 days before (n = 3) or 4) 10 mg of EDP 10 days (n = 3) before PGF2α treatment. Artificial lactation was induced in seven pseudopregnant sows (53.8%) by exogenous hormonal treatment. There was no significant effect of either an increased EDP dosage or interval from the EDP treatment to PGF2α treatment on the induction rate of artificial lactation. In experiment 2, milk samples were collected from artificial lactating and natural lactating sows (n = 6). IgG and IgA levels in the milk collected from both groups were significantly associated with time during the experimental period. Milk IgG levels 24 h after PGF2α treatment in artificial lactating sows were higher than those in the colostrum of lactating sows. In experiment 3, hormonal profiles in pseudopregnant sows with (n = 3) or without (n = 3) EDP treatment were determined. There was a significant difference in estradiol-17β levels on days 8, 7 and 5 before PGF2α treatment between groups. Progesterone and prolactin concentrations did not differ between groups. The present study revealed for the first time that lactation could be induced by exogenous hormonal treatment in non-pregnant sows and that the milk collected from these sows contained high immunoglobulin levels.
International Journal of Behavioral Nutrition and Physical Activity Environmental Supportiveness for Physical Activity in English Schoolchildren: a Study Using Global Positioning Systems

Background: There is increasing evidence that the environment plays a role in influencing physical activity in children and adults. As children have less autonomy in their behavioural choices, neighbourhood environment supportiveness may be an important determinant of their ability to be active. Yet we know rather little about the types of environment that children use for bouts of physical activity. This study uses accelerometery and global positioning system technologies to identify the charactieristics of environments being used for bouts of continuous moderate to vigorous physical activity (MVPA) in a sample of English schoolchildren.
Patient stratification and identification of adverse event correlations in the space of 1190 drug related adverse events

Purpose: New pharmacovigilance methods are needed as a consequence of the morbidity caused by drugs. We exploit fine-grained drug related adverse event information extracted by text mining from electronic medical records (EMRs) to stratify patients based on their adverse events and to determine adverse event co-occurrences. Methods: We analyzed the similarity of adverse event profiles of 2347 patients extracted from EMRs from a mental health center in Denmark. The patients were clustered based on their adverse event profiles and the similarities were presented as a network. The set of adverse events in each main patient cluster was evaluated. Co-occurrences of adverse events in patients (p-value < 0.01) were identified and presented as well. Results: We found that each cluster of patients typically had a most distinguishing adverse event. Examination of the co-occurrences of adverse events in patients led to the identification of potentially interesting adverse event correlations that may be further investigated as well as provide further patient stratification opportunities. Conclusions: We have demonstrated the feasibility of a novel approach in pharmacovigilance to stratify patients based on fine-grained adverse event profiles, which also makes it possible to identify adverse event correlations. Used on larger data sets, this data-driven method has the potential to reveal unknown patterns concerning adverse event occurrences.
Could Alkali Production Be Considered an Approach for Caries Control?

This study investigated the relationship of arginine deiminase (ADS) and urease activities with dental caries through a case-control study. ADS and urease activities were measured in dental smooth-surface supragingival plaque and whole saliva samples from 93 subjects, who were in three different groups: caries-free (n = 31), caries-active (n = 30), and caries-experienced (n = 32). ADS activity was measured by quantification of the ammonia generated from the incubation of plaque and saliva samples in a mixture containing 50 mM arginine-HCl and 50 mM Tris-maleate buffer, pH 6.0. ADS-specific activity was defined as nanomoles of ammonia generated per minute per milligram of protein. Urease activity was determined by quantification of ammonia produced from 50 mM urea. For bacterial identification and enumeration real-time qPCR analysis was used. Groups were compared using Kruskal-Wallis tests. Spearman correlations were used to analyze plaque metabolic activity and bacterial relationships. The results revealed significantly higher ammonia production from arginine in saliva (1.06 vs. 0.18; p < 0.0001) and plaque samples (1.74 vs. 0.58; p < 0.0001) from caries-free subjects compared to caries-active subjects. Urease levels were about 3-fold higher in the plaque of caries-free subjects (p < 0.0001). Although higher urease activity in saliva of caries-experienced and caries-free subjects was evident, no significant difference was found between the groups.
Diversity Analysis of MIMO Decode-and-Forward Relay Network by Using Near-ML Decoder

SUMMARY The probability of making mistakes on the decoded signals at the relay has been used for the maximum-likelihood (ML) decision at the receiver in the decode-and-forward (DF) relay network. It is well known that deriving the probability is relatively easy for the uncoded single-antenna transmission with M-pulse amplitude modulation (PAM). However, in the multiplexing multiple-input multiple-output (MIMO) transmission, the multi-dimensional decision region is getting too complicated to derive the probability. In this paper, a high-performance near-ML decoder is devised by applying a well-known pairwise error probability (PEP) of two paired-signals at the relay in the MIMO DF relay network. It also proves that the near-ML decoder can achieve the maximum diversity of MS MD + MR min(MS , MD), where MS , MR ,a ndMD are the number of antennas at the source, relay, and destination, respectively. The simulation results show that 1) the near-ML decoder achieves the diversity we derived and 2) the bit error probability of the near-ML decoder is almost the same as that of the ML decoder.
Genetics and molecular biology.

Different intrauterine exposures are associated with different metabolic profiles leading to growth and development characteristics in children and also relate to health and disease patterns in adult life. The objective of this work was to evaluate the impact of four different intrauterine environments on the telomere length of newborns. This is a longitudinal observational study using a convenience sample of 222 mothers and their term newborns (>37 weeks of gestational age) from hospitals in Porto Alegre, Rio Grande do Sul (Brazil), from September 2011 to January 2016. Sample was divided into four groups: pregnant women with Gestational Diabetes Mellitus (DM) (n=38), smoking pregnant women (TOBACCO) (n=52), mothers with small-for-gestational age (SGA) children due to idiopathic intrauterine growth restriction (n=33), and a control group (n=99). Maternal and newborn genomic DNA were obtained from epithelial mucosal cells. Telomere length was assessed by qPCR, with the calculation of the telomere and single copy gene (T/S ratio). In this sample, there was no significant difference in telomere length between groups (p>0.05). There was also no association between childbirth weight and telomere length in children (p>0.05). For term newborns different intrauterine environments seems not to influence telomere length at birth.
Phosphatidylinositol 3-kinase/akt and ras/raf-mitogen-activated protein kinase pathway mutations in anaplastic thyroid cancer.

CONTEXT Anaplastic thyroid carcinoma (ATC) can occur in the setting of differentiated thyroid carcinoma (DTC), which suggests a continuum in malignant progression from DTC to ATC. The Ras/Raf-MAPK and the phosphatidylinositol 3-kinase/Akt signaling pathways play critical roles in DTC tumorigenesis, but their roles in the pathogenesis of ATC are poorly defined. OBJECTIVE Our objective was to explore the potential contributions of these two pathways in ATC pathogenesis. DESIGN, SETTING, AND SUBJECTS The mutational status of BRAF, PIK3CA, PTEN, and RAS genes was analyzed in genomic DNA from microdissected tumor specimens of 36 cases of ATC, and in 16 samples of paired-matched lymph node metastases. PIK3CA copy number gain was assessed by real-time quantitative PCR. We performed immunohistochemistry for phospho-ERK and phospho-AKT in 26 cases of ATC. RESULTS DTC was present in half of the cases. BRAF V600E mutation was identified in nine of 36 (25%) ATCs; seven cases had identical mutations in both the ATC and DTC components. PIK3CA kinase domain mutations were found in five (14%) ATCs, one of which had mutations in both differentiated and anaplastic areas. RAS and PTEN mutations were each found in two (6%) ATCs. PIK3CA gain copy number was found notably increased in 14 (39%) ATCs. CONCLUSIONS BRAF mutations appear to play a role in the tumorigenesis of a subset of ATCs, and the majority of lymph node metastases. PIK3CA alterations occur preferentially in the later stages of ATC and were the most relevant events during thyroid cancer progression. The activation of both pathways suggests an important role in ATC dedifferentiation.
Thermal evolution of Tethyan surface waters during the Middle‐Late Jurassic: Evidence from δ18O values of marine fish teeth

[1] Oxygen isotope compositions of phosphate from vertebrate tooth enamel were measured to determine the evolution of tropical sea surface ( 0‰ owing to limited growth of continental ice during the early middle Oxfordian. The resulting sea level fall is estimated to be at least 50 m and is compatible with a global regression stage. The middle Oxfordian thermal minimum is followed by a new warming stage of 3–4°C from the middle to the late Oxfordian.
Update on fi eld use of the available drugs for the chemotherapy of human African trypanosomiasis

Despite the fact that eflornithine was considered as the safer drug to treat human African trypanosomiasis (HAT) and has been freely available since 2001, the difficulties in logistics and cost burden associated with this drug meant that the toxic melarsoprol remained the drug of choice. TheWorldHealth Organization responded to the situation by designing amedical kit containing all the materials needed to use eflornithine, and by implementing a training and drugs distribution programmewhich has allowed a transition to this much safer treatment. The introduction of the combination of nifurtimox and eflornithine (NECT) has accelerated the shift from melarsoprol to the best treatment available, due to reduced dosage and treatment time for eflornithine that has significantly lessened the cost and improved the burden of logistics encountered during treatment and distribution. The decrease in the use of more dangerous but cheaper melarsoprol has meant a rise in the per patient cost of treating HAT. Although NECT is cheaper than eflornithine monotherapy, an unexpected consequence has been a continuing rise in the per patient cost of treating HAT. The ethical decision of shifting to the best available treatment imposes a financial burden on HAT control programmes that might render long-term application unsustainable. These factors call for continuing research to provide new safer and more effective drugs that are simple to administer and cheaper when compared to current drugs.
The effects of thermal cycling on aging of Neodymium-Iron-Boron magnets

In this paper, the effects of temperature cycling on Neodymium-Iron-Boron (NdFeB) magnet aging are investigated. An accelerated lifetime test is parameterized and performed. In order to separate the aging mechanism, the temperature limits given by the manufacturer are not exceeded and the thermal aftereffects, observed during the first cycles, are separated. 80 magnets with four different temperature indices and coatings are tested. The required heating and cooling half-cycle times are measured. It is proven than no secondary aging mechanisms distorts the results. A Coffin-Manson-type aging well known from other aging mechanisms and a logarithmic drop in remanence and coercive force is shown.
Visualization of urban growth: a case study of Nairobi

Current urban growth planning initiatives for Nairobi city mainly rely on single-epoch static maps as base data in conjunction with other non-spatial attribute information. This approach falls short of offering an optimal interactive environment to planners that is helpful in making decisions about the best mix of land uses, and their temporal and spatial dimensions. With increasing availability of cartographic multimedia tools for handling spatial-temporal data, urban growth phenomena can be analysed through cartographic visualization. Cartographic animation has emerged as a potentially effective visualization technique that has an intuitive power in representing dynamic geographical phenomena through its ability to show interrelations amongst geospatial data components, location, attribute and time. Whereas cartographic animations have featured prominently in communicating geospatial information, their use as visual exploration tools is hampered by lack of necessary functionality that is capable of allowing users to interact with the dynamic display. This report gives the findings of a research study for visualizing Nairobi’s urban growth, from 1995 to 2002, through cartographic animation. Showing a series of images in sequence generated an animation of land use change for an area of approximately 1600 sq. km. The animation was created on the basis of the number of original data frames available, the optimal animation display speed, the number of intermediate frames to create between the known frames and the media on which the animation was to be displayed. Urban growth spatial themes identified for the study were built-up, unbuilt and vegetated areas. Creating the animation involved generating raster images for the temporal and spatial land use themes, converting them to bitmap thematic frames and subsequently importing the frames to a movie file. The results of this study are useful for visual thinking and communication of information on temporal and spatial components for the land use categories. The results from this animation can be improved by analyzing them in conjunction with other non-spatial urban growth data for Nairobi.
Novel Particle Swarm Optimization for Low Pass FIR Filter Design

A bstract: This paper presents an optimal design of linear phase digital low pass finite impulse response (FIR) filter using Novel Particle Swarm Optimization (NPSO). NPSO is an improved particle swarm optimization (PSO) that proposes a new definition for the velocity vector and swarm updating and hence the solution quality is improved. The inertia weight has been modified in the PSO to enhance its search capability that leads to a higher probability of obtaining the global optimal solution. The key feature of the proposed modified inertia weight mechanism is to monitor the weights of particles, which linearly decrease in general applications. In the design process, the filter length, pass band and stop band frequencies, feasible pass band and stop band ripple sizes are specified. FIR filter design is a multi6modal optimization problem. Evolutionary algorithms like real code genetic algorithm (RGA), particle swarm optimization (PSO), and the novel particle swarm optimization (NPSO) have been used in this work for the design of linear phase FIR low pass (LP) filter. A comparison of simulation results reveals the optimization efficacy of the algorithm over the prevailing optimization techniques for the solution of the multimodal, non6differentiable, highly non6linear, and constrained FIR filter design problems.
Murine Dishevelled 3 Functions in Redundant Pathways with Dishevelled 1 and 2 in Normal Cardiac Outflow Tract, Cochlea, and Neural Tube Development

Dishevelled (Dvl) proteins are important signaling components of both the canonical β-catenin/Wnt pathway, which controls cell proliferation and patterning, and the planar cell polarity (PCP) pathway, which coordinates cell polarity within a sheet of cells and also directs convergent extension cell (CE) movements that produce narrowing and elongation of the tissue. Three mammalian Dvl genes have been identified and the developmental roles of Dvl1 and Dvl2 were previously determined. Here, we identify the functions of Dvl3 in development and provide evidence of functional redundancy among the three murine Dvls. Dvl3 −/− mice died perinatally with cardiac outflow tract abnormalities, including double outlet right ventricle and persistent truncus arteriosis. These mutants also displayed a misorientated stereocilia in the organ of Corti, a phenotype that was enhanced with the additional loss of a single allele of the PCP component Vangl2/Ltap (LtapLp/+). Although neurulation appeared normal in both Dvl3 −/− and LtapLp/+ mutants, Dvl3 +/−;LtapLp/+ combined mutants displayed incomplete neural tube closure. Importantly, we show that many of the roles of Dvl3 are also shared by Dvl1 and Dvl2. More severe phenotypes were observed in Dvl3 mutants with the deficiency of another Dvl, and increasing Dvl dosage genetically with Dvl transgenes demonstrated the ability of Dvls to compensate for each other to enable normal development. Interestingly, global canonical Wnt signaling appeared largely unaffected in the double Dvl mutants, suggesting that low Dvl levels are sufficient for functional canonical Wnt signals. In summary, we demonstrate that Dvl3 is required for cardiac outflow tract development and describe its importance in the PCP pathway during neurulation and cochlea development. Finally, we establish several developmental processes in which the three Dvls are functionally redundant.
A comparative review of the fisheries resource management systems in New Zealand and in the European Union.

This review aims at comparing the fisheries management systems existing in New Zealand and in the European Union. The involvement of stakeholders at all stages of the management process is generally more transparent and better established in New Zealand than in the EU. Both systems aim at achieving an adequate balance between sustainability and utilisation and consider the precautionary approach as a founding principle. The social objectives are probably more explicit in the EU management system. In New Zealand, B-MSY is a legal management target for all stocks in the quota management system (QMS), but management strategies were poorly explicit until most recently. In the EU, there have not been any legal management targets or strategies until 1999. Since 1999, a number of multi-annual recovery and management plans have been established, including both management targets and strategies. Both management systems include conservation and access regulation measures. The EU management measures aim at regulating fisheries outputs and inputs, and discarding is tolerated. New Zealand management is almost exclusively output-based, and discarding practices are banned. In the EU, while individual quotas (IQs) are implicit in several countries, there is no consistent pattern across Member States for allocating TACs. In New Zealand, individual transferable quotas (ITQs) are implemented, and some flexibility in catch-quota balancing is provided by a carry-over allowance and the payment of a landing tax, the deemed value, for every fish landed above quota. If rights-based management were introduced in the EU based on, e. g. , the New Zealand model, we suggest that concentration rules be set in accordance with the social objectives of the Common Fisheries Policy, and also that the deemed value should be set based on science and economics.
Various interference models for multicellular scenarios: A comparative study

Statistical modeling of interference power is a useful tool to study and investigate the outage probabilities in homogeneous and heterogeneous cellular networks. Also, the ability to analyze and accurately predict the impact of interference via the use of an interference model is an essential way to improve the average throughput (cell edge throughput). There have been several statistical models for aggregating the interference power yielding in results for homogeneous sources, but focus lies on various multicellular scenarios such as heterogeneous networks. Finally, the analytical conditions on the system model parameters are derived and the distributions are determined, on which the statistical properties of interference power can be accurately modeled. This paper presents a comprehensive survey of interference models for various multicellular scenarios emphasizing their domains of application, advantages and disadvantages illustrated with examples. In addition, it gives insights which can facilitate system performance analysis and interference management.
Ennoblement of Stainless Steel by the Manganese-Depositing Bacterium Leptothrix discophora

The noble shift in open-circuit potential exhibited by microbially colonized stainless steel (ennoblement) was investigated by examining the relationship among surface colonization, manganese deposition, and open-circuit potential for stainless steel coupons exposed to batch cultures of the manganese-depositing bacterium Leptothrix discophora. Open-circuit potential shifted from -100 to +330 mV(infSCE) as a biofilm containing 75 nmol of MnO(infx) cm(sup-2) formed on the coupon surface but changed little further with continued MnO(infx) deposition up to 270 nmol cm(sup-2). Increased open-circuit potential corresponded to decreasing Mn(II) concentration in solution and to increased MnO(infx) accumulation and attached cell density on the coupon surfaces. MnO(infx) deposition was attributable to biological activity, and Mn(II) was observed to enhance cell attachment. The experimental results support a mechanism of ennoblement in which open-circuit potential is fixed near +350 mV(infSCE) by the cathodic activity of biomineralized MnO(infx).