Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin

Understanding the genetic and evolutionary impacts of fish stocking on wild populations has long been of interest as negative consequences such as reduced fitness and loss of genetic resources are commonly reported. Nearly five decades of extensive stocking of over a million Muskellunge (Esox masquinongy) in the Lower St. Lawrence River (Québec, Canada) was implemented by managers in an attempt to sustain a fishery. We investigated the effect of stocking on this native species’ genetic structure and allelic diversity in the St. Lawrence river and its tributaries as well as several stocked inland lakes. Using Genotype-By-Sequencing (GBS), we genotyped 643 individuals representing 22 sampling sites and combined this information with forward simulations to investigate the genetic consequences of stocking. Individuals native to the St. Lawrence watershed were genetically divergent from the sources used for stocking and both the St. Lawrence tributaries and inland lakes were also naturally divergent from the main stem. Empirical data and simulations revealed weak effects of stocking on admixture patterns within the St. Lawrence despite intense stocking in the past, whereas footprints of admixture were higher in the smaller stocked populations from tributaries and lakes. Altogether, our data suggests that selection against introgression has been relatively efficient within the large St. Lawrence River. In contrast, the smaller populations from adjacent tributaries and lakes still displayed stocking related admixture which apparently resulted in higher genetic diversity, suggesting that, while stocking stopped at the same time, its impact remained higher in these populations. Finally, the origin of populations from inland lakes that were established by stocking confirmed their close affinity with these source populations. This study illustrates the benefit of combining extensive genomic data with forward simulations for improved inferences regarding outcomes of population enhancement by stocking, as well as its relevance for fishery management decision making.
Diplodia sapineafound on Scots pine in Finland

Diplodia sapinea is an important pathogen of Pinus spp. in many parts of the the world’s temperate and sub-tropical zones. In Central Europe, this fungus has been known since its first description in the 19 century. But it was only in 2007 that the fungus was identified using DNA-markers in Northern Europe (in Estonia). Viljo Kujala reported observing D. sapinea on logging debris of Norway spruce in Finland in 1945, but we have not been able to verify the identifications from his herbarium samples. In 2004, we collected cones under asymptomatic Scots pine (Pinus sylvestris) trees at one location near the southern coast of Finland but failed to isolate D. sapinea from the samples. In 2015 and 2016, we collected fallen Scots pine cones in 15 Scots pine stands in various parts of Finland and the fungus was found at five locations in southwestern Finland including the location investigated in 2004. Frequency of cones with pycnidia of D. sapinea varied from 1 to 12 % in the infested stands. No symptoms of Diplodia tip blight or resinous cankers were detected in trees in the stands where the cones were collected. The results suggest a recent introduction after 2004 of the D. sapinea in Finland.
G-quadruplex dynamics contribute to epigenetic regulation of mitochondrial function

Single-stranded DNA or RNA sequences rich in guanine (G) can adopt non-canonical structures known as G-quadruplexes (G4). Predicted G4-forming sequences in the mitochondrial genome are enriched on the heavy-strand and have been associated with formation of deletion breakpoints that cause mitochondrial disorders. However, the functional roles of G4 structures in regulating mitochondrial respiration in non-cancerous cells remain unclear. Here, we demonstrate that RHPS4, previously thought to be a nuclear G4-ligand, localizes primarily to mitochondria in live cells by mechanisms involving mitochondrial membrane potential. We find that RHPS4 exposure causes an acute inhibition of mitochondrial transcript elongation, leading to respiratory complex depletion. At higher ligand doses, RHPS4 causes mitochondrial DNA (mtDNA) replication pausing and genome depletion. Using these different levels of RHPS4 exposure, we describe discrete nuclear gene expression responses associated with mitochondrial transcription inhibition or with mtDNA depletion. Importantly, a mtDNA variant with increased anti-parallel G4-forming characteristic shows a stronger respiratory defect in response to RHPS4, supporting the conclusion that mitochondrial sensitivity to RHPS4 is G4-structure mediated. Thus, we demonstrate a direct role for G4 perturbation in mitochondrial genome replication, transcription processivity, and respiratory function in normal cells and describe the first molecule that differentially recognizes G4 structures in mtDNA.
Capital Structure as a Mediating Factor in the Relationship between Uncertainty, CSR, Stakeholder Interest and Financial Performance

We examine the mediating role of capital structure in the perceived relationship of uncertainty, corporate social responsibility (CSR), stakeholder interest and financial performance. We collect data through questionnaires, and survey the Chief Financial Officers (CFOs) of the service sector of Pakistan. We apply Structure Equation Modeling (SEM) for data analysis. We find that CFOs perceive uncertainty, CSR and stakeholder interest to have both direct and indirect impacts on financial performance. In particular, we find evidence of the mediating effect of capital structure in the relationship. Our findings imply that firms screen out uncertain situations while making capital structure decision and pursuing CSR-related activities.
The student experience of final year in an undergraduate degree programme in Education Studies

This case study explores the student experience of the final year of a four year undergraduate degree in ‘Education Studies’, with a focus on the perceived impact of curriculum design of the programme. The context is an Irish college of education, and the programme structure has been designed to allow for flexibility to accommodate varying student interests and professional pathways. As the first full iteration of the programme came to a close, it was considered an opportune time to ascertain if the programme was meeting its curriculum design objectives in terms of preparation for the chosen professional pathway post-graduation from both the student and staff perspective. Literature explored included learning ecologies, work-based learning, and the final year experience. Data was collected through a student survey, individual interviews with self-selecting students, and a focus-group interview with the programme development team. Findings suggest that students could clearly identify the development of skills, knowledge and competencies for the workplace through an internship; also highlighted was value in undertaking a dissertation for researching a topic of personal interest, with it noted as a challenging, intense experience. Having appropriate levels and different types of support for students facing the challenges in final year was a significant outcome. A model emerged for final year support in three contexts: pedagogic, workplace and research, and we argue that this is a main research contribution that this study makes to educational research. A discussion of implications for curriculum development in ‘Education Studies’ highlights the need for ‘cohesion’ workshops to be integrated to final year to synthesise student learning, embedding a formalised support structure in order for students to have a greater understanding of choices available to them post-graduation, and introducing a scaffolded approach to ePortfolio development to encourage innovation.
Bessel-Beam Photoacoustic Microscopical Simulation Platform Based on k-Wave

We developed a Bessel-beam photoacoustic microscopical simulation platform by using the k-Wave: MATLAB toolbox. The simulation platform uses the ring slit method to generate Bessel beam. By controlling the inner and outer radius of the ring slit, the depth-of-field (DoF) of Bessel beam can be controlled. And the large volumetric image is obtained by point scanning. The simulation experiments on blood vessels were carried out to demonstrate the feasibility of the simulation platform. This simulation work can be used as an auxiliary tool for the research of Bessel-beam photoacoustic microscopy.
TLC profiling and antioxidant activity of phenolic compound from Sterculia oblongata bark extract

Abstract. Murningsih T, Praptiwi, Liana, Fathoni A. 2019. TLC profiling and antioxidant activity of phenolic compound from Sterculia oblongata bark extract. Nusantara Bioscience 11: 44-48. In the present study, we investigated the total phenolic content and in- vitro antioxidant activity of Sterculia oblongata. Total phenolic content (TPC) of the methanol extract was examined by Folin-Ciocalteu reagent and gallic acid as standard. The in-vitro antioxidant activity was performed by DPPH free radical scavenging activity and β-carotene bleaching assay. The result showed that the TPC of methanol extract was the highest (P<0.05) compared to other extracts. There is a positive and significantly very high Pearson’s correlation between antioxidant activity index (AAI) and TPC (r = 0.996). A negative and significantly high Pearson’s correlation was obtained between IC50 value and TPC (r = -0.885). The result of β-carotene bleaching assay showed that the rate of the decreased antioxidant activity of S.oblongata extract was lower than that of β-carotene/linoleic acid. The results suggest that the extract of S. oblongata can be used as a natural antioxidant. However, further investigation to isolate and identify the chemical compounds responsible for antioxidant was needed
Multi-Informative and Specific Detection of Blood inFingermarks via MALDI-MS Based Strategies

Currently employed enhancement and detection techniques for blood are not confirmatory due to targeting generic compound classes like proteins. As such, they are not sufficiently specific and are prone to false positives. The aim of this work was to confidently determine whether a crime scene sample is in fact blood and more specifically human blood. To achieve this, an in-solution bottom up proteomic approach was developed, targeting blood-specific proteins and employing MALDI-MS. The work was developed further to devise a protocol for proteomic in situ analysis of bloodied fingermarks with MALDI-MS imaging, enabling the mapping of blood peptides to fingermark ridges and thus establishing a strong link between the suspect and the event of bloodshed. Putative peptide identifications were made for signals originating from a number of different blood-specific proteins, including not only the most abundant blood proteins like haemoglobin, but also several other proteins (e.g. complement C3 and hemopexin). To further validate the method, a blind study was conducted analysing unknown samples ranging from different species' blood and human biofluids to other substances known to produce false positives with conventional techniques. Employing MALDI-MS, it was possible to confidently identify human blood samples of up to 34 years in age. This is potentially a huge step forward in the forensic analysis of suspected blood samples and shows potential for re-analysis of cold case samples or samples of disputed origin. It was found in this study that further optimisation of the data analysis approach is required for provenance determination of animal blood samples. Traditionally, establishing the order of deposition of fingermarks associated with blood is difficult and subjective. Infinite focus microscopy was investigated for its potential to facilitate quantitative differentiation between the different deposition scenarios. However, results were highly dependent on the surface of deposition and thus the technique was shown to be unsuitable due to the wide range of surfaces potentially encountered in a forensic investigation.
A deep learning framework for imputing missing values in genomic data

Motivation The presence of missing values is a frequent problem encountered in genomic data analysis. Lost data can be an obstacle to downstream analyses that require complete data matrices. State-of-the-art imputation techniques including Singular Value Decomposition (SVD) and K-Nearest Neighbors (KNN) based methods usually achieve good performances, but are computationally expensive especially for large datasets such as those involved in pan-cancer analysis. Results This study describes a new method: a denoising autoencoder with partial loss (DAPL) as a deep learning based alternative for data imputation. Results on pan-cancer gene expression data and DNA methylation data from over 11,000 samples demonstrate significant improvement over standard denoising autoencoder for both data missing-at-random cases with a range of missing percentages, and missing-not-at-random cases based on expression level and GC-content. We discuss the advantages of DAPL over traditional imputation methods and show that it achieves comparable or better performance with less computational burden. Availability https://github.com/gevaertlab/DAPL Contact ogevaert@stanford.edu
Genetic diversity of ACC-deaminase positive bacteria in Colorado soil under winter wheat cultivars (Triticum aestivum L.)

ii AKNOWLEDGMENTS . v LIST OF TABLES . ix LIST OF FIGURES . xii CHAPTER 1: LITERATURE REVIEW . 1 1.Introduction . 1 1.1 Plant Growth Promoting Rhizobacteria (PGPR) . 2 1.2. ACC-deaminase producing bacteria . 4 1.3. Implications for ACC-Deaminase Positive Bacteria for Improving Drought Tolerance of Winter Wheat . 8 1.3. Objectives and Hypotheses . 11 REFERENCES.13 CHAPTER 2: GENOTYPE-SPECIFIC ENRICHMENT OF ACC-DEAMINASE POSITIVE BACTERIA IN WINTER WHEAT RHIZOSPERES . 20 1.Introduction. 20 2. Materials and Methods . 22 2.1. Field study 1 – Greeley . 22 2.2. Field study 2 – Fort Collins . 26 3. Results . 30
DIVERSE STRATEGIES OF RHODODENDRON (Rhododendron sp.) GENOTYPES IN THE WATER SHORTAGE MANAGEMENT

Rhododendrons in numerous gardens in Central Europe are frequently endangered by adverse summer drought periods associated with the climate change. Therefore, in this work drought-resistance strategies in recent genotypes of these highly aesthetic shrubs were investigated. Dehydrated Rhododendron groenlandicum ‘Helma’, R. obtusum ‘Michiko’ and R. hybridum ‘Polarnacht’ showed high initial stomatal conductances (gS), after few days steeply falling to the stable minimum at ca. 20, 85 and 70% leaf relative water content (RWC), respectively. Except of ‘Polarnacht’, they had relatively large specific leaf area and ‘Michiko’ also free proline accumulation. On the other hand, R. repens ‘Scarlet Wonder’ and R. hybridum ‘Red Jack’ started with half gS values, continuously declining 1.5–2 fold longer compared to the first group of genotypes (RWC of ca. 60 and 75%, respectively). Both produced relatively thick leaves but did not show any osmotic adjustment. Among observed drought-resistance strategies, lower and longer period active transpiration with stomata sensitive to the water loss, as found in R. repens ‘Scarlet Wonder’ and R. × hybridum ‘Red Jack’, were accepted as the most effective for drought-affected rhododendron plantations.
Optimization of Activated Charcoal on in vitro Growth and Development of Potato (Solanum tuberosum L.)

Potato (Solanum tuberosum L.) is the fourth most important food crop of the world. It is an amenable crop which can be used in tissue culture techniques, ranging from in vitro propagation via shoot cultures for regeneration of whole plants from protoplasts (Buckseth et al., 2016). This whole plant can be regenerated from a range of cultured tissues like roots, leaves, tubers and stems or from single cells. In general terms, these all involve the growth of plant cells, tissues and organs in sterile conditions, supported by an appropriate culture medium (Harshal and Gautam, 2014). Murashige and Skoog medium (MS medium) is most widely used for the vegetative propagation of many plant species in vitro (Murashige and Skoog, 1962). Tissue culture based hi-tech seed potato production is spreading very fast in the country (Buckseth et al., 2017). Micropropagation at faster rate and free from cultural contamination is an integral component for the success of in vitro mass Activated charcoal is often used in plant tissue culture to improve cell growth and development by absorbing the beneficial plant growth promoting substances from the media. Thus the main aim of this study was to evaluate the influence of different concentrations of activated charcoal on the recalcitrant varieties of potato. The MS media strength (full and half) did not influence the plant growth and development of potato varieties as both the strengths did equally well in combination with lower concentration of activated charcoal (200mg/l). The use of activated charcoal could be done in a controlled manner (tested concentrations) in order to maintain the endophytes / microplant balance. However, studies in this line need further investigations for lowering the concentrations with a view to avoid the negative effects. K e y w o r d s
Genetic Variants of Targetable Cancer-related Genes in Vestibular Schwannomas

Background: Vestibular schwannoma is an intracranial tumor which can lead to devastating neurological deficit and is prone to recurrence after surgery. Patients with inherited neurofibromatosis type 2 (NF2) syndrome are particularly susceptible to bilateral and aggressive schwannomas. However, the genome of vestibular schwannomas is not well known. NF2-related cases. The results were confirmed by Sanger sequencing. Conclusion: Our study successfully detected some genetic variants in important cancer-related genes in schwannomas, and further elucidation of their relationship to drug-response will be pursued.
Discovery of Relevant Response in Infected Potato Plants from Time Series of Gene Expression Data

The paper presents a methodology for analyzing time series of gene expression data collected from the leaves of potato virus Y (PVY) infected and non-infected potato plants, with the aim to identify significant differences between the two sets of potato plants’ characteristic for various time points. We aim at identifying differentially-expressed genes whose expression values are statistically significantly different in the set of PVY infected potato plants compared to non-infected plants, and which demonstrate also statistically significant changes of expression values of genes of PVY infected potato plants in time. The novelty of the approach includes stratified data randomization used in estimating the statistical properties of gene expression of the samples in the control set of non-infected potato plants. A novel estimate that computes the relative minimal distance between the samples has been defined that enables reliable identification of the differences between the target and control datasets when these sets are small. The relevance of the outcomes is demonstrated by visualizing the relative minimal distance of gene expression changes in time for three different types of potato leaves for the genes that have been identified as relevant by the proposed methodology.
Understanding liaison psychiatry commissioning: an observational study

The purpose of this paper is to explore the challenges that are experienced by staff responsible for commissioning liaison psychiatry services and to establish if these are shared by other health professionals. ,Using a mixed-methods design, the findings from a mental health commissioner workshop (n = 12) were used to construct a survey that was distributed to health care professionals using an opportunistic framework (n = 98). ,Four key themes emerged from the workshop, which was tested using the survey. The importance of secure funding; a better understanding of health care systems and pathways; partnership working and co-production and; access to mental health clinical information in general hospitals. There was broad convergence between commissioners, mental health clinicians and managers, except in relation to gathering and sharing of data. This suggests that poor communication between professionals is of concern. ,There were a small number of survey respondents (n = 98). The sampling used an opportunistic framework that targeted commissioner and clinician forums. Using an opportunistic framework, the sample may not be representative. Additionally, multiple pairwise comparisons were conducted during the analysis of the survey responses, increasing the risk that significant results were found by chance. ,A number of steps were identified that could be applied in practice. These mainly related to the importance of collecting and communicating data and co-production with commissioners in the design, development and monitoring of liaison psychiatry services. ,This is the first study that has specifically considered the challenges associated with the commissioning of liaison psychiatry services.
Novel Hybrid Pulse Width Modulation Technique for Solar Fed Cascaded Multilevel DC-Link Inverter

Multilevel inverter plays an important role especially in solar based renewable energy sources due to its modularity in structure and medium or high power applications. It is well known that there are three types of inverters which are Diode clamped multilevel inverter, flying capacitor multilevel inverter and cascaded multilevel inverter. One of the drawback of these inverters are, more switching losses due to which quality of power get decreases. The main intention of this work is to improve the quality of power, thereby increasing the life and performance of the overall system at consumer side. One of the reduced switched multilevel inverters have been used to perform so called multilevel DC link inverter. In earlier days, Sinusoidal Pulse Width Modulation (SPWM) technique is used to reduce the switching losses of the inverter. Present work proposes a new Hybrid Pulse Width Modulation (HPWM) technique to control the switching losses in the system. In this HPWM technique, multi level DC link inverter having combination of SPWM (at level generation), and Fuzzy controller(at polarity generation) are used to reduce the losses, and the results are compared with conventional SPWM technique considering R and R-L load.
Effects of temperature, dissolved oxygen, and substrate on the development of metabolic phenotypes in age-0 lake sturgeon (Acipenser fulvescens): implications for overwintering survival

The impact of early rearing environment on phenotypic development in teleosts has been reasonably well-documented, but only recently has attention been paid to sturgeon raised for conservation purposes. In the present study, we hypothesized that rearing environment will result in the development of distinct metabolic phenotypes in age-0 lake sturgeon (Acipenser fulvescens) and that these phenotypes will drive differential survival rates during a simulated overwintering event. Lake sturgeon gametes were fertilized and raised in one of three different environments: 16 °C + 100% dissolved oxygen (DO), 14 °C + 100% DO, and 16 °C + 80% DO, each with or without substrate. We measured standard metabolic rate, forced maximum metabolic rate, metabolic scope, energy density, hepatosomatic index, Fulton’s condition factor, and enzyme activities associated with ATP production. Our results suggest that subtle changes in abiotic environments during early life history result in the development of distinct metabolic phenotypes during the first year of life. These have important implications for survival of age-0 lake sturgeon when stocked in the fall of their first year.