Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of landscape composition on sharp-tailed grouse lek location and attendance in Wisconsin pine barrens1

Abstract: Populations of sharp-tailed grouse (Tympanuchus phasianellus) in the upper Midwest are in danger of extirpation due to habitat loss caused by succession, tree planting, and control of wildfire. Sharp-tailed grouse in Wisconsin have persisted primarily on reserves maintained in early succession using prescribed burning and mechanical disturbance. However, during the late 1990s the highest and densest populations of sharp-tailed grouse in Wisconsin were found in a complex of clearcuts in southeastern Douglas County. We compared landcover composition and fragmentation at multiple scales within 2.4 km of 36 sharp-tailed grouse leks and 213 unused locations in a 1,350-km2 study area in the pine barrens of northwestern Wisconsin. Leks were located on managed reserves (n = 11) and habitats recently created by timber harvest (n = 23) and wildfire (n = 2). Leks were clustered in the landscape, with distance to nearest neighbour lek shorter for leks than unused points. Leks were characterized by higher proportions of grass and shrub cover classes, lower proportions of forest, fewer forest patches, and greater distances to forest edge relative to unused points. Proportions of grass and shrub cover classes, distance to nearest lek, and distance to forest edge were strong predictors of lek presence in a logistic regression model. Differences between leks and unused points varied with scale of sampling. Response of sharp-tailed grouse to indices of fragmentation varied among scales and metrics. Number of sharp-tailed grouse attending leks was positively associated with recently created habitat and proportion of grass cover in the landscape.
Genetic structure of indigenous non-nodulating and nodulating populations of Bradyrhizobium in soils from Thailand

One hundred and thirty symbiotic and non-symbiotic strains of Bradyrhizobium were directly isolated from inoculated soybean and uninoculated legume-free virgin field soils in Thailand using a direct selection medium. About 47% and 58% of the isolates obtained from inoculated and uninoculated fields, respectively, were characterized as being non-symbiotic bradyrhizobia. Partial and nearly full-length sequence analyses of regions encoding 16S rRNA indicated that the non-symbionts were closely related to Bradyrhizobium elkanii (79-99% identity) and Bradyrhizobium japonicum (96-100% identity). Southern hybridization analyses showed that DNA from the non-symbiotic bradyrhizobia failed to hybridize to n if and nod gene probes. rep-PCR DNA fingerprint analyses, done using the BOXA1R primer, indicated the symbionts and non-symbionts could be separated into two distinct clusters. There was no relationship between the geographical origin of isolates and groups made based on serological reaction or their ability to nodulate soybean, cowpea, mungbean, or siratro. These results indicate that a relatively large percentage of non-nodulating bradyrhizobia are present in Thai soils.
Merkel Cell Polyomavirus Large T Antigen is Dispensable in G2 and M-Phase to Promote Proliferation of Merkel Cell Carcinoma Cells

Merkel cell carcinoma (MCC) is an aggressive skin cancer frequently caused by the Merkel cell polyomavirus (MCPyV), and proliferation of MCPyV-positive MCC tumor cells depends on the expression of a virus-encoded truncated Large T antigen (LT) oncoprotein. Here, we asked in which phases of the cell cycle LT activity is required for MCC cell proliferation. Hence, we generated fusion-proteins of MCPyV-LT and parts of geminin (GMMN) or chromatin licensing and DNA replication factor1 (CDT1). This allowed us to ectopically express an LT, which is degraded either in the G1 or G2 phase of the cell cycle, respectively, in MCC cells with inducible T antigen knockdown. We demonstrate that LT expressed only in G1 is capable of rescuing LT knockdown-induced growth suppression while LT expressed in S and G2/M phases fails to support proliferation of MCC cells. These results suggest that the crucial function of LT, which has been demonstrated to be inactivation of the cellular Retinoblastoma protein 1 (RB1) is only required to initiate S phase entry.
Microbubbles and Nanobubbles with Ultrasound for Systemic Gene Delivery

The regulation of gene expression is a promising therapeutic approach for many intractable diseases. However, its use in clinical applications requires the efficient delivery of nucleic acids to target tissues, which is a major challenge. Recently, various delivery systems employing physical energy, such as ultrasound, magnetic force, electric force, and light, have been developed. Ultrasound-mediated delivery has particularly attracted interest due to its safety and low costs. Its delivery effects are also enhanced when combined with microbubbles or nanobubbles that entrap an ultrasound contrast gas. Furthermore, ultrasound-mediated nucleic acid delivery could be performed only in ultrasound exposed areas. In this review, we summarize the ultrasound-mediated nucleic acid systemic delivery system, using microbubbles or nanobubbles, and discuss its possibilities as a therapeutic tool.
Optical and magnetic resonance imaging approaches for investigating the tumour microenvironment: state-of-the-art review and future trends

The tumour microenvironment (TME) strongly influences tumorigenesis and metastasis. Two of the most characterized properties of the TME are acidosis and hypoxia, both of which are considered hallmarks of tumours as well as critical factors in response to anticancer treatments. Currently, various imaging approaches exist to measure acidosis and hypoxia in the TME, including magnetic resonance imaging (MRI), positron emission tomography and optical imaging. In this review, we will focus on the latest fluorescent-based methods for optical sensing of cell metabolism and MRI as diagnostic imaging tools applied both in vitro and in vivo. The primary emphasis will be on describing the current and future uses of systems that can measure intra- and extra-cellular pH and oxygen changes at high spatial and temporal resolution. In addition, the suitability of these approaches for mapping tumour heterogeneity, and assessing response or failure to therapeutics will also be covered.
Reply to a Letter to the Editor “Is there an exposure–effect relationship between body mass index and invasive mechanical ventilation, severity, and death in patients with COVID‐19? Evidence from an updated meta‐analysis”

We thank the authors, Liu et al., for commenting on our paper entitled “Obesity is a risk factor for developing critical condition in COVID-19 patients: A systematic review and meta-analysis” and for updating our analysis. Although their analytical approach was different, and more articles were available at the time of their update, we both concluded that obesity is a risk factor for critical condition in COVID-19 patients. Concerning the comments on our methodology:
Polymeric Microspheres Containing Human Vocal Fold Fibroblasts for Vocal Fold Regeneration

Most acellular injectable biomaterials for vocal fold (VF) wound treatment have limited regenerative potential due to their fast enzymatic degradation and limited recruitment of native cells postinjection. The injection of cells as therapeutic treatment often results in apoptosis due to stresses within the needle and the immune response of the host. Degradable microspheres may improve treatment effectiveness by increasing cell residence time, shielding cells during injection, and offering early protection against the immune system response. The objective of the present study was to investigate the potential of human VF fibroblasts encapsulated in polymeric microspheres as an injectable therapeutic treatment in vitro.
Protocol for a definitive randomised controlled trial and economic evaluation of a community-based rehabilitation programme following hip fracture: fracture in the elderly multidisciplinary rehabilitation—phase III (FEMuR III)

Introduction Proximal femoral (hip) fracture is common, serious and costly. Rehabilitation may improve functional recovery but evidence of effectiveness and cost-effectiveness are lacking. An enhanced rehabilitation intervention was previously developed and a feasibility study tested the methods used for this randomised controlled trial (RCT). The objectives are to compare the effectiveness and cost-effectiveness of the enhanced rehabilitation programme following surgical repair of proximal femoral fracture in older people compared with usual care. Methods and analysis Protocol for phase III, parallel-group, two-armed, superiority, pragmatic RCT with 1:1 allocation ratio; allocation sequence by minimisation programme with a built-in random element; secure web-based allocation concealment. The two treatments will be usual care (control) and usual care plus an enhanced rehabilitation programme (intervention). The enhanced rehabilitation will consist of a patient-held information workbook, goal setting diary and up to six additional therapy sessions. Outcome assessment and statistical analysis will be performed blind; patient and carer participants will be unblinded. Outcomes will be measured at baseline, 17 and 52 weeks’ follow-up. Primary outcome at 52 weeks will be the Nottingham Extended Activities of Daily Living scale. Secondary outcomes will measure anxiety and depression, health utility, cognitive status, hip pain intensity, falls self-efficacy, fear of falling, grip strength and physical function. Carer strain, anxiety and depression will be measured in carers. All safety events will be recorded, and serious adverse events will be assessed to determine whether they are related to the intervention and expected. Concurrent economic evaluation will be a cost-utility analysis from a health service and personal social care perspective. An embedded process evaluation will determine the mechanisms and processes that explain the implementation and impacts of the enhanced rehabilitation programme. Ethics and dissemination National Health Service research ethics approval reference 18/NE/0300. Results will be disseminated by peer-reviewed publication. Trial registration number ISRCTN28376407; Pre-results registered on 23 November 2018.
Recent collapse of crop belts and declining diversity of US agriculture since 1840

Over the last century, US agriculture greatly intensified and became industrialized, increasing in inputs and yields while decreasing in total cropland area. In the industrial sector, spatial agglomeration effects are typical, but such changes in the patterns of crop types and diversity would have major implications for the resilience of food systems to global change. Here, we investigate the extent to which agricultural industrialization in the United States was accompanied by agglomeration of crop types, not just overall cropland area, as well as declines in crop diversity. Based on county‐level analyses of individual crop land cover area in the conterminous United States from 1840 to 2017, we found a strong and abrupt spatial concentration of most crop types in very recent years. For 13 of the 18 major crops, the widespread belts that characterized early 20th century US agriculture have collapsed, with spatial concentration increasing 15‐fold after 2002. The number of counties producing each crop declined from 1940 to 2017 by up to 97%, and their total area declined by up to 98%, despite increasing total production. Concomitantly, the diversity of crop types within counties plummeted: in 1940, 88% of counties grew >10 crops, but only 2% did so in 2017, and combinations of crop types that once characterized entire agricultural regions are lost. Importantly, declining crop diversity with increasing cropland area is a recent phenomenon, suggesting that corresponding environmental effects in agriculturally dominated counties have fundamentally changed. For example, the spatial concentration of agriculture has important consequences for the spread of crop pests, agrochemical use, and climate change. Ultimately, the recent collapse of most agricultural belts and the loss of crop diversity suggest greater vulnerability of US food systems to environmental and economic change, but the spatial concentration of agriculture may also offer environmental benefits in areas that are no longer farmed.
Overcoming the Solubility Barrier of Ibuprofen by the Rational Process Design of a Nanocrystal Formulation

Wet media milling, coupled with spay drying, is a commonly proposed formulation strategy for the production and solidification of nanosuspensions in order to overcome the solubility barrier of BCS Class II substances. However, the application of mechanically and thermally intensive processes is not straightforward in the cases of ductile and/or low melting point substances that may additionally be susceptible to eutectic formation. Using ibuprofen (IBU) as a model drug with non-favorable mechanical and melting properties, we attempt to rationalize nanocrystal formulation and manufacturing in an integrated approach by implementing Quality by Design (QbD) methodology, particle informatics techniques and computationally assisted process design. Wet media milling was performed in the presence of different stabilizers and co-milling agents, and the nanosuspensions were solidified by spray-drying. The effects of key process parameters (bead diameter, milling time and rotational speed) and formulation variables (stabilizer type and drug/stabilizer ratio) on the critical quality attributes (CQAs), i.e., Z-average size, polydispersity index (PDI), ζ-potential and redispersibility of spray-dried nanosuspensions were evaluated, while possible correlations between IBU free surface energy and stabilizer effectiveness were studied. The fracture mechanism and surface stabilization of IBU were investigated by computer simulation of the molecular interactions at the crystal lattice level. As a further step, process design accounting for mass-energy balances and predictive thermodynamic models were constructed to scale-up and optimize the design space. Contemplating several limitations, our multilevel approach offers insights on the mechanistic pathway applicable to the substances featuring thermosensitivity and eutectic tendency.
Modulation of Inflammasome and Pyroptosis by Olaparib, a PARP-1 Inhibitor, in the R6/2 Mouse Model of Huntington’s Disease

Pyroptosis is a type of cell death that is caspase-1 (Casp-1) dependent, which leads to a rapid cell lysis, and it is linked to the inflammasome. We recently showed that pyroptotic cell death occurs in Huntington’s disease (HD). Moreover, we previously described the beneficial effects of a PARP-1 inhibitor in HD. In this study, we investigated the neuroprotective effect of Olaparib, an inhibitor of PARP-1, in the mouse model of Huntington’s disease. R6/2 mice were administered Olaparib or vehicle from pre-symptomatic to late stages. Behavioral studies were performed to investigate clinical effects of the compound. Immunohistochemical and Western blotting studies were performed to evaluate neuroprotection and the impact of the compound on the pathway of neuronal death in the HD mice. Our results indicate that Olaparib administration starting from the pre-symptomatic stage of the neurodegenerative disease increased survival, ameliorated the neurological deficits, and improved clinical outcomes in neurobehavioral tests mainly by modulating the inflammasome activation. These results suggest that Olaparib, a commercially available drug already in use as an anti-neoplastic compound, exerts a neuroprotective effect and could be a useful pharmaceutical agent for Huntington’s disease therapy.
Ondansetron use in early pregnancy and the risk of late pregnancy outcomes

The effects of ondansetron, used off‐label to treat nausea and vomiting during pregnancy, on common pregnancy complications are understudied. Modest effects of a commonly used drug could result in adverse events for large numbers of pregnant women. Therefore, our objective was to compare the risk of stillbirth, preterm birth, gestational hypertensive disorders, small for gestational age, and differences in birth weight between women prescribed ondansetron and women prescribed alternative antiemetics in early pregnancy.
Production de masse d'Ageniaspis citricola, parasitoïde de la mineuse des agrumes, en Tunisie

Introduction. Un programme de lutte biologique a ete etabli en Tunisie visant a introduire Ageniaspis citricola, parasitoide de la mineuse des agrumes, Phyllocnistis citrella, pour renforcer l'action des auxiliaires locaux et pour limiter les effets nefastes des traitements chimiques. Afin de disposer regulierement d'un effectif suffisant d'adultes vivants, une technique d'elevage de masse a ete mise au point. Materiel et methodes. A. citricola est un endoparasitoide polyembryonnaire des œufs et des jeunes stades larvaires de la mineuse des agrumes. Son elevage a ete conduit sous un tunnel plastique abritant des jeunes plants de bigaradier (Citrus aurantium) infestes par P. citrella. Des adultes d'A. citricola ont ete deposes delicatement sur les jeunes feuilles de bigaradier, infestees d'œufs et de jeunes larves de P. citrella, stades preferentiels du parasitoide. Les pupes ont ete ensuite prelevees sur des feuilles d'agrumes infestees et mises a incuber jusqu'a emergence des adultes lâches le jour meme dans les vergers d'agrumes. Resultats et discussion. Du 30 avril au 14 juillet 1996, 19 549 nymphes d'A. citricola renfermant 51 270 pupes ont ete obtenues qui ont donne, par la suite, 18 870 adultes d'A. citricola. Une variation du taux de parasitisme a ete observee, etroitement liee a la disponibilite en stades receptifs de P. citrella, sous le tunnel. Conclusion. La methode d'elevage experimentee, efficace et peu couteuse, a pourtant l'inconvenient de ne pouvoir fonctionner que quelques mois par an; elle permet, cependant, de poursuivre les premiers lâchers inoculatifs d'A. citricola, afin de favoriser l'acclimatation du parasitoide en Tunisie.
One-step Preparation of Red-emitting Carbon Dots for Visual and Quantitative Detection of Copper Ions.

A one-step solvothermal method for the preparation of Carbon Dots with red fluorescence (R-CDs) was put forward, in which sodium citrate and formamide were chosen as precursors, while formamide was adopted as the solvent. The fluorescence emission peak of the as-prepared R-CDs remained the same (600 nm) when the excitation wavelength increased from 490 nm to 560 nm, and the fluorescence quantum yield is 35.3%. Furthermore, the fluorescence intensity of the as-prepared R-CDs could be selectively quenched by copper ions, and the mechanism of Cu2+ quenching R-CDs is the combination of static and dynamic quenching. As a result, the R-CDs were applied for the construction of a fluorescent sensor without any modification for the quantitative and visual detection of copper ions, which is a typical contaminant in water. The limit of detection (LOD) for the fluorescent sensor is as low as 5 nmol/L, and it can be used to fast and directly confirm whether the content of copper ions in drinking water meet criterion of the United States Environmental Protection Agency and the World Health Organization.
Formulation and Evaluation of Supramolecular Food-Grade Piperine HP β CD and TPGS Complex: Dissolution, Physicochemical Characterization, Molecular Docking, In Vitro Antioxidant Activity, and Antimicrobial Assessment

The purpose of the present study was to improve the aqueous solubility, dissolution, and antioxidant activity of the water-insoluble drug piperine (PIP). The study was performed by preparing PIP binary inclusion complex (PIP BIC) and piperine ternary inclusion complex (PIP TIC) by different methods. The effect of a hydrophilic auxiliary substance (TPGS) was assessed with addition to PIP and hydroxypropyl beta cyclodextrin (HP β CD) complex. The phase solubility study was performed to evaluate the complexation efficiency and stability constant. The aqueous solubility, dissolution, physicochemical assessment, antioxidant activity, antimicrobial activity, and molecular docking were further evaluated to check the effect of the complexation of PIP. The stability constant (Ks) value was found to be 238 and 461 M−1 for the binary and ternary inclusion complex. The dissolution study results showed a marked enhancement of release in comparison to pure drug. XRD and SEM studies revealed the presence of more agglomerated and amorphous structures of PIP, which confirmed the formation of complexes. The results of DPPH radical scavenging and antimicrobial activity showed a significant (p < 0.05) enhancement in scavenging activity for PIP TIC (microwave irradiation (MI)). The docking studies have revealed that the binding affinity of TPGS at the PIP-HP β CD complex was −5.2 kcal/mol.
Measurement of Early Disease Blueberries Based on Vis/NIR Hyperspectral Imaging System

Blueberries, which are rich in nutrition, are susceptible to fungal infection during postharvest or storage. However, early detection of diseases in blueberry is challenging because of their opaque appearance and the inconspicuousness of spots in the early stage of disease. The goal of this study was to investigate the potential of hyperspectral imaging over the spectral range of 400–1000 nm to discriminate early disease in blueberries. Scanning electron microscope observation verified that fungal damage to the cellular structure takes place during the early stages. A total of 400 hyperspectral images, 200 samples each of healthy and early disease groups, were collected to obtain mean spectra of each blueberry samples. Spectral correlation analysis was performed to select an effective spectral range. Partial least square discrimination analysis (PLSDA) models were developed using two types of spectral range (i.e., full wavelength range of 400–1000 nm and effective spectral range of 685–1000 nm). The results showed that the effective spectral range made it possible to provide better classification results due to the elimination of the influence of irrelevant variables. Moreover, the effective spectral range combined with an autoscale preprocessing method was able to obtain optimal classification accuracies, with recognition rates of 100% and 99% for healthy and early disease blueberries. This study demonstrated that it is feasible to use hyperspectral imaging to measure early disease blueberries.
Refining Boolean queries to identify relevant studies for systematic review updates

OBJECTIVE Systematic reviews are important in health care but are expensive to produce and maintain. The authors explore the use of automated transformations of Boolean queries to improve the identification of relevant studies for updates to systematic reviews. MATERIALS AND METHODS A set of query transformations, including operator substitution, query expansion, and query reduction, were used to iteratively modify the Boolean query used for the original systematic review. The most effective transformation at each stage is identified using information about the studies included and excluded from the original review. A dataset consisting of 22 systematic reviews was used for evaluation. Updated queries were evaluated using the included and excluded studies from the updated version of the review. Recall and precision were used as evaluation measures. RESULTS The updated queries were more effective than the ones used for the original review, in terms of both precision and recall. The overall number of documents retrieved was reduced by more than half, while the number of relevant documents found increased by 10.3%. CONCLUSIONS Identification of relevant studies for updates to systematic reviews can be carried out more effectively by using information about the included and excluded studies from the original review to produce improved Boolean queries. These updated queries reduce the overall number of documents retrieved while also increasing the number of relevant documents identified, thereby representing a considerable reduction in effort required by systematic reviewers.