Miracle-dz/UniFAR-FTUs huggingface dataset:
A coupled mechano-biochemical model for cell polarity guided anisotropic root growth

Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.
Application of artificial intelligence to enhance collection of E-waste: A potential solution for household WEEE collection and segregation in India

Our society has undergone a massive technological revolution over the past decade and electronic appliances have now become ubiquitous. The increase in production of electronic products and the growing inherent need to own the latest technology available has led to a significant increase in the amount of E-waste produced each year. India generated 3.2 million tonnes of E-waste in 2020, with metropolitan cities like Mumbai, Delhi and Bangalore leading the list. Proper management and recycling of E-wastes are critical for the sustainability of any modern city today. While industrial and commercial collection of E-wastes has been in the spotlight, solutions for collection of E-wastes from individual households are limited. This article proposes the implementation of a mobile robot that identifies common electronic wastes based on transfer learning and serves as an attachment to existing municipality garbage trucks. The robot moves around, identifies electronic wastes and performs segregation of the identified material via its arm-based lift and storage mechanism. A convolutional neural network–based identification system has been employed for categorising the E-wastes and yields 96% accuracy. This is a first of its kind attempt, especially in India, to collect and segregate E-wastes from homes and individuals. The system will relieve unskilled labour from the hazardous process while providing a 20% decrease in costs over a 5-year period. The application of this article aims to provide a viable mobile solution for E-waste collection from households with minimal human intervention.
2021 Dietary Guidance to Improve Cardiovascular Health: A Scientific Statement From the American Heart Association

Poor diet quality is strongly associated with elevated risk of cardiovascular disease morbidity and mortality. This scientific statement emphasizes the importance of dietary patterns beyond individual foods or nutrients, underscores the critical role of nutrition early in life, presents elements of heart-healthy dietary patterns, and highlights structural challenges that impede adherence to heart-healthy dietary patterns. Evidence-based dietary pattern guidance to promote cardiometabolic health includes the following: (1) adjust energy intake and expenditure to achieve and maintain a healthy body weight; (2) eat plenty and a variety of fruits and vegetables; (3) choose whole grain foods and products; (4) choose healthy sources of protein (mostly plants; regular intake of fish and seafood; low-fat or fat-free dairy products; and if meat or poultry is desired, choose lean cuts and unprocessed forms); (5) use liquid plant oils rather than tropical oils and partially hydrogenated fats; (6) choose minimally processed foods instead of ultra-processed foods; (7) minimize the intake of beverages and foods with added sugars; (8) choose and prepare foods with little or no salt; (9) if you do not drink alcohol, do not start; if you choose to drink alcohol, limit intake; and (10) adhere to this guidance regardless of where food is prepared or consumed. Challenges that impede adherence to heart-healthy dietary patterns include targeted marketing of unhealthy foods, neighborhood segregation, food and nutrition insecurity, and structural racism. Creating an environment that facilitates, rather than impedes, adherence to heart-healthy dietary patterns among all individuals is a public health imperative.
Cryo-EM structures of PI3Kα reveal conformational changes during inhibition and activation

Significance Phosphoinositide 3-kinases (PI3Ks) are of critical importance in cell signaling and can function as drivers of disease. Information on the PI3K structure is essential for an understanding of the function of these proteins and for the identification of specific and effective small-molecule inhibitors. Here we present a single-particle cryo-electron microscopy (cryo-EM) analysis of PI3Kα, the dimer consisting of the p110α catalytic subunit bound to the p85α regulatory subunit. We investigated three conformational states of PI3Kα: the unbound dimer, the dimer bound to the isoform-specific inhibitor BYL-719, and the dimer associated with an activating phosphopeptide. Each of these conformations reveals specific structural features that provide insights into conformation-associated functions. Phosphoinositide 3-kinases (PI3Ks) are lipid kinases essential for growth and metabolism. Their aberrant activation is associated with many types of cancers. Here we used single-particle cryoelectron microscopy (cryo-EM) to determine three distinct conformations of full-length PI3Kα (p110α–p85α): the unliganded heterodimer PI3Kα, PI3Kα bound to the p110α-specific inhibitor BYL-719, and PI3Kα exposed to an activating phosphopeptide. The cryo-EM structures of unbound and of BYL-719–bound PI3Kα are in general accord with published crystal structures. Local deviations are presented and discussed. BYL-719 stabilizes the structure of PI3Kα, but three regions of low-resolution extra density remain and are provisionally assigned to the cSH2, BH, and SH3 domains of p85. One of the extra density regions is in contact with the kinase domain blocking access to the catalytic site. This conformational change indicates that the effects of BYL-719 on PI3Kα activity extend beyond competition with adenosine triphosphate (ATP). In unliganded PI3Kα, the DFG motif occurs in the “in” and “out” positions. In BYL-719–bound PI3Kα, only the DFG-in position, corresponding to the active conformation of the kinase, was observed. The phosphopeptide-bound structure of PI3Kα is composed of a stable core resolved at 3.8 Å. It contains all p110α domains except the adaptor-binding domain (ABD). The p85α domains, linked to the core through the ABD, are no longer resolved, implying that the phosphopeptide activates PI3Kα by fully releasing the niSH2 domain from binding to p110α. The structures presented here show the basal form of the full-length PI3Kα dimer and document conformational changes related to the activated and inhibited states.
Labeled Cycle Graph for Transposition and Indel Distance

In the comparative genomics field, one way to infer the evolutionary distance between two organisms of related species is by finding the minimum number of large-scale mutations, called genome rearrangements, that transform one genome into the other. This number is referred to as the rearrangement distance. Since problems in this area emerged in the mid-1990s, several genome rearrangements have been proposed. Rearrangements that do not alter the genome content are called conservative, and in this group we have the following: the reversal, which inverts a segment of the genome; the transposition, which exchanges two consecutive segments; and the double cut and join, which cuts two different pairs of adjacent blocks and joins them differently. Seminal works compared genomes sharing the same set of conserved blocks, but nowadays, researchers started looking at genomes with unequal gene content, by allowing the use of nonconservative rearrangements such as insertion and deletion (jointly called indel). The transposition distance and the transposition and indel distance are both NP-hard. We investigate the transposition and indel distance and present a structure called labeled cycle graph, representing an instance of rearrangement distance problems for genomes with unequal gene content. This structure is used to devise a lower bound and a 2-approximation algorithm for the transposition and indel distance.
The two‐handed template for planning fibular free flap reconstruction of the head and neck

Fibular free flap reconstruction of head and neck defects is complex, and the anatomic relationships among components of the fibular flap pose challenges to reconstructive surgeons. Various techniques have been employed in planning for fibular free flap procedures, but these are often cumbersome and difficult to implement in clinically. We devised a simplistic tool for pre‐operative leg selection, wherein the surgeon uses two hands to represent the various components of the fibular flap. The senior author has used this method to aid in leg selection for fibular free flaps. In all cases, utilization of this technique allowed for appropriate leg selection relative to the location of the vascular pedicle and posterior crural septum. The two‐handed template for fibular free flap reconstruction is a simple, reproducible, and affordable tool that can aid reconstructive surgeons when they are planning to use a fibular flap.
Abscisic acid is required for exodermal suberization to form a barrier to radial oxygen loss in the adventitious roots of rice (Oryza sativa).

To acclimate to waterlogged conditions, wetland plants form a barrier to radial oxygen loss (ROL) that can enhance oxygen transport to the root apex. We hypothesized that one or more hormones are involved in the induction of the barrier and searched for such hormones in rice. We previously identified 98 genes that were tissue-specifically upregulated during ROL barrier formation in rice. The RiceXPro database showed that most of these genes were highly enhanced by exogenous abscisic acid (ABA). We then examined the effect of ABA on ROL barrier formation by using an ABA biosynthesis inhibitor (fluridone, FLU), by applying exogenous ABA and by examining a mutant with a defective ABA biosynthesis gene (osaba1). FLU suppressed barrier formation in a stagnant solution that mimics waterlogged soil. Under aerobic conditions, rice does not naturally form a barrier, but 24 h of ABA treatment induced barrier formation. osaba1 did not form a barrier under stagnant conditions, but the application of ABA rescued the barrier. In parallel with ROL barrier formation, suberin lamellae formed in the exodermis. These findings strongly suggest that ABA is an inducer of suberin lamellae formation in the exodermis, resulting in an ROL barrier formation in rice.
PEG mediated destabilization of holo α-lactalbumin probed by in silico and in vitro studies: deviation from excluded volume effect

Abstract Crowded and confined macromolecular milieus surround proteins, and both are stabilizing if the nature of the interaction between crowder and proteins are considered hard-core repulsive interactions. However, non-specific chemical interactions between a protein and its surroundings also play a significant role and the sum effect of both hard-core repulsion and soft interaction balances the overall effect of crowding/confinement. Previous studies showing the effect of polyethylene glycol (PEG) on protein and nucleic acid may be interpreted as either primarily excluded volume effect or, in some cases, chemical effect by changing solvent properties. In case of destabilizing interactions, charge-charge and hydrophobic contact have to gain more attention. For instance, in vitro and in vivo studies using protein as crowding agent revealed the destabilization of proteins induced by charge-charge interactions. To investigate the effect of PEG 10 kDa on holo α-lactalbumin (holo α-LA), structure and thermal stability of the protein were measured at different pH values using several techniques. Structural characterization by Trp-fluorescence, near-UV CD and far-UV measurements at different pH values clearly shows perturbation of tertiary and secondary structure of holo α-LA by PEG 10 kDa. Furthermore, the dynamic light scattering measurement shows that the protein is homogeneous under all experimental conditions. Analysis of the heat-induced denaturation profile in the presence of the crowder shows destabilization of the protein in terms of T m (midpoint of denaturation) and ΔG D 0 (Gibbs free energy change at 25 °C). To evaluate the interaction of PEG 10 kDa with holo α-LA and stability of PEG-α-LA complex, docking and molecular dynamic simulation were carried out for 100 ns. Communicated by Ramaswamy H. Sarma
Functional relevance and health benefits of soymilk fermented by lactic acid bacteria

The growing interest of consumers towards nutritionally enriched, and health promoting foods, provoke interest in the eventual development of fermented functional foods. Soymilk is a growing trend that can serve as a low‐cost non‐dairy alternative with improved functional and nutritional properties. Soymilk acts as a good nutrition media for the growth and proliferation of the micro‐organism as well as for their bioactivities. The bioactive compounds produced by fermentation of soymilk with lactic acid bacteria (LAB) exhibit enhanced nutritional values, and several improved health benefits including antihypertensive, antioxidant, antidiabetic, anticancer and hypocholesterolaemic effects. The fermented soymilk is acquiring a significant position in the functional food industry due to its increased techno‐functional qualities as well as ensuring the survivability of probiotic bacteria producing diverse metabolites. This review covers the important benefits conferred by the consumption of soymilk fermented by LAB producing bioactive compounds. It provides a holistic approach to obtain existing knowledge on the biofunctional attributes of fermented soymilk, with a focus on the functionality of soymilk fermented by LAB.
Delayed parenthood and its influence on offspring health: what have we learned from the mouse model

Abstract Delayed parenthood is constantly increasing worldwide due to various socio-economic factors. In the last decade, a growing number of epidemiological studies have suggested a link between advanced parental age and an increased risk of diseases in the offspring. Also, poor reproductive outcome has been described in pregnancies conceived by aged parents. Similarly, animal studies showed that aging negatively affects gametes, early embryonic development, pregnancy progression, and the postnatal phenotype of resulting offspring. However, how and to what extent parental age is a risk factor for the health of future generations is still a subject of debate. Notwithstanding the limitation of an animal model, the mouse model represents a useful tool to understand not only the influence of parental age on offspring phenotype but also the biological mechanisms underlying the poor reproductive outcome and the occurrence of diseases in the descendants. The present review aims at i) providing an overview of the current knowledge from mouse model about the risks associated with conception at advanced age (e.g. neurodevelopmental and metabolic disorders), ii) highlighting the candidate biological mechanisms underlying this phenomenon, and iii) discussing on how murine-derived data can be relevant to humans. Summary sentence This review summarizes the current state of the art on the impact of parental age on reproduction and offspring health in the mouse and discusses on candidate mechanisms behind the increased disease risks for the offspring in the short, medium, and long term.
A Combination of Amino Acid Mutations Leads to Resistance to Multiple Nucleoside Analogs in Reverse Transcriptases from HIV-1 Subtypes B and C

Resistance to anti-HIV drugs has been a problem from the beginning of antiviral drug treatments. The recent expansion of combination antiretroviral therapy worldwide has led to an increase in resistance to antiretrovirals; understanding the mechanisms of resistance is increasingly important. ABSTRACT Resistance to anti-HIV drugs has been a problem from the beginning of antiviral drug treatments. The recent expansion of combination antiretroviral therapy worldwide has led to an increase in resistance to antiretrovirals; understanding the mechanisms of resistance is increasingly important. In this study, we analyzed reverse transcriptase (RT) variants based on sequences derived from an individual who had low-level rebound viremia while undergoing therapy with abacavir, azidothymidine (AZT) (zidovudine), and (−)-l-2′,3′-dideoxy-3′-thiacytidine (3TC) (lamivudine). The RT had mutations at positions 64, 67, 70, 184, and 219 and a threonine insertion after amino acid 69 in RT. The virus remained partially susceptible to the nucleoside RT inhibitor (NRTI) regimen. We show how these mutations affect the ability of NRTIs to inhibit DNA synthesis by RT. The presence of the inserted threonine reduced the susceptibility of the RT mutant to inhibition by tenofovir.
Visualizing Knowledge Evolution Trends and Research Hotspots of Personal Health Data Research: Bibliometric Analysis

Background The recent surge in clinical and nonclinical health-related data has been accompanied by a concomitant increase in personal health data (PHD) research across multiple disciplines such as medicine, computer science, and management. There is now a need to synthesize the dynamic knowledge of PHD in various disciplines to spot potential research hotspots. Objective The aim of this study was to reveal the knowledge evolutionary trends in PHD and detect potential research hotspots using bibliometric analysis. Methods We collected 8281 articles published between 2009 and 2018 from the Web of Science database. The knowledge evolution analysis (KEA) framework was used to analyze the evolution of PHD research. The KEA framework is a bibliometric approach that is based on 3 knowledge networks: reference co-citation, keyword co-occurrence, and discipline co-occurrence. Results The findings show that the focus of PHD research has evolved from medicine centric to technology centric to human centric since 2009. The most active PHD knowledge cluster is developing knowledge resources and allocating scarce resources. The field of computer science, especially the topic of artificial intelligence (AI), has been the focal point of recent empirical studies on PHD. Topics related to psychology and human factors (eg, attitude, satisfaction, education) are also receiving more attention. Conclusions Our analysis shows that PHD research has the potential to provide value-based health care in the future. All stakeholders should be educated about AI technology to promote value generation through PHD. Moreover, technology developers and health care institutions should consider human factors to facilitate the effective adoption of PHD-related technology. These findings indicate opportunities for interdisciplinary cooperation in several PHD research areas: (1) AI applications for PHD; (2) regulatory issues and governance of PHD; (3) education of all stakeholders about AI technology; and (4) value-based health care including “allocative value,” “technology value,” and “personalized value. ”
Fruits of Ruta chalepensis L. (Rutaceae) as a Source of 2-undecanone

Abstract The chemical composition of the essential oils of spontaneous aromatic plants is severely affected by edapho-climatic factors as well as the development stage of the plant. Therefore, the objective of the present work is to better understand the essential oil quality of Ruta chalepensis L. (Rutaceae), a medicinal plant widely used in folk medicine, collected at the fruiting stage from two populations of south-east of Tunisia. Each organ of Ruta chalepensis (leaves, stems, and fruits) was hydrodistillated by a Clevenger-type apparatus. Gas chromatography-flame ionization detector (GC-FID) and GC-mass spectrometry (GC-MS) analyses of the essential oils resulted in the identification of nineteen compounds, where esters and ketones represented the main chemical classes. The major compounds in the essential oils of leaves and stems were 2-undecanone (23.0-37.7%), 2-nonanone (16.7-23.0%) and octyl acetate (11.0-26.8%), whereas 2-undecanone (57.5-58.4%) and 2-nonanone (19.0-23.3%) were found to be the most abundant compounds in the fruits essential oil.
Interobserver variability in target volume delineation for CT/MRI simulation and MRI-guided adaptive radiotherapy in rectal cancer

Objectives: Quantify target volume delineation uncertainty for CT/MRI simulation and MRI-guided adaptive radiotherapy in rectal cancer. Define optimal imaging sequences for target delineation. Methods: Six experienced radiation oncologists delineated clinical target volumes (CTVs) on CT and 2D and 3D-MRI in three patients with rectal cancer, using consensus contouring guidelines. Tumour GTV (GTVp) was also contoured on MRI acquired week 0 and 3 of radiotherapy. A STAPLE contour was created and volume and interobserver variability metrics were analysed. Results: There were statistically significant differences in volume between observers for CT and 2D-MRI-defined CTVs (p < 0.05). There was no significant difference between observers on 3D-MRI. Significant differences in volume were seen between observers for both 2D and 3D-MRI-defined GTVp at weeks 0 and 3 (p < 0.05). Good interobserver agreement (IOA) was seen for CTVs delineated on all imaging modalities with best IOA on 3D-MRI; median Conformity index (CI) 0.74 for CT, 0.75 for 2D-MRI and 0.77 for 3D-MRI. IOA of MRI-defined GTVp week 0 was better compared to CT; CI 0.58 for CT, 0.62 for 2D-MRI and 0.7 for 3D-MRI. MRI-defined GTVp IOA week three was worse compared to week 0. Conclusion: Delineation on MRI results in smaller volumes and better IOA week 0 compared to CT. 3D-MRI provides the best IOA in CTV and GTVp. MRI-defined GTVp on images acquired week 3 showed worse IOA compared to week 0. This highlights the need for consensus guidelines in GTVp delineation on MRI during treatment course in the context of dose escalation MRI-guided rectal boost studies. Advances in knowledge: Optimal MRI sequences for CT/MRI simulation and MRI-guided adaptive radiotherapy in rectal cancer have been defined.