Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of the stability of thymine tautomers and the interaction of its tautomers with Na+, K+, Mg2+ and Ca2+ in gas and solvent phases

The present study compared the interactions among Na +, K +, Mg2+ and Ca2+, thymine and its tautomers in the gas and solvent phase, an interaction dependent upon the electronic construction of the tautomers. Three types of cation interaction with thymine and its tautomers were observed. In the first one, the metal cations interacted with a lone pair of nitrogen or oxygen of the tautomers. In the second type, there was an interaction among the cations, nitrogen and oxygen at the same time; the last one was that of cations with the electron density of thymine π-system, where the cations were perpendicular to the ring of thymine. The interaction of metals cation with tautomers was studied in the gas and solvent phases; a comparison was then made between interactions in two phases. The interaction energy for all complexes indicated the stability of complexes, an energy which was higher in Ca2+ and Mg2+ compared with Na+ and K+. Concerning K+ and Na+, the stability of all complexes of tautomers was greater than that of thymine complexes; however, the stability of certain Ca2+ and Mg2+ complexes was lower than the complexes of thymine. GRAPHICAL ABSTRACT
Evolutionary Covariant Positions within Calmodulin EF-hand Sequences Promote Ligand Binding

: Intracellular calcium signaling is an essential regulatory mechanism through calcium-mediated signal transduction pathways involved in many cell processes, such as exocytosis, motility, apoptosis, excitability, transcription, and muscle contraction. The calcium-binding, ubiquitous, and highly conserved protein calmodulin (CaM) is an important regulator of hundreds of target proteins involved in cellular calcium signaling. CaM comprises of two pairs of EF-hand calcium-binding domains and these structural regions of the protein are highly conserved. Studying the molecular mechanisms underlying the binding of calcium to the EF-hands of CaM is critical in understanding the calcium-mediated cellular processes and how improper binding of calcium can lead to various human pathologies. Previous site-specific binding measurements indicate that each of the four EF-hands of CaM have distinct affinities for calcium. In this study, we have utilized covariance patterns and site-specific mutagenesis to analyze calcium affinity in the two EF-hands of the N-lobe of CaM in order to determine the specific amino acids that are evolutionarily conserved to coordinate calcium. The specific amino acids in CaM that we studied are theorized to coevolve, which means that in their protein coding genes, when a mutation occurs, a compensatory mutation is likely to follow to conserve structure and function of CaM. Since CaM is a highly conserved protein with a known structure, covariance analyses will help in understanding which amino acid contacts are most important for the coordination of calcium in the EF-hands of CaM and to determine which amino acids are under evolutionary constraint. Covariance algorithms, multiple sequence analyses and accompanied protein structure analyses were used to identify the two high scoring amino acid pairs in the N-lobe EF-hands: positions 22 and 24 in EF-hand site 1 and positions 58 and 60 in EF-hand site 2. The amino acids in these locations were mutated and accompanied calcium binding was measured to better understand the effects of the mutations on calcium binding. We have found that both the D24N mutation in site 1 and the D58N mutation in site 2 disrupt binding likely due to the removal of a necessary aspartate in the binding site. However, the combined D58N and N60D mutations restore binding in site 2 by providing the necessary aspartate in the covariant The N60D mutation by impact on calcium in site 2. that evolution conserves at least one aspartate in the covariant positions of the binding site and the presence of two aspartates in the covariant positions of the binding site has little affect on calcium binding. We are currently studying the covariant positions in site 1 and future work includes structurally analyzing the covariant positions in the C-lobe of CaM and studying covariance patterns of other calcium-binding proteins with EF-hand binding domains.
Grapevine Non-vinifera Genetic Diversity Assessed by Simple Sequence Repeat Markers as a Starting Point for New Rootstock Breeding Programs

Microsatellite markers are a valuable tool to facilitate the management of germplasm collections and assess genetic diversity. This study reports the genetic characterization of a large collection of 379 rootstocks and other non-vinifera accessions maintained at the University of Milan, Italy. Accessions were genotyped with 22 highly polymorphic microsatellite markers, including the nine “international” loci used for grapevine identification, three VMC, three VrZAG, and seven VChr loci; 17 loci were retained to identify cultivars, investigate genetic diversity, analyze pedigrees, infer population structure, and design a core collection. This study identified 232 unique genotypes; the allelic profiles of 70 rootstocks were confirmed according to the literature and databases, while the profiles of 43 rootstocks were proposed for the first time. Pedigree analysis highlighted 77 parents-offspring trios and 44 parent-offspring relationships, some of them already known and others new. Genetic-structure analysis showed a more likely number of three ancestral groups, with a high percentage of admixed samples. A structure based on the genetic background of genotypes was not observed. A core collection of 70 genotypes captured 100% of the entire number (373) of detected alleles. Most of these genotypes were unidentified or poorly characterized. The information provided in this paper could assist breeders in their efforts to exploit still unexplored individuals useful for long-term breeding plans.
Manipulation of the illumination of an Adaptive Optics Flood Illumination Ophthalmoscope for functional imaging of the retina in-vivo

L’œil etant la seule fenetre optique transparente de notre corps, il donne un acces unique a l’observation de reseaux neuronaux et vasculaires. Mais aujourd’hui une nouvelle ere s’ouvre pour l’imagerie haute resolution, qui ne doit plus se contenter de donner acces aux structures des tissus, mais aussi d’en apprecier les fonctions. En effet, on peut trouver dans l’imagerie retinienne des biomarqueurs du fonctionnement de l’ensemble du corps humain. Des maladies neurodegeneratives (Parkinson,Alzheimer) ou l’hypertension arterielle pourraient etre ainsi precocement diagnostiquees par une imagerie de haute precision de la retine. L’optique adaptative, adaptee a l’imagerie retinienne des 1997, a ameliore nettement la resolution spatiale des images retiniennes entrainant la multiplication des etudes de retine par ophtalmoscope. Elle a notamment ete couplee avec l’ophtalmoscope a balayage, qui devint le choix le plus populaire par sa superiorite en resolution spatiale et sectionnement optique par rapport au plein champ. Cependant, contrairement aux systemes a balayage, l’ophtalmoscope plein champ produit des images grand champ a forte cadence d’acquisition et sans distorsion. Dans mon travail de these, j’ai cherche a montrer qu’un tel systeme, associe a des modalites d’imagerie jouant sur la geometrie d’eclairement, pourrait apporter a la recherche sur la retine. Pour atteindre cet objectif ambitieux, nous avons modiﬁe l’ophtalmoscope plein champ construit au Centre Hospitalier National des Quinze-Vingts avec un traitement d’image speciﬁque et deux nouveaux instruments inspires de la microscopie plein champ. Nous avons integre ces instruments dans le trajet d’illumination de l’ophtalmoscope aﬁn de manipuler la geometrie de l’eclairage de la retine. Ces nouvelles implementations nous permettent de mettre en œuvre des techniques d’imagerie plus avancees, comme par exemple l’imagerie en champ sombre ou l’angiographie non invasive en proche infrarouge. Ces modalites d’imagerie ont ete exploitees pour imager la retine de facon fonctionnelle. Nous nous sommes interesses principalement a la fonction de couplage de lumiere des photorecepteurs et a la perfusion sanguine.
GO-based filtration membrane for removal of Endocrine Disrupting Compounds (EDCs) from water

In the present study, an attempt is made to utilize the superior water selective transport properties of Graphene Oxide (GO) laminates as filtration membranes for Endocrine Disrupting Compounds (EDCs) with high permeate flux rates. A layer-by-layer (L-b-L) approach was utilized to prepare thin film composite membranes with a polymer support and a few layers of GO interlinked via poly(allylamine hydrochloride) (PAH). The prepared membrane showed a fourfold increase in the permeate flux in comparison to the commercially available nanofiltration (NF) membranes. The rejection performance of the membrane was evaluated by studying the permeation of ibuprofen and a rejection rate of 75% was obtained.
Edge Detection For Eye States Using Color Image Sequence

In this work, an automatic and real time method for detecting eye states is proposed. The method is based on the fact that the regions of iris and white regions of an eyeball can be detected when it is open. In this case, color images contain more information helpful for detecting irises than intensity images. The saturation of color is used to detect whether the eye is open or closed, then the edge map of the eye image is used to detect the irises. Using the color information to detect the locations of irises is more accurate than using only the edge image. يعلا ت0احل فاوحلا فاشتكا ةنولملا روصلا نم ةلسلس مادختساب ن م / مظاك سابع لما تابساحلا مولع مسق / ةيبرتلا ةيلك / ةيرصنتسملا ةعماجلا
SINOMA - A new approach for estimating linear relationships between noisy serial data streams

Reconstructions of past climates are based on the calibration of available proxy data. This calibration is usually achieved by means of linear regression models. In the recent paleo-climate literature there is an ongoing discussion on the validity of highly resolved climate reconstructions. The reason for this is that the proxy data are noisy, i.e. in addition to the variability that is related to the climate variable of interest, they contain other sources of variability. Inadequate treatment of such noise leads to a biased estimation of regression slopes, resulting in a wrong representation of the real amplitude of past climate variations. Methods to overcome this problem have had a limited success so far. Here, we present a new approach - SINOMA - for noisy serial data streams that are characterized by different spectral characteristics of signal and noise. SINOMA makes use of specific properties of the data streams temporal or spatial structure and by this is able to deliver a precise estimate of the true regression slope and, simultaneously, of the ratio of noise variances present in the predictor and predictand. The paper introduces the underlying mathematics as well as a general description of the presented algorithm. The validity of SINOMA is illustrated with two test data-sets. Finally we address methodological limitations and further potential applications.
On the Gain of NOMA in Wireless Powered Networks With Circuit Power Consumption

This letter investigates when non-orthogonal multiple access (NOMA) outperforms time-division multiple access (TDMA) for use in the uplink of wireless powered networks, assuming non-negligible circuit power consumption and a non-linear energy harvesting model. To this end, we propose a resource allocation scheme that maximizes the minimum rate among the users, by optimizing the allocated time to energy harvesting and information transmission. The formulated problem is optimally and efficiently solved by using a novel algorithm, which is based on the derived analytical expressions and the bisection method. The simulations results show that NOMA is superior to TDMA for practical values of circuit power consumption.
An FPGA Implementation of Hough Transform using DSP blocks and block RAMs

Since FPGA chips maintain relatively low price and its programmable features, it is widely used in those fields which need to update architecture or functions frequently such as communication and education areas. Especially, in mobile devices that recently require the ability to perform computation such as real-time image processing, FPGAs are promising devices. The main contribution of this paper is to present a new FPGA architecture for the Hough transform that identifies straight lines in a binary image. Recent FPGAs have hundreds of embedded DSP blocks and block RAMs. For example, Xilinx Virtex-6 Family FPGAs have a DSP48E1 block, which is a configurable logic block equipped with fast multipliers, adders, pipeline registers, and so on. They also have a dual-port memory with 18Kbits as a block RAM. One of the most important key techniques for accelerating computation using FPGAs is an efficient usage of DSP blocks and block RAMs. Our new architecture for the Hough transform uses 178 DSP48E1 blocks and 180 block RAMs with 18Kbits that work in parallel. As far as we know, there is no previously published work that fully utilizes DSP blocks and block RAMs for the Hough transform. Roughly speaking, a conventional sequential implementation performs 180 m voting operations for m edge points. Our architecture performs voting operations in parallel, and outputs identified straight lines in m +97 clock cycles. Since 180 m voting operations are performed using 178 DSP48E1 blocks, the lower bound of the computing time is m clock cycles. Hence our implementation is close to optimal. The implementation results show that the Hough transform for a 512×512 image with 33232 edge points can be done in only 135. 75µs.
Design of Online Application for Agricultural Machinery Service based on Android Operating System

Utilization of agricultural machinery recently becoming big issue to increase agriculture production in Indonesia. In these couple years Indonesian Ministry of Agriculture massively granted agricultural machineries to the farmers for increasing rice production. Considering that farmer’s paddy field are scattered in villages area, it can be happening that agricultural machinery in one village may overutilize where the other still underutilize. The objective of this research is to design an online application for agricultural machinery service for optimizing the utilization of agricultural machinery. The application was developed under Android operating system which is commonly used for mobile phone. The method of this research was following System Development Life Cycle which include investigation, system analysis, design, implementation, installation and testing steps. There are three sub systems in this application i.e. system for operator, machinery provider and machinery user. The application contains several functions such as machinery data management, order management and machinery services scheduling. In the user application, detail data such as field location, type of machinery, order time, and supporting map of the location can be input and read by the machinery provider easily. The application was tested under several Android operating systems and the results showed that the application can run satisfactorily.
Animated rendering of cardiac model simulations

Heart disease has been the leading cause of death both in the world and the United States in the past decade. Computational cardiac modeling and simulation, especially patient-specific cardiac modeling has been recognized as one of the best ways to improve diagnosis of heart disease by providing insights in individual disease characteristics that cannot be obtained by other means. However presenting the results of cardiac simulations to cardiologists in an interactive manner can considerably improve the utility of cardiac models in understanding the heart function. In this work, we have developed virtual reality and animated volume rendering techniques to render the results of cardiac simulations. We have developed a GPU accelerated algorithm that produces time varying voxelized representation of the quantities of interest in a cardiac model, which can then be interactively rendered in real time. We voxelize the different time frames of the analysis model and transfer the time-varying data to the GPU memory using a flat data structure. This technique allows us to visualize and interact with animation in real time. As a proof-of-concept, we test our method on interactively rendering the simulation results of cardiac biomechanics simulations. We also present the timing results on post-processing and rendering two different cardiac IGA at different resolutions. We achieve an interactive frame rate of over 50 fps for all test cases.
Coarse and giant particles are ubiquitous in Saharan dust export regions and are radiatively significant over the Sahara

<p>Mineral dust is an important component of the climate system, interacting with radiation, clouds, and biogeochemical systems and impacting atmospheric circulation, air quality, aviation, and solar energy generation. These impacts are sensitive to dust particle size distribution (PSD), yet models struggle or even fail to represent coarse (diameter (<span><em>d</em></span>)&#160;<span>>2.5</span>&#8201;<span>&#181;</span>m) and giant (<span><em>d</em>>20</span>&#8201;<span>&#181;</span>m) dust particles and the evolution of the PSD with transport. Here we examine three state-of-the-art airborne observational datasets, all of which measured the full size range of dust (<span><em>d</em>=0.1</span>&#160;to&#160;<span>>100</span>&#8201;<span>&#181;</span>m) at different stages during transport with consistent instrumentation. We quantify the presence and evolution of coarse and giant particles and their contribution to optical properties using airborne observations over the Sahara (from the Fennec field campaign) and in the Saharan Air Layer (SAL) over the tropical eastern Atlantic (from the AER-D field campaign). </p><p>Observations show significantly more abundant coarse and giant dust particles over the Sahara compared to the SAL: effective diameters of up to 20&#8201;<span>&#181;</span>m were observed over the Sahara compared to 4&#8201;<span>&#181;</span>m in the SAL. Excluding giant particles over the Sahara results in significant underestimation of mass concentration (40&#8201;%), as well as underestimates of both shortwave and longwave extinction (18&#8201;% and 26&#8201;%, respectively, from scattering calculations), while the effects in the SAL are smaller but non-negligible. The larger impact on longwave extinction compared to shortwave implies a bias towards a radiative cooling effect in dust models, which typically exclude giant particles and underestimate coarse-mode concentrations. </p><p>A compilation of the new and published effective diameters against dust age since uplift time suggests that two regimes of dust transport exist. During the initial 1.5&#8201;d, both coarse and giant particles are rapidly deposited. During the subsequent 1.5 to 10&#8201;d, PSD barely changes with transport, and the coarse mode is retained to a much greater degree than expected from estimates of gravitational sedimentation alone. The reasons for this are unclear and warrant further investigation in order to improve dust transport schemes and the associated radiative effects of coarse and giant particles in models. </p><p>This work has been recently published in ACP (Ryder, C. L., Highwood, E. J., Walser, A., Seibert, P., Philipp, A., and Weinzierl, B.: Coarse and giant particles are ubiquitous in Saharan dust export regions and are radiatively significant over the Sahara, Atmos. Chem. Phys., 19, 15353&#8211;15376, https://doi.org/10.5194/acp-19-15353-2019, 2019). </p>
An online routing algorithm for space division multiplexing-based elastic optical networks

We focus on the optimisation of lightpath routing in an online space division multiplexing-based elastic optical network (SDM-b-EON). We propose a new online routing algorithm, named as online routing algorithm (ORA), which accounts for the presence of the transceivers in the network, and also ensures the routing of the transparent lightpaths through the spectral super-channels over spatial multiple core fibres (MCFs) links. We conduct extensive simulations considering two realistic network topologies and two different MCF crosstalk values which result in different transmission reach values. The obtained results demonstrate that: 1) ORA significantly outperforms the various reference routing techniques in terms of the bandwidth blocking probability (BwBP); 2) in regard to the use of modulation formats, for low crosstalk values, the most used format is QPSK rather than BPSK which results in lesser traffic being accepted by the SDM-b-EON; 3) as the transceivers amount increases, more frequent demands blocking occurs owing to spectrum scarcity. Overall, our study shows that in a SDM-b-EON, larger amount of transceivers can be efficiently used in comparison to the less efficient spectrum usage, since the spectrum significantly experiences fragmentation owing to the spectrum-contiguity and spectrum-continuity constraints.
Secure and Differentially Private Logistic Regression for Horizontally Distributed Data

Scientific collaborations benefit from sharing information and data from distributed sources, but protecting privacy is a major concern. Researchers, funders, and the public in general are getting increasingly worried about the potential leakage of private data. Advanced security methods have been developed to protect the storage and computation of sensitive data in a distributed setting. However, they do not protect against information leakage from the outcomes of data analyses. To address this aspect, studies on differential privacy (a state-of-the-art privacy protection framework) demonstrated encouraging results, but most of them do not apply to distributed scenarios. Combining security and privacy methodologies is a natural way to tackle the problem, but naive solutions may lead to poor analytical performance. In this paper, we introduce a novel strategy that combines differential privacy methods and homomorphic encryption techniques to achieve the best of both worlds. Using logistic regression (a popular model in biomedicine), we demonstrated the practicability of building secure and privacy-preserving models with high efficiency (less than 3 min) and good accuracy [<1% of difference in the area under the receiver operating characteristic curve (AUC) against the global model] using a few real-world datasets.
A typical weather pattern for the ozone pollution events in North China

Abstract. Ground-level observations, reanalyzed meteorological fields and a 3-D global chemical and transport model (GEOS-Chem) were applied in this study to investigate ozone (O3) pollution events (OPEs) in North China (36.5° N–40.5° N, 114.5° E–119.5° E) during 2014–2017. Ozone pollution days (OPDs) were defined as days with maximum daily averaged 8-h (MDA8) concentrations over North China larger than 160 μg m−3, and OPEs were defined as periods with 3 or more consecutive OPDs. Observations showed that there were 167 OPDs and 27 OPEs in North China during 2014–2017, in which 123 OPDs and 21 OPEs occurred in May–July. We found that OPEs in North China occurred under a typical weather pattern with high daily maximum temperature (Tmax), low relative humidity (RH), anomalous southerlies and divergence in the lower troposphere, an anomalous high-pressure system at 500 hPa and an anomalous downward air flow from 500 hPa to the surface. Under such a weather pattern, chemical production of O3 was high between 800 and 900 hPa, which was then transported downward to enhance O3 pollution at the surface. A standardized index I_OPE was defined by applying four key meteorological parameters, including Tmax, RH, meridional winds at 850 hPa (V850) and zonal winds at 500 hPa (U500). I_OPE can capture approximately 80 % of the observed OPDs and OPEs, which has implications for forecasting OPEs in North China.