Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes

Abstract Microbial species play important roles in different environments and the production of high-quality genomes from metagenome data sets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and simplifies metagenome assembly, binning, bin improvement, bin quality (completeness and contamination), bin annotation, and evolutionary placement of bins via detailed maximum-likelihood phylogeny based on multiple marker genes using different amino acid substitution models, next to average nucleotide identity analysis of genomes for delineation of species boundaries and operational taxonomic units. MAGO offers streamlined execution of the entire metagenomics pipeline, error checking, computational resource distribution and compatibility of data formats, governed by user-tailored pipeline processing. MAGO is an open-source-software package released in three different ways, as a singularity image and a Docker container for HPC purposes as well as for running MAGO on a commodity hardware, and a virtual machine for gaining a full access to MAGO underlying structure and source code. MAGO is open to suggestions for extensions and is amenable for use in both research and teaching of genomics and molecular evolution of genomes assembled from small single-cell projects or large-scale and complex environmental metagenomes.
Fast correction of B0 field inhomogeneity for pH‐specific magnetization transfer and relaxation normalized amide proton transfer imaging of acute ischemic stroke without Z‐spectrum

The magnetization transfer and relaxation normalized amide proton transfer (MRAPT) analysis is promising to provide a highly pH‐specific mapping of tissue acidosis, complementing commonly used CEST asymmetry analysis. We aimed to develop a fast B0 inhomogeneity correction algorithm for acute stroke magnetization transfer and relaxation normalized amide proton transfer imaging without Z‐spectral interpolation.
Minor Physical Anomalies and Hyperactivity

The paper by Quinn and Rapoport1 in the May issue of Pediatrics indicates a higher incidence of minor physical anomalies ("stigmata") in hyperactive boys compared to a control group. The authors believe that the presence of stigmata are a clue to the occurrence of insults affecting the fetus during early development. It is suggested that the hyperactive behavior disorder is also a result of the same insult affecting the central nervous system during early morphogenesis.
Does early life programming influence arterial stiffness and central hemodynamics in adulthood?

OBJECTIVES We aimed to investigate possible associations between birth weight and adult life carotid-femoral pulse wave velocity (cfPWV) and augmentation pressure index (AIx). DESIGN AND METHOD This study included 1598 participants, that is, 340 elderly individuals from the Malmö Birth Data Cohort (MBDC) and 1258 young-middle aged individuals from the Malmö Offspring Study (MOS) with full data on birth weight and gestational age. Participants underwent cfPWV and AIx measurements with Sphygmocor (AtCor, Australia). Analysis of data was performed with multiple linear regression models including adjustments for age, sex, gestational age and risk factors. Furthermore, comparisons were made between participants born prematurely or at term or born small-for-gestational age (SGA) or appropriate-for-gestational age (AGA). RESULTS Birth weight was positively associated with cfPWV after full adjustment (β = 0.057; P < 0.001), a finding that remained significant in the younger age group 18-27 years (β = 0.138, P = 0.008). Furthermore, birth weight was inversely associated with AIx (β = -0.058, P = 0.001). Participants born SGA had significantly higher AIx (P = 0.007) and MAP (P = 0.037) compared with AGA born. Preterm-born participants showed significantly higher SBP compared with term-born (P = 0.034). Finally, birth weight was inversely associated with MAP (β = -0.058, P = 0.017) and SBP (β = -0.047, P = 0.031), respectively. CONCLUSION Birth weight is positively associated with cfPWV, shown strongest in the youngest individuals, a finding that could possibly be explained by increasing trends for maternal overweight/obesity in recent decades. Furthermore, birth weight is inversely associated with AIx, a risk marker of cardiovascular disease. This calls for screening of risk factors in subjects with adverse conditions at birth.
Plant organellar RNA editing: what 30 years of research has revealed.

The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-to-U base transitions) is highly prevalent within organelles (i.e., mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.
DNS-aided explicitly filtered LES of channel flow.

The equations for LES are formally derived by low-pass filtering the NS equations with the effect of the small scales on the larger ones captured by a SGS model. However, it is known that the LES equations usually employed in practical applications are inconsistent with the filter operator when no explicit filter is used. Moreover, even for explicitly filtered LES, some inconsistencies remain in the wall-normal direction due to the constraining effect of the wall. A typically undesirable effect stemming from the inconsistency between LES and the filtered NS (fNS) equations is that DNS data can not be used to aid SGS modeling. Using the proposed form of the incompressible fNS equations for flows over flat walls in which the continuity equation, the filter operator, and the boundary condition at the wall are consistently formulated, we compute a set of plane turbulent channel flow explicitly filtered LES at different grid resolutions with the SGS term computed from a parallel DNS computation starting with an equivalent initial condition. The results show that the SGS term computed from DNS provide a truthful SGS model for short times until the numerical errors compound and the two parallel computations diverge. The effective time where the statistics remain similar is longer for lower-order statistics such as mean velocity profile, as expected. This demonstrates that with the consistent fNS equations, the abundant DNS data can be used to inform SGS model development for explicitly filtered LES. Moreover, the diverging of statitics at longer times shows that the SGS contribution is not necessarily homogeous as most SGS models assume, and a more precise correlation between the instantaneous LES velocity field and SGS model is required to capture the dynamics of turbulence.
WHO Multi-country Study on Women's Health and Domestic Violence against Women: Initial Results on Prevalence, Health Outcomes and Women's Responses

This report of the WHO Multi-country Study on Womens Health and Domestic Violence against Women analyses data collected from over 24 000 women in 10 countries representing diverse cultural geographical and urban/rural settings: Bangladesh Brazil Ethiopia Japan Peru Namibia Samoa Serbia and Montenegro Thailand and the United Republic of Tanzania. The Study was designed to: estimate the prevalence of physical sexual and emotional violence against women with particular emphasis on violence by intimate partners; assess the association of partner violence with a range of health outcomes; identify factors that may either protect or put women at risk of partner violence; document the strategies and services that women use to cope with violence by an intimate partner. (excerpt)
Contribution of single‐gene defects to congenital cardiac left‐sided lesions in the prenatal setting

To explore the contribution of single‐gene defects to the genetic cause of cardiac left‐sided lesions (LSLs), and to evaluate the incremental diagnostic yield of whole‐exome sequencing (WES) for single‐gene defects in fetuses with LSLs without aneuploidy or a pathogenic copy‐number variant (pCNV).
Feasibility of a community‐based cervical cancer screening with “test and treat” strategy using self‐sample for an HPV test: Experience from rural Cameroon, Africa

To achieve higher coverage and effectiveness in limited‐resource settings, World Health Organization (WHO) guidelines for cervical cancer prevention recommend a screen‐and‐treat strategy with high‐risk human papillomavirus (HPV) testing. We piloted a real‐word project to examine the feasibility of this approach in rural Cameroon. Nurses from the Women's Health Program (WHP) of the Cameroon Baptist Convention Health Services (CBCHS) educated women in remote villages on cervical cancer prevention. At a follow‐up visit, they explained to nonpregnant women aged 30–65 how to self‐collect vaginal specimens for HPV testing with the careHPV assay. The cytobrush specimens were transported in coolers to a CBCHS laboratory for analysis. The nurses returned to villages to inform women of their results, examined HPV‐positive women in the primary health centers (PHCs) using visual inspection with acetic acid and Lugol's iodine (VIA/VILI) enhanced by digital cervicography (DC) to guide treatment. Of the 1,270 eligible women screened (mean age: 44.7 years), 196 (15.4%) were HPV‐positive, of whom 185 (94.4%) were examined, 16 (8.6%) were VIA/VILI‐positive, 8 (4.3%) were VIA/VILI‐inadequate, one (0.5%) was VIA/VILI‐uncertain and 161 (87.0%) were treated with thermal ablation. One woman had LEEP, and another woman with invasive cancer was treated at a referral facility. The cytobrushes broke off in the vaginas of two women (removed in the village) and in the bladder of another (surgically removed). Community‐based cervical cancer screening with self‐collected specimens for HPV testing is feasible in rural Cameroon. Education on the proper sampling procedure and follow‐up of women who are HPV‐positive are essential.
[Mycobacterium Tuberculosis Rv3084 Encodes Functional Esterase and Suppresses the Pro-inflammatory Cytokines in vivo].

Objective To explore the biological characteristics of the esterase LipR encoded by Mycobacterium tuberculosis (MTB) Rv3084 and its immunomodulatory function in vivo. Methods The LipR gene was amplified from MTB H37Rv strain to construct recombinant expression plasmid. After sequencing, the recombinant plasmid was transformed into E. coli for expression and purification of LipR protein. The expressed protein was confirmed with Western blot assay. The hydrolyzing activity of LipR was detected and the factors affecting LipR enzyme activity were analyzed. Mice were intramuscularly injected with 0.1 mL (containing plasmid DNA 100 μg) recombinant eukaryotic plasmid three times (day 1, 8, and 15); seven days after the last injection, the mice were executed, and the lung and spleen were taken for cytokine detection. Results The recombinant expression plasmid was successfully constructed and it was found that LipR protein was mainly expressed in the form of inclusion bodies in E. coli with the relative molecular mass of about 33×10 3. LipR was demonstrated as an alkaline eurythermic esterase, due to the preference of hydrolyzing short carbon chain esters with optimal hydrolyzing activity on pNP-acetate (pNPA, C2) and the capability in tolerance of high pH and temperature; in the presence of different detergents or metal ions, the activity of LipR hydrolyzing pNP-butyrate (pNPB, C4) was inhibited to some extent. In the mouse model, it was found that LipR could inhibit the secretion of interferon-γ (IFN- γ) and interleukin-2 (IL-2), but to stimulate the secretion of IL-10. Conclusion The esterase LipR may be one of the esterases help M. tuberculosis withstand harsh environment inside the host in collaboration, and simultaneously act as an immune modulator to inhibit the secretion of pro-inflammatory cytokines and consequently impact the killing effect of host immune system against M. tuberculosis.
A LoRa Wireless Mesh Network for Wide-Area Animal Tracking

The continuous evolution in technology and innovation empowers mankind to strive for more and move ahead towards living an easier and more convenient life with better safety measures and assisting systems. However, parallel to the aforementioned patterns are some contrastingly petrifying and frightening patterns. Mankind’s greed for resources and inefficiency in using the same has led to the destruction of various lifeforms and their natural habitats. Animal tracking is key to conservation and protection of the beings itself as well as their habitats. It is mankind’s responsibility to right what he has wronged. LoRa, a wireless technology, is of communicating over long distances while sipping efficiently on power. However, the vastness of the savannas and the deserts and the densities of the forests are out of bounds for existing conventional wireless communication technologies. Tracking via satellite would turn out to be expensive and infeasible in many scenarios. Tracking over the cellular network in such expansive remote regions would be quixotic and impractical. This work proposes a novel design of a mesh network formed by LoRa based animal collars or tags, for tracking location and monitoring other factors via sensors over very wide areas. Furthermore, the work proposes different models to choose from, based on the expanse of the area desired to be covered and it’s geographical conditions.
Preliminary performance assessment of Radar-aided monocular Visual Odometry for small aerial platforms

Monocular Visual Odometry (VO) is widely used for small aerial platforms navigation. However, environment conditions can limit the use of cameras. Radar Odometry (RO) can be envisaged when illumination conditions hinder visual navigation. Indeed, radar can help estimation of platform speed and interframe platform displacement, thus solving also the inherent monocular VO scale estimation problem. Performance of radar-aided monocular VO navigation solution, to be used then within the framework of all-illumination multi-sensor navigation, is assessed with test in real operational scenario. Results show acceptable standalone performance, that can be further improved with more complex architectures.
Road Intersection Intelligent Traffic Management Based on V2V Wireless Communication

An autonomous vehicles use various kinds of sensors to communication to other vehicles with the aim to manage traffic in road intersection. Autonomous vehicles are installed with sensors and modern technologies for self-management communication. Autonomous vehicles are used communication to manage the traffic in highways and urban roads. To reduce the communication delay, we have proposed V2V communication based MIMO technology
Intent-Aware Conditional Generative Adversarial Network for Pedestrian Path Prediction

Learning to understand human behaviors and forecast their motions is a prerequisite for an automated car to navigate in urban traffic safely and efficiently. When pedestrians interact with a vehicle, they follow specific motion patterns based on their intentions. This work presents a conditional generative adversarial network based architecture that explicitly model human intention as a conditional variable to robustly learn the multi-modal nature of pedestrian motion for accurate future trajectory prediction. The generator in our framework uses a LSTM encoder-decoder conditioned on human intention for motion prediction while the discriminator consisting of a LSTM classifier learns to distinguish whether a predicted trajectory is consistent with a given intention. Through experiments on two real-world datasets, it demonstrates that our proposed architecture outperforms state-of-the-art methods in terms of the average displacement error of predicted positions. Additionally, qualitative analysis shows that our model is capable of predicting a multi-modal distribution with respect to human intentions.
EMBLICA OFFICINALIS: A MERITOCRATIC DRUG FOR TREATING VARIOUS DISORDERS

Article history anti-diabetic, anti-oxidant, anti-cancer, anti-hyperlipidemic anti-inflammatory. Phytogenic agents have traditionally been used by herbalists and indigenous healers for the prevention and treatment of various diseases. Emblica officinalis (Amla) is a deciduous tree belonging to family Euphorbiacea. Growing body of evidences have shown that amla possess anti diabetic activity and have been used to treat diabetes-induced complications. Amla is a potent antioxidant. Wide array of studies such as hepatoprotective, anticancer, anti inflammatory, analgesic, anti hyperlipidemic etc are associated with this plant. The present review demonstrates the pleiotropic actions of amla in various disorders. Moreover, the underlying mechanisms of amla-induced protection in various diseases have been delineated.
Peptide self-assembling and Lys/His exchange features in BDS

We studied broadband dielectric spectra (10-2-1014 Hz) in a wide range of temperatures (10-300 K) and at thoroughly controlled levels of ambient humidity of two peptides built of natural amino acids: n-HFEFHFEF-c and n-FKFEFKFE-c. Preliminary results demonstrate remarkable differences between properties of these two peptide systems with respect to water sorption and consequent spectral peculiarities.
Fruit Localization and Environment Perception for Strawberry Harvesting Robots

This work presents a machine vision system for the localization of strawberries and environment perception in a strawberry-harvesting robot for use in table-top strawberry production. A deep convolutional neural network for segmentation is utilized to detect the strawberries. Segmented strawberries are localized through coordinate transformation, density base point clustering and the proposed location approximation method. To avoid collisions between the gripper and fixed obstacles, the safe manipulation region is limited to the space in front of the table and underneath the strap. Therefore, a safe region classification algorithm, based on Hough Transform algorithm, is proposed to segment the strap masks into a belt region in order to identify the pickable strawberries located underneath the strap. Similarly, a safe region classification algorithm is proposed for the table, to calculate its points in 3D and fit the points onto a 3D plane based on the 3D point cloud, so that pickable strawberries in front of the table can be identified. Experimental tests showed that the algorithm could accurately classify ripe and unripe strawberries and could identify whether the strawberries are within the safe region for harvesting. Furthermore, harvester robot’s optimized localization method could accurately locate the strawberry targets with a picking accuracy rate of 74.1% in modified situations.
Generation of Biological Electromagnetic Field by Microtubules

General mechanism of organization, information and controlling in biological systems is based on internal electromagnetic field. Electromagnetic field is generated by microtubules composed of identical tubulin heterodimers containing electric dipoles. Classical dipole theory of generation of the electromagnetic field enables analysis of the space-time coherence. Structure of microtubules with the spiral and axial periodicity enables interaction of the field in time shifted by one or more periods of oscillation and generation of coherent signals. Due to ordered water layers at charged surfaces their low effective temperature provides low energy losses. Supplied energy is coherently stored in oscillators with a high electrical quality, microtubule inner cavity, and in excited electrons at molecular orbitals and in "semiconduction" and "conduction" bands.
Musculoskeletal Modeling of Elbow Joint under Functional Electrical Stimulation

Recent advances in Functional Electrical Stimulation technologies allow for progressive, selective and reproducible muscle control. It becomes possible to control and simulate its behavior in order to optimize the generation and control of restricted movement for the flexion-extension study of the paraplegic limb elbow. In order to achieve this, the first step is to develop muscle models and geometric and dynamic models of all activated members. In the particular context of our application, this paper aims to define the modeling of musculoskeletal.
A Fast Global Method Combined with Local Features for 6D Object Pose Estimation

With the advancement of intelligent manufacturing, robots are increasingly involved in industrial production, for example, replacing human beings to identify and manipulate objects. However, it is still a challenging task for object recognition and pose estimation in industrial environment, especially under large environmental noise, mutual occlusions and high-speed requirements. In this paper, we propose a new method for 6D object pose estimation, Super Key 4-Points Congruent Sets (SK-4PCS), which is a fast global method combined with local features. The proposed method includes three steps. Firstly, the key points in 3D point clouds are extracted by local features, which are invariant with respect to rotation and translation. Secondly, the smart indexing scheme is used to realize the query of 4-points congruent sets globally. Finally, the coarse pose obtained quickly is further refined by the Iteration Closest Point algorithm (ICP) [1]. The proposed method is also compared with existing methods by the evaluation indicator Visible Surface Discrepancy (VSD) on the LINEMOD dataset [2]. The experimental results show that the refined SK-4PCS results in significant speedup and satisfactory accuracy in 6D object pose estimation.