Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of dietary selenium requirement for Chinese egg-laying ducks

The purpose of this study was to estimate the selenium (Se) requirement of egg-laying ducks based on daily egg production and the selenoprotein glutathione peroxidase (Gpx). Five-hundred and forty laying ducks were divided into six treatments, each containing six replicates of 15 ducks. The birds were caged individually and received a Se-deficient basal diet (0.04 mg/kg) or diets supplemented with 0.08, 0.16, 0.24, 0.32, 0.40 mg/kg Se (as sodium selenite) for 6 months. The experiment consisted of two periods: an early-laying period of 2 months and the peak-laying period of 4 months. Egg production and feed intake were recorded daily. At the end of the experiment, blood samples were drawn for determination of Gpx activity in plasma (Gpx3) and in erythrocytes (Gpx1). Hepatic Gpx1 activity and relative expression of Gpx1 mRNA were also determined. Eggs (n = 6) were sampled for quality determination and Se content at the end of the experiment. The activities of plasma Gpx3, erythrocyte Gpx1 and liver Gpx1 increased in a quadratic manner (P < 0.001) with increasing supplemental Se. The mRNA abundance of hepatic Gpx1 increased linearly (P < 0.001) with dietary Se supplementation. Egg shell thickness was significantly reduced in the ducks fed 0.44 mg Se/kg (P < 0.05), indicating that higher dietary Se tends to compromise egg shell quality. Yolk and albumen contents of Se increased linearly (P < 0.0001) with dietary Se supplementation. Using quadratic broken line models, the Se requirement for daily egg production was 0.18 mg/kg for early-laying ducks and 0.24 mg/kg for peak-laying ducks; for optimal function of Gpx (peak-laying ducks), it was 0.37 mg Se/kg.
Within- and among-population genetic variation in the Southern Upland Designatable Unit of Maritime Atlantic Salmon (Salmo salar L.) Dans- et inter-population la variation génétique dans l'unité du Sud désignable Upland des Maritimes Saumon Atlantique (Salmo salar L.)

Genetic variation was surveyed at 17 microsatellite loci from 1,039 individuals from 11 rivers of the Southern Upland of Nova Scotia, and several small and large reference populations from elsewhere in Atlantic Canada. Levels of within-population genetic variation were lower in sample collections obtained from rivers of the Southern Upland compared to those obtained from New Brunswick, but generally speaking, similar to or slightly greater than those from endangered populations of the inner Bay of Fundy. Within the Southern Upland, south and southwest sample collections, including Salmon River Digby, Tusket, and Round Hill, were more genetically depauperate, with the latter exhibiting nearly half the level of allele richness observed in the more variable northeast Southern Upland collections. Based on several indicators, contemporaneous sample collections from Medway, St. Mary’s East Branch, and Salmon River Guysborough are the most genetically variable of those analyzed here from this Designatable Unit.
The flow field around a freely swimming copepod in steady motion. Part I: Theoretical analysis

The three-dimensional flow field around a free-swimming copepod in steady motion was studied theoretically. This study was based on coupling the Navier-Stokes equations with the dynamic equations for an idealized body of a copepod. To allow analytical solutions to the flow field, three simplifications were made: (a) to simulate the effect of the beating movement of the cephalic appendages, a force-field was added to the Navier-Stokes equations, (b) to linearize the problem, Stokes flow was used, and (c) to simplify the morphologies of the copepods, a spherical body shape was assumed. Analytical solutions were derived for five steady motions: (1) hovering, (2) sinking, (3) upwards swimming, (4) backwards swimming and (5) forwards swimming. The results show that the geometry of the flow field around a freely swimming copepod varies significantly with the different swimming behaviours. When a copepod hovers in the water, or swims very slowly, it generates a wide, cone-shaped flow field. In contrast, when a copepod sinks, or swims fast, the flow geometry is not cone-shaped, but cylindrical, narrow and long. These results are consistent with published observations on live copepods. It is shown that the differences in the flow geometry with the different swimming behaviours are due to the relative importance between the two factors in generating the flow field: the copepod's swimming motion and the requirement to counterbalance the copepod's excess weight. The results also highlight the importance of considering freely swimming copepods as self-propelled rather than as towed bodies. Self-propelled' means a freely swimming copepod must gain thrust from the surrounding water in order to counterbalance the dragforce by water and its excess weight. Regardless of swimming behaviours and velocities, the far-field velocity field decays to that of the velocity field generated by a point force of magnitude equal to the copepod's excess weight in an infinite domain. On the other hand, using the towed body model yields a flow field with much different far- and nearfield flow characteristics. Hence, the towed body model is inherently unable to reproduce fundamental characteristics of the flow field around a freely swimming copepod.
Associations Between Postoperative Management in the Critical Care Unit and Adolescent Developmental Outcomes Following Cardiac Surgery in Infancy: An Exploratory Study*

Supplemental Digital Content is available in the text. Objectives: Children with congenital heart disease are at high risk for developmental sequelae. Most studies focus on preoperative and intraoperative predictors of developmental impairment, with less attention to the postoperative period. The relationship between patient-related factors specific to the postoperative course in the PICU following cardiac surgery with long-term neurodevelopmental outcomes in adolescence was examined. Design: Retrospective chart review of patients previously recruited to a study describing their developmental outcomes in adolescence. Setting: Single tertiary care pediatric hospital in Canada. Patients: Eighty adolescents, born between 1991 and 1999, with congenital heart disease who required open-heart surgery before 2 years old. Measurements and Main Results: Several variables related to acuity of illness and complexity of postoperative course in the PICU were collected. Outcome measures included the Movement-Assessment Battery for Children-2 (motor), Leiter Brief Intelligence Quotient (cognition), and Strength and Difficulties Questionnaire (behavior). Analyses examined associations between PICU variables and long-term outcomes. Longer mechanical ventilation (β = –0.49; p = 0.013) and dopamine use (β = –14.41; p = 0.012) were associated with lower motor scores. Dopamine use was associated with lower cognitive scores (β = –14.02; p = 0.027). Longer PICU stay (β = 0.18; p = 0.002), having an open chest postoperatively (β = 3.83; p = 0.017), longer mechanical ventilation (β = 0.20; p = 0.001), longer inotrope support (β = 0.27; p = 0.002), hours on dopamine (β = 0.01; p = 0.007), days to enteral feeding (β = 0.22; p = 0.012), lower hemoglobin (β = –0.11; p = 0.004), and higher creatinine (β = 0.05; p = 0.014) were all associated with behavioral difficulties. Conclusions: Several important developmental outcomes in adolescents were associated with factors related to their postoperative course in the PICU as infants. Findings may highlight those children at highest risk for neurodevelopmental sequelae and suggest new approaches to critical care management following open-heart surgery, with the aim of mitigating or preventing adverse long-term outcomes.
N-Adamantyl-4-methylthiazol-2-amine suppresses glutamate-induced autophagic cell death via PI3K/Akt/mTOR signaling pathways in cortical neurons

We recently reported that N-adamantyl-4-methylthiazol-2-amine (KHG26693) attenuates glutamate-induced oxidative stress and inflammation in the brain. In this study, we investigated KHG 26693 as a therapeutic agent against glutamate-induced autophagic death of cortical neurons. Treatment with KHG26693 alone did not affect the viability of cultured cortical neurons but was protective against glutamate-induced cytotoxicity in a concentration-dependent manner. KHG26693 attenuated the glutamate-induced increase in protein levels of LC3, beclin-1, and p62. Whereas glutamate decreased the phosphorylation of PI3K, Akt, and mTOR, these levels were restored by treatment with KHG26693. These results suggest that KHG26693 inhibits glutamate-induced autophagy by regulating PI3K/Akt/mTOR signaling. Finally, KHG26693 treatment also attenuated glutamate-induced increases in reactive oxygen species, glutathione, glutathione peroxidase, and superoxide dismutase levels in cortical neurons, indicating that KHG26693 also protects cortical neurons against glutamate-induced autophagy by regulating the reactive oxygen species scavenging system.
Switching from TDF to TAF in HIV/HBV co-infected individuals with renal dysfunction - a prospective cohort study.

BACKGROUND Whereas tenofovir disoproxil fumarate (TDF) can lead to renal adverse events, tenofovir alafenamide (TAF) has a more favorable renal safety profile. However, the impact of replacing TDF with TAF on renal function and liver parameters among HIV/hepatitis B virus (HBV) co-infected individuals with renal dysfunction remains unclear. METHODS We included all participants from the Swiss HIV Cohort Study with an HIV/HBV-coinfection who switched from TDF to TAF and had an estimated glomerular filtration rate (eGFR) <90 mL/min/1.73m and a suppressed HIV viral load (<200 cp/mL). We assessed changes in eGFR, urine protein-to-creatinine ratio and alanine aminotransferase (ALT) after one year using mixed-effect models with interrupted time-series. RESULTS Among 106 participants (15.1% women, median age 53 years), eGFR was 60-89 mL/min/1.73m in 84 (79.2%) and <60 mL/min/1.73m in 22 (20.8%) individuals at the time of switch. One year after the switch from TDF to TAF, individuals with an eGFR between 60-89 mL/min/1.73m experienced increases in eGFR of 3.2 mL/min/1.73m (95% confidence interval [CI] 1.2 to 5.2), while those with an eGFR <60 mL/min/1.73m experienced improvements of 6.2 mL/min/1.73m (95% CI 2.4 to 10.0). Urine protein-to-creatinine ratio decreased overall (-6.3 mg/mmol, 95% CI -10.0 to -2.7), and ALT levels declined in patients with elevated baseline levels (-11.8 IU/L, 95% CI -17.3 to -6.4) one year after replacing TDF with TAF. CONCLUSIONS Switching from TDF to TAF among HIV/HBV-coinfected individuals with renal impairment led to improvements in eGFR, a decline in proteinuria, and to ALT normalization in those with elevated ALT levels.
C. elegans ACAT regulates lipolysis and its related lifespan in fasting through modulation of the genes in lipolysis and insulin/IGF‐1 signaling

Overly active acyl‐coenzyme A: cholesterol acyltransferases (ACATs) are known to contribute to the development of atherosclerosis, cancer cell proliferation and de novo lipogenesis. However, the role of ACAT in systemic lipid metabolism and its consequence of aging is unknown. Using avasimibe, a clinically proven ACAT inhibitor, and mboa‐1 mutant strain, a homologous to mammalian ACAT, herein, we found that Ava treatment and mboa‐1 mutant exhibited a decreased fat accumulation during feeding and increased lipolysis with extended lifespan of C. elegans during fasting. Our study highlights the essential role of ACAT inhibitor and mboa‐1 in fat mobilization and the survival of C. elegans in fasting through the modulation of the genes involved in lipolysis and insulin/IGF‐1 signaling.
Rapid adaptation for fibre degradation by changes in plasmid stoichiometry within Lactobacillus plantarum at the synthetic community level

The multi‐enzyme cellulosome complex can mediate the valorization of lignocellulosic biomass into soluble sugars that can serve in the production of biofuels and valuable products. A potent bacterial chassis for the production of active cellulosomes displayed on the cell surface is the bacterium Lactobacillus plantarum, a lactic acid bacterium used in many applications. Here, we developed a methodological pipeline to produce improved designer cellulosomes, using a cell‐consortium approach, whereby the different components self‐assemble on the surface of L. plantarum. The pipeline served as a vehicle to select and optimize the secretion efficiency of potent designer cellulosome enzyme components, to screen for the most efficient enzymatic combinations and to assess attempts to grow the engineered bacterial cells on wheat straw as a sole carbon source. Using this strategy, we were able to improve the secretion efficiency of the selected enzymes and to secrete a fully functional high‐molecular‐weight scaffoldin component. The adaptive laboratory process served to increase significantly the enzymatic activity of the most efficient cell consortium. Internal plasmid re‐arrangement towards a higher enzymatic performance attested for the suitability of the approach, which suggests that this strategy represents an efficient way for microbes to adapt to changing conditions.
The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity1

An intrinsically disordered protein interacts with HYPONASTIC LEAVES1 and ARGONAUTE1 in a post-miRNA processing complex to promote ARGONAUTE1 stability and miRNA activity. In plants, small RNAs are loaded into ARGONAUTE (AGO) proteins to fulfill their regulatory functions. MicroRNAs (miRNAs), one of the most abundant classes of endogenous small RNAs, are preferentially loaded into AGO1. Such loading, long believed to happen exclusively in the cytoplasm, was recently proposed to also occur in the nucleus. Here, we identified CONSTITUTIVE ALTERATIONS IN THE SMALL RNAS PATHWAYS9 (CARP9), a nuclear-localized, intrinsically disordered protein, as a factor promoting miRNA activity in Arabidopsis (Arabidopsis thaliana). Mutations in the CARP9-encoding gene led to a mild reduction of miRNAs levels, impaired gene silencing, and characteristic morphological defects, including young leaf serration and altered flowering time. Intriguingly, we found that CARP9 was able to interact with HYPONASTIC LEAVES1 (HYL1), but not with other proteins of the miRNA biogenesis machinery. In the same way, CARP9 appeared to interact with mature miRNA, but not with primary miRNA, positioning it after miRNA processing in the miRNA pathway. CARP9 was also able to interact with AGO1, promoting its interaction with HYL1 to facilitate miRNA loading in AGO1. Plants deficient in CARP9 displayed reduced levels of AGO1-loaded miRNAs, partial retention of miRNA in the nucleus, and reduced levels of AGO1. Collectively, our data suggest that CARP9 might modulate HYL1-AGO1 cross talk, acting as a scaffold for the formation of a nuclear post-primary miRNA-processing complex that includes at least HYL1, AGO1, and HEAT SHOCK PROTEIN 90. In such a complex, CARP9 stabilizes AGO1 and mature miRNAs, allowing the proper loading of miRNAs in the effector complex.
TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler

Abstract Motivation Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate. Results We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations. Availability and implementation TreeSAPP was developed in Python 3 as an open-source Python package and is available on GitHub at https://github.com/hallamlab/TreeSAPP. Supplementary information Supplementary data are available at Bioinformatics online.
Cooperative Full-Duplex V2V-VLC in Rectilinear and Curved Roadway Scenarios

We study here the vehicle-to-vehicle (V2V) visible light communication (VLC) between two cars moving along different roadway scenarios: (i) a multiple-lane rectilinear roadway and (ii) a multiple-lane curvilinear roadway. Special emphasis was given to the implementation of full-duplex (FD) cooperative communication protocols to avoid communication disruption in the absence of a line-of-sight (LOS) channel. Importantly, we found that the cooperative FD V2V-VLC is promising for avoiding communication disruptions for cars traveling in realistic curvilinear roadways. Results in this work can be easily extended to the case of vehicle-to-infrastructure (V2I), which can also be promising in cases of low-car-density environments.
Influence of subsurface tile drainage operational performance on nutrient losses under semi-arid environment.

The total geographical area of Pakistan is 79.61 mha cultivated area of about 22.06 million ha and its economy mainly depends on irrigated agriculture, which is 73% of the total cultivated area. Being dominant sector of Pakistan’s economy, it contributes about 24% to the country’s GDP, employs 48.4% of total workforce and facilitates 70% of export revenues (MINFAL, 2013). Although, the country has a history of successful irrigation, as a results of continuous evolvement in irrigation and resulting seepage from the canal system, agricultural lands of Pakistan have suffered from the problem of water logging and salinity, one of the main threats to rural development in Pakistan. Some parts of Pakistan have alluvial deposit and consist of poorly drained soils. For improved crop production these area may be artificially drained through subsurface drainage systems. Subsurface drainage systems dispose extra water and enhance crop production; however, it also increases the leaching of nitrate nitrogen (NO3-N) from the respective agricultural area. This leaching is mainly caused by an increase in subsurface drainage rate, which remove NO3-N from the soil profile into the main drain (Vos et al., 2000; Kladivlo et al., 2004; Rekha et al., 2011). The excesses removal of NO3-N, particularly from productive agricultural areas is recognized as a major non-point source of contamination of the water resources. Water in a stream comes out usually from overland flow as well as generally from groundwater seepage into the bed of streams (Fetter, 2001). A portion of the groundwater is lost by the tile drains where it is available. Leveled topography and well maintained subsurface drainage systems have created difficulties in understanding the hydrology of a watershed. They have produced more problems than solutions about water and crop management in those areas (Mitchell et al., 2000; Pir et al., 2014). Although, surface runoff occurs sometime in these highly fruitful areas (Mitchell et al., 2001), more questions are often upraised about the individual assistances of subsurface drainage systems and conventional base flow to total watershed nutrient loadings, and the dynamics of the N cycle in such watersheds (Dinnes et al., 2002; Kladivko et al., 2004; Rurak et al., 2010). A suitable water table management rules for crop production and environmental profits may be developed, if we know the answer of these questions. Neither the base flow into drainage drains in subsurfacedrained watersheds areas is thoroughly understood nor has it been widely documented by field research. To calculate the influences of tile drains drainage schemes on water quality, a thought of tile drains-drained watershed hydrology, more Pak. J. Agri. Sci., Vol. 52(1), 159-167; 2015 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 http://www.pakjas. com.pk
Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles

Simple Summary Oxygen-binding proteins that mediate oxygen-binding for storage and consumption, to reduce energy, are very diverse in fish, depending on their habitats. In the present study, oxygen-binding protein gene expression in the skeletal muscle of 25 diverse fish species was examined by a meta-transcriptomic approach. By using RNAseq data, this is the first study to examine the high level of myoglobin, one of the oxygen-binding proteins, transcripts in pacu and loach fish that might be related to their high tolerance for the oxygen-deficient environment. In addition, this study presents the power of the current method to compare the fish oxygen-binding protein expression and its putative gene expansion event. Abstract Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-binding protein expression in diverse fish species. Taking advantage of substantial RNAseq data deposited in the NCBI (National Center for Biotechnology Information) database, we adopted a meta-transcriptomic approach to explore and compare four oxygen-binding protein gene expression levels in the skeletal muscle of 25 diverse fish species for the first time. RNAseq data were downloaded from the NCBI Sequence Read Archive (SRA) database, and de novo assembly was performed to generate transcript contigs. The genes encoding oxygen-binding proteins were then identified by the BLAST search, and the relative expression level of oxygen-binding protein genes was normalized by the RPKM (Reads per Kilobase Million) method. By performing expression profiling, hierarchy clustering, and principal component analysis, pacu and loach fish were noticed by their high myoglobin expression levels in skeletal muscle tissues among 25 diverse fish species. In conclusion, we demonstrated that meta-transcriptomic analysis of RNAseq data is an informative approach to compare the oxygen-binding protein expression and putative gene expansion event in fish.
Time and Singular Causation - A Computational Model

Causal queries about singular cases, which inquire whether specific events were causally connected, are prevalent in daily life and important in professional disciplines such as the law, medicine, or engineering. Because causal links cannot be directly observed, singular causation judgments require an assessment of whether a co-occurrence of two events c and e was causal or simply coincidental. How can this decision be made? Building on previous work by Cheng and Novick (2005) and Stephan and Waldmann (2018), we propose a computational model that combines information about the causal strengths of the potential causes with information about their temporal relations to derive answers to singular causation queries. The relative causal strengths of the potential cause factors are relevant because weak causes are more likely to fail to generate effects than strong causes. But even a strong cause factor does not necessarily need to be causal in a singular case because it could have been preempted by an alternative cause. We here show how information about causal strength and about two different temporal parameters, the potential causes' onset times and their causal latencies, can be formalized and integrated into a computational account of singular causation. Four experiments are presented in which we tested the validity of the model. The results showed that people integrate the different types of information as predicted by the new model.