Miracle-dz/UniFAR-FTUs huggingface dataset:
Propagation for conserving endangered taxol producing tree Taxus sumatrana through shoot cuttings technique

Taxus sumatrana or commonly known as Sumatran yew is native endangered taxol producing trees from Indonesia and promising drug for cancer source. Due to very limited and restricted natural growing habitat, small population size and the tendency of habitat deterioration, their sustainable occurrence is facing a serious threats. Urgent task for conserving this species was needed. Shoot cutting is promising methods for solving natural regeneration problems of this species. This research was conducted to determine appropriate shoot cutting technique for propagating the species and hence conserving Sumatran yew. Completely Randomized Design Factorial with 2 factors and 20 replications was used in this research. The first factor was cutting medium the second factor was auxin addition. The observed parameters were survival rate, rooting percentage, primary root number and primary root length. The result showed that the percentage of rooted cuttings were varied from 50 to 65 percent depend on the treatment. Cutting media and auxin treatment significantly only affected primary root number. Combination of soil and husk with auxin addition produced the highest rooting percentage.
Adaptive Introgression Promotes Fast Adaptation In Oaks Marginal Populations

Range shifts and species range limits are two fundamental, related processes in population and evolutionary genetics that have received much attention since a large impact of climate change in species’ distributions was predicted. In general, there is a broad consensus on the effects of abiotic interactions on range limits, but comprehensive evidence supporting/rejecting the impact of biotic interactions is lacking. Hybridization has long been recognized as a biotic interaction favoring marginal populations establishment and range expansion through transgressive segregation or adaptive introgression, but recently new roles have been claimed for hybridization, such as the trigger of adaptive radiations, or indirect effects on population sizes that would allow persistence until new mutations arises or the environment changes. In this work, we selected two Mediterranean oak species with ecological discrimination based on soil pH, and intensively sampled three interspecific pairs of marginal populations from taxon-extreme environments under heterogeneous climate conditions. We genotyped 110 EST-SSR markers evenly distributed across their genomes and applied a variety of population and landscape genetics models to validate candidate genes for local adaptation. Then, several introgression screens on shared candidates showed that the three inter-specific population pairs contain evidences of adaptive introgression and that events occur in both directions. Other significant findings from our work are: (i) Aproximate Bayesian Computation coupled to coalescent simulations supports small hybridization rates since recent secondary contact in two population pairs affected by Quaternary climatic oscillations but continuous old interspecific gene flow in the pair less affected by climate, (ii) introgression at loci involved in local adaptations leads to strong geographic structure of marginal oak populations when sampling is large enough, and (iii) sampling efforts can be targeted to reveal different components of populations structure. Finally, we review evidences that support our conclusions and discuss some evolutionary implications of adaptive introgression on range expansion.
Global Economic and Food Security Impacts of Demand-Driven Water Scarcity—Alternative Water Management Options for a Thirsty World

Global freshwater demand will likely continue its expansion under current expectations of economic and population growth. Withdrawals in regions which are already water-scarce will impose further pressure on the renewable water resource base threatening the long-term availability of freshwater across the many economic activities dependent on this resource for various functions. This paper assesses the economy-wide implications of demand-driven water scarcity under a ‘middle-of-the-road’ socio-economic development pathway by considering the trade-offs between the macroeconomic and food security impacts. The study employs a global CGE model comprising an advanced level of detail regarding water uses across economic activities and which allows for a sector-specific endogenous adaptation to water scarcity. A sustainable withdrawal threshold is imposed in regions with extended river-basin overexploitation (India, South Asia, the Middle East, and Northern Africa) whilst different water management options are considered through four alternative allocation methods across users. The scale of macroeconomic effects is dependent on the relative size of sectors with low-water productivity, the amount of water uses in these sectors, and the flexibility of important water users to substitute away from water inputs in conditions of scarcity. The largest negative GDP deviations are obtained in scenarios with limited mobility to re-allocate water across users. A significant alleviation is obtained when demand patterns are shifted based on differences in water productivity, however, with a significant imposition on food security prospects.
Effect of herbicides on weed dynamics, phytotoxicity and seed yield of linseed (Linum usitatissimum L.).

A field experiment was conducted during rabi season of 2016-17 and 2017-18 at Research cum Instructional Farm of Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh. The treatment was comprised i.e. metribuzin + oxyflurofen @ 250 g a.i.+ 125 g a.i. ha-1 as pre-emergence (T1), oxyflurofen @125 g a.i.ha -1 as pre-emergence (T2), oxadiargyl @ 80 g a.i. ha -1 as pre-emergence (T3), imazethapyr 10 EC @ 75 g a.i. ha -1 as post-emergence (T4), metsulfuron-methyl @ 4 g a.i. ha -1 as postemergence (T5), isoproturon @ 1 kg a.i. ha -1 as post-emergence (T6), isoproturon + metsulfuron-methyl @ 1 kg a.i. + 4 g a.i. ha 1 as post-emergence (T7), pendimethalin + fb metsulfuron-methyl @ 1 kg a.i.+ fb 4 g a.i. ha -1 as pre + post-emergence (T8), hand weeding twice 21 and 45 DAS (T9) and weedy check (T10). The experiment was laid out in RBD and thrice replicated with the variety of ‘RLC-92’. The lowest weed density of total weeds and dry matter of weeds were observed with hand weeding treatment, however among herbicide treatment, application of isoproturon + metsulfuron-methyl @ 1 kg a.i.+ 4 g a.i. ha-1 as post-emergence (T7) was found lowest density of total weeds and dry matter at 60, 90 DAS and at harvest stages. The treatments of imazethapyr 10 EC @ 75 g ha-1 as post-emergence (T4) and pendimethalin + fb metsulfuron-methyl @ 1 kg a.i.+ fb 4 g a.i. ha -1 as pre + postemergence (T8) was found phytotoxic on linseed. The seed yield of linseed was recorded highest with hand weeding treatment (1940 kg ha-1) however, application of isoproturon + metsulfuron-methyl @ 1 kg + 4 g ha-1 as post-emergence (T7), metsulfuronmethyl @ 4 g a.i. ha-1 as post-emergence (T5), pendimethalin + fb metsulfuron-methyl @ 1 kg a.i. + fb 4 g a.i. ha -1 as pre + postemergence (T8) and isoproturon @ 1 kg a.i. ha -1 as post-emergence (T6) were found statistically at par. In case of economical analysis, the application of metsulfuron-methyl @ 4 g a.i. ha-1 as post-emergence (T5) was found highest value (3.91). Hence, sole application of metsulfuron-methyl @ 4 g a.i. ha-1 as post-emergence (T5) was most effective herbicide against broad leaf of weed flora i.e. Medicago dendiculata.
ACCESSING HEART HEALTH: A NORTHERN EXPERIENCE

Background and Research Purpose: Coronary heart disease (CHD) continues to be a major cause of death and disability across the globe. Regional differences in CHD exist throughout Canada, including Ontario. It is important to explore the complex interplay between geographical regions and individuals’ efforts at reducing their cardiovascular risk. This study explored barriers and supports to heart healthy lifestyles and associated meanings within various regions of Ontario. The focus of this paper is on the northern context to better understand the issues these individuals face when making heart healthy lifestyle changes. Sample and Method: The study used an ethnographic approach and photo-elicitation interviews. Participants took photographs of places that represented the barriers and supports to lifestyle changes for cardiovascular risk modification. These photographs were used as the basis for interview dialogue. Twelve informants from a larger study comprised the northern sub-sample considered in this paper. Results and Conclusions: When the data were analyzed, health care access and access concerns related to heart healthy lifestyles for people in northern Ontario emerged as key findings. Findings suggest that the concept of place is pivotal to recognizing issues related to health care access, which should be incorporated as part of our understanding of health and cardiovascular risk modification.
Cascade Probability Control to Mitigate Bufferbloat under Multiple Real-World TCP Stacks

Persistently full buffer problem, commonly known as bufferbloat, causes unnecessary additional latency and throughput degradation whenever congestion happens in Internet. Several proposed queue management schemes, with the debloat mission, are almost based on the modification of one-loop feedback control where the instability and bad transient behavior are still big challenges. In this paper, we present a cascade probability control scheme using margin optimal method to address such challenges under different kinds of real-world TCP stacks. Simulation results guarantee the measured round trip time tracking to a low value of delay (e.g., ≈180 ms under TCP Reno, and ≈130 ms under TCP Cubic) and ≈50% delay reduction in comparison to current deployed queue management schemes in network devices.
Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis

Gene-based association tests aggregate genotypes across multiple variants for each gene, providing an interpretable gene-level analysis framework for genome-wide association studies (GWAS). Early gene-based test applications often focused on rare coding variants; a more recent wave of gene-based methods, e.g. TWAS, use eQTLs to interrogate regulatory associations. Regulatory variants are expected to be particularly valuable for gene-based analysis, since most GWAS associations to date are non-coding. However, identifying causal genes from regulatory associations remains challenging and contentious. Here, we present a statistical framework and computational tool to integrate heterogeneous annotations with GWAS summary statistics for gene-based analysis, applied with comprehensive coding and tissue-specific regulatory annotations. We compare power and accuracy identifying causal genes across single-annotation, omnibus, and annotation-agnostic gene-based tests in simulation studies and an analysis of 128 traits from the UK Biobank, and find that incorporating heterogeneous annotations in gene-based association analysis increases power and performance identifying causal genes.
PuMA: A papillomavirus genome annotation tool

High-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of ‘viral metagenomics’ has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are experts on the genomic organization of that virus. There is a need to develop analytical approaches to reconstruct, annotate, and classify viral genomes. We have developed the papillomavirus annotation tool (PuMA) to provide researchers with a convenient and reproducible method to annotate novel papillomaviruses. PuMA provides an accessible method for automated papillomavirus genome annotation. PuMA currently has a 98% accuracy when benchmarked against the 481 reference genomes in the papillomavirus episteme (PaVE). Finally, PuMA was used to annotate 168 newly isolated papillomaviruses, and successfully annotated 1424 viral features. To demonstrate its general applicability, we developed a version of PuMA that can annotate polyomaviruses. PuMA is available on GitHub (https://github.com/KVD-lab/puma) and through the iMicrobe online environment (https://www.imicrobe.us/#/apps/puma)
INVESTIGATING THE FACTORS AFFECTING RISK MANAGEMENT EFFICIENCY OF COMMERCIAL BANKS

As a bank’s risk profile continually evolves, it leads to losses and a bank’s capital base and profitability drive the banking sector’s capacity to absorb risks. The proper functioning of this system depends on the proper use of resources collected and this requires accurate assessment of hazards and risks, and recognition methods to deal with the risks that lie ahead. Due to this issue, this study focuses on factors affecting the efficiency of risk management in the Pakistani banking industry. For empirical findings, Panel regression analysis has been employed taking a stratum of time series data and cross-sectional variants of macro and bank-specific factors for the period covering 2009 to 2013. Empirical results show a positive relationship between the liquidity, profitability, operating efficiency, merger and economic growth with capital adequacy ratio while the asset portfolio risk and inflation rates have the opposite effect
Constructing the Cultural Repertoire in a Natural Disaster : The Role of Social Media in the Thailand Flood of 2011

In 2011, Thailand witnessed its worst flooding catastrophe in half a century. In this study, we explored social media as a new and promising weapon to address the physical and morale challenges caused by the natural disaster. A case study was conducted in the context of crisis response, which investigated the use of social media to contribute to the collective cultural repertoire during the natural disaster. By investigating two paths toward the cultural repertoire construction considering different social groups, this study also identified the roles of social media as an information market and an information threshold in the crisis response.
Exploring the Pathological Mechanism of Bladder Cancer Based on Tumor Mutational Burden Analysis

Although immunotherapy has progressed in the treatment of bladder cancer, some patients still have poor prognosis. New therapeutic targets are eager to be discovered to improve the outcomes of bladder cancer. With the development of high-throughput sequencing and tumor profiling, potential tumor biomarkers were identified. Through the interpretation of related data from the Cancer Genome Atlas database (TCGA), some key genes have been discovered to drive the development and prognosis of urinary bladder neoplasm. On account of the success of immunotherapy in many cancer types, we established the relationship between tumor mutation burden and immune microenvironment of bladder cancer and found the changes of several immune cells in this disease. Based on the understanding of the bladder tumor genome and immune environment, this study is supposed to provide new therapies for the treatment of bladder neoplasm.
Solid Oxide Electrolyzer Cell Modeling: A Review

Solid Oxide Electrolyzer Cell (SOEC) is a very good candidate technology for securing sustainable development for the future. It allows CO 2 to be recycled into usable fuels and has potential for hydrogen economy. In this work the authors focus on development of SOEC through modeling different aspects of the cell: from design of specific elements to final incorporation of electrolyzers in the global energy system and network. The publications reviewed span from the 1970s to the present day and cover a selection of most contributed works. The selected publications provide means for modeling the solid oxide electrolyzer cell in both steady and transient states. The scale of the models ranges from micro to macro and to global energy system levels. The thrust of this work is to summarize the current level of development in modeling the solid oxide electrolyzer cell and to highlight unresolved problems and provide pointers in terms of research gaps requiring closer attention by engineers and scientists.
Determining the serotype composition of mixed samples of pneumococcus using whole genome sequencing

Serotyping of Streptococcus pneumoniae is a critical tool in the surveillance of the pathogen and development and evaluation of vaccines. Whole-genome DNA sequencing and analysis is becoming increasingly common and is an effective method for pneumococcal serotype identification of pure isolates. However, because of the complexities of the pneumococcal capsular loci, current analysis software requires samples to be pure (or nearly pure) and only contain a single pneumococcal serotype. We introduce a new software tool called SeroCall, which can identify and quantitate the serotypes present in samples, even when several serotypes are present. The sample preparation, library preparation and sequencing follow standard laboratory protocols. The software runs as fast or faster than existing identification tools on typical computing servers and is freely available under an open source license at https://github.com/knightjimr/serocall. Using samples with known concentrations of different serotypes as well as blinded samples, we were able to accurately quantify the abundance of different serotypes of pneumococcus in mixed cultures, with 100% accuracy for detecting the major serotype and up to 86% accuracy for detecting minor serotypes. We were also able to track changes in serotype frequency over time in an experimental setting. This approach could be applied in both epidemiologic field studies of pneumococcal colonization as well as in experimental lab studies and could provide a cheaper and more efficient method for serotyping than alternative approaches.
“Our culture does not allow that”: Exploring the challenges of sexuality education in rural communities

Within sub-Saharan Africa, AIDS is becoming a greater threat to rural communities due to the high numbers of urban dwellers and migrant labourers who return to their rural villages when they fall ill and due to the lack of information and health services. Previous studies have found a reduced rate of infection among people who have high educational attainment, and thus advocate for education as the vaccine against new HIV infections among the youth. However, very little research has focussed on the delivery of sexuality and HIV&AIDS education in rural classrooms. With teachers positioned at the forefront of the pandemic, especially in rural communities, it is important to understand how teachers experience teaching about sexuality in rural schools. In this paper, I explore the experiences of eight women teachers through focus group discussions. Thematic inductive analysis was used to identify the stumbling blocks within sexuality education classrooms in rural schools. Societal constructions of childhood and nostalgia for past traditional practices were found to be the major challenges to teaching. The findings highlight the need for a sexuality education curriculum that integrates traditional ways of knowing into formal sexuality education in order for it to be effective in reducing further spread of HIV.
2-Dimensional HP Foldings of Dermaseptin-J2

Although the hydrophobic-polar (HP) model is a simple model to study protein folding, it is an approximation to the real-life case. Dermaseptin is a subfamily of frog skin active peptide family, which has various antimicrobial activities, and dermaseptin-J2 is a newly found peptide composed of 26 amino acids. In this study, the 2-dimensional HP model was used to analyze the foldings of dermaseptin-J2 and its nine mutants, which were converted to different HP sequences according to the normalized amino acid hydrophobicity index with respect to pH levels and the conversion of glycine as hydrophobic or polar, and each has 847,288,609,443 possible foldings. The results show that the foldings with minimal energy have different native states, which are chiral and can be numerically distinguished and ranked according to the normalized amino acid hydrophobicity index. The nine mutants of dermaseptin-J2 do not affect the minimal energy but affect their native states at pH 7. The results demonstrate that two pH levels and conversion of glycine as hydrophobic or polar affect the native state and minimal energy, suggesting these are two ways to modify dermaseptin-J2.
Can we predict nutrient limitation in streams and rivers

Summary 1. Anthropogenic impacts on the biogeochemical cycles of nitrogen (N) and phosphorus (P) affect natural ecosystems worldwide. Modelling is required to predict where and when these key nutrients limit primary production in freshwaters. 2. We reviewed 382 nutrient-enrichment experiments to examine which factors promote limitation of microphytobenthos biomass by N or P in streams and rivers. Using regression models, we examined whether the response of microphytobenthos biomass to N and P additions could be predicted by the absolute N and P concentrations in the water, the water N:P ratio or a combination of the two. 3. The absolute N concentration in the water was the best predictor of the magnitude of the response of microphytobenthos biomass to N additions. In comparison, the N:P ratio was the best predictor of whether or not N was limiting. However, predictions were uncertain except at extreme N:P ratios 100 : 1. 4. The absolute P concentration in the water was the best predictor of the magnitude of the response of microphytobenthos biomass to P additions. Neither the absolute nor the relative N and P concentrations predicted whether or not P was limiting. 5. The absolute and the relative N and P water concentrations contribute significant and complementary insights into the responses of microphytobenthos biomass to nutrient enrichment in running waters. However, ability to predict nutrient limitation from these concentrations is constrained by substantial error in the models. In the future, the prediction ability of models of nutrient limitation might be improved by focussing on regional scales and accounting for additional factors such as light and disturbance.
Thermal energetics of Nyctophilus geoffroyi (Chiroptera : Vespertilionidae) at the southern limits of its distribution

The energetics of the lesser long-eared bat, Nyctophilus geoffroyi, at the southern limits of its distribution was examined to determine whether this species shows any latitudinal variation in this aspect of its physiological ecology. Estimates of metabolic rate were obtained from the oxygen consumption of adult bats in a non-reproductive condition. Values for the thermoneutral zone were similar but thermal conductance was lower than for bats from mainland of Australia. Euthermic body temperature was higher (37.4 ± 0.2°C) and the ambient temperature at which N. geoffroyi entered torpor has a downward shift of 10°C at the southern limits of its distribution. The basal metabolic rate (1.12 ± 0.14 mL O2 g –1 h –1 ) also was lower than in lower latitudes. Thermal conductance of the bats in Tasmania was lower than that found in New South Wales or Western Australia (0.29 v. 0.38–0.39 mL O2 g –1 h –1 °C –1 ). All of these differences are apparently adaptations to a cooler environment. ZO en Ny l K. J o R