Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

The world’s herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.
Numerical relativity simulations of precessing binary neutron star mergers

We present the first set of numerical relativity simulations of binary neutron mergers that include spin precession effects and are evolved with multiple resolutions. Our simulations employ consistent initial data in general relativity with different spin configurations and dimensionless spin magnitudes $\sim 0.1$. They start at a gravitational-wave frequency of $\sim392$~Hz and cover more than $1$ precession period and about 15 orbits up to merger. We discuss the spin precession dynamics by analyzing coordinate trajectories, quasi-local spin measurements, and energetics, by comparing spin aligned, antialigned, and irrotational configurations. Gravitational waveforms from different spin configuration are compared by calculating the mismatch between pairs of waveforms in the late inspiral. We find that precession effects are not distinguishable from nonprecessing configurations with aligned spins for approximately face-on binaries, while the latter are distinguishable from a nonspinning configurations. Spin precession effects are instead clearly visible for approximately edge-on binaries. For the parameters considered here, precession does not significantly affect the characteristic postmerger gravitational-wave frequencies nor the mass ejection. Our results pave the way for the modeling of spin precession effects in the gravitational waveform from binary neutron star events.
Effect of OCR on sampling disturbance of cohesive soils and evaluation of laboratory reconsolidation procedures

The paper presents the results of an experimental investigation of sampling disturbance in cohesive soils through single-element triaxial tests on resedimented Boston blue clay (RBBC). The first part of the paper discusses the effect of the overconsolidation ratio (OCR) (18) of the soil on postdisturbance compression and undrained shear behavior. The results demonstrate that sensitivity to disturbance decreases markedly with OCR. It is also found that for the medium-sensitivity soil tested, the estimate of the preconsolidation pressure is not significantly affected by OCR. The second part of the paper discusses laboratory reconsolidation procedures. For OCR1 RBBC, the recompression method is not effective in recovering the stressstrain behavior of the soil and, for greater disturbance, provides an increasingly unsafe estimate of the strength. For OCR4, provided the reconsolidation path reproduces the path that occurred in the field, this procedure succeeds in recovering the intact stressstrainstrength.
On Propeller Performance of DTC Post-Panamax Container Ship

The propeller performance has been investigated using a benchmark Duisburg Test Case ship with RANSE. First, the hydrodynamic characteristics of propeller in case of open water have been analyzed by a commercial CFD program and the results are compared with those of experimental data. Later, the flow around the bare hull has been solved and the frictional resistance value and form factor of the ship have been obtained and compared with those of ITTC57 formulation and experimental results for validation. The free surface effect has been ignored. A good agreement has been obtained between the results of RANSE and experiments at both stages. Then the ship - propeller interaction problem was solved by RANSE and the differences in thrust, torque and efficiency of propeller as compared with the open-water numerical results have been discussed.
Statistical methods for microbiome data and antimicrobial resistance analysis

This thesis consists of three projects motivated by biological problems: (i) detecting differentially abundant taxa in multiple metagenomic samples (chapter 2), (ii) developing a two-stage causal mediation model for identifying taxa mediating the effect of environmental conditions on an outcome in the analysis of microbiome data (chapter 3), and (iii) analyzing temporal changes of the antimicrobial susceptibility (chapter 4). Although the emerging field of metagenomics has revolutionized our understanding of the microbial world, the analysis of metagenomic data raises some statistical challenges, including modeling high-dimensional overdispersed count data with excessive zeros. In the first project (chapter 2), we propose a hypothesis testing framework based on a Poisson Hurdle hierarchical model to address the considerable zeros issue in the metagenomic data, and a full Bayesian inference is performed to identify the differentially abundant taxa among multiple treatment groups. Simulation studies demonstrate our model outperforms the existing approaches in terms of false discovery rate control at desired level of significance and statistical power as well. In the second project (chapter 3), we develop a causal mediation model to investigate the effect of a treatment on an outcome transmitted through microbes. Considering the sparsity and high-dimensional overdispersed count natures of the metagenomic data, we propose a novel screening procedure to reduce the dimension to a moderate size. Then a Bayesian variable selection strategy with a shrink and diffuse prior is used to select the key taxa with mediation effects. The performance of the proposed method is illustrated via simulation studies. In the third project (chapter 4), we present a hierarchical Bayesian latent class mixture model to detect the temporal changes in antibiotic resistance using minimum inhibitory concentration (MIC) values. By taking the censorship into account, our proposed approach would achieve less bias in the estimation of mean MIC. We also apply this proposed method to the data from CDC xi NARMS program and show that evidence of temporal changes in mean MIC exist in spite of no changes or changes of adverse direction in the proportion of resistance.
MAXIMIZING THE HYDROLOGICAL IMPACT OF STREET TREES THROUGH SIDEWALK DESIGN

Urbanization increases the total area of impervious ground cover leading to post- development rain runoff quantities that can damage and flood the natural downstream catchment. The Low Impact Development aim is to ensure that a resulting runoff from a given area is equivalent to pre-development levels. Trees, both in a natural and urban environment, play a vital role in the surrounding hydrology through interception, transpiration, evaporation, and infiltration. This increase of rain runoff created by a greater percentage of impervious surfaces can be in-part accommodated and improved by sidewalk design engineered to support healthy urban trees. Engineered soils can be used to meet the required bearing capacity of traditional compacted sidewalk subgrade soils while increasing volume available for root growth and water retention. Different engineered soils will be tested for their compatibility with pervious pavement materials to determine the most effective draining system that still meets the required load carrying capacity demanded by municipal sidewalk regulations. In combination with the structural soils further changes to the traditional sidewalk design are proposed to create beneficial growing conditions and maximize tree health. An assessment of the initial investment and cost of maintenance for this street tree catchment design will be explored to determine if the relief afforded to the stormwater management of a developed area justifies the expense. This paper will focus on the tools and methods used to pursue the analysis of the hydrological effect of sidewalk design centered on urban trees, with a specific concentration on application in Montreal, Canada.
The Importance of the Brand in Brand Extension

Recent research has identified two factors that influence consumer perceptions of a brand extension: brand affect and the similarity between the original and extension product categories. However, surprisingly little attention has been paid to other associations specific to the brand itself. The authors perform three experiments to explore the relative importance of these associations. The experiments reveal that brand-specific associations may dominate the effects of brand affect and category similarity, particularly when consumer knowledge of the brands is high. The authors conclude by discussing the implications of these findings for managerial decision making and the process by which consumers evaluate brand extensions.
Computer Security Awareness and Vulnerabilities: An Exploratory Study for Two Public Higher Institutions in Ghana

The study is an exploratory study that evaluates computer security awareness and computer security vulnerabilities based on user practices among computer users in two public higher institutions in Ghana. Using a cross-sectional survey and a convenient sampling technique, the target population was identified as three subgroups namely faculty staff, administrative staff and students. The study reveals that different levels of computer security awareness exist among sub groups of each institution. Sub groups also differ in computer security vulnerabilities in some areas for each institution and between institutions. Key findings include differences in perception of remote connection to computer while on a network, seemingly inappropriate usage of anti-virus protection among computer users, computer security vulnerabilities created by the computer and password sharing behavior of users, among others. Limitations and future research have been suggested. The study also provides important managerial implications.
Association of Host and Pathogenic Variation with Sexual Transmission of HIV

Human immunodeficiency virus (HIV) is genetically extremely variable due to the poor proof reading activity of its reverse transcriptase enzyme. Human immunodeficiency virus isolates are highly variable over time, and exhibit changes in biological phenotype during the course of infection. Different HIV variants exist in different tissues, cells and secretions; including genital secretions and cells of human males and females. Virus present in the urogenital cells and secretions determines the risk for sexual transmission of HIV. The precise association of viral variants from genital secretions and cells in the sexual transmission of HIV to the partner is not fully understood. The presence of viral variants may influence affinity to different host cell receptors which may affect the transmission, infectivity, cellular immunity and pathogenesis of HIV. Delineation of the role of host and pathogenic variation will lead to a better understanding of the process of sexual transmission of HIV. Furthermore, it will also help in designing the strategies for development of preventive or therapeutics vaccines and microbicides for control and management of HIV/AIDS.
Identification of RFLP Markers Linked to the Unifoliate Leaf, Cauliflower Head Mutation of Alfalfa

The cauliflower head and unifoliate leaf mutation (uni) is a unique developmental mutation of alfalfa that may shed some light on the relationship between leaves and fbral organs. RFLP loci linked to uni were identified using bulk segregant analysis of an F2 diploid alfalfa population segregating for this trait. Two bulks, one unifoliate leaf and one trifoliate leaf, were formed with each composed of 20 F2 plants and screened using 110 RFLP clones. Seven clones detected polymorphisms between the bulks. Linkage analysis confirmed that three of the clones were tightly linked to uni and located on linkage group 4 of a previously published linkage map. The clones provide useful tools for future genetic and molecular studies.
Director’s Cut - Analysis of VR Film Cuts for Interactive Storytelling

The usage of film cuts, or transitions, is a powerful technique in interactive storytelling to express the film story by leading the viewers attention. To explore how existing transition techniques are currently being used by professional 360° filmmakers, this paper investigates the impact of transitions and additional graphical elements from a storytelling perspective. We base this on the recently published Director’s Cut dataset [1] which contains professional 360° films with the directors’ intending viewing direction (i.e., director’s cut) and test subjects’ scan-paths. Our objective is to examine widely used transition techniques in professional 360° film, and with our finding guide filmmakers in the storytelling and editing process. To the authors knowledge, this is the first study to analyze professionally prepared VR film cuts concerning the distance of viewers’ scan-paths and director’s cut. We observed that the intended viewing direction is required for the viewer to understand the story best and not miss the director’s plot points. The transition is a point where the viewers are presented with a new scene and are required to orientate themselves within it. Thus if there is a considerable distance mismatch between the intended and actual viewing, the viewer is not in the best position to understand the scene properly. Our results show that the use of simple graphics can serve as a reference for viewers as the transition happens and they are presented with a new immersive environment.
Multiple host use and the dynamics of host switching in host–parasite systems

The link between multi‐host use and host switching in host–parasite interactions is a continuing area of debate. Lycaenid butterflies in the genus Maculinea, for example, exploit societies of different Myrmica ant species across their ranges, but there is only rare evidence that they simultaneously utilise multiple hosts at a local site, even where alternative hosts are present. We present a simple population‐genetic model accounting for the proportion of two alternative hosts and the fitness of parasite genotypes on each host. In agreement with standard models, we conclude that simultaneous host use is possible whenever fitness of heterozygotes on alternative hosts is not too low. We specifically focus on host‐shifting dynamics when the frequency of hosts changes. We find that (i) host shifting may proceed so rapidly that multiple host use is unlikely to be observed, (ii) back and forth transition in host use can exhibit a hysteresis loop, (iii) the parasites' host use may not be proportional to local host frequencies and be restricted to the rarer host under some conditions, and (iv) that a substantial decline in parasite abundance may typically precede a shift in host use. We conclude that focusing not just on possible equilibrium conditions but also considering the dynamics of host shifting in non‐equilibrium situations may provide added insights into host–parasite systems.
A generic, process‐based model of microbial pollution in aquatic systems

Based on a comprehensive synthesis of data available within the literature, a new process‐based model of microbial pollution is presented, which is applicable for surface and coastal waters. The model is based on a generic set of parameterisations that describe the dynamics of most protozoan, bacterial and viral organisms of interest, including pathogens and microbial indicator organisms. The parameterisations dynamically account for the effects of temperature, salinity, pH, dissolved oxygen, sunlight, nutrients and turbidity on the growth and mortality of enteric organisms. Parameters for a range of organisms are also presented which are based on collation of literature data. The model has been implemented within an aquatic ecology model, Computational Aquatic Ecosystem Dynamics Model (CAEDYM), which can couple to multidimensional hydrodynamic models. Without adjustment of the literature derived parameter values, a 3‐D implementation is validated against observed data from three freshwater systems that differ in their climatic zone, trophic status and operation. The simulations highlight the spatial and temporal variability that may be encountered by operators. Additionally, large differences in the fate and distribution of different species originate from variable rates of growth, mortality and sedimentation and it is emphasized that the use of surrogates for quantifying risk is problematic. The model can be used to help design targeted monitoring programs, explore differences between species, and to support real‐time decision‐making. Areas where insufficient understanding and data exist are discussed.
Extending the boundaries of energy management for assessing manufacturing business strategies

Manufacturers are responsible for about one third of global energy demand, and thus have a responsibility for reducing their reliance on rapidly depleting non-renewable energy sources. Consequently, a plethora of research has arisen to develop novel ways of improving energy efficiency in factories by focusing on changes to energy intensive production processes and other energy using systems that support manufacturing activities. However, the ultimate goal of manufacturing companies is to maximise profit by refining their business strategy, highlighting the importance of assessing the impact of different business strategies on energy demand. Therefore, one of the key research challenges is to assign anticipated energy demand to various decisions within a business. This paper presents a hierarchical approach to attribute the potential energy demand of manufacturing activities to alternative business decisions, thus informing selection of the most energy efficient business strategies.
Oligometastatic breast cancer : a case report and literature review

Introduction Oligometastatic breast disease is a potentially curable state of distant cancer spread, but there is still no standard approach for treatment. The aim of this article is to present a clinical case of oligometastatic breast cancer and short data of the latest literature sources. Case report This case report presents 58 years old postmenopausal women diagnosed with oligometastatic breast carcinoma who underwent a successful simultaneous nipple-sparing mastectomy with sentinel node biopsy and right upper lobectomy in National Cancer Institute, Vilnius, Lithuania. Conclusions Multidisciplinary approach and modern imaging studies allows us to diagnose and successfully treat this rare pathological state. Scientific trials to delineate proper indications for oligometastatic breast disease are needed
Serum Biochemistry of Broiler Chicken Supplemented with Detoxifying Microbial Enzymes to Ameliorate Feed Toxins

Mycotoxins are the toxic metabolites produced by certain fungi, mainly by the Aspergillus, Penicillium and Fusarium genera. They are always a hazard to man and domestic animals and had come to public interest since the past 30 years. Aflatoxins constitute a great threat to the health of animals and humans due to their teratogenic, carcinogenic, mutagenic and immunosuppressive effects (Guan et al., 2008; Yunus et al., 2011). Additionally, in terms of the livestock industry aflatoxins cause huge economic loss by retarding animal growth, increasing feed consumption and reducing meat production (Fan et al., 2013; International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 07 (2019) Journal homepage: http://www.ijcmas. com
Macrobenthos communities of Cambridge, McBeth and Itirbilung fiords, Baffin Island, Northwest Territories, Canada

Thirty-eight marine invertebrates, including molluscs, echinoderms, polychaetes and several minor taxa, have been added to the previously described benthic macrofauna inhabiting Cambridge, McBeth and Itirbilung fiords in northeastern Baffin Island, Northwest Territories, Canada. The fiords lie fully within the marine arctic zone and organisms exhibiting panarctic distributions constitute the majority of species collected from them. Macrobenthic associations recorded in the fiords are comparable, both with respect to species composition and habitat, to benthic invertebrate associations occurring on the Baffin Island continental shelf and in east Greenland fiords, reflecting the broad environmental tolerances of the organisms constituting the benthic associations. Deposit-feeding organisms dominate the fiord macrobenthos, notably nuculanid bivalves, ophiuroid echinoderms and elasipod holothurians. The foraging and locomotory activities of these organisms may influence benthic community structure by reducing the abundance of sessile and/or tubiculous benthos. Key words: marine benthos, eastern Baffin Island, fiords, continental shelf, zoogeography, ecology