Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthesis of α-brominated phosphonates and their application as phosphate bioisosteres

Substrate phosphorylation is a key modulator of signal transduction. Abnormal phosphorylation in vivo is implicated in many diseases including cancer, diabetes, and Alzheimer's disease. Inhibitors of phosphate-recognizing proteins have potential as medicinal agents as well as tools to study phosphorylation pathways. A well-known and common inhibition strategy is to synthetically replace the labile phosphate moiety with a non-hydrolyzable phosphonate. Fully saturated, α-fluoro and α,α-difluorophosphonates are often effective phosphate bioisosteres and have been well studied. More recently α-brominated phosphonates have begun to emerge as inhibitors of phosphate recognizing enzymes, some of which operate by irreversible mechanisms. Herein we discuss the synthetic approaches to aliphatic and benzylic α-bromophosphonates and their biological activities.
Pre‐dispersal acorn predation in mixed oak forests: interspecific differences are driven by the interplay among seed phenology, seed size and predator size

1. Pre‐dispersal seed predation (PSP) often occurs in multi‐host–predator systems (e.g. several plant species exposed to a common array of granivorous insects). However, whether the interaction among seed phenology, seed size and predator size accounts for interspecific differences in PSP remains elusive.
Designed peptides as potential fusion inhibitors against SARA-CoV-2 coronavirus infection

Inspired by fusion-inhibitory peptides from heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains from human immuno-deficiency virus type 1 (HIV-1) envelope glycoprotein gp41 and severe acute respiratory syndrome-coronavirus (SARS-CoV) based on viral fusogenic mechanism in the present work, we provided a similar approach to design the synthesized peptides against the entry into host cells of SARA-CoV-2 virus that causes 2019 novel coronavirus disease (COVID-19). These peptides derived from HR1 and HR2 of SARA-CoV-2 spike protein were further tested for their interaction and potential fusion possibility through circular dichroism spectrum. Here we used the peptide COVID-2019-HR1P1 (40 amino acids) as the target, which was derived from HR1 of SARA-CoV-2 spike protein, while the designed peptides including COVID-2019-HR2P1 (37 amino acids), COVID-2019-HR2P2 (32 amino acids) and others derived from HR2 of SARA-CoV-2 were tested for their binding to COVID-2019-HR1P1. Interestingly, results showed that both COVID-2019-HR2P1 and COVID-2019-HR2P2 can form the complex with COVID-2019-HR1P1, respectively. This implied that these designed peptides could play an important role in blocking SARA-CoV-2 entry into mammalian host cells via viral fusogenic mechanism, and thus could be used for preventing SARA-CoV-2 infection.
Forecasting virus diffusion with simple Bayesian forecast combination

There are various diffusion models for S shaped processes like virus diffusion and these models are typically not nested. In this note it is proposed to combine the forecasts using a simple Bayesian forecast combination algorithm. An illustration to daily data on cumulative Covid-19 cases in the Netherlands shows the ease of use of the algorithm and the accuracy of the thus combined forecasts.
SCeVE

Authoring a collaborative, interactive Mixed Reality (MR) tour requires flexible design and development of various software modules for tasks such as managing geographically distributed participants, adaptable travel and virtual camera techniques, data logging for assessment of the incorporated techniques, as well as for evaluating the Quality of Experiences (QoE). In most cases, authors might have to develop all these software modules, instead of focusing only on the virtual environment design. In this article, we propose SCeVE, a component-based framework that supports flexible design and authoring of interactive MR tours by offering ease of access to four major design choices: (i) Synchronization, (ii) Collaborative exploration, (iii) Visualization, and (iv) Evaluation. Based on tour requirements, an author can access one or more components (or software libraries) of design choices via SCeVE’s API (Application Programming Interface) services, as demonstrated by the two case studies on group travel in a plant walk MR tour. SCeVE framework is innovative in the sense that it facilitates group travel in virtual environments involving “live” models of participants from geographically distributed sites. SCeVE empowers authors to focus only on the design of the required virtual environments. They can quickly build a diverse set of collaborative MR tours by utilizing the flexibility of SCeVE in terms of the various available options for traveling, rendering on multiple devices, and virtual camera viewpoint computation strategies. By providing data logs of various components, SCeVE facilitates performance evaluation of the various strategies used as well as the user experience in collaborative MR tours. SCeVE is designed in an extensible manner, allowing authors to add devices and software services as additional components.
Articulating the “So, What?” in Clinical Research: Insight from the M-CHOIR Group

Summary: With the academic culture of “publish or perish,” authors must ensure that they are delivering high-quality data with a meaningful impact on clinical practice. Even for physician–scientists at the top of their fields, establishing the relevance of a study to clinical practice is a challenge. Thus, it is essential that research proposals ask questions that are clinically important, use appropriate methodologies, and examine outcomes that are relevant to both the physicians and the patients. The question of “so, what? ” or in other words, “who cares? ” is one that can make or break a study’s impact on clinical practice. Researchers should use models such as PICOS (Population, Intervention, Comparison, Outcomes, and Study design) and FINER (Feasible, Interesting, Novel, Ethical, Relevant) and ask why readers will care about their study’s findings before the study is conducted. By doing so, researchers can ensure the successful execution of their study and a meaningful impact of their findings, in both academia and clinical practice. This Special Topic article aims to guide researchers in producing relevant, impactful conclusions of their studies by providing input and resources from the Michigan Center for Hand Outcomes and Innovation (M-CHOIR) group.
Aerosol Inhalation in the Rat Lung Part I: Analysis of the Rat Acinus Morphometry and Construction of a Stochastic Rat Lung Model

ABSTRACT Morphometric data of four ventilatory units of the lung of a male Sprague-Dawley rat were statistically analyzed. Because of the rather monopodial structure of the rat lung, airways were classified by their diameters rather than by their generation numbers, as is general practice. The statistical analyses provided information on the distributions of a variety of geometric parameters of a rat acinus and the correlations among them. Together with the previously analyzed tracheobronchial morphometric data they form the basis of a stochastic morphometric model of the whole rat lung. This morphometric model can then be used for Monte Carlo simulations of the transport and deposition of inhaled aerosol particles in the rat lung.
Pitfalls and Promise of 3-dimensional Image Comparison for Craniofacial Surgical Assessment

Summary: Three-dimensional (3D) photography is becoming widely used in plastic surgery. It provides an accurate and reproducible record of the facial surface anatomy and could be a versatile tool for treatment planning and assessment. However, the existing software tools available for the assessment of 3D facial imaging often give highly misleading results. The goal of this special topic article is to give clinicians an insight into methods of 3D image assessment and explain the reasons why results may be misleading. We point toward the advantages of an alternative approach using “nonrigid surface registration” for the comparison of pre- and postsurgical images. This approach is compared with the regular rigid surface registration, and this is illustrated by the assessment of a child with Crouzon syndrome before and after LeFort III osteotomy and distraction. Findings of the standard method imply that changes have occurred that are anatomically not possible, whereas the alternative approach indicates realistic changes. Furthermore, we demonstrate an exciting capacity of 3D image analysis to construct reference populations of normal head size and shape. These can be used to assess the parts of the head that are normal and abnormal pre- and posttreatment of the same child. We conclude that, while 3D image analysis has great potential in surgical assessment, existing software does not always give an adequate assessment. Collaboration among surgeons and engineering and computer science specialists should be encouraged. This way, more comprehensive and accurate techniques in patient assessment and surgical planning can be developed and applied in clinical practice.
Impact of Intermediate Hyperglycemia and Diabetes on Immune Dysfunction in Tuberculosis

Abstract Background People with diabetes have an increased risk of developing active tuberculosis (TB) and are more likely to have poor TB-treatment outcomes, which may impact on control of TB as the prevalence of diabetes is increasing worldwide. Blood transcriptomes are altered in patients with active TB relative to healthy individuals. The effects of diabetes and intermediate hyperglycemia (IH) on this transcriptomic signature were investigated to enhance understanding of immunological susceptibility in diabetes-TB comorbidity. Methods Whole blood samples were collected from active TB patients with diabetes (glycated hemoglobin [HbA1c] ≥6.5%) or IH (HbA1c = 5.7% to <6.5%), TB-only patients, and healthy controls in 4 countries: South Africa, Romania, Indonesia, and Peru. Differential blood gene expression was determined by RNA-seq (n = 249). Results Diabetes increased the magnitude of gene expression change in the host transcriptome in TB, notably showing an increase in genes associated with innate inflammatory and decrease in adaptive immune responses. Strikingly, patients with IH and TB exhibited blood transcriptomes much more similar to patients with diabetes-TB than to patients with only TB. Both diabetes-TB and IH-TB patients had a decreased type I interferon response relative to TB-only patients. Conclusions Comorbidity in individuals with both TB and diabetes is associated with altered transcriptomes, with an expected enhanced inflammation in the presence of both conditions, but also reduced type I interferon responses in comorbid patients, suggesting an unexpected uncoupling of the TB transcriptome phenotype. These immunological dysfunctions are also present in individuals with IH, showing that altered immunity to TB may also be present in this group. The TB disease outcomes in individuals with IH diagnosed with TB should be investigated further.
Differentiation of Mitochondrial DNA in Largemouth Bass

Abstract Mitochondrial DNA (mtDNA) variation was examined for two nominal subspecies of largemouth bass, Micropterus salmoides salmoides (northern largemouth bass) and M. s. floridanus (Florida largemouth bass). Mitochondrial DNA nucleon diversity values within samples ranged from 0.378 to 0.911; the value over all individuals surveyed was 0.917. Estimated percentage nucleotide sequence divergence among the 19 haplotypes ranged from 0.081 to 5.80 (mean ± SE, 2.72 ± 0.459). The average percentage nucleotide sequence divergence within populations ranged from 0.137 to 0.526 (mean ± SE, 0.312 ± 0.067). The average percentage nucleotide sequence divergence among pairwise comparisons of populations ranged from 0.174 to 5.11 (mean ± SE, 2.91 ± 0.523). Parsimony and phenetic analysis of populations yielded strong differentiation between the two subspecies and provided enough resolution to discriminate among populations within the same subspecies. These data suggest that restriction fragment length polymorphism (R.
Cytokine storm and leukocyte changes in mild versus severe SARS-CoV-2 infection: Review of 3939 COVID-19 patients in China and emerging pathogenesis and therapy concepts

Clinical evidence indicates that the fatal outcome observed with severe acute respiratory syndrome‐coronavirus‐2 infection often results from alveolar injury that impedes airway capacity and multi‐organ failure—both of which are associated with the hyperproduction of cytokines, also known as a cytokine storm or cytokine release syndrome. Clinical reports show that both mild and severe forms of disease result in changes in circulating leukocyte subsets and cytokine secretion, particularly IL‐6, IL‐1β, IL‐10, TNF, GM‐CSF, IP‐10 (IFN‐induced protein 10), IL‐17, MCP‐3, and IL‐1ra. Not surprising, therapies that target the immune response and curtail the cytokine storm in coronavirus 2019 (COVID‐19) patients have become a focus of recent clinical trials. Here we review reports on leukocyte and cytokine data associated with COVID‐19 disease in 3939 patients in China and describe emerging data on immunopathology. With an emphasis on immune modulation, we also look at ongoing clinical studies aimed at blocking proinflammatory cytokines; transfer of immunosuppressive mesenchymal stem cells; use of convalescent plasma transfusion; as well as immunoregulatory therapy and traditional Chinese medicine regimes. In examining leukocyte and cytokine activity in COVID‐19, we focus in particular on how these levels are altered as the disease progresses (neutrophil NETosis, macrophage, T cell response, etc.) and proposed consequences to organ pathology (coagulopathy, etc.). Viral and host interactions are described to gain further insight into leukocyte biology and how dysregulated cytokine responses lead to disease and/or organ damage. By better understanding the mechanisms that drive the intensity of a cytokine storm, we can tailor treatment strategies at specific disease stages and improve our response to this worldwide public health threat.
Graph-convolutional-network-based interactive prostate segmentation in MR images.

PURPOSE Accurate and robust segmentation of the prostate from magnetic resonance (MR) images is extensively applied in many clinical applications in prostate cancer diagnosis and treatment. The purpose of this study is the development of a robust interactive segmentation method for accurate segmentation of the prostate from MR images. METHODS We propose an interactive segmentation method based on a graph convolutional network (GCN) to refine the automatically segmented results. An atrous multiscale convolutional neural network (CNN) encoder is proposed to learn representative features to obtain accurate segmentations. Based on the multiscale feature, a GCN block is presented to predict the prostate contour in both automatic and interactive manners. To preserve the prostate boundary details and effectively train the GCN, a contour matching loss is proposed. The performance of the proposed algorithm was evaluated on 41 in-house MR subjects and 30 PROMISE12 test subjects. RESULTS The proposed method yields mean Dice similarity coefficients of 93.8±1.2% and 94.4±1.0% on our in-house and PROMISE12 datasets, respectively. The experimental results show that the proposed method outperforms several state-of-the-art segmentation methods. CONCLUSION The proposed interactive segmentation method based on the GCN can accurately segment the prostate from MR images. Our method has a variety of applications in prostate cancer imaging.
Eradications and People: Lessons from the Plant Eradication Program in Galapagos

It is often argued that the benefit of eradication of an invasive species—a one‐off injection of funds and the problem is solved—far outweighs the cost of a perennial control program. Furthermore, these are very attractive projects for funding agencies as outcomes are clear and easy to assess. Galapagos is in the early stage of the invasion process, with most alien species not yet naturalized and still restricted to gardens and farms. These species should be easy targets for early and cost‐effective eradication projects, which would prevent many future problems. We review 30 plant eradication projects covering 23 potentially invasive species with limited distributions on four of the Galapagos Islands. Of the 30 projects, only four were successful: these were all less than 1 ha in net area, on land with a single owner and did not have persistent seed banks. Of the other 26 projects, most failed due to a lack of support from institutions that did not offer continuity of resources, from land owners who denied permission to carry out the work or from being too ambitious. As a result of these problems, 64.3% of the funding secured for the program was spent on discontinued projects. We highlight lessons learned to inform plant eradication programs in the future.
Resource: A multi‐species multi‐timepoint transcriptome database and webpage for the pineal gland and retina

The website and database https://snengs.nichd. nih.gov provides RNA sequencing data from multi‐species analysis of the pineal glands from zebrafish (Danio rerio), chicken (White Leghorn), rat (Rattus novegicus), mouse (Mus musculus), rhesus macaque (Macaca mulatta), and human (Homo sapiens); in most cases, retinal data are also included along with results of the analysis of a mixture of RNA from tissues. Studies cover day and night conditions; in addition, a time series over multiple hours, a developmental time series and pharmacological experiments on rats are included. The data have been uniformly re‐processed using the latest methods and assemblies to allow for comparisons between experiments and to reduce processing differences. The website presents search functionality, graphical representations, Excel tables, and track hubs of all data for detailed visualization in the UCSC Genome Browser. As more data are collected from investigators and improved genomes become available in the future, the website will be updated. This database is in the public domain and elements can be reproduced by citing the URL and this report. This effort makes the results of 21st century transcriptome profiling widely available in a user‐friendly format that is expected to broadly influence pineal research.
Fortified Foods Are Major Contributors to Apparent Intakes of Vitamin A and Iodine, but Not Iron, in Diets of Women of Reproductive Age in 4 African Countries

ABSTRACT Background Food fortification is implemented to increase intakes of specific nutrients in the diet, but contributions of fortified foods to nutrient intakes are rarely quantified. Objectives We quantified iron, vitamin A, and iodine intakes from fortified staple foods and condiments among women of reproductive age (WRA). Methods In subnational (Nigeria, South Africa) and national (Tanzania, Uganda) cross-sectional, clustered household surveys, we assessed fortifiable food consumption. We estimated daily nutrient intakes from fortified foods among WRA by multiplying the daily apparent fortifiable food consumption (by adult male equivalent method) by a fortification content for the food. Two fortification contents were used: measured, based on the median amount quantified from individual food samples collected from households; and potential, based on the targeted amount in national fortification standards. Results for both approaches are reported as percentages of the estimated average requirement (EAR) and recommended nutrient intake (RNI). Results Fortified foods made modest contributions to measured iron intakes (0%–13% RNI); potential intakes if standards are met were generally higher (0%–65% RNI). Fortified foods contributed substantially to measured vitamin A and iodine intakes (20%–125% and 88%–253% EAR, respectively); potential intakes were higher (53%–655% and 115%–377% EAR, respectively) and would exceed the tolerable upper intake level among 18%–56% of WRA for vitamin A in Nigeria and 1%–8% of WRA for iodine in Nigeria, Tanzania, and Uganda. Conclusions Fortified foods are major contributors to apparent intakes of vitamin A and iodine, but not iron, among WRA. Contributions to vitamin A and iodine are observed despite fortification standards not consistently being met and, if constraints to meeting standards are addressed, there is risk of excessive intakes in some countries. For all programs assessed, nutrient intakes from all dietary sources and fortification standards should be reviewed to inform adjustments where needed to avoid risk of low or excessive intakes.
The Developmental Morphology of Leea guineensis. I. Vegetative Development

The early ontogeny of the compound leaves and their associated stipules in Leea guineensis G. Don was studied using SEM. At initiation, the leaf primordium uses up most of the shoot apical meristem, which fluctuates greatly in size at different stages of development. Continuous meristematic regions at the base of the leaf primordium, later recognized as stipules, grow around and enclose the apical meristem. The continuity between the leaf, the stipules, and the shoot axis is striking at early stages of development, making it difficult to delimit these different structures. If growth processes such as timing and duration of growth and meristem fusion or extension are used to explain the vegetative morphology of L. guineensis, visualizing the relationship between the leaf, the stipules, and the shoot axis becomes easier.
Valorization of Eucalyptus globulus bark as a growing-media component for potted plants

Eucalyptus globulus bark is a waste from pulp and paper industries. This work aims to use E. globulus bark as raw-material for substrates formulation. Three types of bark were used: fresh bark (FB) milled to 6 mm particle size, and two hydrothermally treated barks (HTB1: 20’ 60°C; HTB2: 40’ 100°C). Barks were mixed at 25 and 50% (v v -1 ) (S25; S50) with peat. FB was phytotoxic, causing low germination (91%) and root growth inhibition (0.1 cm length) of Lepidum sativum seeds. HTB1 and HTB2 reduced significantly toxicity with germination rates of 98 and 100%, and root lengths of 5.1 and 5.2 cm, respectively. Potting test, using Chinese cabbage, revealed lower germination (95%) in FB mixtures than in HTB1, HTB2 and commercial substrate (CS) (98-100%), reinforcing the FB phytotoxic. S50 decreased plant growth, probably related with lower water retention, as well as nitrogen immobilization inherent to woody substrates. S25 showed shoot weight, and roots growth statistically equal or higher than CS, encouraging use of this proportion of hydrothermally treated bark in substrate formulation.
Service-Life Study of Polycarbonate Outdoors Using Python with Incomplete Data

The deterioration of polycarbonate (PC) depends on various environmental factors. Meanwhile, the complexity of the related weathering processes inhibits the prediction of service life based on the environmental factors. To elucidate the nonlinear correlation between PC weathering and the environmental factors, three-year-long natural weathering tests were conducted at eight experimental stations in China. The relationship between tensile-property data of PC and environmental and pollutant data is analyzed by extra-trees and multilayer perceptron networks implemented in Python. The results indicated that (1) the degradation of PC tensile properties is mainly affected by the experimental period (76.37%), whilst the effect of the environmental or pollutant factors on the degradation is less pronounced (23.63%); (2) the classification accuracy of the trained model on the training set is 91% (91/100), and on the testing set is 72.13% (44/61); and lastly, (3) it is inferred from the error analysis of the classification results that the performance change of polycarbonate in Qionghai and Wuhan is characterized by an initial reduction followed by a slight improvement. Lastly, we show that the proposed method performs well, especially in the case of areas with incomplete data available.