Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural studies of surfactant protein D in complex with bacterial lipopolysaccharide ligands

Abstract This work is focused on the recognition of natural lipopolysaccharide (LPS) by the innate immune protein human lung surfactant protein D (hSP-D) in the form of a biologically active recombinant fragment (rfhSP-D), containing the α-helical coiled-coil and three carbohydrate recognition domains (CRD). Intact LPS from two bacterial strains, S. minnesota (R5 mutant) and H. influenzae type b Eagan (CA7 mutant), were delipidated by means of mild acid hydrolysis, leaving the purified polysaccharide (PS) to be used in X-ray diffraction studies by means of co-crystallisation with rfhSP-D. S. minnesota R7 full LPS was also investigated following development of a suitable solubilisation method which also utilised the LPS from E. coli O111:B4.This work is focused on the recognition of natural lipopolysaccharide (LPS) by the innate immune protein human lung surfactant protein D (hSP-D) in the form of a biologically active recombinant fragment (rfhSP-D), containing the α-helical coiled-coil and three carbohydrate recognition domains (CRD). Intact LPS from two bacterial strains, S. minnesota (R5 mutant) and H. influenzae type b Eagan (CA7 mutant), were delipidated by means of mild acid hydrolysis, leaving the purified polysaccharide (PS) to be used in X-ray diffraction studies by means of co-crystallisation with rfhSP-D. S. minnesota R7 full LPS was also investigated following development of a suitable solubilisation method which also utilised the LPS from E. coli O111:B4. The structural studies of rfhSP-D bound to H. influenzae Eagan CA7 PS (solved and refined at 2.98 Å) and to S. minnesota rough mutant LPS/PS (solved and refined at 3.3 Å) reveal that rfhSP-D binds to LPS preferentially through the non-terminal inner core heptose HepI via the O6’ and O7’ hydroxyls. rfhSP-D recognition of S. minnesota HepI shows a similar bound heptose orientation to that previously reported for heptose binding by rfhSP-D in the literature with an indication of normal Kdo in the inner core Kdo-HepHep trisaccharide. rfhSP-D recognition of the HepI of H. influenzae Eagan CA7 reveals a novel bound heptose orientation, with the heptose rotated by 180° about C5-C6, resulting in the O6’ and O7’ hydroxyls being interchanged with respect to coordination to Ca1 and protein. The novel orientation of HepI is accompanied by a salt bridge being formed between the flanking residue Arg343 and Glu347, both of which adopt a previously unseen conformation. The novel binding mechanism of rfhSP-D for Eagan CA7 suggests flexibility in recognition and offers evidence to explain why this mutant binds more weakly than the Eagan 4A mutant to both rfhSP-D and hSP-D.
Interaction between micronutrients; vitamin a, zinc and iron in the eye (biochemical and histological studies)

The association of visual impairment and poor diet has long been recognized. The retina and retinal pigment epithelium have the highest trace mineral content as compared to any body tissue. Malnutrition as a cause of blindness has been under estimated. This study aimed to investigate the relation between both deficiency as well as the excess of micronutrients (Vitamin A, zinc and iron) and the ocular eye diseases. This work was done on 48 albino rats divided into six groups. Group one fed on control basal diet, group two, three and four were fed on a diet free from vitamin A, iron, and zinc respectively. Group five was fed on a diet free from all the above micronutrients while group six was fed on a diet contain excess of all these micronutrients. At the end of the feeding period, ophthalmological and histological examinations were done to all rats. The level of vitamin A was estimated in the serum and the concentration of zinc and iron were determined in the cornea, lens and retina. Also total protein and its fractions were estimated in the lens. The result of this study showed that cortical cataract was detected in the rats fed on the diet containing deficient or excess micronutrients. The level of vitamin A in serum and the concentration of iron and zinc in cornea, lens and retina revealed a significant change in different tissues studied due to different treatment especially in deficient and excess groups. Histological examination revealed photoreceptor degeneration in the retina and intact endothelial cells of the cornea. The data of this work also revealed that the level of these micronutrients in the diet affect ocular function, therefore they have to be provided in adequate amounts that satisfy the physiological requirements to avoid eye complications.
Development of BIM process through knowledge management

Building Information Modelling [BIM] is a tool enabling management of information of a built asset from planning to demolition. Previous research has focused on its technical use cases, neglecting the organizational support processes. The link between knowledge management actions, more specifically knowledge transfer, and BIM development are studied with this research. The studied elements are measuring the level of BIM use, knowledge transfer and finding possible solutions to take BIM development work forward, using the principles of knowledge management. This qualitative research is conducted as a single case study. Primary data sources are semi-structured interviews. The studied organization is a big organization in the Finnish infrastructure industry. The findings were that supporting knowledge transfer does create benefits for the BIM process. Knowledge transfer can be used to enhance the organizational capability of BIM use.
Off-line and on-line optical monitoring of microalgal growth

The growth of Chlamydomonas reinhardtii microalgae cultures was successfully monitored, using classic off-line optical techniques (optical density and fluorescence) and on-line analysis of digital images. In this study, we found that the chlorophyll fluorescence ratio F685/F740 has a linear correlation with the logarithmic concentration of microalgae. By using digital images, the biomass concentration correlated with the luminosity of the images through an exponential equation and the length of penetration of a super luminescent blue beam (λ = 440 nm) through an inversely proportional function. The outcomes of this study are useful to monitor both research and industrial microalgae cultures.
Making friends in online games: gender differences and designing for greater social connectedness

ABSTRACT While online multiplayer games provide an opportunity for players to both maintain and establish new connections, male and female players have been found to experience these environments differently. Interviews (n = 22) and focus groups (n = 14) were used to explore these differences as they impact on creating new social connections, as well as to provide recommendations for the development of new social tools and features that account for these differences. While all participants experienced toxicity and performance pressure as barriers to forming new connections, female players uniquely reported the impacts of misogynistic targeting and stereotype threat. In turn, female players wishing to avoid these stresses would often mask their gender. The common practice of gender misrepresentation by both male and female players impacted female players’ ability to create social connections through voice technology, as well as building their distrust of unknown others. Recommendations are made to build social connectedness between players taking into account the specific constraints faced by female players. These include establishing mentoring opportunities as well as profiling players beyond their immediate skill or rank. Additionally, the desire for control of one’s online identity presents practical challenges that may be overcome through thoughtful design.
Effect of Chitosan Addition on Kinetic of Mass Transfer during Deep Fat Frying of Kurdish Cheese Nugget

Background: Frying is the cooking of food in fat, which involves heat and mass transfer simultaneously. During frying, moisture loss creates cavities or pores as well as passageways in the food. These cavities are known as capillary pores and the oil penetrates through them during frying. Materials and Methods: This study aimed to evaluate the effect of chitosan on mass transfer during deep-fat frying of Kurdish cheese nuggets. Moreover, the effect of chitosan level (0, 0.5, and 1.5%), frying temperature (150, 170, and 190°C), and frying time (0, 1, 2, 3, and 4 min) on mass transfer in the breading coating and the core parts were determined in this study. The data were statistically analyzed using ANOVA and Duncan post-hoc test in SPSS software (Version 21.0). In addition, MATLAB software was utilized to fit the equations. Results: The results showed an interaction effect of these processing conditions on mass transfer. Battercoated samples with 1.5% chitosan had the lowest oil content in core and breading among all formulations. The model based on Fick’s law was used to describe moisture transfer data. The oil absorption rate constants in the breading and core parts were within the range of 0.19-0.27 s−10.22-0.41 s−1, respectively. Activation energy obtained from the Arrhenius plot ranged between 13.65 and 54.93 kJ/mol. Conclusions: Moisture loss during frying increased with the increase of frying time and temperature and was significantly affected by batter formulation. The kinetic models gave a good fit for moisture diffusion and oil transfer.
Prediksi Penggunaan Aktual E-Toll Card dengan Pendekatan Persamaan Model Struktural

The purpose of this study is to examine the relationships between variables in predicting the actual use of innovation services. The variables in this study include resistance to change, perceived value, attitude towards innovation services, the intention to use the innovation services, and innovative personality. Data collection techniques in this study conducted by questionnaire with non-probability sampling method. The number of respondents was 212 respondents. Data was then analyzed by Structural Equation Modeling (SEM). Results showed that three out of five hypotheses are supported. Those hypotheses include the intention of a significant predictor of the use of innovation services. Intention itself is also influenced by the attitude towards innovation services. The perceived value is a significant predictor of the attitude towards innovation services. However, the results showed that the resistance to change and innovative personality is not a significant predictor of the intention to use the innovation services. This study also provides research limitations and suggestions for further research.
Enhancing methane production from anaerobic co‐digestion of cow manure and barley: Link between process parameters and microbial community dynamics

The effects of selected process parameters (i.e., temperature, inoculum to substrate ratio [I:S], and inoculum source) on methane production and microbial community structure were investigated in lignocellulose‐based anaerobic digestion tests. The results highlighted that dynamic response of microbial communities in changing process parameters subsequently affected anaerobic digestion performance. Co‐inoculation of cow rumen fluid to the seed sludge improved the methane yield by 18%. The overall highest methane yield (278 mL CH4/g volatile solids) was obtained when cow rumen fluid was co‐inoculated with anaerobic seed sludge with an I:S ratio of 1:2 at mesophilic temperature. Based on 16S rRNA gene amplicon sequencing results, Clostridium, Bacteroides, and Bacillus were the predominant bacterial genera in all anaerobic digesters. The highest relative abundances of Clostridum and Bacillus were detected in the thermophilic anaerobic digester. The relative abundance of Rikenella; known for high cellulolytic activity, was significantly higher only in the cow rumen fluid‐added digester. Comparatively higher abundances of these lignocellulose‐degraders synergistically affected volatile fatty acids as well as methane production in these anaerobic digestion set ups. Methanobacterium was the most abundant methanogen in the digesters inoculated only with anaerobic seed sludge; whereas, Methanobrevibacter dominated the digester that was co‐inoculated with cow rumen fluid.
Transferring Adaptive Bit Rate Streaming Quality Models from H.264/HD to H.265/4K-UHD

SUMMARY In this paper the quality of adaptive bit rate video streaming is investigated and two state-of-the-art models, i.e., the NTT audiovisual quality-estimation and ITU-T P.1203 models, are considered. This paper shows how these models can be applied to new conditions, e.g., 4K ultra high deﬁnition (4K-UHD) videos encoded using H.265, considering that they were originally designed and trained for HD videos encoded with H.264. Six subjective evaluations involving up to 192 participants and a large variety of test conditions, e.g., durations from 10sec to 3min, coding-qualityvariation,andstallingevents,wereconductedonbothTVandmobile devices. Using the subjective data, this paper addresses how models and coeﬃcients can be transferred to new conditions. A comparison between state-of-the-art models is conducted, showing the performance of transferred and retrained models. It is found that other video-quality estimation models, such as VMAF, can be used as input of the NTT and ITU-T P.1203 long-term pooling modules, allowing these other video-quality-estimation models to support the speciﬁcities of adaptive bit-rate-streaming scenarios. Finally, all retrained coeﬃcients are detailed in this paper allowing future work to directly reuse the results of this study.
From Cells to Residues: Flame-Retarded Rigid Polyurethane Foams

ABSTRACT Rigid polyurethane foams (RPUFs) exhibit short times to ignition as well as rapid flame spread and are therefore considered to be hazardous materials. This paper focuses on the fire phenomena of RPUFs, which were investigated through a multimethodological approach. Water-blown polyurethane (PUR) foams without flame retardants (FRs) as well as water-blown PUR foams containing triethyl phosphate as a gas phase-active FR were examined. The aim of this study is to clarify the influence of the FR on the fire phenomena during combustion of the foams. Additionally, materials’ densities were varied to range from 30 to 100 kg/m3. Thermophysical properties were studied by means of thermogravimetry; fire behavior and flammability were investigated via cone calorimeter and limiting oxygen index, respectively. During the cone calorimeter test, the temperature development inside the burning specimens was monitored with thermocouples, and cross sections of quenched specimens were examined visually, giving insight into the morphological changes during combustion. The present paper delivers a comprehensive study, illuminating phenomena occurring during foam combustion and the influence of a FR active in the gas phase. The superior fire performance of flame-retarded PUR foams was found to be based on flame inhibition, and on increased char yield leading to a more effective protective layer. It was proven that in-depth absorption of radiation is a significant factor for estimation of time to ignition. Cross sections investigated with the electron scanning microscope exhibited a pyrolysis front with an intact foam structure underneath. The measurement of temperature development inside burning specimens implied a shift of burning behavior towards that of non-cellular materials with rising foam density.
Dialing-Up Distal Sites in Proteins: The Search for the Mechanical Consequences of Thermodynamic Coupling in eglin C

Proteins have evolved to exploit long-range structural and dynamic effects as a means of regulating function. Understanding this communication between distal sites in proteins is therefore vital to our comprehension of such phenomena as allostery, catalysis, and ligand binding/ejection. By quantifying the additivity/thermodynamic coupling in globallymonitored phenomena such as ligand binding, catalysis, or folding free-energy, mutant cycles have long been used to determine the existence of communication between various sites— proximal or distal—in proteins. The absence of ligands or products in protein stability/folding studies provides a simple background for examining this most basic communication, non-additivity. Typically, non-additivity is measured through global transitions in concert with a single probe. Mechanistic insight is often limited by the probes Single Probe vs. Multi-probe Detection of Non-additivity. Representations of the native state and an unfolded state of the Two-State model (left) and an ensemble of states (right).
Wheat Straw Biochar Increases Potassium Concentration, Root Density, and Yield of Faba Bean in a Sandy Loam Soil

ABSTRACT A greenhouse experiment was conducted to study the effect of different irrigation levels (100%, 75%, and 50% of water requirement) and wheat straw biochar levels (0%, 1.25%, 2.5%, 3.75%, and 5% w/w) on faba bean yield, water productivity, root length density, and different ions concentration in soil solution, using a factorial arrangement in complete randomized design with three replications. Results showed that application of high level of biochar (5% w/w) destroyed the plants before they reached maturity. The maximum yield was obtained in 1.25% w/w biochar under full irrigation, while the maximum water productivity was obtained in 2.5% w/w biochar and 50% of water requirement. Further, the root length density in soil top layer (0–8 cm) was significantly more than those in 8–16 cm, due to holding more water content in top layer and no drainage from the pots. Sodium, potassium, calcium and magnesium ions’ concentrations in soil solution were significantly increased by increasing biochar levels; however, the rate of increase in potassium was higher than other ions due to high potassium concentration in biochar in comparison with the soil. In conclusion, application of biochar in the level of 1.25% w/w is suggested as a suitable agent to decrease water consumption and improving the crop performance.
Study on drying kinetics of coriander leaves using different drying techniques

Coriander (Coriandrum sativum) is a herbaceous annual plant with fan-shaped feathery leaves and clusters of pale mauve flowers. Its aromatic leaves are used as a herb in many oriental dishes and soups, but in terms of international trade, it is mainly grown for the round, aromatic seeds, which are used as a spice. In the present study, coriander leaves which were procured from the local market of Udaipur were dried by using tray dryer and fluidized bed dryer. Also, the drying kinetics of coriander leaves were compared. The fresh and blanched leaves weighing 100 g were dried in tray dryer and fluidized bed dryer at air temperature of 45, 55 and 65 oC at fixed air velocity of 2m/s. The results showed that drying of coriander leaves took place in falling rate period and constant rate period was absent in both tray drying and fluidized bed drying experiments.
Modular Supercomputing Architecture: From Idea to Production

1.1 The Jülich Supercomputing Centre (JSC) . 2 1.2 Supercomputing architectures at JSC . 3 1.2. 1 The dual supercomputer strategy . 3 1.2. 2 The Cluster-Booster concept . 5 1.2. 3 The Modular Supercomputing architecture . 7 1.3 Applications and workloads . 9 1.3. 1 Co-design applications in the DEEP projects . 11 1.4 Systems overview . 13 1.4. 1 Sponsors . 13 1.4. 2 Timeline . 14 1.5 Hardware implementation . 15 1.5. 1 First generation (DEEP) prototype . 15 1.5. 2 Second generation (DEEP-ER) prototype . 19 1.5. 3 JURECA . 21 1.6 System Software . 24 1.6. 1 System administration . 24 1.6. 2 Schedulers and resource management . 24 1.6. 3 Network-bridging protocol . 27 1.6. 4 I/O software and file system . 28 1.7 Programming model . 28 1.7. 1 Inter-module MPI Offloading . 29 1.7. 2 OmpSs abstraction layer . 30 1.7. 3 Resiliency software . 31 1.8 Cooling and facility infrastructure . 33 1.9 Conclusions and next steps . 35 1.10 Acknowledgments . 36 Bibliography . 38
Semantic approaches for the meta-optimization of complex biomolecular networks (Approches sémantiques pour la méta-optimisation des réseaux biomoléculaires complexes)

Systems biology models aim to understand the behaviour of a cell trough a complex biomolecular network. In the literature, most research focuses on modelling isolated parts of this network, such as metabolic networks.However, to fully understand the cell’s behaviour we should analyze the biomolecular network as a whole. Avail-able approaches do not address these requirements sufficiently. In this context, we aim at developing a platform that enables biologists to simulate the state changes of biomolecular networks with the goal of steering their be-haviours. The platform employs rules, knowledge and experience, much like those that an expert biologist mightderive. This platform consists of four modules: a logic-based modelling module, a semantic modelling module,a qualitative discrete-event simulation module and an optimization module. For this purpose, we first present alogic-based approach for modelling complex biomolecular networks including the structural, functional and be-havioural aspects. Next, we propose a semantic approach based on four ontologies to provide a rich description of biomolecular networks and their state changes. Then, we present a method of qualitative discrete-event simulation to simulate the biomolecular network behaviour over time. Finally, we propose a multi-objective optimization method for optimizing the transittability of complex biomolecular networks in which we take into account various criteria such as minimizing the number of external stimuli, minimizing the cost of these stimuli, minimizing the number of target nodes and minimizing patient discomfort. Based on these four contributions, a prototype called the CBNSimulator was developed. We describe our approaches and show their applicability through real cases studies, the bacteriophage T4 gene 32, the phage lambda, and the p53 signaling network. Results demonstrate that these approaches provide the necessary elements to model, reason and analyse the dynamic behaviour and the transition states of complex biomolecular networks.