Miracle-dz/UniFAR-FTUs huggingface dataset:
Extractive distribution in Pseudotsuga menziesii: effects on cell wall porosity in sapwood and heartwood

Douglas-fir (Pseudotsuga menziesii) has distinctly colored heartwood as a result of extractive deposition during heartwood formation. This is known to affect natural durability and treatability with preservatives, as well as other types of wood modification involving infiltration with chemicals. The distribution of extractives in sapwood and heartwood of Douglas-fir was studied using fluorescence microscopy. Several different types of extractive including flavonoids, resin acids, and tannins were localized to heartwood cell walls, resin canals, and rays, using autofluorescence or staining of flavonoids with Naturstoff A reagent. Extractives were found to infiltrate the cell walls of heartwood tracheids and were also present to a lesser extent in sapwood tracheid cell walls, especially in regions adjacent to the resin canals. Forster resonance energy transfer measurements showed that the accessibility of lignin lining cell wall micropores to rhodamine dye was reduced by about 50%, probably as a result of cell wall-bound tannin-like materials which accumulate in heartwood relative to sapwood, and are responsible for the orange color of the heartwood. These results indicate that micro-distribution of heartwood extractives affects cell wall porosity which is reduced by the accumulation of heartwood extractives in softwood tracheid cell walls.
Altered apoptosis and biotransformation signaling in HCT-116 colorectal carcinoma cells induced by Teucrium chamaedrys L. extract

The aim of this study was an investigation of pro-apoptotic activity of methanol extract from T. chamaedrys, a more detailed determination of the signal molecules activated in the process of apoptosis, and effects on mRNA expression of enzymes involved in biotransformation (CYP1A1 and GSTP1) and membrane transporter, MRP-2 in HCT-116 colorectal carcinoma cells. The results show pronounced proapoptotic activity of T. chamaedrys extract, due to activation of both extrinsic and intrinsic pathways. The death receptor associated signaling pathway was activated in HCT-116 following treatment by T. chamaedrys, via increased Fas receptor expression and activity of caspase 8. Activation of caspase 9 suggests that mitochondrial signalling also has an impact. The extract reduced mRNA expression of GSTP1 and MRP-2 genes, as one of the causes of multi drug resistance in cancer cells. Observed results offer the possibility for the use of T. chamaedrys extract in the context of cancer prevention and therapy.
Guiding users in learning a complex user interface

In interface design, technology is a medium in the communication between a designer and a user (Norman, 2004). The diﬃculty in good design is that the user’s mental model, deﬁned as ‘what the user believes about the system at hand’ (Nielsen, 2010), should be similar to the designer’s conceptual mental model and this can only be achieved through the technology. The user interface should thus be self-explanatory and provide the user with the functionality that is needed for the task at hand, while maintaining simplicity. Theusage of software also depends on its users and their expertise with the software or similar software. Large diﬀerences in expertise lead to a wide range in user types and fulﬁlling their needs in one user interface is a huge challenge. A solution to this are personalized interfaces, which are interfaces that can be or are altered to ‘make useful features more accessible for a user’s current task’ (Findlater & McGrenere, 2010, p. 121). Even though good solutions have been provided, personalization and customization also have some strong downsides, for instance its potential negative eﬀect on the learning curve of expertise. Applications supporting software learnability have been reviewed by Cockburn, Gutwin, Scarr, & Malacria (2014), from which ephemeral adaptation has been chosen to overcome the initial eﬀort needed to familiarize with complex software and its design. Ephemeral adaptation means that user attention is steered towards relevant items by making them appear immediately, while the other items fade in over time (Findlater, Moﬀatt, McGrenere, & Dawson, 2009). This concept has only been tested in a simple experimental set-up with selecting from simple drop-down menu‘s. The current study was designed to apply ephemeral adaptation within complex software and to explore its potential value beyond initial exposure. A between-subjects experiment was performed, comparing software learnability with either ephemeral adaptation applied to the interface or not. Results indicated ephemeral adaptation is beneﬁcial when ﬁrst exposed to a complex interface, as shown by faster task-completion times. Furthermore, ephemeral adaptation applied to form ﬁlling has the same positive eﬀects as shown in a previous study with drop-down menus. Applying the concept of ephemeral adaptation diminishes the needed eﬀort to learn a
An evaluation of the geographical influence on the α-amylase bioactivity of actinomycetes - isolated from Coringa Mangroves

Mangroves are the versatile and indomitable plant community for a wide range of bioactivities owing to its unique marine terrestrial extreme interface. The objective of the current study is to evaluate the hypothesis, to what extent the geography (distance from the shore) influences the α-Amylase production from mangrovian actinomycetes. Six different soil samples (A1, A2, A3, A4, A5 and A6) were collected from Coringa mangroves based on shore to distant shore and were subjected to serial dilution and isolation techniques. A total of nine strains were identified based on colony characteristics. The primary screening for α Amylase recognized two strains (ANUKCJV1:132135 – A5 and ANUKCJV2:130305 – A2) as the potential candidate strains and were subjected to α-Amylase production, the two strains exhibited 0.491 and 0.303 IU of α-Amylase activity. The two potential strains were identified as Streptomyces pluripotens and Streptomyces chilikensis respectively based on 16S r DNA sequencing. The sequences of the two potential strains were deposited in the NCBI with accession codes; ANUKCJV1 – MH973320 and ANUKCJV2 – MH973321 respectively. Based on the current study it may be concluded that both the extremeness and favourability of the mangrovian environ influences the α-Amylase production.
Automated Ventricular System Segmentation in Paediatric Patients Treated for Hydrocephalus Using Deep Learning Methods

Hydrocephalus is a common neurological condition that can have traumatic ramifications and can be lethal without treatment. Nowadays, during therapy radiologists have to spend a vast amount of time assessing the volume of cerebrospinal fluid (CSF) by manual segmentation on Computed Tomography (CT) images. Further, some of the segmentations are prone to radiologist bias and high intraobserver variability. To improve this, researchers are exploring methods to automate the process, which would enable faster and more unbiased results. In this study, we propose the application of U-Net convolutional neural network in order to automatically segment CT brain scans for location of CSF. U-Net is a neural network that has proven to be successful for various interdisciplinary segmentation tasks. We optimised training using state of the art methods, including “1cycle” learning rate policy, transfer learning, generalized dice loss function, mixed float precision, self-attention, and data augmentation. Even though the study was performed using a limited amount of data (80 CT images), our experiment has shown near human-level performance. We managed to achieve a 0.917 mean dice score with 0.0352 standard deviation on cross validation across the training data and a 0.9506 mean dice score on a separate test set. To our knowledge, these results are better than any known method for CSF segmentation in hydrocephalic patients, and thus, it is promising for potential practical applications.
Macrobiotusnoemiae sp. nov., a new tardigrade species(Macrobiotidae: hufelandi group) from Spain

A reexamination of the tardigrade collection from the Museo Nacional de Ciencias Naturales (MNCN) in Madrid was carried out. Specimens from the genera Milnesium, Macrobiotus, and Paramacrobiotus were verified in order to provide their correct identification and 15 taxa were identified. Moreover, a list of corrected species identifications from MNCN is provided. Fourteen specimens and 16 eggs, identified previously as Macrobiotus recens, were attributed to a species new for science. Macrobiotus noemiae sp. nov. is most similar to Mac. naskreckii and Mac. recens but it differs from them by details of egg morphology, mainly by the presence of thin flexible filaments on the tops of egg processes.
Psychrotrophic Microbiota in Milk and Fermented Milk Products

Milk and dairy products form a significant part of the human diet. temperature control is considered as the key to extend shelf life for dairy products. Psychrotrophs grow at temperature such as 7oC or lower but had higher optimal growth temperature. Most psychrotrophs produce extracellular enzymes while growing in milk and deteriorate its quality. six types of samples constituting buffalo milk, flavored milk, curd, shrikhand, lassi and butter were collected in different seasons to study the psychrotrophic microbiota. sixty psychrotrophic bacteria were grouped into fifteen clusters of very similar isolates. One isolate from each of the fifteen clusters of closely related isolates was identified by phylogenetic analysis namely Stenotrophomonas maltophilia, Pseudomonas putida, Pseudomonas stutzeri, Enterobacter hormaechei, Macrococcus caseolyticus, Exiguobacterium acetylicum, Exiguobacterium indicum, Micrococcus luteus, Kocuria rosea, Staphylococcus equorum, Ornithinmicrobium humiphilum, Planococcus psychrotoleratus, Bacillus cereus and two isolates upto genus level namely Exiguobacterium spp. and Kocuria spp. Fatty acid profile of milk sample inoculated with lipolytic psychrotrophic bacterial isolate was determined using hydrolytic extraction Gas Chromatographic method.
Bayesian Regularized Neural Networks for Small n Big p Data

Artificial neural networks (ANN) mimic the function of the human brain and they have the capability to implement massively parallel computations for mapping, function approximation, classification, and pattern recognition processing. ANN can capture the highly nonlinear associations between inputs (predictors) and target (responses) variables and can adaptively learn the complex functional forms. Like other parametric and nonparametric methods, such as kernel regression and smoothing splines, ANNs can introduce overfitting (in particular with highlydimensional data, such as genome wide association -GWAS-, microarray data etc.) and resulting predictions can be outside the range of the training data. Regularization (shrinkage) in ANN allows bias of parameter estimates towards what are considered to be probable. Most common techniques of regularizations techniques in ANN are the Bayesian regularization (BR) and the early stopping methods. Early stopping is effectively limiting the used weights in the network and thus imposes regularization, effectively lowering the Vapnik-Chervonenkis dimension. In Bayesian regularized ANN (BRANN), the regularization techniques involve imposing certain prior distributions on the model parameters and penalizes large weights in anticipation of achieving smoother mapping.
Mortality of the Western corn rootworm, Diabrotica virgifera virgifera larvae caused by entomopathogenic fungi

Mortality of the Western corn rootworm (WCR) larvae caused by entomopathogenic fungi Beauveria bassiana, Beauveria brongniartii, Metarhizium anisopliae was investigated in a laboratory. Larvae were treated with a spore suspension (concentration of 2.0 x 107 conidia/ml) by immersion. Only one strain of entomopathogenic fungi, a strain of B. brongniartii, significantly influenced mortality of WCR larvae after 7 days. Average mortality of the larvae was 17.63%. After 14 days, five strains of B. bassiana, two strains of B. brongniartii and one strain of M. anisopliae significantly influenced mortality of WCR larvae, with average mortality ranging from 25.83% to 60.57%. After 21 days from exposure of the larvae to spores, four strains of B. bassiana, two strains of B. brongniartii and one strain of M. anisopliae significantly influenced mortality of the WCR larvae with average mortality ranging from 62.5% to 86.6%. Results confirmed that interaction is possible between fungal strains and insect of a various geographical provenance. More than half of the tested fungal strains significantly influenced the mortality of WCR larvae after 14 and 21 days. We found that differences between strains were more important than differences between fungal species.
Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense

Liriodendron chinense (Hemsl.), a Tertiary relic tree, is mainly distributed in subtropical China. The causes of the geographical distribution pattern of this species are poorly understood. In this study, we inferred historical dispersal routes and glacial refugia of this species by combining genetic data (chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and nuclear DNA (nDNA)) and geospatial data (climate and geology) with the methods of landscape genetics. Additionally, based on sequence variation at multiple loci, we employed GenGIS and Barrier software to analyze L. chinense population genetic structure. Dispersal corridors and historical gene flow between the eastern and western populations were detected, and they were located in mountainous regions. Based on species distribution model (SDMs), the distribution patterns in paleoclimatic periods were consistent with the current pattern, suggesting the presence of multiple refuges in multiple mountainous regions in China. The genetic structure analysis clustered most eastern populations into a clade separated from the western populations. Additionally, a genetic barrier was detected between the eastern and western populations. The dispersal corridors and historical gene flow detected here suggested that the mountains acted as a bridge, facilitating gene flow between the eastern and western populations. Due to Quaternary climatic fluctuations, the habitats and dispersal corridors were frequently inhabited by warm-temperate evergreen forests, which may have fragmented L. chinense habitats and exacerbated the differentiation of eastern and western populations. Ultimately, populations retreated to multiple isolated mountainous refugia, shaping the current geographical distribution pattern. These dispersal corridors and montane refugia suggested that the mountains in subtropical China play a crucial role in the conservation of genetic resources and migration of subspecies or related species in this region.
Fisheries biology and interaction in the northern Australian small mackerel fishery

The small mackerels comprising school mackerel (Scomberomorus queenslandicus), spotted mackerel (S. munroi) and grey mackerel (S. semifasciatus) are important and valued species to recreational and commercial fishers in northern Australia. Prior to this project very little was known about the basic biology of, or fisheries for, small mackerels. Each species was found to exhibit distinct life history patterns with differing stock structures. Though there is some overlap between fisheries, there was much spatial and temporal separation of the fisheries, with gill net specialisation for each species targeted by the commercial fishery. Recreational hook and line fisheries for school mackerel and spotted mackerel were important with most of the grey mackerel harvest taken by the commercial sector.
Virtual Instructor-Student Interaction: A New Method for Stimulating Class Participation in an Asynchronous Learning Network

The goal of this paper is to describe a new virtual form of instructor-student interaction that can enable students to interact with their instructors without the pressures inherent in a traditional setting where they must face other students. Virtual instructor-student interaction (VISI) is a new pedagogical technique, developed by the author, which involves the transformation of an online survey into a medium that can simultaneously present course material, ask questions, obtain feedback and deliver responses. The interaction takes place asynchronously in a private space between the student and the instructor. By using this method instructors can enable students to grow their knowledge of subject material through brainstorming and direct communication with the instructor, in an intellectual space that is devoid of the peer pressure that pervades both traditional face-to-face interactions as well as the public interaction that takes place in online courses on open access websites.
Formation of phage lysis patterns and implications on co-propagation of phages and motile host bacteria

Coexistence of bacteriophages, or phages, and their host bacteria plays an important role in maintaining the microbial communities. In natural environments with limited nutrients, motile bacteria can actively migrate towards locations of richer resources. Although phages are not motile themselves, they can infect motile bacterial hosts and spread in space via the hosts. Therefore, in a migrating microbial community coexistence of bacteria and phages implies their co-propagation in space. Here, we combine an experimental approach and mathematical modeling to explore how phages and their motile host bacteria coexist and co-propagate. When lytic phages encountered motile host bacteria in our experimental set up, a sector-shaped lysis zone formed. Our mathematical model indicates that local nutrient depletion and the resulting inhibition of proliferation and motility of bacteria and phages are the key to formation of the observed lysis pattern. The model further reveals the straight radial boundaries in the lysis pattern as a tell-tale sign for coexistence and co-propagation of bacteria and phages. Emergence of such a pattern, albeit insensitive to extrinsic factors, requires a balance between intrinsic biological properties of phages and bacteria, which likely results from co-evolution of phages and bacteria. Author summary Coexistence of phages and their bacterial hosts is important for maintaining the microbial communities. In a migrating microbial community, coexistence between phages and host bacteria implies that they co-propagate in space. Here we report a novel phage lysis pattern that is indicative of this co-propagation. The corresponding mathematical model we developed highlights a crucial dependence of the lysis pattern and implied phage-bacteria co-propagation on intrinsic properties allowing proliferation and spreading of the microbes in space. Remarkably, extrinsic factors, such as overall nutrient level, do not influence phage-bacteria coexistence and co-propagation. Findings from this work have strong implications for dispersal of phages mediated by motile bacterial communities, which will provide scientific basis for the fast-growing applications of phages.
Software Adaptation through Dynamic Updating

Software systems evolve continuously. They need to be updated to fix bugs, to improve their performance or to adapt their functionality to new user requirements. In their first approaches, these updating techniques required that the corresponding program was not in use, substituting it with its new version and using such new version thereafter. This is still a valid procedure for single-user programs being run in personal computers. However, there are other kinds of software that should be always available, demanding a dynamic (i.e., at run-time) software update. This paper surveys the regular goals and currently existing mechanisms able to drive a dynamic software updating procedure.
Role of ETS1 in the Transcriptional Network of Diffuse Large B Cell Lymphoma of the Activated B Cell-Like Type

Diffuse large B cell lymphoma (DLBCL) is a heterogenous disease that has been distinguished into at least two major molecular entities, the germinal center-like B cell (GCB) DLBCL and activated-like B cell (ABC) DLBCL, based on transcriptome expression profiling. A recurrent ch11q24.3 gain is observed in roughly a fourth of DLBCL cases resulting in the overexpression of two ETS transcription factor family members, ETS1 and FLI1. Here, we knocked down ETS1 expression by siRNA and analyzed expression changes integrating them with ChIP-seq data to identify genes directly regulated by ETS1. ETS1 silencing affected expression of genes involved in B cell signaling activation, B cell differentiation, cell cycle, and immune processes. Integration of RNA-Seq (RNA sequencing) data and ChIP-Seq (chromatin immunoprecipitation sequencing) identified 97 genes as bona fide, positively regulated direct targets of ETS1 in ABC-DLBCL. Among these was the Fc receptor for IgM, FCMR (also known as FAIM3 or Toso), which showed higher expression in ABC- than GCB-DLBCL clinical specimens. These findings show that ETS1 is contributing to the lymphomagenesis in a subset of DLBCL and identifies FCMR as a novel target of ETS1, predominantly expressed in ABC-DLBCL.
Correlation and genetic analysis of seed shell thickness and yield factors in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.)

In order to solve the difficult problem of the outer shell covering in the processing of Tartary buckwheat, we conducted a genetic analysis in segregating F2 and F3 populations derived from a hybrid between ‘Yunqiao No. 1’ and ‘Rice buckwheat’, and the F3 population was used to analyze the phenotypic and genetic correlation among the traits. The results showed that the variety with a value of trait for seed shell thickness over 0.20 mm is a hard-shelled type (The thick shell type = seed shell rate > 20%), and that with a value of trait for seed shell thickness below 0.15 mm is a easily-shelled type (The thin shell type = seed shell rate < 20%), while that with a value of trait for seed shell thickness ranging from 0.15 mm to 0.20 mm is a hard-shelled type or easily-shelled type. In addition, alleles for traits of number of seed per plant and total seed weight per plant have larger dominance variance relative to their additive variance, indicating that genes controlling these traits have larger dominant effects, it is not suitable for the selection of single plant in offspring plants at the early stage of development, because these traits do not show up then. The alleles for traits of 1000 kernel weight and seed shell thickness have larger additive variance relative to their dominant variance, indicating that genes governing these traits have greater additive effects, with which the single plant can be selected in the progeny at the early stage of development. Although, the value of seed shell thickness has been shown to correlated positively with that of 1000 kernel weight, almost all the seeds of easily-shelled type are those with thin shell. However, ideal single plants with easily-shelled trait are those with intermediate phenotypes of seed shell thickness and 1000 kernel weight, by which the traits of large number of seeds per plant and total seed weight per plant could be selected. In the progeny population of this study, there were excellent single plants with high-yield and easily-shelled traits, of which the value of seed shell thickness was 0.17 mm (0.15 mm to 0.20 mm), the value of 1000 kernel weight was 14 g, the value of number of seeds per plant was 1137 and value of total seed weight per plant was 15.9 g. The results showed that taking the hybrid combinations of easily-shelled trait with the trait of seed shell thickness was the most effective selection indexes to breed the high-yield buckwheat varieties with the trait of easy shelling.