Miracle-dz/UniFAR-FTUs huggingface dataset:
Dehydration and low ozone in the tropopause layer over the Asian monsoon caused by tropical cyclones: Lagrangian transport calculations using ERA-Interim and ERA5 reanalysis data

Abstract. Low ozone and high water vapour mixing ratios are common features in the Asian summer monsoon (ASM) anticyclone; however, low ozone and low water vapour values were observed near the tropopause over Kunming, China, within the ASM using balloon-borne measurements performed during the SWOP (sounding water vapour, ozone, and particle) campaign in August 2009 and 2015. Here, we investigate low ozone and water vapour signatures in the upper troposphere and lower stratosphere (UTLS) using FengYun-2D, FengYun-2G, and Aura Microwave Limb Sounder (MLS) satellite measurements and backward trajectory calculations. Trajectories with kinematic and diabatic vertical velocities were calculated using the Chemical Lagrangian Model of the Stratosphere (CLaMS) trajectory module driven by both ERA-Interim and ERA5 reanalysis data. All trajectory calculations show that air parcels with low ozone and low water vapour values in the UTLS over Kunming measured by balloon-borne instruments originate from the western Pacific boundary layer. Deep convection associated with tropical cyclones over the western Pacific transports ozone-poor air from the marine boundary layer to the cold tropopause region. Subsequently, these air parcels are mixed into the strong easterlies on the southern side of the Asian summer monsoon anticyclone. Air parcels are dehydrated when passing the lowest temperature region (< 190 K) at the convective outflow of tropical cyclones. However, trajectory calculations show different vertical transport via deep convection depending on the employed reanalysis data (ERA-Interim, ERA5) and vertical velocities (diabatic, kinematic). Both the kinematic and the diabatic trajectory calculations using ERA5 data show much faster and stronger vertical transport than ERA-Interim primarily because of ERA5's better spatial and temporal resolution, which likely resolves convective events more accurately. Our findings show that the interplay between the ASM anticyclone and tropical cyclones has a significant impact on the chemical composition of the UTLS during summer.
EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions

Long-range regulation by distal enhancers is crucial for many biological processes. The existing methods for enhancer-target gene prediction often require many genomic features. This makes them difficult to be applied to many cell types, in which the relevant datasets are not always available. Here, we design a tool EAGLE, an enhancer and gene learning ensemble method for identification of Enhancer-Gene (EG) interactions. Unlike existing tools, EAGLE used only six features derived from the genomic features of enhancers and gene expression datasets. Cross-validation revealed that EAGLE outperformed other existing methods. Enrichment analyses on special transcriptional factors, epigenetic modifications, and eQTLs demonstrated that EAGLE could distinguish the interacting pairs from non- interacting ones. Finally, EAGLE was applied to mouse and human genomes and identified 7,680,203 and 7,437,255 EG interactions involving 31,375 and 43,724 genes, 138,547 and 177,062 enhancers across 89 and 110 tissue/cell types in mouse and human, respectively. The obtained interactions are accessible through an interactive database enhanceratlas.org. The EAGLE method is available at https://github.com/EvansGao/EAGLE and the predicted datasets are available in http://www.enhanceratlas.org/. Author summary Enhancers are DNA sequences that interact with promoters and activate target genes. Since enhancers often located far from the target genes and the nearest genes are not always the targets of the enhancers, the prediction of enhancer-target gene relationships is a big challenge. Although a few computational tools are designed for the prediction of enhancer-target genes, it’s difficult to apply them in most tissue/cell types due to a lack of enough genomic datasets. Here we proposed a new method, EAGLE, which utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions. Comparing with other existing tools, EAGLE displayed a better performance in the 10-fold cross-validation and cross-sample test. Moreover, the predictions by EAGLE were validated by other independent evidence such as the enrichment of relevant transcriptional factors, epigenetic modifications, and eQTLs. Finally, we integrated the enhancer-target relationships obtained from human and mouse genomes into an interactive database EnhancerAtlas, http://www.enhanceratlas.org/.
The Use of Organic Nano-Supplements of Fertilizer for Lily Forcing Period

Lilium is one of the most important ornamental plants after roses, carnations and chrysanthemum in the world that is requested as potted of cut flowers. It is so important to consider its quality along with its production rate in terms of yield (quantity). However, it always needs to intend the product costs aside from quantity and quality. Fertilizer utilization is so important and this may be improved by compounds that promote it and also have synergetic effects themselves. We examined both carboxymethylated chitosan (CMC) and magnetic nano-carbocymethylated chitosan (MNCC) to produce Lilium bulb and advised them especially magnetic chitosan. In this study, these compounds (magnetic and non-magnetic chitosan) at concentrations of zero, 2.5, 5, 10 and 15 mg/l were examined during lily forcing in three cultivars, including Cherbourg, Navona, Brunello, which are from Asiatic and Oriental lilies. The results showed that highest concentrations (10 and 15 mg/l) among between examined concentrations regardless of compounds types and cultivars did not make toxicity and had significant effects on plants biology and physiology [contents of carbohydrates and enzymes affecting these carbohydrates (amylases)]. However, for observing morphological changes may be need to use higher concentrations of these compounds. Note that this needs to examine the non-toxicity of higher concentrations in future studies.
Real-Time Object Tracking with Motion Information

Motion is a vital information for object tracking. However, most existing methods, including the classic Siamese FC network [1], only consider the object appearance, and ignore the vital motion feature. In this paper, we design a dual-network object tracker, which is called DOT for short, to effectively combine the appearance and motion information. Our method employs two branches, S-net and M-net, to exploit the appearance and motion information respectively. Moreover, an attention fusion module is also introduced to effectively integrate these two aspects. The experiments carried out on OTB-2013 demonstrate the improvement on object tracking by the integration of motion information with our dual-network and attention fusion.
Liver Glycogen Phosphorylase Deficiency Leads to Profibrogenic Phenotype in a Murine Model of Glycogen Storage Disease Type VI

Mutations in the liver glycogen phosphorylase (Pygl) gene are associated with the diagnosis of glycogen storage disease type VI (GSD‐VI). To understand the pathogenesis of GSD‐VI, we generated a mouse model with Pygl deficiency (Pygl−/−). Pygl−/− mice exhibit hepatomegaly, excessive hepatic glycogen accumulation, and low hepatic free glucose along with lower fasting blood glucose levels and elevated blood ketone bodies. Hepatic glycogen accumulation in Pygl−/− mice increases with age. Masson's trichrome and picrosirius red staining revealed minimal to mild collagen deposition in periportal, subcapsular, and/or perisinusoidal areas in the livers of old Pygl−/− mice (>40 weeks). Consistently, immunohistochemical analysis showed the number of cells positive for alpha smooth muscle actin (α‐SMA), a marker of activated hepatic stellate cells, was increased in the livers of old Pygl−/− mice compared with those of age‐matched wild‐type (WT) mice. Furthermore, old Pygl−/− mice had inflammatory infiltrates associated with hepatic vessels in their livers along with up‐regulated hepatic messenger RNA levels of C‐C chemokine ligand 5 (Ccl5/Rantes) and monocyte chemoattractant protein 1 (Mcp‐1), indicating inflammation, while age‐matched WT mice did not. Serum levels of aspartate aminotransferase and alanine aminotransferase were elevated in old Pygl−/− mice, indicating liver damage. Conclusion: Pygl deficiency results in progressive accumulation of hepatic glycogen with age and liver damage, inflammation, and collagen deposition, which can increase the risk of liver fibrosis. Collectively, the Pygl‐deficient mouse recapitulates clinical features in patients with GSD‐VI and provides a model to elucidate the mechanisms underlying hepatic complications associated with defective glycogen metabolism.
Cryopreservation of horse semen with a liposome and trehalose added extender

The aim of the study was to evaluate the effect of cryopreserved equine semen in the presence of trehalose-loaded liposomes on the integrity and function of sperm cells. Six ejaculations of five stallions collected with an artificial vagina were used. The ejaculates were diluted with INRA 96® 2:1 v/v and transported at 22 °C to the laboratory. Before cryopreservation, the semen was diluted with INRA Freeze® to obtain the following treatments: T1) INRA Freeze® (control), T2) INRA Freeze® + liposomes, T3) INRA Freeze® + liposomes+trehalose. Data were analysed using the Kruskal Wallis test. The percentages of sperm with intact DNA were 54.5, 57.9, and 64.8% for T1, T2 and T3, respectively (P>0.05). When evaluating the acrosomal and capacitation state after filtering with Percoll®, the percentages of spermatozoa without acrosome reaction and without capacitation were 67.8, 79.2 and 68.1% in T1, T2, and T3, respectively (P>0.05), while the capacitated sperm without acrosome reaction and without capacitation was similar in T1 (47%) and T3 (32%) (P>0.05), and lower in T2 (16%) before filtering with Percoll®. The use of liposomes and liposome-trehalose did not affect on the functional status and nuclear chromatin of the equine sperm after freezing, but it did affect the percentage of capacitated sperm without acrosome reaction after selecting the thawed semen using the Percoll® gradient.
Investigating the Potential of Different Modeling Setups in Simulating a Flameless Furnace Using Global and Detailed Kinetic Mechanisms

ABSTRACT Attempts were made to reproduce the laboratory measurements of flameless combustion systems using numerical simulation tools, for different chambers designs. In many cases, a significant discrepancy is reported between the experimental measurements and the numerical results. In this work, we have successfully reproduced the reported experimental results (velocity field, temperature field, and the outlet dry NOx emissions) of the “FOUR” MILD combustion facility (proposed by C. Rottier). An acceptable accuracy was achieved in two reference test cases. A concise discussion is presented on the available literature on the subject of numerical modeling for the flameless combustion mode. The use of two turbulence models was explored (standard k-ε, and modified k-ε), along with two kinetic mechanisms (a global 2-step CH4 combustion mechanism, and the more detailed KEE-58 mechanism). The commercial ANSYS FLUENT® software was used in these simulations. The results of seven different modeling setups are presented, comparing the predictions of temperature fields, and NOX emissions. Features such as the onset of premature ignition and the reactants entrainment ratio are also discussed. Our results show that the most accurate model setup employs the following: SKE – KEE-58 – EDC with a reduced volume fraction constant. In regards to reproducing the measurements from the “FOUR” facility, we are not aware of a similar research that runs a concise discussion on the predictions of such broad and different modeling setups.
Origin and protection of middle-European bees in Europe

The population of the honey bee, Apis mellifera, continues to shrink. The middle-European bee, Apis m. mellifera, is particularly at risk in Europe. The drop in the number of middle-European bees is so huge that the insect is under the threat of extinction. Today, they live on small areas covered by the protection of genetic resources. Apis m. mellifera is protected mainly in areas where this species evolved: for instance, in Switzerland, Latvia, Norway, Sweden, Finland, Denmark, France, Germany, Poland or Russia. This paper presents methods used to preserve and protect Apis m. mellifera in Europe and research on the descent and original extent of the species. It also reviews opportunities created by the implementation of various types of programs for the protection of genetic resources of Apis m. mellifera and ways of employing morphological and genetic studies for the conservative breeding of middle-European bees. The paper demonstrates that the protection of Apis m. mellifera in Europe is necessary, considering the decreasing size, and the threat of hybridization, of this population. The use of the morphometric evaluation and DNA analysis methods have made it possible to track and compare likely directions of propagation of genes in the long history of evolution of bees. Moreover, these methods have given us better insight into the ongoing processes. The current use of these methods for reliable identification of bee breeds helps to protect Apis m. mellifera more effectively. European programs for the protection of genetic resources of bees are based on the following two main paradigms: the breeding of local isolated populations on islands and establishment of protected inland areas for the conservative breeding of contained swarms. All these programs share and are successful in achieving the goal that consists in the preservation of the characteristics of Apis m. mellifera as unchanged as possible, with retention of the maximum genetic diversity of the species.
Back to the Basics: Resting State Functional Connectivity of the Reticular Activation System in PTSD and its Dissociative Subtype

Background Brainstem and midbrain neuronal circuits that control innate, reflexive responses and arousal are increasingly recognized as central to the neurobiological framework of post-traumatic stress disorder (PTSD). The reticular activation system represents a fundamental neuronal circuit that plays a critical role not only in generating arousal but also in coordinating innate, reflexive responding. Accordingly, the present investigation aims to characterize the resting state functional connectivity of the reticular activation system in PTSD and its dissociative subtype. Methods We investigated patterns of resting state functional connectivity of a central node of the reticular activation system, namely, the pedunculopontine nuclei, among individuals with PTSD (n = 77), its dissociative subtype (PTSD+DS; n = 48), and healthy controls (n = 51). Results Participants with PTSD and PTSD+DS were characterized by within-group pedunculopontine nuclei resting state functional connectivity to brain regions involved in innate threat processing and arousal modulation (i.e., midbrain, amygdala, ventromedial prefrontal cortex). Critically, this pattern was most pronounced in individuals with PTSD+DS, as compared to both control and PTSD groups. As compared to participants with PTSD and controls, individuals with PTSD+DS showed enhanced pedunculopontine nuclei resting state functional connectivity to the amygdala and the parahippocampal gyrus as well as to the anterior cingulate and the ventromedial prefrontal cortex. No group differences emerged between PTSD and control groups. In individuals with PTSD+DS, state derealization/depersonalization was associated with reduced resting state functional connectivity between the left pedunculopontine nuclei and the anterior nucleus of the thalamus. Altered connectivity in these regions may restrict the thalamo-cortical transmission necessary to integrate internal and external signals at a cortical level and underlie, in part, experiences of depersonalization and derealization. Conclusions The present findings extend the current neurobiological model of PTSD and provide emerging evidence for the need to incorporate brainstem structures, including the reticular activation system, into current conceptualizations of PTSD and its dissociative subtype.
Effect of Extract Crushed Fenugreek Seeds as Feed Additive on some Blood Parameters, Milk Yield and Its Composition of Lactating Egyptian Buffaloes

Milk production & composition and some blood parameters were examined in Egyptian buffaloes as affected by supplemented basal diet by crushed Fenugreek seeds. Sixteen lactating buffaloes aged 5-7 years (at the third and fifth seasons of lactation); 45 days from calving were divided into four dietary treatments, 4 animals per each. Buffaloes were fed individually on basal diet ration [concentrate feed mixture (CFM) and rice straw (RS)] according to developing of body weight and milk production during the whole experimental periods. The crushed Fenugreek seeds were given as feed additives to the basal ration at a level 100, 150 and 200 g/buffalo/ day for 2, 3 and 4 treatments, respectively, while the 1 treatment considered as control.The results indicated that the dry matter intake (DMI) was significantly (P<0.05) increased in T3 and T3 than other groups. Also, crushed fenugreek seeds significantly(P<0.05) increased nutrient digestibilities (DM, OM, CP and EE). The total milk yields were 806.4, 896.0, 952.0 and 907.2 Kg, respectively. Also, the overall daily milk yield was 7.2, 8.0, 8.5 and 8.1 Kg/h/d for T1, T2, T3 and T4, respectively. Lactose percentage significantly (P<0.05) increased in treated buffaloes. However, fat percentage was significantly (P<0.05) decreased with treated buffaloes. The calculated efficiency of milk yield/DMI was increased (P<0.05) in Fenugreek treated buffaloes. The addition of crushed Fenugreek seeds increased (P<0.05) the level of blood plasma prolactin and GPT in lactating buffaloes.It could be concluded that adding fenugreek seeds to buffalo's rations at 100, 150 and 200 g /buffalo/day led to raising economic efficiency by about 6.6, 3.95 and 7.89 %, respectively and it could be recommended to improve feed efficiency, milk yield and economic efficiency.
Martin's peripheral embryo – unique but not a phylogenetic ‘orphan’ at the base of his family tree: a tribute to the insight of a pioneer seed biologist

Abstract As a tribute to A.C. Martin's classic work on embryos in seeds, we have attempted to gain a better understanding of the peripheral embryo, which puzzled Martin. The peripheral embryo is strongly curved and in contact with the inner surface of the seed coat, and Martin placed it at the base of his family tree of seed phylogeny and called it a ‘phylogenetic orphan’. We evaluated ovule/seed development, kind of embryo and occurrence of perisperm in families with and without a peripheral embryo. All families with a peripheral embryo occur in the Caryophyllales. Seeds with a peripheral embryo have a low cotyledon width:radicle width ratio that coincides with Martin's (full-sized) linear embryo. The peripheral embryo develops in campylotropous and/or amphitropous ovules and is pushed to the side of the seed as the perisperm develops. Linear-full embryos and perisperm are widely distributed across extant angiosperms but are rarely found together, except in core Caryophyllales. The non-core Caryophyllales with endosperm and various kinds of embryos, including the linear-full, diverged before the core Caryophyllales. Thus, the ancestral linear-full embryo appears to have been retained when the core lineage developed campylotropous and/or amphitropous ovules and perisperm. Seeds with a peripheral embryo merit a position on Martin's family tree; however, the position should be a side branch (‘orphan’) slightly above (more advanced than) his linear embryo and not at the base. We conclude that Martin had great insight into the relationships between the kinds of embryos and rightly questioned the position of the peripheral embryo.
EXAMINATION OF MORPHOLOGY AND SURFACE STRUCTURE OF COCCI LACTIC ACID BACTERIA BY SCANNING ELECTRON MICROSCOPE AND IMAGE ANALYSIS.

Lactic acid bacteria (LAB) widely distributed in nature and play an important role in much food fermentation. Bacteria cell morphology is useful and valuable characteristics used in the classification and identification of bacteria. Therefore, cell morphological shape and size of six strains of cocci LAB were studied in broth and milk media using scanning electron microscope (SEM) and image analysis technique. Results indicated that, Pediococcus acidilactica was the smallest strain in size and Streptococcus thermophilus was smaller than Enterococcus and lactococcus strains. Except Pediococcus acidilactica, cells of other strains were generally smaller in size when grown in milk media than in broth media. Cells of cocci LAB were not perfect spherical cells. In conclusion, cell shape and size parameters can be used for identification and classification of cocci LAB with determination of define standard conditions for growth.
Exploring the effect of mono- and di-fluorinated triphenylamine-based molecules as electron donors for dye-sensitised solar cells

ABSTRACT Dye that is consisting of donor-π-π-linkers-acceptor (D-π-π-A) is characterised by enhancement of light-harvesting capability in dye-sensitised solar cell (DSSC) applications. In this work, the DFT and TDDFT using the CAM-B3LYP XC-functional with 6-31G+(d) basis set and were used to study the geometrical, electronic, and photovoltaic properties of four dyes. Two of the investigated dyes are previously reported as successful photosensitisers with power conversion efficiencies of 8.22 and 7.0%, and two are novel designed ones. The investigated dyes are based on triphenylamine (TPA) as electron-donor and cyanoacrylic acid (CA) as electron-acceptor groups, and two π-linkers, i.e. dihydrothieno-dioxine (DHO) and fluorophenylene (FP). The four dyes are different in the FP unit which has Fluorine (F) atom/s in different position and with a different number. The study aims to: (1) justify the reported superiority performance of T2FC (with one F atom at the ortho-position with respect to the CA unit) over the T3FC (with one F atom at the meta-position), and (2) explore the effect of incorporating another F atom at the second ortho-position (T26FC) or at the meta-position (T35FC). The results are supported by the data obtained from calculations of adsorption parameters of dyes adsorbed on (TiO2)24 anatase (1 0 1).