Miracle-dz/UniFAR-FTUs huggingface dataset:
Projection layers improve deep learning models of regulatory DNA function

With the increasing application of deep learning methods to the modelling of regulatory DNA sequences has come an interest in exploring what types of architecture are best suited to the domain. Networks designed to predict many functional characteristics of noncoding DNA in a multitask framework have to recognise a large number of motifs and as a result benefit from large numbers of convolutional filters in the first layer. The use of large first layers in turn motivates an exploration of strategies for addressing the sparsity of output and possibility for overfitting that result. To this end we propose the use of a dimensionality-reducing linear projection layer after the initial motif-recognising convolutions. In experiments with a reduced version of the DeepSEA dataset we find that inserting this layer in combination with dropout into convolutional and convolutional-recurrent architectures can improve predictive performance across a range of first layer sizes. We further validate our approach by incorporating the projection layer into a new convolutional-recurrent architecture which achieves state of the art performance on the full DeepSEA dataset. Analysis of the learned projection weights shows that the inclusion of this layer simplifies the network’s internal representation of the occurrence of motifs, notably by projecting features representing forward and reverse-complement motifs to similar positions in the lower dimensional feature space output by the layer.
Evidence for asymmetric migration load in a pair of ecologically divergent stickleback populations

Gene flow between ecologically divergent populations can prevent local adaptation, resulting in lower mean fitness and directional selection within a population. Such maladaptation should tend to be stronger in populations receiving a relatively larger fraction of immigrants. We test this expectation by comparing the strength of selection in a pair of three-spine stickleback populations in adjoining but unequal-sized lake basins in British Columbia. A larger deeper basin is connected to a smaller shallower basin by a short channel that allows extensive migration between populations. The two basins contain distinct habitats and prey communities, and stickleback stomach contents and isotope ratios differ accordingly. Trophic morphology is correlated with diet, so we would expect these ecological differences to be accompanied by morphological divergence. However, high gene flow appears to constrain adaptive divergence: microsatellites indicate that the two basins represent a single panmictic gene pool, and phenotypic divergence is very subtle. As a result, fish in the smaller lake basin are subject to persistent directional selection towards a more benthic phenotype, whereas the larger population exhibits no significant selection. The results illustrate the potentially asymmetrical effect of migration-selection balance, and its effect on fitness within populations. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 273–287. ADDITIONAL KEYWORDS: gene flow – local adaptation – maladaptation – niche variation – relative gonad mass – stable isotopes.
Comparison of foot loading and foot strike pattern in women running in minimalist and conventional sports shoes

Background: At present, most runners use conventional sports shoes to protect and absorb the impacts that may cause overloading of the feet and joints. On the other hand, some runners tend to run almost barefoot or in minimalist footwear that may lead to foot strike pattern changes. Objective: The aim of this study was to analyse and to compare the foot strike pattern and foot loading when running in conventional running shoes (CRS) and minimalist running shoes (MRS) in a group of recreational women runners. Methods: A group of 14 experienced recreational women runners participated in this research. A Pedar-X system (Novel, Munich, Germany) was used to analyse the interaction of the foot with the ground while running in different type of shoes from as it relates to vertical force and plantar pressure distribution. The participants ran over a distance of 100 m with their habitual foot strike pattern in minimalist and also in conventional running shoes and data was always obtained while running along a straight 50 m long section (v = 3.33 ± 0.2 m ⋅ s -1 ). For assessment of the temporal and kinetics variables differences, the Wilcoxon test and the unpaired t-tests were used. Results: Recreational women runners showed statistically significant shift of the plantar pressures towards the forefoot when running in MRS compared to CRS (p = .047). Duration of swing phase in MRS and in CRS was similar (p = .291). When running in MRS, foot loading during initial contact was significantly higher than when running in CRS. Loading in the area of midfoot and forefoot was significantly higher in MRS too. Conclusions: Runners shifted their foot strike pattern forward when running in MRS; running in MRS may increase the foot loading and we recommend the use of minimalist footwear only after adequate foot strengthening and adaptation to avoid possible risk of foot injuries.
SOCIAL STRESS AND DOMINANCE AMONG GROUP MEMBERS AFTER MIXING BEEF COWS

Three groups of 10 spring-calving Angus and Hereford purebred and crossbred cows were placed in drylot paddocks from mid-November until calving to determine the influence of mixing mature beef cows from two different sources on social behavior and stress. Two Angus cows from an outside herd (alien cows) were placed in each paddock, and eight cows selected from the resident herd were added 1 d later. Agonistic behavior was recorded during a total of 21 30-min observation sessions over a period of 13 wk. Blood samples were drawn on days 2, 28 and 84 after penning and analyzed for cortisol, glucose and differential leucocyte counts. Breed-origin influenced (P < 0.01) social dominance values, which averaged 49.8, 48.7, 40.1 and 35.0 for crossbred, resident Angus, Hereford and alien Angus cows, respectively. Alien Angus received the most aggression during the first observation period (0–36 d after mixing) and initiated less aggression throughout the study as compared to resident cows. Physiological measures di.
Pricing Kernels

Pricing kernels or stochastic discount factors (SDFs) (see Stochastic Discount Factors) are used to represent valuation operators in dynamic stochastic economies. A kernel is a commonly used mathematical term for representing an operator. The term stochastic discount factor (SDF) extends concepts from economics and finance to include adjustments for risk. As we will see, there is a close connection between the two terms. The terms pricing kernel and SDF are often used interchangeably. After deriving convenient representations for prices, we provide several examples of stochastic discount factors and discuss econometric methods for estimating and testing asset pricing models that restrict stochastic discount factors.
Assessment of Rational Prescribing in General Outpatient Department of Kampala International University Teaching Hospital, Western Uganda

Introduction: Prevention of irrational use of medicines may reduce healthcare costs and potentially save lives. Aim: The aim of this study was to assess rational drug prescribing using World Health Organization (WHO) and International Network of Rational Use of Drugs (INRUD) indicators on prescribing in the General Outpatient Department of Kampala International University Teaching Hospital, Ishaka-Bushenyi, Western Uganda. Methodology: The study design was retrospective, descriptive and cross-sectional. A total of 884 prescriptions were selected by systematic sampling using an interval of 27 from 23,868 prescriptions available in the medical records of the General Out-Patient Department (GOPD) of Kampala International University Teaching Hospital (KIUTH) from April, 2016 to March, 2017. The selected samples were analyzed using Microsoft Excel 2013, to assess for conformity with the prescribing indicators. Results: The results showed that the percentage of recording of diagnosis was 90.72% (index of diagnosis—0.91). The average number of drugs per encounter was 2.6 (index of non-polypharmacy—0.77), and the percentage of drugs prescribed with the generic name was 90.21% (index of generics—0.9). Percentages of encounters with antibiotics and injectable drugs prescribed were 61.88% (index of antibiotics—0.48) and 5.43% (index of injectable drugs—1) respectively. Only 78.96% (index of EMSLU—0.79) of the medicines prescribed were from the Essential Medicines Supplies List of Uganda (EMSLU) or Uganda Clinical Guidelines 2016. The index of rational drug prescribing (IRDP) was found to be 4.85. Conclusion: The findings showed that only the percentage of encounters with injectable drugs was in line with WHO/INRUD prescribing indicators. On the over all, the index of rational drug prescribing (IRDP) was poor (observed 4.85 versus optimum 6). The authors recommended continuous sensitization, counselling and education of prescribers in KIUTH in order to achieve rational prescribing.
Quality of life and willingness-to-pay in patients with androgenetic alopecia

Objective The objective of the study was to assess the quality of life (QoL) in patients with androgenetic alopecia (AGA). A secondary aim was to determine the correlation between dermatology life quality index and willingness-to-pay (WTP) among subjects of different disease duration, severity, and socioeconomic factors. Patients and methods A self-administered multiple-choice questionnaire distributed to subjects diagnosed with AGA attending the dermatology clinic at three specialized hospitals in Riyadh from June 2016 to March 2017. Results Of the 233 subjects, 207 (88%) completed the questionnaires. The dermatology life quality index scores ranged from 0 to 29, with a mean score of 7.8±5.8 indicating a moderate effect on QoL. In 28.5% of subjects, QoL was affected very large to extremely large by AGA. Women showed a significantly higher WTP than men (P<0.001). Conclusion The present study suggests a moderate effect of AGA on the QoL. AGA impact women more than in men and women show more WTP than mem. More studies should pay more attention on the psychological status of patients with AGA.
In vitro tuberization of glory lily (Gloriosa superba L.)

Gloriosa superba L. , a climber belonging to the family, Colchicaceae is a high value medicinal plant cultivated in Tamil Nadu. Colchicine is one major tropalone alkaloids of medicinal importance which cures gout, cancer, rheumatism. Vegetative propagation through V or L shaped tubers is a commonly followed practice but is considered slow with poor multiplication ratio of 1: 1 every year. The cost involved towards planting material (800 kg of tubers/acre) alone accounts to 2.0 lakhs at Rs. 250 per kg of tuber prevailing for the last three years. In this context, a suitable protocol for in vitro tuberisation using non-dormant tubers of Gloriosa superba L. on Murashige and Skoog medium supplemented with various concentrations growth regulators have been reported in the present study. Sprouted tuber node explants were sterilized with 70% ethanol for 30 s followed by 60 s in HgCl2 which reduced the contamination percentage (8.00%). MS medium supplemented with 4.0 mgL-1BAP and 1.0 mgL-1 NAA recorded the highest response for primary tuber (100%) and secondary tuber (100%) formation. This also recorded the maximum number of tuber (1.77) from single explants. GA3 (1.0 mgL-1) was observed to be vital for the elongation of shoot whereas, IAA (1.0 mgL-1) in combination with IBA (0.5 mgL-1) was effective for induction of roots on MS medium. Key words: Glory lily, ms medium, tuber node, shooting, rooting, primary tubers.
The Influence of the Bright Light Exposure during Daytime on Melatonin Excreting Rate in Urine

The present study was conducted to know the effects of different light intensities exposed during daytime for several hours on melatonin excreting rate in urine and tympanic temperature. Eleven healthy female subjects were exposed to bright light of 6000 lx (Bright) or dim light of 100 lx (Dim) during daytime from 09:00 h to 13:30 h, and then the light condition was kept at 100 lx until the end of test at 14:30 h. The urinary samples were collected from 10:00 h to 14:30 h every 1.5 hours, and melatonin excreting rate in urine was measured by enzyme immunoassay. Melatonin excreting rate in urine was significantly higher in Bright than in Dim at 11:30 h and 14:30 h, and not significant but at high level at 13:00 h (p <0.07). Moreover, average tympanic temperatures were significantly lower in Bright than in Dim from 11:43 h to 14:30 h. These results showed that the bright light exposure during daytime could reduce tympanic temperature, which might result from the increase of melatonin level.
Direct and indirect effects of species displacements: an invading freshwater amphipod can disrupt leaf-litter processing and shredder efficiency

Abstract Invasive species may threaten the fundamental role played by native macroinvertebrate shredders in determining energy flow and the trophic dynamics of freshwater ecosystems. Functionally, amphipods have long been regarded as mainly shredders, but they are increasingly recognized as major predators of other macroinvertebrate taxa. Furthermore, intraguild predation (IGP) between native and invasive amphipods underlies many species displacements. We used laboratory mesocosms to investigate what might happen to shredders and leaf-litter processing in water bodies invaded by the highly predatory Ponto-Caspian amphipod Dikerogammarus villosus, which is spreading rapidly throughout Europe and may soon invade the North American Great Lakes. The leaf-shredding efficiency of D. villosus was significantly lower than that of 3 Gammarus species (2 native and 1 invasive) that D. villosus has either already displaced or may be currently displacing in The Netherlands. In addition, D. villosus was a major predator of all of these native and invasive amphipod shredders and of a common isopod shredder Asellus aquaticus. Leaf processing in Gammarus and Asellus mesocosms declined rapidly in the presence of D. villosus and ceased altogether within 4 d because by then, all potential shredders had been killed and consumed. Furthermore, the shredding efficiency of surviving amphipods and isopods declined significantly within 2 d of the release of D. villosus, a result indicating that predator-avoidance behavior may override leaf processing. We discuss the implications of these direct and indirect effects of D. villosus invasions and species displacements on community structure and litter processing in aquatic ecosystems.
The Effect of Mechanical Cold Work on the Magnetic Flux Expulsion of Niobium

Expulsion of ambient flux has been shown to be crucial to obtain high quality factors in bulk niobium SRF cavities. However, there remain many questions as to what properties of the niobium material determine its flux expulsion behavior. In this paper, we present first results from a new study of two cavities that were specially fabricated to study flux expulsion. Both cavities were made from large grain ingot niobium slices, one of which had its slices rolled prior to fabrication, and none these slices were annealed prior to measurement. Expulsion measurements indicate that a dense network of grain boundaries is not necessary for a cavity to have near-complete flux trapping behavior up to large thermal gradients. The results also contribute to a body of evidence that cold work is a strong determinant of flux expulsion behavior in SRF-grade niobium.
Dual-Polarization NFDM Transmission With Continuous and Discrete Spectral Modulation

Nonlinear distortion experienced by signals during their propagation through optical fibers strongly limits the throughput of optical communication systems. Recently, a strong research focus has been dedicated to nonlinearity mitigation and compensation techniques. At the same time, a more disruptive approach, the nonlinear Fourier transform, aims at designing signaling schemes more suited to the nonlinear fiber channel. In a short period, impressive results have been reported by modulating either the continuous spectrum or the discrete spectrum. Additionally, very recent works further introduced the opportunity to modulate both spectra for single polarization transmission. Here, we extend the joint modulation scheme to dual-polarization transmission by introducing the framework to construct a dual-polarization optical signal with the desired continuous and discrete spectra. After a brief analysis of the numerical algorithms used to implement the proposed scheme, the first experimental demonstration of dual-polarization joint nonlinear frequency division multiplexing modulation is reported for up to 3200 km of low-loss transmission fiber. The proposed dual-polarization joint modulation schemes enables to exploit all the degrees of freedom for modulation (both polarizations and both spectra) provided by a single-mode fiber.
Loss of Jak 2 protects cardiac allografts from chronic rejection by attenuating Th 1 response along with increased regulatory T cells

Chronic rejection acts as the most formidable obstacle for organ transplantation in clinical settings. Herein we demonstrated in a cardiac transplantation model that blockade of Janus kinase 2 (Jak2) provides protection for cardiac allografts against chronic rejection. Specifically, loss of Jak2 almost completely abolished the production of IFN-γ+ Th1 cells, while the percentage of Foxp3+ regulatory T cells (Tregs) was significantly increased. As a result, loss of Jak2 significantly prolonged allograft survival (58 ± 30.6 days vs. 7 ± 0.3 days). Particularly, 4 out of 13 Jak2 deficient recipients (30%) showed long-term acceptance of allografts as manifested by the graft survival time > 100 days. Cellular studies revealed that Jak2 deficiency did not impact the intrinsic proliferative capability for CD4+ T cells in response to nonspecific polyclonal and allogenic stimulation. Mechanistic studies documented that the impaired Th1 development was caused by the attenuated IFN-γ/STAT1 and IL-12/STAT4 signaling along with repressed expression of Th1 transcription factors T-bet, Hlx and Runx3. However, the IL-2/STAT5 signaling remained intact, which ensured normal Treg development in Jak2-/naïve CD4 T cells. Together, our data support that blockade of Jak2 may have therapeutic potential for prevention and treatment of allograft rejection in clinical settings.
The Effects of Socio-demographic Characteristics on Indonesian Women’s Knowledge of HIV/AIDS: A Cross-sectional Study

Objectives The purpose of this study was to characterize Indonesian women’s knowledge of HIV/AIDS and to investigate the effects of socio-demographic characteristics thereupon with the goal of supporting the prevention and early detection of HIV/AIDS. Methods This cross-sectional study was conducted using secondary data from the standard Indonesian Demographic and Health Survey (IDHS) in 2012. A total of 34 984 subjects ranged in age from 15 years to 49 years. Data were analyzed using the chi-square test and logistic regression to identify the effects of socio-demographic characteristics on Indonesian women’s knowledge of HIV/AIDS. Results All socio-demographic characteristics except marital status were related to knowledge of HIV/AIDS among Indonesian women in the univariate analysis (p<0.05). Multivariate analysis revealed that only age group, education level, location of residence, and wealth index were related to Indonesian women’s knowledge of HIV/AIDS (p<0.05). Conclusions Indonesian women’s insufficient knowledge related to HIV/AIDS shows that the provision of accurate and comprehensive information related to HIV/AIDS are components of prevention and control interventions that should be improved. With greater knowledge, women are expected to be more likely to determine their own and their partners’ human immunodeficiency virus status and to take appropriate preventive steps.
Study of Environmental Impacts Before and After Using the Organic-Chemical Fertilizer in Rice Paddy Fields

The environmental impact of an organic-chemical fertilizer developed by the Institute of National Science and Technology has been studied at Bansrangsabaeng Posai Ubonratchathani. The study revealed that the values of pH, EC, OC, total N, available P, and exchangeable K in soils from two varieties of rice tested Kor-Khor 10 and Kor-Khor 15 paddy fields are almost the same. The concentrations of VOC, NH 3, and CH 4 in the air from the rice paddy fields mentioned above are lower than 0.001 mg/m 3 indicating no air pollution problems. Analysis of the water supply (ground water) and surface water within the studied area before and after using organic-chemical fertilizer, found that most of the water supply parameters including pH, Total Hardness, TDS, SS, Fe, Mn, and NO 3-N were not significantly changed and all of them met water supply standards. In terms of surface water quality, slightly different values of pH, TDS, SS, NO 3-N, TKN, PO 4-P, BOD, COD, and DO were observed compared with a standard fertilizer. In conclusion, the organic-chemical fertilizer is a viable alternative to standard chemical fertilizer and may help to reduce the environmental impact of such chemicals upon the land.
Contribution scientifique A model of opinion diffusion and deliberation

In this article, we propose an agent-based model of opinion diffusion and voting where agents influence each other through deliberation. The model is inspired from social modeling as it describes a process of collective decision-making that iterates on a series of dyadic inter-individual influence steps and collective deliberation procedures. We study the evolution of opinions and the correctness of decisions taken within a group. We also aim at founding a comprehensive model to describe collective decision-making as a combination of two different paradigms : argumentation theory and agent-based influence models, which are not obvious to link since a formal translation and interpretation of their relationship is required. We find that deliberation, modeled as an exchange of arguments, reduces the variance of opinions and the number of extremists as long as not too much deliberation takes place during the decision-making process. Insofar as we define “correct” decisions as those whose supporting arguments survive deliberation, promoting deliberative discussion favors convergence towards correct decisions.