Miracle-dz/UniFAR-FTUs huggingface dataset:
Fibroblast-specific IL11 signaling is required for lung fibrosis and inflammation

Tissue injury leads to activation of resident stromal, parenchymal and immune cells to initiate reparative processes that, if unresolved, can lead to fibrosis and organ damage. The directionality of effect between fibrosis and inflammation in the lung has been a point of debate for many years. Here, we tested the hypothesis that Interleukin 11 (IL11) signaling in fibroblasts is of primary importance for pulmonary fibrosis and that this event is upstream of lung inflammation. We generated mice with loxP-flanked Il11ra1 alleles and crossed them to a Col1a2-CreERT strain to enable Il11ra1 deletion in adult fibroblasts (Il11ra1-CKO mice). Lung fibroblasts from Il11ra1-CKO mice were selectively deleted for Il11ra1 and refractory to TGFβ1 stimulation. In the mouse model of bleomycin-induced lung fibrosis, Il11ra1-CKO mice had markedly reduced pulmonary fibrosis and lesser lung damage, which was accompanied by diminished ERK activation in the stromal compartment. Bleomycin lung injury in Il11ra1-CKO mice was also associated with diminished STAT3 activation in inflammatory cells, fewer pulmonary immune cell infiltrates and almost complete inhibition of NF-kB activation. These data reveal an essential role for IL11 signaling in fibroblasts for lung fibrosis and show that inflammation in the lung can be secondary to stromal activation.
Parameters of Soybean Cultivated in Succession With Intercropping System of Out-of-Season Corn With Green Manure

Most Brazilian soils have low organic matter content, and the current management systems used in agriculture contribute to worsening this situation. The introduction of practices that lead to the increase of soil organic matter becomes more necessary for agrosystems to be sustainable, ensuring high yields because only then the production chain becomes profitable and enables agricultural production. The present work aimed to investigate the effect of intercropping practices among corn crop with different green manures in soybean agronomic parameters. The work consisted of five treatments using Brachiaria ruziziensis (Brachiaria); Raphanus sativus (Forage Turnip); Crotalaria spectabilis cv. Common (Crotalaria); Avena strigosa (Black Oats); and a control area (single maize) with five replications. Different aspects related to successor cultivation with soybean were evaluated taking into consideration agronomic aspects such as stem thickness, number of pods, plant height, the weight of one thousand grains and yield per hectare presented by the crop. The work demonstrated that brachiaria green manure in consortium with out-of-season corn crop promoted the highest plant height and number of pods for the soybean crop in succession.
Complete mitochondrial genome of Agapornis lilianae (Psittaciformes: Psittacidae), with its phylogenetic analysis

Abstract In this paper, we reported the complete mitogenome of Agapornis lilianae. A. lilianae mitogenome is 16,720bp base pairs long. The overall base compositions of complete mitogenomes of A. lilianae is 29.66% A, 21.5% T, 34.59% C, 14.25% G. All genes exhibit the typical mitochondrial gene arrangement and transcribing directions. The phylogenetic analysis based on 21 mitochondrial sequence data suggested that A. lilianae are closely related to the same genus specie Agapornis roseicollis. The results obtained here would be useful for the conservation and phylogeny of A. lilianae.
Germination of spores of Amazonian ferns Polypodium aureum in different culture media

Abstract The greatest diversity of ferns occurs in the tropics, where approximately three in four of the species are found. In the Brazilian flora, the ferns have megadiversity, being an important plant group. The objective was to evaluate the spores germination of ferns Polypodium aureum in different types of culture medium. The sporangia were removed from fertile fronds and sterilized with sodium hypochlorite 0.57% during 30 minutes. After sterilization, the sporangia were seeded in culture media agar, MS, SH, White and B5. The experimental design was completely randomized being composed of 5 treatments (agar media, B5, SH, White and MS) and 10 replications. The ratings occurred every 3 days over a period of 45 days, counting the number of spores germinated. After this period, the germination percentage, germination time on medium, germination speed index and timing of germination were calculated. The germination percentage and the index of synchronization have not changed in function of different culture media. The medium White presented the highest average for the germination speed index whereas the agar media, MS, SH and B5 had the same germination speeds. The percentage of mortality was higher in MS medium, the White medium presented the lowest percentage of mortality, and the media composed by agar, SH and B5 showed intermediate values. The lowest average germination time occurred at the media SH and B5, since the environment composed by agar showed higher average germination time. The media MS and White showed similar results to the agar, SH and B5. Based on the obtained results, it can be concluded that the White medium is the most effective on the germination of spores of Polypodium aureum.
A 5’ UTR G-quadruplex controls localisation and translation of a potassium leak channel mRNA

RNA G-quadruplexes (G4s) are non-canonical secondary structures that have been proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within 3’ UTRs of some neuronal mRNAs are known to control their distal localisation and local translation, contributing to the distinct local proteomes that facilitate the synaptic remodelling attributed to normal cellular function. In this study, we characterise the G4 formation of a (GGN)13 repeat found within the 5’ UTR of KCNK9 mRNA, encoding the potassium 2-pore domain leak channel Task3. Using circular dichroism, we show that this (GGN)13 repeat forms a parallel G4 that exhibits the stereotypical potassium specificity of a G4, remaining thermostable under physiological ionic conditions. The G4 is inhibitory to translation of Task3, which can be overcome through the activity of the G4-specific helicase DHX36, consequently increasing K+ leak currents and decreasing resting membrane potentials in HEK293 cells. Additionally, we observe that this G4 is fundamental to ensuring the delivery of Task3 mRNA to distal primary cortical neurites. It has previously been shown that abnormal Task3 expression correlates with neuronal dysfunction, we therefore posit that this G4 is required for regulated local expression of Task3 leak channels that maintain K+ leak currents within neurons.
Dataset Decay: the problem of sequential analyses on open datasets

Open data has two principal uses: (i) to reproduce original findings and (ii) to allow researchers to ask new questions with existing data. The latter enables discoveries by allowing a more diverse set of viewpoints and hypotheses to approach the data, which is self-evidently advantageous for the progress of science. However, if many researchers reuse the same dataset, multiple statistical testing may increase false positives in the literature. Current practice suggests that the number of tests to be corrected is the number of simultaneous tests performed by a researcher. Here we demonstrate that sequential hypothesis testing on the same dataset by multiple researchers can inflate error rates. This finding is troubling because, as more researchers embrace an open dataset, the likelihood of false positives (i.e. type I errors) will increase. Thus, we should expect a dataset’s utility for discovering new true relations between variables to decay. We consider several sequential correction procedures. These solutions can reduce the number of false positives but, at the same time, can prompt undesired challenges to open data (e.g. incentivising restricted access).
DEVELOPMENTS IN THE FIELD OF AYURVEDA - PAST TO PRESENT

In the present era of competition and globalization, every branch of science is trying to retain its identity in the globe by reorientation and developing itself according to the needs by conducting various kinds of research. The present practice of Ayurveda emphasizes on traditional way. The Globalization, Patent, Intellectual Property Rights issues and Bio-piracy are becoming major challenges in the indigenous traditional medical systems like Ayurveda . In order to promote as a global medicine and equip Ayurveda to meet the global healthcare needs of the 21st century, there is an urgent need to modernize the ancient system in pace with the development of science and information technology. So considering all these facts, Ayurveda is needed to restructure in the global context to meet the rising demands of a cyber society with the application of Information, Education and Communication (IEC) technology. This review article highlights how the advancements have been taken in different fields of Ayurveda over the decades till the current scenario.
The spatial analysis of biological interactions: morphological variation responding to the co‐occurrence of competitors and resources

By sharing geographic space, species are forced to interact with one another and the contribution of this process to evolutionary and ecological patterns of individual species is not fully understood. At the same time, species turnover makes that species composition varies from one area to another, so the analysis of biological interaction cannot be uncoupled from the spatial context. This is particularly important for clades that show high degree of specialization such as hummingbirds, where any variation in biotic pressures might lead to changes in morphology. Here, we describe the influence of biological interactions on the morphology of Hylocharis leucotis by simultaneously considering potential competition and diet resources. We characterized the extent of local potential competition and local available floral resources by correlating two measurements of hummingbird diversity, floral resources and the size of morphological space of H. leucotis along its geographic distribution. We found that H. leucotis shows an important morphological variability across its range and two groups can be recognized. Surprisingly, morphological variation is not always linked to local hummingbird richness or the phylogenetic similarity of. Only in the southern part of its distribution, H. leucotis is morphologically more variable in those communities where it coexist with closely related hummingbird species. We also found that morphological variation in H. leucotis is independent from the availability of floral resources. Our results suggest that abiotic factors might be responsible for morphological differences across populations in Hylocharis leucotis being biological interactions of minor importance.
Induction of cardiac anomalies with all-trans retinoic acid in the chick embryo

Summary To study the interaction between hemodynamics and morphology in abnormal development of the heart, it is essential to have an animal model with specific and reproducible cardiac malformations. A standardized method was developed for inducing such an anomaly in the chick embryo. For this purpose, all-trans retinoic acid, dissolved in 2% dimethylsulphoxide, was applied on the vitelline membrane of the embryo in concentrations of 1.0 μgm and 0.3 μgm. A total of 207 embryos, staged according to Hamburger and Hamilton, were treated at stages 10 (33 hours of incubation) and 15 (50–55 hours of incubation). Three control groups consisted of embryos solely treated with dimethylsulphoxide, sham operated chicks, and untreated embryos, respectively. The embryos were sacrificed on the 9th, 10th and 11th days of incubation and hearts were examined by microdissection. Additional histologic studies were undertaken in 110 cases. Embryos treated with retinoic acid at both stages of development showed a high percentage of lesions falling within the general spectrum of double outlet right ventricle. The abnormality varied from merely a rightward shift of the aorta to cases with an additional subaortic ventricular septal defect, which, in combination with the rightward positioned aorta, was classified as a double outlet right ventricle. Histologic examination showed the presence of muscular tissue between the leaflets of the aortic and mitral valves. No other types of cardiac malformations were seen. Our results, with respect to timing, resemble data from studies made of hearts after surgical ablation of neural crest at comparable stages. Both method and timing of treatment with retinoic acid are important factors for the induction of specific and reproducible cardiac anomalies. This chick model allows for further detailed study of development of double outlet right ventricle, as well as the assessment of early detectable hemodynamic changes.
Analyzing Pattern of Head Injuries Sustained by Patients due to fall from Height: A Prospective Study

We analyzed the pattern of head injuries in patients of fall from a height of 9–10 feet and aged 2070 years. This prospective study was done at JNMCH, Aligarh, on 100 patients who sustained a fall and came to the casualty for treatment during a 12-month period i.e. from January 1, 2011 to December 31, 2011. Male: female ratio was 2.13:1. Maximum number of cases was in the age group of 30–40 years. Skull fractures were seen in 79 cases (79%) and intracranial injuries occurred in 87 cases (87%). The most common fracture was linear un-displaced fracture and was observed in 62 cases (62/79; 78.48%) and the most common intracranial injury was extra-axial bleed seen in 73 cases (73/87; 83.91%). Skull fractures and intracranial injuries were seen either alone or together. Fall related injuries can be prevented by avoiding excess alcohol intake and multiple self-medications without prescription during working at height, and by using appropriate footwear.
Changing ecological communities along an elevation gradient in seasonally dry tropical forest on Hispaniola (Sierra Martín García, Dominican Republic)

We report the results of systematic vascular plant and bird surveys in Seasonally Dry Tropical Forest (SDTF) across leeward and windward elevation gradients (31–884 masl) in the Sierra Martín García (SMG), Dominican Republic. We expected to see gradual, systematic changes in plant distributions with elevation owing to the strong effect of topoclimate. In contrast, we predicted bird community composition to be related only weakly to elevation, because we expected bird distributions to be more strongly related to vegetation structure than composition. Based on 48 vegetation transects, we identified seven groups that differed in their species composition, which was correlated with elevation and precipitation. The most distinctive vegetation community occurs in dry, warm, and low elevations on the leeward slope, featuring large numbers of non‐woody indicator species (those species found frequently within one group but not in other groups) even though most of its trees and shrubs represent species that are widespread. Low rainfall and shale bedrock (rather than limestone) may be the primary drivers of distinctiveness in the low‐elevation leeward plots. On the leeward slope, where we also surveyed the birds, the vegetation community changes gradually with elevation at mid‐ to high elevations. The most distinctive bird community also was associated with the low‐elevation forest on shale bedrock and was dominated by widespread species. At higher elevations, but still within leeward SDTF, the bird communities had a stronger component of species endemic either to Hispaniola or to Caribbean islands, and species turnover did not correspond to the elevation gradient.
Nondestructive and Continuous Fresh Weight Measurements of Bell Peppers Grown in Soilless Culture Systems

Fresh weight is a direct index of crop growth. It is difficult to continuously measure the fresh weight of bell peppers grown in soilless cultures, however, due to the difficulty in identifying the moisture condition of crops and growing media. The objective of this study was to develop a continuous and nondestructive measuring system for the fresh weight of bell peppers grown in soilless cultures considering the moisture content of growing media. The system simultaneously measures the trellis string’s supported weight and gravitational weight using tensile load cells. The moisture weight of growing media was calibrated during the growth period using changes in moisture content before and after the first irrigation of the day. The most stable time period for the measurement, from 03:00 to 06:00, was determined by analyzing the diurnal change in relative water content. To verify the accuracy of the system, the fruits, stems, leaves, and roots’ fresh weights were measured manually. The fresh weights measured by the developed system were in good agreement with those manually measured. The results confirm that our system can reliably and accurately measure fresh weights of bell peppers grown in soilless cultures. This method can be applied to continuous growth data collection for other crops grown in soilless cultures.
Reward Prediction Error Signaling during Reinforcement Learning in Social Anxiety Disorder is altered by Social Observation

BACKGROUND Dysfunctional expectations of impending social or performance outcomes are core features of Social Anxiety Disorder (SAD) but often lack formal definition in clinical research. Reinforcement learning (RL) models offer a framework to define changes in outcome expectations in a formal way by computing the prediction error (PE). This study quantifies the updating of expectations by PEs in SAD and investigates alterations in RL regions associated with PE signaling. METHOD 48 adult participants (24 diagnosed with SAD and 24 age-, gender-, and education- matched healthy controls (HC)) underwent event-related functional magnetic resonance imaging while learning from probabilistic feedback. Crucially, both groups completed two parallel versions of the task: one in which they learned under scrutiny (social observation) and one in which they learned without being overtly evaluated (non-social control condition). RESULTS Coupling to prediction errors in SAD was elevated in dorsomedial prefrontal cortex (DMPFC) when learning under observation. These findings provide the first evidence that PE signaling during social performance situations in SAD is associated with hypersensitive response signatures in DMPFC, a brain region associated with using others’ value standards as a proxy for one’s own value standards. Dynamic Causal Modelling further revealed that RPE-modulated connectivity from ventral pallidum to DMPFC during observation was reduced in SAD. CONCLUSIONS The present results corroborate a crucial role of DMPFC in SAD, which corresponds to dysfunctional expectations about others’ alleged performance standards that play a prominent role in current models of the disorder.
An exploration into the effectiveness of the transition made between the Early Years Foundation Stage to Key Stage One

A small scale research study is to explore aspects that influence the success of the transition made from the Early Years Foundation Stage (FS) to Key Stage One (KSO); in order to ascertain how effective it is for children. Furthermore, the study intends to research how children feel about this transition that they have to make; to understand if practitioners and policy have it right for them.
The complete chloroplast genome of Swertia cordata

Abstract Swertia cordata, a herbaceous plant, has been used in medicines as an alternative febrifuge and anthelmintic. In this study, the complete chloroplast DNA sequence of S. cordata was assembled. It is 153,429 bp in length, including a large single-copy region of 83,613 bp and a small single-copy region of 18,038 bp separated by a pair of inverted repeat regions of 25,889 bp each. A total of 129 genes are detected, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The complete chloroplast genome of S. cordata will help to study the genetic diversity and phylogenetic analysis of Swertia.
Energy landscape steering in SecYEG mediates dynamic coupling in ATP driven protein translocation

The Sec translocon is a transmembrane assembly highly conserved among all forms of life as the principal route for transport of polypeptides across or into lipid bilayers. In bacteria translocation involves allosteric communication between the membrane pore SecYEG and the associated SecA ATPase. Using singlemolecule fluorescence we reveal that slow conformational changes associated with the ATPase SecA modulate fast opening and closure of the SecY lateral gate. Such a mismatch of timescales is not compatible with direct coupling between SecA and SecYEG. A dynamic allosteric model is proposed in which the SecA ATPase cycle ‘steers’ the energy landscape for SecY pore opening. We map the experimental traces onto reduced reaction coordinates derived from molecular dynamics trajectories, providing a model for the energy landscape and a structural interpretation of the associated dynamics. Dynamic allostery may be common among motor ATPases that drive conformational changes in molecular machines.
a universal method of protoplast isolation and transient expression in plants

Protoplasts isolated from plant tissues have been testified as useful and versatile materials for performing cell-based experiments such as protein subcellular localization, in vivo protein-protein interaction, determination of vacuolar pH and promoter activity. Protoplast isolation and transient expression methods have already been reported in some plants, which with some limitations for universal application to some extent. In this report, we presented an improved method of protoplast isolation and transient expression, which was verified by using four representative plant materials including Arabidopsis, chrysanthemum, tomato and apple. To illustrate the practicability of the method, we transiently expressed the Green Fluorescent Protein (GFP) using chrysanthemum leaf protoplasts, and observed that the fluorescent protein could be successfully delivered into protoplasts under optimal conditions. In all, the results including protoplast isolation and plastid transfection can be obtained in only two days, which efficiently saving much time compared with corresponding protocols. The cell system offers reliable guidelines for further comprehensive analysis of complex regulatory mechanisms in whole-plant physiology, immunity, growth and development.
Complete mitochondrial genome of the Partridge Shank chicken (Galliformes: Phasianidae)

Abstract Partridge Shank chicken is a valuable broiler breed in China. The first complete mitochondrial DNA (mtDNA) sequence of Partridge Shank chicken had been obtained using PCR amplification, sequencing and assembling. The complete mitochondrial genome was 16,788 bp in length, with the base composition of 30.2% for A, 23.7% for T, 32.5% for C and 13.5% for G. It exhibited the typical mitochondrial structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a non-coding control region (D-loop region). The phylogenetic tree construced with maximum-likelihood (ML) method based on the complete chicken mitochondrial genomes showed that the 26 chicken breeds could be divided into two groups.