Miracle-dz/UniFAR-FTUs huggingface dataset:
Tocilizumab for Treatment of Mechanically Ventilated Patients With COVID-19

Abstract Background Severe coronavirus disease 2019 (COVID-19) can manifest in rapid decompensation and respiratory failure with elevated inflammatory markers, consistent with cytokine release syndrome for which IL-6 blockade is an approved treatment. Methods We assessed effectiveness and safety of IL-6 blockade with tocilizumab in a single-center cohort of patients with COVID-19 requiring mechanical ventilation. The primary endpoint was survival probability postintubation; secondary analyses included an ordinal illness severity scale integrating superinfections. Outcomes in patients who received tocilizumab compared with tocilizumab-untreated controls were evaluated using multivariable Cox regression with propensity score inverse probability of treatment weighting (IPTW). Results 154 patients were included, of whom 78 received tocilizumab and 76 did not. Median follow-up was 47 days (range, 28–67). Baseline characteristics were similar between groups, although tocilizumab-treated patients were younger (mean: 55 vs 60 years), less likely to have chronic pulmonary disease (10% vs 28%), and had lower D-dimer values at time of intubation (median: 2.4 vs 6.5 mg/dL). In IPTW-adjusted models, tocilizumab was associated with a 45% reduction in hazard of death (HR, .55; 95% CI, .33–.90) and improved status on the ordinal outcome scale [OR per 1-level increase, . 58; . 36–. 94). Although tocilizumab was associated with an increased proportion of patients with superinfections (54% vs 26%; P < .001), there was no difference in 28-day case fatality rate among tocilizumab-treated patients with versus without superinfection (22% vs 15%; P = .42). Staphylococcus aureus accounted for ~50% of bacterial pneumonia. Conclusions In this cohort of mechanically ventilated COVID-19 patients, tocilizumab was associated with lower mortality despite higher superinfection occurrence.
Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.)

Summary Although upland cotton (Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole‐genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome‐wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.
Biyoçeşitlilik ve Türkiye deki Endemik Bitkilere Örnekler

This work is on the importance of biodiversity, attempts in international cooperation and the international convention signed. The richness of Turkiye in terms of biodiversity and its relationship with geographical location are given on maps together with their justificaiton. The number of species in Turkiye is compared with neighboring countries and European total. Depicting plants for which Turkiye is the gene center are discussed in terms of food resources providing additional evidence for biodiversity richness of Turkiye.
Drug Sensitivity Assay of Xanthomonas citri subsp. citri Using REMA Plate Method

[Abstract] Resazurin Microtiter Assay (REMA) is a simple, rapid, reliable, sensitive, safe and cost-effective measurement of cell viability. Resazurin detects cell viability by converting from a nonfluorescent dye to the highly red fluorescent dye resorufin in response to chemical reduction of growth medium resulting from cell growth (Palomino et al., 2002). The REMA assay can be used as a fluorogenic oxidation-reduction indicator in a variety of cells, including bacteria, yeast and eukaryotes (Silva et al., 2013).
Algal oil production: Research Paper

Three naturally occurring algal samples were collected from different areas of kothi satna m.p. Algae were identified in the botany lab as green algae Pithophora, Spirogyra, Hydrodictyon, Oil was extracted from the all the three dried algal samples and their physicochemical properties such as, lipid content, viscosity, density and pH were analysed. The physico - chemical properties of algal oil meet all the properties given by American society for testing and materials (ASTM) D6751, ISO 15607and EN14214 - Europe. It is concluded that the algal oil can be used as a potential source of bio fuel for the production of biodiesel.
Container Substrate-pH Response to Differing Limestone Type and Particle Size

The objective of this study was to develop reactivity indices to describe the pH response for liming materials incorporated into container substrates. Three reactivity indices (particle size efficiency (PSE), fineness factor (FF), and effective calcium carbonate equivalence (ECC)) were developed based on lime particle size distribution and lime neutralizing value (NV) in CaCO3 equivalent. Six lime particle size fractions (2000 to 850, 850 to 250, 250 to 150, 150 to 75, 75 to 45, and <45 mm) separated from each of three calcitic limes and seven dolomitic limes were used to calibrate PSE, and were based on the increase in substrate pH (DpH) incited by the particle size fraction relative to reagent grade CaCO3 when mixed in a sphagnum peat substrate at 5 g CaCO3 equivalents per liter of peat. PSE for calcitic carbonate limes at day 7 (short-term pH response) were 0.13, 0.40, 0.78, 0.97, 1.00, and 1.00 for 2000 to 850, 850 to 250, 250 to 150, 150 to 75, 75 to 45, and <45 mm particle fractions, respectively. Other PSE values were described for dolomitic carbonate limestones and for long-term pH response, and PSE was modeled with a function over time. FF was calculated for a liming material by summing the percentages by weight in each of the six size fractions multiplied by the appropriate PSE. ECC rating of a limestone was the product of its NV and FF. ECC multiplied by the applied lime incorporation rate could be used to predict substrate-pH response. Estimated PSE values were validated in two experiments that compared expected and observed substrate pH using 29 unscreened carbonate and hydrated lime sources blended with peat. Validation trials resulted in a close correlation and no bias between expected and observed pH values. Revised PSE values are useful to evaluate the reactivity of different limestone sources for container substrates given the fine particle size, short crop duration, and pH sensitivity of many container-grown crops.
Proposal for a New Family, Campylobacteraceae

The genera Campylobacter, Arcobacter, Helicobacter, Wolinella, and “Flexispira” constitute, within the class Proteobacteria, a separate eubacterial lineage identified as rRNA superfamily VI. A considerable number of common genotypic and phenotypic features differentiate the genera Campylobacter and Arcobacter from the other members of this group. Therefore, we propose that the genera Campylobacter and Arcobacter should be included in a separate family, for which the name Campylobacteraceae is proposed.
Ureidothiophene inhibits interaction of bacterial RNA polymerase with –10 promotor element

Abstract Bacterial RNA polymerase is a potent target for antibiotics, which utilize a plethora of different modes of action, some of which are still not fully understood. Ureidothiophene (Urd) was found in a screen of a library of chemical compounds for ability to inhibit bacterial transcription. The mechanism of Urd action is not known. Here, we show that Urd inhibits transcription at the early stage of closed complex formation by blocking interaction of RNA polymerase with the promoter –10 element, while not affecting interactions with –35 element or steps of transcription after promoter closed complex formation. We show that mutation in the region 1.2 of initiation factor σ decreases sensitivity to Urd. The results suggest that Urd may directly target σ region 1.2, which allosterically controls the recognition of –10 element by σ region 2. Alternatively, Urd may block conformational changes of the holoenzyme required for engagement with –10 promoter element, although by a mechanism distinct from that of antibiotic fidaxomycin (lipiarmycin). The results suggest a new mode of transcription inhibition involving the regulatory domain of σ subunit, and potentially pinpoint a novel target for development of new antibacterials.
Hibernation versus Daily Torpor in Mammals and Birds: Physiological Variables and Classification of Torpor Patterns

Hibernation and daily torpor are usually considered to be two distinct patterns of heterothermia. In the present comparison we evaluated (1) whether physiological variables of torpor from 104 avian and mammalian species warrant the distinction between hibernation and daily torpor as two different states of torpor and (2), if so, whether this distinction is best based on maximum torpor bout duration, minimum body temperature (Tb), minimum metabolic rate during torpor, or the reduction of metabolic rate expressed as percentage of basal metabolism (BMR). Initially, animals were grouped into species displaying either daily torpor or prolonged torpor (hibernation) according to observations from original sources. Both cluster and discriminant analyses supported this division, and further analyses were therefore based on these two groups. Frequency distributions for all tvariables tested differed significantly (P < 0.001) between daily torpor and hibernation. The average maximum torpor bout duration was 355.3 h in hibernators and 11.2 h in daily heterotherms. Mean minimum Tb's were lower in hibernators than in daily heterotherms (5.8° C vs. 17.4° C) as were minimum metabolic rates measured as rate of oxygen consumption (V̇o2; 0.037 vs. 0.535 mL O₂ g⁻¹h⁻¹), and the metabolic rate reduction expressed as percentage of BMR (5.1% vs. 29.5%). Furthermore, mean body weights were significantly higher in hibernators (2384 g) than in daily heterotherms (253 g; P < 0.001). Thus, the comparisons of several physiological variables appear to justify a distinction between the two torpor patterns. However, of all variables tested, only the frequency distributions of maximum torpor bout duration (1.5-22 h for daily torpor; 96-1,080 h for hibernation) showed a clear gap between daily heterotherms and hibernators. The minimum V̇o2 also distinguished clearly between daily heterotherms and hibernators. All other variables, including minimum Tb during torpor, did not show a complete separation between the two patterns of heterothermia. We therefore suggest that classification of torpor patterns should be based on the duration of torpor bouts or the minimum V̇o2 during torpor.
NEW REMAINS OF EOCENE AND OLIGOCENE AFROSORICIDA (AFROTHERIA) FROM EGYPT, WITH IMPLICATIONS FOR THE ORIGIN(S) OF AFROSORICID ZALAMBDODONTY

Abstract Molecular estimates for the divergence of Chrysochloridae (golden moles) and Tenrecoidea (tenrecs) date back to near the K-T boundary, but at present the oldest undoubted fossil members of these clades are early Miocene in age (∼20 Ma). The only Paleogene African genus that has been proposed as a possible stem tenrecoid is late Eocene (∼34 Ma) Widanelfarasia from Egypt, heretofore known only from the lower dentition. Here we employ high-resolution computed tomography to reveal the morphology of the maxillary post-canine dentition of Widanelfarasia, and describe fragmentary dental and mandibular remains of early Oligocene Jawharia (gen. nov.) and Eochrysochloris (gen. nov.). The upper molar dentition of Widanelfarasia provides evidence for an intermediate morphological stage between moderate dilambdodonty and incipient zalambdodonty. Phylogenetic analysis employing the morphological character matrix of Asher and Hofreiter (2006) places Widanelfarasia within crown Tenrecoidea, but an alternative placement of that genus as a stem tenrecoid could not be statistically rejected. Additional support for the latter hypothesis, and for the hypothesis of convergent evolution of zalambdodonty within Afrosoricida, is provided by Eochrysochloris gen. nov., which shares apomorphic premolar features with Miocene Prochrysochloris and extant chrysochlorids, but retains a well-developed talonid basin on its lower molars. Jawharia gen. nov. is interpreted as an advanced stem tenrecoid that provides additional support for the hypothesis that tenrecoid zalambdodonty evolved from moderate dilambdodonty. Some of the apomorphic morphological features shared by Widanelfarasia and early Miocene Protenrec are also seen in Todralestes, from the oldest (late Paleocene) placental mammal-bearing locality in Africa. As such Todralestes may be a stem or crown afrosoricid, and, if so, the oldest known Afro-Arabian member of Afrotheria.
PPPYEPTAP Motif Is the Late Domain of Human T-Cell Leukemia Virus Type 1 Gag and Mediates Its Functional Interaction with Cellular Proteins Nedd4 and Tsg101

ABSTRACT The human T-cell leukemia virus type 1 (HTLV-1) Gag polyprotein contains two adjacent proline-rich motifs (sequence PPPYEPTAP) in the C terminus of the matrix domain. Proline-to-alanine mutations were introduced into either or both motifs of HTLV-1 to determine the effect on the release of HTLV-1 virus-like particles from 293T cells. The release of both single mutants was significantly reduced, whereas a double mutation in both motifs abolished the release of the HTLV-1 particles. Two-hybrid and in vitro binding assays showed that the HTLV-1 Gag polyprotein binds both Tsg101 and Nedd4 proteins. The interaction with HTLV-1 Gag required the central WW domain of Nedd4 and the ubiquitin enzyme variant (UEV) domain of Tsg101. We expressed various fragments of Nedd4 and Tsg101 proteins in 293T cells and tested for their ability to interfere with virion release mediated by the HTLV-1 Gag-Pro polyprotein. Fragments consisting of the N-terminal UEV domain of Tsg101 and the central WW and C-terminal Hect domains of Nedd4 protein all caused transdominant inhibition of HTLV-1 particle release. Similarly, inhibition of the proteasome significantly decreased HTLV-1 particle release. Furthermore, the WW domain overexpression caused an early arrest of HTLV-1 particle morphogenesis before the membrane is deformed into the typical half-shell structure. This result suggests that Nedd4 is involved early in budding of HTLV-1.
Factors Influencing Bryophyte Assemblage at Different Scales in the Western Canadian Boreal Forest

Abstract This study examined bryophyte community composition in relation to microsite and microenvironmental variation at different scales in three conifer-dominated stands in the boreal forest of Alberta, Canada. We documented bryophyte assemblage on specific microsite types (physiognomic forms providing substrates for moss colonization: logs, stumps, tree bases, undisturbed patches of forest floor, disturbed patches of forest floor), and at coarser scales: mesosites (625 m2 plots within stands), and stands (10 ha). Patterns of variation in bryophyte composition arising from the microsite sampling were clearly related to microsite type and, for woody substrates, to microsite quality (decay class; hardwood vs. softwood). Microenvironment (moisture, pH, temperature, light) also had some influence on bryophyte composition of woody microsite types. Forest floor moisture, pH, and light were related to bryophyte composition of undisturbed patches of forest floor while forest floor moisture and temperature were significant correlates for disturbed forest floor. At the coarser-scale, surface moisture and forest floor moisture were related to bryophyte assemblage of mesosites; this was partially reflective of differences among stands. We conclude that bryophyte species composition in these forests is related to a hierarchy of factors including fine scale variation in the type and quality of available microsites along with microenvironmental variation at different scales. Management efforts to preserve bryophyte biodiversity will need to incorporate this complexity.
Space Food for Thought: Challenges and Considerations for Food and Nutrition on Exploration Missions.

Throughout human history, food and nutrition have been key determinants in the success—or failure—of exploration missions. The National Aeronautics and Space Administration (NASA) is planning missions that will put the first woman and next man on the moon this decade and will send humans to Mars next decade. Greater propulsion capability is needed to supply missions as distance from Earth increases and planetary physics makes regular resupply unfeasible. Hence, providing food and nutrition becomes a significant challenge. The 20th anniversary of continuous human presence on the International Space Station (ISS) is approaching. NASA has provided a safe food system for astronauts on 4to 11-mo missions in low-Earth orbit. However, limited water, storage, crew time, and food preparation capability (e.g., add water, heat) restrict the crew to a limited choice of shelfstable, single-serving food products either in their natural form or preserved by dehydration, retort thermostabilization, or irradiation. Astronauts select ∼20% of their food items and beverages, whereas ∼80% of their diet comes from a shared, standard set of foods. Resupply vehicles arrive several times a year, bringing some fresh fruits and vegetables and some semi-shelf-stable specialty items. Astronauts report that these deliveries provide profound psychological benefits. The degree to which these intermittent deliveries stave off nutritional deficiencies is not easy to quantify because the variety and amount of fresh fruit and vegetables vary, and they are shelflife limited to a few days or weeks. Although Apollo astronauts reported hot water to be “essential and non-negotiable” on ∼10-d lunar missions (1), resource constraints on upcoming lunar missions may preclude hot water or a food warmer for at least part of the mission. Food mass and volume will be highly constrained, despite frequent and intense lunar walks increasing energy expenditure and limiting available time to eat. Concerns arise as to whether a limited diet of cold foods for up to 8 d will affect intake,
The Sound of Silence in Plants

RNA silencing appears as one of the most exciting discoveries in the field of molecular biology of the last decade. Double-stranded small RNA species ranging from 20 to 26 nt, named siRNAs, were initially identified as a plant defense mechanism to target viral RNA upon infection. siRNAs can bind to a complementary RNA and induce its degradation. In addition, single stranded miRNAs have been characterized as endogenous small non-coding RNAs involved in mRNA inhibition of translation or cleavage in both plants and animals. A broad range of physiological processes are related to this class of RNAs such as control of development, defense against viral infection and cancer. RNA silencing involves several RNA processing enzymes which are well conserved between plants and animals. However plants have developed specific features of RNA silencing that will be reviewed here. Plants and C. elegans are the only organisms capable of producing double stranded RNA from single stranded molecules when these possess specific qualitative and quantitative features. RNA dependent RNA polymerases (RDR) are the critical enzymes for this step. A special focus will be made in this review on the recent progress in characterizing the ability of plants to send short and long distance signals from the initially silenced cell.
Synthesis of Antiviral Perfluoroalkyl Derivatives of Teicoplanin and Vancomycin

The limited scope of antiviral drugs and increasing problem of antiviral drug resistance represent a global health threat. Glycopeptide antibiotics and their lipophilic derivatives have emerged as relevant inhibitors of diverse viruses. Herein, we describe a new strategy for the synthesis of dual hydrophobic and lipophobic derivatives of glycopeptides to produce selective antiviral agents without membrane‐disrupting activity. Perfluorobutyl and perfluorooctyl moieties were attached through linkers of different length to azido derivatives of vancomycin aglycone and teicoplanin pseudoaglycone, and the new derivatives were evaluated against a diverse panel of viruses. The teicoplanin derivatives displayed strong anti‐influenza virus activity at nontoxic concentrations. Some of the perfluoroalkylated glycopeptides were also active against a few other viruses such as herpes simplex virus or coronavirus. These data encourage further exploration of glycopeptide analogues for broad antiviral application.
Chemistry and antioxidant potential of phytoconstituents from Aegle marmelos fruit-shell.

BACKGROUND Oxidative stress is among the main causes of metabolic disorders. Hence, there is need to discover potent antioxidants for therapeutic applications. OBJECTIVE The objective of this study has been to investigate the phytoconstituents of the methanolic extract of hard shell of Aegle marmelos fruit and their antioxidant potential. METHODS Methanolic extract was fractionated using different solvents by liquid-liquid extraction. Characterization of the phytoconstituents was done by using phytochemical tests and GC-MS analysis. The free radical scavenging activity, total reducing power, lipid peroxidation inhibition and cell protection assays against oxidative stress were performed with methanolic extract and its fractions. RESULTS Therapeutically significant class of compounds, for example, polyphenols, glycosides and sterols were revealed in the hard-shell extract. Differential separation of compounds was achieved by liquid - liquid extraction using different solvents. Six compounds: 4-Hydroxybenzeneacetic acid; 5-Oxo-pyrrolidine-2-carboxylic acid methyl ester; 1-[3-Methyl-3- Butenyl] Pyrrolidine; Trans-sinapyl alcohol; 5-[Hydroxymethyl]-2-furaldehyde and 2,4-Dihydroxy-2,5-dimethyl-3[2H]- furan-3-one, identified in the fruit-shell extract, are being reported for the first time from this plant. Strong antioxidant potential of the extract was evident from efficient scavenging of free radicals. The extract also conferred protection to yeast cells against oxidative damage. CONCLUSION Results showed that the hard shell of the Aegle marmelos fruit was a potent source for antioxidant compounds, which can be developed for therapeutic applications in control and management of metabolic diseases.