Miracle-dz/UniFAR-FTUs huggingface dataset:
Importance of phosphorus application in Acacia mangium plantation

Fertilizers (nitrogen/N, phosphorous/P, and potassium/K) have been widely applied to increase the productivity of forest plantation, especially in poor soils. This study was to test the effects of fertilization at planting and additional fertilization in the following two years on growth and aboveground biomass (AGB) of a 30-month old plantation of Acacia mangium in Northeast Vietnam. There were four treatments including (1) 1 kg compost/tree at planting and 0.2 kg NPK (16:16:8)/tree/year in the following two years (IC-A-NPK), (2) 1 kg compost/tree at planting and 0.2 kg P (16.5% P2O5) + 0.1 kg K (60% K2O)/tree/year in the following two years (IC-A-PK), (3) 1 kg compost + 0.2 kg NPK/tree at planting and 0.2 kg NPK/tree/year in the following two years (IM-A-NPK), and (4) 1 kg compost + 0.2 kg NPK/tree at planting and 0.6 kg P + 0.1 kg K/tree/year in the following two years (IM-A-PK). The results indicated there was no significant effect of fertilization at planting and additional fertilization on diameter at breast height (DBH), basal area, and AGB between IC-A-NPK (DBH of 8.9 cm, basal area of 7.4 m2 ha-1, and AGB of 37.8 Mg ha-1) and IM-A-NPK (DBH of 10.1 cm, basal area of 9.2 m2 ha-1, and AGB of 47.5 Mg ha-1). Meanwhile, DBH (9.6 cm), basal area (8.6 m2 ha-1) and AGB (44.2 Mg ha-1) in IM-A-PK were significantly higher than that in IC-A-PK (DBH of 8.4 cm, basal area of 6.4 m2 ha-1, and AGB of 31.6 Mg h-1). It was concluded that fertilization at planting of both compost and NPK is not required for A. mangium plantation. While additional fertilization of phosphorus should be applied for higher productivity.
A Novel Antenna Protein Complex in the Life Cycle of Cyanobacterial Photosystem II

In oxygenic photosynthetic organisms, photosystem II (PSII) is a unique membrane protein complex that catalyzes light-driven oxidation of water. PSII undergoes frequent damage due to its demanding photochemistry. However, many facets of its repair and reassembly following photodamage remain unknown. We have discovered a novel PSII subcomplex that lacks five key PSII core reaction center polypeptides: D1, D2, PsbE, PsbF, and PsbI. This pigment-protein complex does contain the PSII core antenna proteins CP47 and CP43, as well as most of their associated low–molecular–mass subunits, and the assembly factor Psb27. Immunoblotting analysis, multiple mass spectrometry techniques, and ultrafast spectroscopic results supported the absence of a functional reaction center in this chlorophyll–protein complex. We therefore refer to it as the ‘no reaction center’ complex (NRC). Additionally, genetic deletion of PsbO on the PSII lumenal side resulted in an increased NRC population, indicative of a faulty PSII repair scheme at the cellular level. Analytical ultracentrifugation studies and clear native acrylamide gel analysis showed that the NRC complex is a stable pigment-protein complex and not a mixture of free CP47 and CP43 proteins. Our finding challenges the current model of the PSII repair cycle and implies an alternative PSII repair strategy. We propose that formation of this pigment-protein complex maximizes PSII repair economy by preserving an intact PSII core antenna shell in a single complex that is available for PSII reassembly, thus minimizing the risk of randomly diluting multiple recycling components in the thylakoid membrane following a photodamage event at the RC. Significance statement Photosystem II (PSII) converts sunlight into chemical energy, powering nearly all life on Earth. The efficiency of this process is maximized under various environmental conditions by a frequent repair and reassembly cycle that follows inevitable PSII damage even during normal oxygenic photosynthesis. We have isolated a novel pigment protein PSII subcomplex in which, surprisingly, the reaction center (RC) components of PSII are absent. Formation of this stable chlorophyll-protein complex suggests a protective mechanism whereby longer-lived PSII subunits are ‘unplugged’ from the damaged RC to prevent harmful, aberrant photochemistry during RC repair. This finding provides intriguing new insight into how PSII is assembled and rebuilt to optimize its performance to optimally catalyze one of the most challenging reactions in biology.
Care managers can be useful for patients with depression but their role must be clear: a qualitative study of GPs’ experiences

Abstract Objective: Explore general practitioners’ (GPs’) views on and experiences of working with care managers for patients treated for depression in primary care settings. Care managers are specially trained health care professionals, often specialist nurses, who coordinate care for patients with chronic diseases. Design: Qualitative content analysis of five focus-group discussions. Setting: Primary health care centers in the Region of Västra Götaland and Dalarna County, Sweden. Subjects: 29 GPs. Main outcome measures: GPs’ views and experiences of care managers for patients with depression. Results: GPs expressed a broad variety of views and experiences. Care managers could ensure care quality while freeing GPs from case management by providing support for patients and security and relief for GPs and by coordinating patient care. GPs could also express concern about role overlap; specifically, that GPs are already care managers, that too many caregivers disrupt patient contact, and that the roles of care managers and psychotherapists seem to compete. GPs thought care managers should be assigned to patients who need them the most (e.g. patients with life difficulties or severe mental health problems). They also found that transition to a chronic care model required change, including alterations in the way GPs worked and changes that made depression treatment more like treatment for other chronic diseases. Conclusion: GPs have varied experiences of care managers. As a complementary part of the primary health care team, care managers can be useful for patients with depression, but team members’ roles must be clear. KEY POINTS A growing number of primary health care centers are introducing care managers for patients with depression, but knowledge about GPs’ experiences of this kind of collaborative care is limited. GPs find that care managers provide support for patients and security and relief for GPs. GPs are concerned about potential role overlap and desire greater latitude in deciding which patients can be assigned a care manager. GPs think depression can be treated using a chronic care model that includes care managers but that adjusting to the new way of working will take time.
De novo β-alanine synthesis in α-proteobacteria involves a β-alanine synthase from the uracil degradation pathway

β-alanine synthesis in bacteria occurs by the decarboxylation of L-aspartate as part of the pantothenate synthesis pathway. In the other two domains of life we find different pathways for β-alanine formation, such as sources from spermine in plants, uracil in yeast and by transamination reactions in insects and mammals. There are also promiscuous decarboxylases that can decarboxylate aspartate. Several bioinformatics studies about the conservation of pantothenate synthesis pathway performed on bacteria, archaea and eukaryotes, have shown a partial conservation of the pathway. As a part of our work, we performed an analysis of the prevalence of reported β-alanine synthesis pathways in 204 genomes of alpha-proteobacteria, with a focus on the Rhizobiales order. The aim of this work was to determine the enzyme or pathway used to synthetize β-alanine in Rhizobium etli CFN42. Our bioinformatics analysis showed that this strain encodes the pyrimidine degradation pathway in its genome. We obtained a β-alanine synthase (amaB) mutant that was a β-alanine auxotroph. Complementation with the cloned gene restored the wild type phenotype. Biochemical analysis confirmed that the recombinant AmaB catalyzed the formation of β-alanine from 3-Ureidopropionic acid in vitro. Here we show a different way in bacteria to produce this essential metabolite. Importance Since the pioneer studies of Cronan (1980) on β-alanine synthesis in E. coli, it has been assumed that the decarboxilation of aspartate by the L-aspartate-α-decarboxylase it’s the main enzymatic reaction for β-alanine synthesis in bacteria. Forty years later, while we were studying the pantothenic acid synthesis in rhizobia, we demonstrate that a numerous and diverse group of bacteria classified as α-proteobacteria synthesize β-alanine de novo using β-alanine synthase, the last enzyme from the reductive pathway for uracil degradation. Additionally, there is a growing interest in β-amino acid due to its remarkable pharmaceuticals properties as hypoglycemic, antiketogenic and anti-fungal agents.
Brief Announcement: Distributed Task Allocation in Ant Colonies

A common problem in both distributed computing and insect biology is designing a model that accurately captures the behavior of a given distributed system or an ant colony, respectively. While the challenges involved in modeling computer systems and ant colonies are quite different from each other, a common approach is to explore multiple variations of different models and compare the results in terms of the simplicity of the model and the quality of the results. We consider the task allocation problem as a case study and explore multiple models inspired from both distributed computing and biological experiments. We compare the models with respect to their significance in understanding real ant behavior and also their technical relevance to distributed computing.
Evaluation of Drought Tolerant Rice Cultivars Using Drought Tolerant Indices under Water Stress and Irrigated Condition

Drought is the most critical abiotic factor reducing rice yield in rainfed and drought prone areas. Majority of rice cultivated area in south Asia are under rainfed, where water stress at any of the critical growth stage causes sharp decline in yield. Research was conducted in western Nepal at farmers field around the close vicinity of Regional Agriculture Research Center (RARS) Nepalgunj. Ten different rice cultivars were evaluated under drought stress and non-stress condition during the year 2017 to identify superior stress tolerant cultivars. Different drought tolerance indices like stress tolerance (TOL), Stress tolerance index (STI), Stress susceptibility index (SSI), were tested in screening superior rice cultivars. Significant reduction in mean grain yield was observed under drought stress in all rice cultivars under the study. The rice cultivars with high STI values and low TOL and SSI were identified as superior drought tolerant cultivars. Based on results of different tolerance indices, Sukha series of rice, Sukha Dhan 1-6 and Radha-4 showed low TOL and SSI and high STI values and were identified as drought tolerant cultivars. The present study reveals that selection based on drought tolerance indices can be an efficient tool in identification of superior drought tolerant cultivars with higher yield and stability.
Use of electronic nicotine delivery systems by pregnant women II: Hair biomarkers for exposures to nicotine and tobacco-specific nitrosamines

INTRODUCTION Public awareness of electronic nicotine delivery systems (ENDS) has increased over time, and the perception that ENDS offer a safer alternative to cigarettes may lead some pregnant women to use them to reduce cigarette smoking during pregnancy. No previous studies have used metabolite levels in hair to measure nicotine exposure for ENDS users during pregnancy. We aimed to measure and compare levels of nicotine, cotinine, and tobacco-specific nitrosamines (TSNAs) in hair samples from pregnant women who were current ENDS users, current smokers, and current non-smokers. We also aimed to estimate the association between ENDS use/smoking and smallness for gestational age (SGA). METHODS We used hair specimens from pregnant women who were dual users (ENDS and cigarettes), smokers, and non-smokers from a prospective cohort study to estimate exposure to nicotine, cotinine, and TSNAs. The exposure biomarkers and self-reports of smoking and ENDS use were used in log-binomial regression models to estimate risk ratios (RRs) for SGA among offspring. RESULTS Nicotine concentrations for pregnant dual users were not significantly different from those for smokers (11.0 and 10.6 ng/mg hair, respectively; p=0.58). Similarly, levels of cotinine, and TSNAs for pregnant dual users were not lower than those for smokers. The RR for SGA was similar for dual users and smokers relative to nonsmokers, (RR=3.5, 95% CI: 0.8–14.8) and (RR=3.3, 95% CI: 0.9–11.6), respectively. Using self-reports confirmed by hair nicotine, the RR values for dual ENDS users and smokers were 8.3 (95% CI: 1.0–69.1) and 7.3 (95% CI:1.0–59.0), respectively. CONCLUSIONS We did not observe lower levels of nicotine, cotinine, and TSNAs for current dual users compared to smokers during pregnancy. The risk of SGA for offspring of pregnant dual users was similar to that for offspring of pregnant smokers. Future studies are needed to further estimate the magnitude of the association between ENDS use and smallness for gestational age.
Computational design and interpretation of single-RNA translation experiments

Advances in fluorescence microscopy have introduced new assays to quantify live-cell translation dynamics at single-RNA resolution. We introduce a detailed, yet efficient sequence-based stochastic model that generates realistic synthetic data for several such assays, including Fluorescence Correlation Spectroscopy (FCS), ribosome Run-Off Assays (ROA) after Harringtonine application, and Fluorescence Recovery After Photobleaching (FRAP). We simulate these experiments under multiple imaging conditions and for thousands of human genes, and we evaluate through simulations which experiments are most likely to provide accurate estimates of elongation kinetics. Finding that FCS analyses are optimal for both short and long length genes, we integrate our model with experimental FCS data to capture the nascent protein statistics and temporal dynamics for three human genes: KDM5B, β-actin, and H2B. Finally, we introduce a new open-source software package, RNA Sequence to NAscent Protein Simulator (RSNAPSIM), to easily simulate the single-molecule translation dynamics of any gene sequence for any of these assays and for different assumptions regarding synonymous codon usage, tRNA level modifications, or ribosome pauses. RSNAPSIM is implemented in Python and is available at: https://github.com/MunskyGroup/rSNAPsim.git. Author summary Translation is an essential step in which ribosomes decipher mRNA sequences to manufacture proteins. Recent advances in time-lapse fluorescence microscopy allow live-cell quantification of translation dynamics at the resolution of single mRNA molecules. Here, we develop a flexible computational framework to reproduce and interpret such experiments. We use this framework to explore how well different single-mRNA translation experiment designs would perform to estimate key translation parameters. We then integrate experimental data from the most flexible design with our stochastic model framework to reproduce the statistics and temporal dynamics of nascent protein elongation for three different human genes. Our validated computational method is packaged with a simple graphical user interface that (1) starts with mRNA sequences, (2) generates discrete, codon-dependent translation models, (3) provides visualization of ribosome movement as trajectories or kymographs, and (4) allows the user to estimate how optical single-mRNA translation experiments would be affected by different genetic alterations (e.g., codon substitutions) or environmental perturbations (e.g., tRNA titrations or drug treatments).
To assume or not to assume blood T1 for AIF measurement in DCE-MRI?

Data Analysis Firstly, signal intensity time series from the aorta were extracted for each of the 25 slices in the volume, taking care to avoid partial volume errors. These AIFs were then converted to units of concentration (Cp) using the methods presented in (1) with the baseline blood T1 estimated using either our measured value of T1 at each slice location or an assumed T1 value (1253 ms, within the blood T1 range found in literature (3) and the blood T1 measured at slice 18 of our volume – the point at which blood inflow effects are negligible in this DCE-MRI data set (2)). A “true” representative tumor residue curve (Ct) was simulated in MATLAB (The Mathworks, Natick, USA) using the exteded Kety model (4) with representative tumor parameter values for K trans (0.1 min -1 ), ve (30%) and vp (5%). Since blood T1 at slice 18 of our DCE-MRI data was reliable, “true” Cp was regarded as the AIF from this slice. Subsequently, for each slice in the volume our “true” Ct curve was fit with the extended Kety model using the slice specfic AIF from both the measured T1 and assumed T1 method in turn to obtain fitted parameter estimates. The error in these fitted parameters was calculated relative to our “true” set of parameter values and used to compare the level of accuracy between the measured and assumed T1 approaches.
The Development of Hypersensitivity Reactions in the Pediatric Population: A Review

Over the past several years, pediatric allergies have come to the forefront of many studies. Reports of immune-mediated hypersensitivity in younger patients have grown and led to an interest researching the causes of pediatric hypersensitivities. There are various risk factors that have been discussed that may lead to the development of allergies including genetic inheritance, genetic mutation, and environmental sensitization. It is important for all of these factors to be discussed in relation to the function of the immune system and its role in hypersensitivity reactions. If the causes of hypersensitivity reactions could be further studied and understood, treatments might be developed to reduce or eliminate these hypersensitivity reactions in younger pediatric populations. Much research has been done regarding the risk factors for pediatric hypersensitivity reactions and many recommendations have been made to combat this growing phenomenon. It is important to review the mechanisms of hypersensitivity reactions, the risk factors for developing them, and to research the incidences of pediatric hypersensitivity reactions and the recommended interventions for future diagnosis and treatment of hypersensitivity reactions in the pediatric population.
THE PREVALENCE OF ORAL MUCOSA DISEASE OF GUSTI HASAN AMAN DENTAL HOSPITAL IN BANJARMASIN, SOUTH KALIMANTAN

Background : Society often underestimate oral health problem. They mostly visit the dentist when the chief complain eventually disturb their mastication, deglutination and speech function. Until recently, there has been no data provided for the prevalence of oral mucosa disease in Indonesia, as well as the prevalence of oral mucosa disease in Banjarmasin, South Kalimantan. Objective : To discover the prevalence of oral mucosa disease in Gusti Hasan Aman Dental Hospital, Banjarmasin, South Kalimantan in 2014-2017. Material and Methods : This is a retrospective descriptive study. The sample of this study was obtained by purposive sampling method from patients' medical record who visited Department of Oral Medicine, Gusti Hasan Aman Dental Hospital Banjarmasin in 2014-2017, complied the inclusion and exclusion criteria. Data was obtained from final diagnosis of patients' disease written in medical record which then presented in graphics. Result : It was found that the prevalence of oral mucosa disease in Gusti Hasan Aman Dental Hospital in 2014-2017 comprised of Reccurent Aphtous Stomatitis (SAR) in 397 patients (45,42%), Traumatic Ulcer in 263 patients (30,08%), Oral Candidiasis in 92 patients (10,53%), Viral Infection in 88 patients (10,07%), Allergic Stomatitis in 26 patients (2,97%), and other diseases in 8 patients (0,92%). Conclusion : The highest prevalence of oral mucosa disease in Gusti Hasan Aman Dental Hospital in 2014-2017 year is Recurrent Aphthous Stomatitis, followed by Traumatic Ulcer, and infectious diseases comprise of oral candidiasis and viral infection.
Integration of a Highway Fill Embankment Case Study in Engineering Design Courses for Instructional Improvement

This paper focuses on the application of a case study of fundamentals of geotechnics to a highway embankment slope failure movement investigation for civil engineering curriculum development and education. The proposed case study is introduced into the first year elementary engineering design course. The proposed highway fill embankment slope case study project is planned to be further introduced for expanded discussions in the later semesters. Early student exposure of case studies in the curriculum will benefit upper level engineering geology and soil mechanics courses. This project will also be helpful by connecting hydrologic engineering and transportation highway pavement engineering research work in the later semesters, especially with senior design projects.
Fibre digestion by rumen microbiota — a review of recent metagenomic and metatranscriptomic studies

Abstract: Plant biomass is the most abundant renewable resource on the planet, and the biopolymers of lignocellulose are the foundation of ruminant production systems. Optimizing the saccharification of lignocellulosic feeds is a crucial step in their bioconversion to ruminant protein. Plant cell walls are chemically heterogeneous structures that have evolved to provide structural support and protection to the plant. Ruminants are the most efficient digesters of lignocellulose due to a rich array of bacteria, archaea, fungi, and protozoa within the rumen and lower digestive tract. Metagenomic and metatranscriptomic studies have enhanced the current understanding of the composition, diversity, and function of the rumen microbiome. There is particular interest in identifying the carbohydrate-active enzymes responsible for the ruminal degradation of plant biomass. Understanding the roles of cellulosomes- and polysaccharide-utilising loci in ruminal fibre degradation could provide insight into strategies to enhance forage utilisation by ruminants. Despite advancements in “omics” technology, the majority of rumen microorganisms are still uncharacterised, and their ability to act synergistically is still not understood. By advancing our current knowledge of rumen fibre digestion, there may be opportunity to further improve the productive performance of ruminants fed forage diets.
Drug utilization study in the paediatric department of a tertiary care teaching hospital

Background: Rational drug use is one of the main concerns of the health care system in India. Paediatric population being more vulnerable require additional focus to achieve this goal. Objectives of the study were to evaluate the prescription patterns according to WHO guidelines and the diseases, for which they are being prescribed, to identify the common diseases and common medications used.Methods: A cross sectional study was done in the paediatrics department for a period of 2 months. All the paediatric prescriptions were evaluated using WHO core indicators like average number of medicines per encounter, percentage of medicines from the essential drug lists and also complimentary indicators like utilization of different dosage forms and diagnostic patterns. Statistical Analysis: Data was analyzed and represented as frequency (n) and percentage (%). Results: 89 out of 302 prescriptions had 2 medicines per encounter, 100% of medicines were included from the Essential Drug List (EDL), 59.4% of the medicines were in generic format of prescription.Conclusions: This study gives a positive outlook at the utilization pattern of drugs with all the indicators specifically Essential Drugs List. Regular auditing, continuous medical education and evidence-based medicine can help in improving the health care.