Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstructing species evolutionary trees using the numerical features of microRNA

Research has revealed that some microRNAs show obvious lineage or species specificity, but others show highly conserved properties among species. Based on these properties, we aimed to reconstruct a species evolution tree using a new technique that refers to the numerical features of microRNA. First, we selected 132 microRNA numerical features that included base content, secondary structure matching state frequency, free energy features and information entropy features, and 32 species that included 22 animals, 9 plants and a representative virus group. Second, we found several significantly different numerical features among lineages or species by statistical analysis and confirmed that differences in each numerical feature were not identical. Third, we designed a comprehensive feature and confirmed that it showed obvious lineage and species specificity. Last, species trees were built using the comprehensive feature. The results showed that the reconstructed species tree was almost in keeping with the actual chronological order of species evolution. This indicated that our analysis was effective. Our research strategy offers a new route for investigating species evolution.
Rauchen im Jugendalter in England und Deutschland, 2001 – 2016

Zusammenfassung Ziel Deskription des Rauchverhaltens Jugendlicher aus England und Deutschland über einen Beobachtungszeitraum von 15 Jahren. Methode 11 wiederholte Querschnittserhebungen mit insgesamt 107 485 Personen im Alter von 11 bis 15 Jahren wurden zwischen 2001 und 2016 in England und Deutschland durchgeführt. Erfasst wurde a) der relative Anteil Jugendlicher, die jemals in ihrem Leben ein konventionelles Tabakprodukt geraucht hatten, und b) der relative Anteil aktuell rauchender Jugendlicher, d. h. Jugendliche, die „gelegentlich“ bzw. „ständig“ oder „regelmäßig“ rauchten. Ergebnisse Es zeigte sich im Beobachtungszeitraum eine signifikant stärkere Reduktion des Anteils Jugendlicher mit Raucherfahrung in Deutschland (von 52 % auf 10 %) im Vergleich zu England (von 44 % auf 19 %). Der Anteil aktuell rauchender Jugendlicher fiel im Beobachtungszeitraum in Deutschland um 16 Prozentpunkte auf 3 % und in England um 12 Prozentpunkte auf 7 % (kein signifikanter Unterschied). Schlussfolgerungen Die Daten liefern einen Hinweis auf einen stärkeren Trend zum Nie-Rauchen in Deutschland im Vergleich zu England und auf einen vergleichbaren Trend zum selteneren aktuellen Rauchen in den beiden Ländern. Kausale Schlussfolgerungen sind aufgrund der Studienanlage nicht möglich.
Effect of Changing Heart Rate on the Ocular Pulse and Dynamic Biomechanical Behavior of the Optic Nerve Head

Purpose To study the effect of changing heart rate on the ocular pulse and the dynamic biomechanical behaviour of the optic nerve head (ONH) using a comprehensive mathematical model. Methods In a finite element model of a healthy eye, a biphasic choroid consisted of a solid phase with connective tissues and a fluid phase with blood, and the lamina cribrosa (LC) was viscoelastic as characterized by a stress-relaxation test. We applied arterial pressures at 18 ocular entry sites (posterior ciliary arteries) and venous pressures at four exit sites (vortex veins). In the model, the heart rate was varied from 60 bpm to 120 bpm (increment: 20 bpm). We assessed the ocular pulse amplitude (OPA), pulse volume, ONH deformations and the dynamic modulus of the LC at different heart rates. Results With an increasing heart rate, the OPA decreased by 0.04 mmHg for every 10 bpm increase in heart rate. The ocular pulse volume decreased linearly by 0.13 µL for every 10 bpm increase in heart rate. The storage modulus and the loss modulus of the LC increased by 0.014 MPa and 0.04 MPa, respectively, for every 10 bpm increase in heart rate. conclusions In our model, the OPA, pulse volume, and ONH deformations decreased with an increasing heart rate, while the LC became stiffer. The effects of blood pressure / heart rate changes on ONH stiffening may be of interest for glaucoma pathology. Support Singapore Ministry of Education, Academic Research Fund, Tier 2 (R-397-000-280-112). Commercial relationship None
Prioritizing management goals for stream biological integrity within the developed landscape context

Stream management goals for biological integrity may be difficult to achieve in developed landscapes where channel modification and other factors constrain in-stream conditions. To evaluate potential constraints on biological integrity, we developed a statewide landscape model for California that estimates ranges of likely scores for a macroinvertebrate-based index that are typical at a site with the observed level of landscape alteration. This context can support prioritization decisions for stream management, like identifying reaches for restoration or enhanced protection based on how observed scores relate to model predictions. Median scores were accurately predicted by the model for all sites in California with bioassessment data (Pearson correlation r = 0.75 between observed and predicted for calibration data, r = 0.72 for validation). The model also predicted that 15% of streams statewide are constrained for biological integrity within their present developed landscape, particularly for urban and agricultural areas in the South Coast, Central Valley, and Bay Area regions. We worked with a local stakeholder group from the San Gabriel River watershed (Los Angeles County, California) to evaluate how the statewide model could support local management decisions. To achieve this purpose, we created an interactive application, the Stream Classification and Priority Explorer, that compares observed scores with predictions from the landscape model to assign priorities. We observed model predictions consistent with the land-use gradient from the upper to lower watershed, where potential limits to achieving biological integrity were more common in the heavily-urbanized lower watershed. However, most of the sites in the lower watershed scored within their predicted ranges, and were therefore given a low priority for restoration. In contrast, 2 low-scoring sites in the undeveloped upper watershed were prioritized for causal assessment and possible future restoration, whereas 3 high-scoring sites were prioritized for protection. The availability of geospatial and bioassessment data at the national level suggests that these tools can easily be applied to inform management decisions at other locations where altered landscapes may limit biological integrity.
Lack of gene flow between Phytophthora infestans populations of two neighboring countries with the largest potato production

Gene flow is an important evolutionary force that enables adaptive responses of plant pathogens in response to changes in the environment and plant disease management strategies. In this study, we made a direct inference concerning gene flow in the Irish famine pathogen Phytophthora infestans between two of its hosts (potato and tomato) as well as between China and India. This was done by comparing sequence characteristics of the eukaryotic translation elongation factor 1 alpha (eEF‐1α) gene, generated from 245 P. infestans isolates sampled from two countries and hosts. Consistent with previous results, we found that eEF‐1α gene was highly conserved and point mutation was the only mechanism generating any sequence variation. Higher genetic variation was found in the eEF‐1α sequences in the P. infestans populations sampled from tomato compared to those sampled from potato. We also found the P. infestans population from India displayed a higher genetic variation in the eEF‐1α sequences compared to China. No gene flow was detected between the pathogen populations from the two countries, which is possibly attributed to the geographic barrier caused by Himalaya Plateau and the minimum cross‐border trade of potato and tomato products. The implications of these results for a sustainable management of late blight diseases are discussed.
Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence

To persist when nutrient sources are limited, aerobic soil bacteria metabolize atmospheric hydrogen (H2). This process is the primary sink in the global H2 cycle and supports the productivity of microbes in oligotrophic environments. H2-metabolizing bacteria possess [NiFe] hydrogenases that oxidize H2 to subatmospheric concentrations. The soil saprophyte Mycobacterium smegmatis has two such [NiFe] hydrogenases, designated Huc and Hhy, that belong to different phylogenetic subgroups. Both Huc and Hhy are oxygen-tolerant, oxidize H2 to subatmospheric concentrations, and enhance bacterial survival during hypoxia and carbon limitation. Why does M. smegmatis require two hydrogenases with a seemingly similar function? In this work, we resolved this question by showing that Huc and Hhy are differentially expressed, localized, and integrated into the respiratory chain. Huc is active in late exponential and early stationary phases, supporting energy conservation during mixotrophic growth and transition into dormancy. In contrast, Hhy is most active during long-term persistence, providing energy for maintenance processes following carbon exhaustion. We also show that Huc and Hhy are obligately linked to the aerobic respiratory chain via the menaquinone pool and are differentially affected by respiratory uncouplers. Consistently, these two enzymes interacted differentially with the respiratory terminal oxidases. Huc exclusively donated electrons to, and possibly physically associated with, the proton-pumping cytochrome bcc–aa3 supercomplex. In contrast the more promiscuous Hhy also provided electrons to the cytochrome bd oxidase complex. These results indicate that, despite their similar characteristics, Huc and Hhy perform distinct functions during mycobacterial growth and survival.
GEO2RNAseq: An easy-to-use R pipeline for complete pre-processing of RNA-seq data

In transcriptomics, the study of the total set of RNAs transcribed by the cell, RNA sequencing (RNA-seq) has become the standard tool for analysing gene expression. The primary goal is the detection of genes whose expression changes significantly between two or more conditions, either for a single species or for two or more interacting species at the same time (dual RNA-seq, triple RNA-seq and so forth). The analysis of RNA-seq can be simplified as many steps of the data pre-processing can be standardised in a pipeline. In this publication we present the “GEO2RNAseq” pipeline for complete, quick and concurrent pre-processing of single, dual, and triple RNA-seq data. It covers all pre-processing steps starting from raw sequencing data to the analysis of differentially expressed genes, including various tables and figures to report intermediate and final results. Raw data may be provided in FASTQ format or can be downloaded automatically from the Gene Expression Omnibus repository. GEO2RNAseq strongly incorporates experimental as well as computational metadata. GEO2RNAseq is implemented in R, lightweight, easy to install via Conda and easy to use, but still very flexible through using modular programming and offering many extensions and alternative workflows. GEO2RNAseq is publicly available at https://anaconda.org/xentrics/r-geo2rnaseq and https://bitbucket.org/thomas_wolf/geo2rnaseq/overview, including source code, installation instruction, and comprehensive package documentation.
A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae

Crocodilians are an economically, culturally, and biologically important group. To improve researchers’ ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple non-coding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, ten in C. porosus and six in A. mississippiensis. The annotated C. porosus genome will serve as an important platform for osmoregulatory, physiological and sex determination studies, as well as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods.
Role of Migratory Birds in Transmission of E. Coli Infection to Commercial Poultry

A total of 100 migratory birds were collected from Dakahlia and Damietta Governorates. All samples were subjected to clinical and postmortem (P.M) examination followed by bacteriological examination for detection of Avian Pathogenic E. coli infection. Out of 100 samples, 25 samples were distinguished as positive for Escherichia coli. Accurately, 4 E. coli serogroupes were identified in 25 positive samples and the most predominant serogroup were O125 (76 %), O126 (8%), O158 (8%), O86 (4%) and untypable E. coli (4 %). Studying antibiotic resistance pattern of E. coli isolates revealed that 64% of the isolates demonstrated multidrug resistance pattern. The highest resistance rates were recorded against Ciprofloxacin (88%) followed by Gentamycin (80%), Streptomycin (68%), Norfloxacin (40%), Colistin (16%) and Doxycycline (4%). Conventional PCR was done for detection of virulence genes (fimH, tsh, eaeA, stx1and stx2) in 10 isolates and the results revealed that; 100%, 60%, 40%, 0% and 0% were positive for these virulence genes, respectively. By studying the effect of one isolate of O125 No. 78 in commercial chicken (cobb) and ducks (pekin) we found that, more sever signs, pathological lesion and 100% mortality rate in cobb chicken than pekin ducks which had less signs nor pathological lesion with 10% mortality rate only.
Utility of Combining Epworth Sleepiness Scale, STOP-BANG and Perioperative Sleep Apnea Prediction Score for Predicting Absence of Obstructive Sleep Apnea

Aims and objective: To correlate and predict obstructive sleep apnea with the help of 3 sleep questionnaire–perioperative sleep apnea prediction score (PSAP), STOP-BANG, Epworth sleepiness scale score (ESS). Materials and methods: Prospective study of 69 patients were subjected to 3 sleep questionnaire (PSAP, STOP-BANG, and ESS), then they all were subjected to polysomnography. Obstructive sleep apnea (OSA) was defined for AHI>15, and all these three questionnaires final score was correlated with apnea-hypopnea index (AHI), and their utility in predicting OSA was calculated (separately as well as when three questionnaire score taken together) using receiver operating characteristic (ROC) curves. Results: Total 69 patients with the mean age of 50.29 ± 11.37 years, and male: female of 2:1 and mean body mass index (BMI) of 31.27 ± 7.253 kg/m, mean AHI was calculated to be 19.63 ± 22. 49 and it significantly correlated with PSAP 4.52 ± 1.596 (r = 0.376,p = 0.001), STOP-BANG 4.493 ± 1.711 (r = 0.303, p = 0.011), ESS 13.00 ± 6.782 (r = 0.395, p = 0.001). PSAP (area under curve (AUC) = 0.761) had a better prediction for OSA than STOP-BANG (AUC = 0.697) and ESS (AUC = 0.669) according to Receiver operating curve. Cut off values for diagnosis of OSA from our data was calculated to be 4 for PSAP (sensitivity: 81% specificity: 59%), 4 for STOP-BANG (sensitivity: 65.4%, specificity: 60%) and 11 for ESS (sensitivity: 73.1%; specificity: 48.8%). Based on these cut off value 18 patients were found to be having all questionnaire positive of which 11 had OSA (AHI>15) and rest seven non-OSA. A total of 11 patients were all questionnaire negative of which 10 were non-OSA (AHI < 15). So when three questionnaires were combined to predict OSA their sensitivity was 91.66% and specificity was 58.8%, a positive predictive value of 61% and negative predictive value of 90.11%. Conclusion: Perioperative sleep apnea prediction score (PSAP), STOP-BANG, ESS when taken together can be very helpful in screening for OSA and if all scores are negative it virtually rules out OSA.
behavioral and physiological consequences of overstocking dairy cattle

Overstocked group pens continue to be a challenge for many dairy producers. There are many reasons why overstocking may occur, including an unexpectedly busy calving month, too many replacement heifers, or herd expansion before barn expansion. While overstocking may be a short-term solution to a management challenge, a growing body of science demonstrates that overcrowding results in both behavioral and physiological changes that could compromise future performance, productivity and animal welfare. Overstocking interferes with normal behavioral time budgets of dairy cows, disrupting both feeding and lying activity. Aggressive competitive interactions are also more frequent when cows are crowded at the feed bunk or lying stalls, particularly for socially subordinate animals. More recent research has found that overstocking can affect physiological processes, including energy metabolism and glucocorticoid secretion. This research has dramatically improved our understanding of the ways in which overstocking affects dairy cattle health and welfare, and collectively will enable improved science-based recommendations on how best to manage intensively housed dairy cattle.
Chemical attributes of soil irrigated with treated sewage effluent and cultivated with bell pepper

The use of treated sewage effluents (TSE) for irrigation purposes is a viable alternative for wastewater reuse and nutrient supply to the soil, which represent the two main environmental benefits. This work therefore evaluated the effect of the application of TSE on the quantity of nutrients added to the soil and changes in the chemical attributes of a Red-Yellow Latosol in the layer from 0.0 to 0.2 m cultivated with the bell pepper F1 Canary hybrid and surface drip irrigated. The experiment was carried out under field conditions from September 2015 to January 2016 in a randomized block statistical design with four replications, including the following treatments: river water, TSE, river water with base fertilization, TSE with base fertilization, TSE with cover fertilization, and TSE with cover and base fertilization. Irrigation of the bell pepper cultivation with TSE increased the level of potassium but did not affect the levels of phosphorus, organic matter and pH of the soil at the end of the growing cycle. The following amounts of nutrients were added to the soil by irrigation with TSE: 10 kg ha-1 of total nitrogen, 10 kg ha-1 of total potassium and 0.5 kg ha-1 of total phosphate. In general, TSE induced greater productivity of the peppers than those irrigated with river water, even when including mineral fertilization.
Regional bean breeding and seed systems approaches for increased impact: evidence from East and Central Africa Bean Research Network (ECABREN)

Bean production in sub-Saharan Africa is largely done by small-scale farmers (less than 2 ha), predominantly by women for both household food security and cash. Bean productivity is limited by biotic and abiotic constraints such as diseases, pests, poor soil fertility and drought (Beebe et al., 2012). One of the major interventions being pursued by regional bean research networks to address bean productivity in smallholder systems is enhancing the use of adapted varieties (Buruchara et al., 2011). Based on bean agro-ecological adaptions and market demand similarities across several African countries, a regional breeding programme based on regional constraints and variety demand was introduced by the Pan-African Bean Research Alliance (PABRA) in 1996. Through the alliance, national bean research programmes (NBRPs) in partnership with the International Center for Tropical Agriculture (CIAT) have developed a range of farmer-preferred bean varieties with useful adaptation and consumerpreferred traits. Through this alliance, countries share germplasm and variety evaluation data that accelerate the release process, often leading to simultaneous release of a variety in several countries. It is therefore logical that seed systems are developed and implemented to facilitate seed access in each member country, and to promote regional seed business development. This paper describes the PABRA approach and experience in the development of regional seed systems to facilitate access to seed of improved bean varieties by farmers.
Untangling the origin of ghost gear within the Maldivian archipelago and its impact on olive ridley (Lepidochelys olivacea) populations

There is little documentation available on the impact of abandoned, lost or discarded fishing nets (‘ghost nets’) on turtle populations. Here, we utilise data collected over a 5 year period to assess (1) if a particular net type or characteristic was identifiable as entangling more turtles and (2) if particular fishing practices (i.e. types of nets) could be managed to reduce turtle entanglement in the Maldivian archipelago. A total of 131 turtles were entangled in the 752 reported ghost nets, and olive ridley turtles Lepidochelys olivacea appeared to be the most vulnerable (making up 97% of entangled turtles). However, we estimate that the 752 nets in this study, reported over a 51 month period, could have entangled between 3400 and 12200 turtles across the Indian Ocean prior to being detected in the Maldives. Mesh size, seasonality (i.e. north east monsoon), and the presence of floats were all identified as variables significantly affecting the likelihood of turtle entanglement. The probability of entanglement increased as the mesh size in creased but decreased when floats were present. Additionally, turtles were more likely to be entangled during the north east monsoon when currents flow from east to west. Cluster analysis indicated that there were at least 11 broadly assigned net types found floating in the study area, and these were dominated by trawl and gill nets. Our analyses highlight the need for a detailed database of existing gear types coupled with gear marking to improve traceability of ghost nets in the Indian Ocean.