Miracle-dz/UniFAR-FTUs huggingface dataset:
Nanoparticles: Synthesis, Morphophysiological Effects, and Proteomic Responses of Crop Plants

Plant cells are frequently challenged with a wide range of adverse environmental conditions that restrict plant growth and limit the productivity of agricultural crops. Rapid development of nanotechnology and unsystematic discharge of metal containing nanoparticles (NPs) into the environment pose a serious threat to the ecological receptors including plants. Engineered nanoparticles are synthesized by physical, chemical, biological, or hybrid methods. In addition, volcanic eruption, mechanical grinding of earthquake-generating faults in Earth’s crust, ocean spray, and ultrafine cosmic dust are the natural source of NPs in the atmosphere. Untying the nature of plant interactions with NPs is fundamental for assessing their uptake and distribution, as well as evaluating phytotoxicity. Modern mass spectrometry-based proteomic techniques allow precise identification of low abundant proteins, protein–protein interactions, and in-depth analyses of cellular signaling networks. The present review highlights current understanding of plant responses to NPs exploiting high-throughput proteomics techniques. Synthesis of NPs, their morphophysiological effects on crops, and applications of proteomic techniques, are discussed in details to comprehend the underlying mechanism of NPs stress acclimation.
B cells are programmed to activate κ and λ for rearrangement at consecutive developmental stages

κ and λ , the two types of immunoglobulin light (L) chains present in mammals, contribute differently to the L chain pool of each species. Here we show that the extreme preponderance of κ in the mouse results from programmed sequential activation of the κ and λ loci. Activation – a prerequisite of rearrangement – was monitored by analyzing transcription of unrearranged J‐C clusters. Upon in vitro differentiation of a rearrangement‐deficient pro/pre‐B line, germ‐line transcripts of the λ J‐C clusters, that are newly described here, became detectable 2 days later than their counterparts of J‐C κ. Clear differences could also be observed in vivo: germ‐line transcripts of κ were already present in large B220+ CD25+ pre B‐II cells whereas germ‐line λ transcripts first became detectable at the consecutive developmental stage of small B220+ CD25+ pre‐B‐II cells. This activation pattern was found to be identical in mice which can not rearrange κ due to a targeted deletion or inactivation of κ. This suggests that pre‐B‐II cells follow a hit‐and‐run mechanism of development which includes programmed transitions and differential activation of the L chain loci, i. e. κ first, then λ. Thus, privileged activation of κ might be the decisive factor in setting the 10 : 1 ratio of κ to λ present in the mouse.
Baking Performance of Durum and Soft Wheat Flour in a Sponge-Dough Breadmaking Procedure

ABSTRACT Breadmaking properties were determined for formulations that included durum, soft, and spring wheat flour, using a pound-loaf sponge-dough baking procedure. Up to 60% durum or soft wheat flour plus 10% spring wheat flour could be incorporated at the sponge stage for optimum dough-handling properties. At remix, the dough stage required 30% spring wheat flour. Bread made with 100% spring wheat flour was used as a standard for comparison. Bread made with 60% durum flour exhibited internal crumb color that was slightly yellow. When storing pound bread loaves for 72 hr, crumb moisture content remained unchanged. Crumb firmness and enthalpy increased the most in bread made with 60% soft wheat flour. Crumb firmness increased the least in bread made with 100% spring wheat flour. Enthalpy changed the least in bread made with 60% durum flour. Crumb moisture content was significantly correlated with crumb firmness (r = -0.82) and enthalpy (r = -0.65). However, crumb moisture content was specific for each ty.
Kinetics and New Mechanism of Azoxystrobin Biodegradation by an Ochrobactrum anthropi Strain SH14

Azoxystrobin is one of the most popular strobilurin fungicides, widely used in agricultural fields for decades.Extensive use of azoxystrobin poses a major threat to ecosystems. However, little is known about the kinetics and mechanism of azoxystrobin biodegradation. The present study reports a newly isolated bacterial strain, Ochrobactrum anthropi SH14, utilizing azoxystrobin as a sole carbon source, was isolated from contaminated soils. Strain SH14 degraded 86.3% of azoxystrobin (50 μg·mL−1) in a mineral salt medium within five days. Maximum specific degradation rate (qmax), half-saturation constant (Ks), and inhibition constant (Ki) were noted as 0.6122 d−1, 6.8291 μg·mL−1, and 188.4680 μg·mL−1, respectively.Conditions for strain SH14 based azoxystrobin degradation were optimized by response surface methodology. Optimum degradation was determined to be 30.2 °C, pH 7.9, and 1.1 × 107 CFU·mL−1 of inoculum. Strain SH14 degraded azoxystrobin via a novel metabolic pathway with the formation of N-(4,6-dimethoxypyrimidin-2-yl)-acetamide,2-amino-4-(4-chlorophenyl)-3-cyano-5,6-dimethyl-pyridine, and 3-quinolinecarboxylic acid,6,8-difluoro-4-hydroxy-ethyl ester as the main intermediate products, which were further transformed without any persistent accumulative product. This is the first report of azoxystrobin degradation pathway in a microorganism. Strain SH14 also degraded other strobilurin fungicides, including kresoxim-methyl (89.4%), pyraclostrobin (88.5%), trifloxystrobin (78.7%), picoxystrobin (76.6%), and fluoxastrobin (57.2%) by following first-order kinetic model. Bioaugmentation of azoxystrobin-contaminated soils with strain SH14 remarkably enhanced the degradation of azoxystrobin, and its half-life was substantially reduced by 95.7 and 65.6 days in sterile and non-sterile soils, respectively, in comparison with the controls without strain SH14. The study presents O. anthropi SH14 for enhanced biodegradation of azoxystrobin and elaborates on the metabolic pathways to eliminate its residual toxicity from the environment.
Interplane bulk motion analysis and removal based on normalized cross‐correlation in optical coherence tomography angiography

Bulk motion seriously degrades the image quality of optical coherence tomography angiography (OCTA). Conventional correction methods focus on in‐plane displacement, while the bulk motion component perpendicular to B‐scans also introduces noise. This work first presents an evaluation of this component using a specific scan protocol and an approximate expression derived from peak‐normalized cross‐correlation values, and then quantitatively assesses how interplane bulk motion noise reduce the sensitivity of cross‐sectional angiograms. Finally, we developed a repetitive bulk motion correction method based on the estimated displacements and redundant volume scans. The correction does not require registration and angiogram reconstruction of low flow sensitivity frames, and the results of in vivo mice skin OCTA imaging experiments show that the proposed method can effectively reduce bulk motion noise caused by cardiac and respiratory motion and occasional shaking, and improve OCTA image quality, which has practical significance for clinical OCTA diagnosis and analysis.
Sediment Control of Soluble Reactive Phosphorus in Hoxie Gorge Creek, New York

Stream sediments were found to regulate the soluble reactive phosphorus (SRP) of stream water by geochemical processes. This conclusion was based on sediment analysis, laboratory sorption experiments, and measurement of the equilibrium phosphorus concentration (EPC). EPC is the concentration of P in the water at which there is neither sorption nor desorption of P by the sediments. At low flow conditions, streamwater SRP was highly correlated with EPC at six sites along Hoxie Gorge Creek (r = 0.979). EPC was inversely related to the ionic strength of the equilibrating solution, with Ca2+ producing larger changes than Na+. Minimum EPC values occurred near the neutral pH of the stream water and increased sharply in acidic and basic solutions. Also, EPC was negatively correlated with the exchangeable Al content of the sediments at the six sites. These data are consistent with a mechanism previously verified for soils in which solution cations displace exchangeable Al(III) from sediments; hydrolyzed Al(III) re.
Locating Forest Management Units Using Remote Sensing and Geostatistical Tools in North-Central Washington, USA

In this study, we share an approach to locate and map forest management units with high accuracy and with relatively rapid turnaround. Our study area consists of private, state, and federal land holdings that cover four counties in North-Central Washington, USA (Kittitas, Okanogan, Chelan and Douglas). This area has a rich history of landscape change caused by frequent wildfires, insect attacks, disease outbreaks, and forest management practices, which is only partially documented across ownerships in an inconsistent fashion. To consistently quantify forest management activities for the entire study area, we leveraged Sentinel-2 satellite imagery, LANDFIRE existing vegetation types and disturbances, monitoring trends in burn severity fire perimeters, and Landsat 8 Burned Area products. Within our methodology, Sentinel-2 images were collected and transformed to orthogonal land cover change difference and ratio metrics using principal component analyses. In addition, the Normalized Difference Vegetation Index and the Relativized Burn Ratio index were estimated. These variables were used as predictors in Random Forests machine learning classification models. Known locations of forest treatment units were used to create samples to train the Random Forests models to estimate where changes in forest structure occurred between the years of 2016 and 2019. We visually inspected each derived polygon to manually assign one treatment class, either clearcut or thinning. Landsat 8 Burned Area products were used to derive prescribed fire units for the same period. The bulk of analyses were performed using the RMRS Raster Utility toolbar that facilitated spatial, statistical, and machine learning tools, while significantly reducing the required processing time and storage space associated with analyzing these large datasets. The results were combined with existing LANDFIRE vegetation disturbance and forest treatment data to create a 21-year dataset (1999–2019) for the study area.
Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs

Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKU1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and the newest SARS-CoV-2 (the causative agent of COVID-19) lead to severe and deadly diseases with mortality rates ranging between ~1 to 35% depending on factors such as age and pre-existing conditions. Despite continuous global health threats to humans, there are no approved vaccines or drugs targeting human CoVs, and the recent outbreak of COVID-19 emphasizes an urgent need for therapeutic interventions. Using computational and bioinformatics tools, here we present the feasibility of reported broad-spectrum RNA polymerase inhibitors as anti- SARS-CoV-2 drugs targeting its main RNA polymerase, suggesting that investigational and approved nucleoside RNA polymerase inhibitors have potential as anti-SARS-CoV-2 drugs. However, we note that it is also possible for SARS-CoV-2 to evolve and acquire drug resistance mutations against these nucleoside inhibitors.
Lecythidaceae Poit. in the Tupé Sustainable Development Reserve, Manaus, Brazil

Lecythidaceae is the family of the Brazil nut, and comprises about 300 species belonging to 17 genera with pantropical distributions. One hundred and twenty-two species belonging to nine genera are distributed throughout Brazil, demonstrating its greatest diversity in the Amazon rainforest where Lecythidaceae is also one of the most abundant families. It is usually difficult to collect fertile material from these trees because of their canopy heights, and species determinations using sterile material can be complex because of their morphological similarities. There have been relatively few studies of this family even though it is one of the most important groups in the Amazon region, and a detailed taxonomic treatment of the species of Lecythidaceae in the Tupe Sustainable Development Reserve was therefore the goal of the present work. Ten species were found, Allantoma lineata (Mart. ex O.Berg) Miers, Bertholletia excelsa Bonpl. , Couratari tenuicarpa A.C. Sm. , Lecythis poiteaui O. Berg; and six species of Eschweilera, the richest genus. The descriptions and identification keys of the species used 56 characters. The main reproductive characters useful for distinguishing the species were the pubescence of the inflorescence rachis, pedicel length and trichomes presence, floral symmetry, hood type, filament shape, stigma shape, fruit shape and size, and aril type. The most diagnostic vegetative characters were the type and color of the outer bark, inner bark color, midrib prominence, and petiole shape and pubescence.
Recent Advances in Hybrid Biomimetic Polymer-Based Films: from Assembly to Applications

Biological membranes, in addition to being a cell boundary, can host a variety of proteins that are involved in different biological functions, including selective nutrient transport, signal transduction, inter- and intra-cellular communication, and cell-cell recognition. Due to their extreme complexity, there has been an increasing interest in developing model membrane systems of controlled properties based on combinations of polymers and different biomacromolecules, i.e., polymer-based hybrid films. In this review, we have highlighted recent advances in the development and applications of hybrid biomimetic planar systems based on different polymeric species. We have focused in particular on hybrid films based on (i) polyelectrolytes, (ii) polymer brushes, as well as (iii) tethers and cushions formed from synthetic polymers, and (iv) block copolymers and their combinations with biomacromolecules, such as lipids, proteins, enzymes, biopolymers, and chosen nanoparticles. In this respect, multiple approaches to the synthesis, characterization, and processing of such hybrid films have been presented. The review has further exemplified their bioengineering, biomedical, and environmental applications, in dependence on the composition and properties of the respective hybrids. We believed that this comprehensive review would be of interest to both the specialists in the field of biomimicry as well as persons entering the field.
Evaluation and Transcriptome Analysis of the Novel Oleaginous Microalga Lobosphaera bisecta (Trebouxiophyceae, Chlorophyta) for Arachidonic Acid Production

Arachidonic acid (AA) is an omega-6 long-chain polyunsaturated fatty acid and is important for human health. The coccoid green microalga Lobosphaera bisecta has been reported to be able to accumulate high AA content under certain conditions. Nutrient management and light intensity had significant effects on the biomass and accumulation of lipids and AA in L. bisecta SAG2043. Both a high nitrogen concentration (18 mM) and high light intensity (bilateral light-300 μmol m−2 s−1) were beneficial to the growth of L. bisecta, and the replacement of culture medium further enhanced the biomass, which reached 8.9 g L−1. Low nitrogen concentration (3.6 mM) and high light significantly promoted the accumulation of lipids and AA. The highest lipid and AA content reached 54.0% and 10.8% of dry weight, respectively. Lipid compositions analysis showed that 88.2% of AA was distributed within the neutral lipids. We then reconstructed the lipid metabolic pathways of L. bisecta for the first time, and demonstrated that the upregulation of a key desaturase and elongase in the Δ6 pathway was conducive to the accumulation of fatty acids toward AA synthesis. L. bisecta SAG2043 exhibits high biomass, lipid and AA production. It may be a potential candidate for AA production.
Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity

Significance Oxidation of cysteines by reactive oxygen species (ROS) initiates thermogenesis in brown and beige adipose tissues. Cellular selenols, where selenium replaces sulfur, exhibit enhanced reactivity with ROS. Here we developed a mass spectrometric method to interrogate incorporation of selenols into proteins. Unexpectedly, this approach revealed facultative incorporation of selenium into proteins that lack canonical encoding for selenocysteine. Selenium was selectively incorporated into regulatory sites on key metabolic proteins, including as selenocysteine replacing cysteine at position 253 in UCP1 uncoupling protein 1 (UCP1). Remarkably, dietary selenium supplementation elevated facultative incorporation into UCP1, elevated energy expenditure through thermogenic adipose tissue, and protected against obesity. Together, these findings reveal the existence of facultative protein selenation, which correlates with effects on thermogenic adipocyte function. Oxidation of cysteine thiols by physiological reactive oxygen species (ROS) initiates thermogenesis in brown and beige adipose tissues. Cellular selenocysteines, where sulfur is replaced with selenium, exhibit enhanced reactivity with ROS. Despite their critical roles in physiology, methods for broad and direct detection of proteogenic selenocysteines are limited. Here we developed a mass spectrometric method to interrogate incorporation of selenium into proteins. Unexpectedly, this approach revealed facultative incorporation of selenium as selenocysteine or selenomethionine into proteins that lack canonical encoding for selenocysteine. Selenium was selectively incorporated into regulatory sites on key metabolic proteins, including as selenocysteine-replacing cysteine at position 253 in uncoupling protein 1 (UCP1). This facultative utilization of selenium was initiated by increasing cellular levels of organic, but not inorganic, forms of selenium. Remarkably, dietary selenium supplementation elevated facultative incorporation into UCP1, elevated energy expenditure through thermogenic adipose tissue, and protected against obesity. Together, these findings reveal the existence of facultative protein selenation, which correlates with impacts on thermogenic adipocyte function and presumably other biological processes as well.
The Effects of Alcohol Warning Labels on Population Alcohol Consumption: An Interrupted Time Series Analysis of Alcohol Sales in Yukon, Canada.

OBJECTIVE There is limited evidence that alcohol warning labels (AWLs) affect population alcohol consumption. New evidence-informed AWLs were introduced in the sole government-run liquor store in Whitehorse, Yukon, that included a cancer warning (Ca), low-risk drinking guidelines (LRDGs) and standard drink (SD) messages. These temporarily replaced previous pregnancy warning labels. We test if the intervention was associated with reduced alcohol consumption. METHOD An interrupted time series study was designed to evaluate the effects of the AWLs on consumption for 28 months before and 14 months after starting the intervention. Neighboring regions of Yukon and Northwest Territories served as control sites. About 300,000 labels were applied to 98% of alcohol containers sold in Whitehorse during the intervention. Multilevel regression analyses of per capita alcohol sales data for people age 15 years and older were performed to examine consumption levels in the intervention and control sites before, during, and after the AWLs were introduced. Models were adjusted for demographic and economic characteristics over time and region. RESULTS Total per capita retail alcohol sales in Whitehorse decreased by 6.31% (t test p < .001) during the intervention. Per capita sales of labeled products decreased by 6.59% (t test p < .001), whereas sales of unlabeled products increased by 6.91% (t test p < .05). There was a still larger reduction occurring after the intervention when pregnancy warning labels were reintroduced (-9.97% and -10.29%, t test p < .001). CONCLUSIONS Applying new AWLs was associated with reduced population alcohol consumption. The results are consistent with an accumulating impact of the addition of varying and highly visible labels with impactful messages.
Me‐too pharmaceutical products: History, definitions, examples, and relevance to drug shortages and essential medicines lists

We define a me‐too drug as a pharmacologically active compound that is structurally related to a first‐in‐class compound, regarded as belonging to the same therapeutic class as the original compound, and used for the same therapeutic purposes, but which may differ in some respects, such as specificity of pharmacological action, adverse reactions profile, or drug–drug interactions. We also offer definitions of related terms, including follow‐on drug and first‐in‐class. The therapeutic advantages of me‐too drugs may include improved target specificity, reduced risks of off‐target adverse reactions and drug–drug interactions, increased chance of benefit in some patients, and improved drug delivery and pharmacokinetics. Me‐too drugs can also demonstrate incremental innovation. Their availability may help in coping with drug shortages. However, they may occasionally cause unexpected adverse reactions that are not class effects. Tricyclic antidepressants, β‐blockers, and statins illustrate the diversity of me‐too drugs. Earlier compounds may be as effective as later ones, or more so. Tricyclic antidepressants have similar chemical structures, and compounds introduced after the first‐in‐class compound (imipramine) mostly offered little in the way of innovative features, but continue to be prescribed. In contrast, me‐too β‐blockers introduced after the first‐in‐class compound, pronethalol, have diverse structures and display several innovative features. Stereoisomers and biosimilars/biobetters provide special examples of me‐too drugs. Although many me‐too drugs offer no significant advantages over their predecessors, over 60% of the drugs listed on the World Health Organization's essential list are me‐toos. Different countries may choose different me‐too drugs when constructing essential medicines lists, partly explaining transnational differences between them.