Miracle-dz/UniFAR-FTUs huggingface dataset:
: An Efficient Sequence Retrieval Software and Comparative Sequence Retrieval Analysis

For any sequence analysis procedure, a single or multiple sequence must be retrieved, stored and organized. Among the most common public databases used for biological sequence retrieval is GenBank, which is a comprehensive public database of nucleotide sequences. However, as the length of the sequence to be retrieved increases such as a chromosome, entire genome, or a scaffold; the elapsed time to download the file is elongated due to slower bandwidth to download/retrieve the sequence. [8] In most cases of sequence analysis, the researcher requires messenger RNA (mRNA), RNA, DNA, and the protein sequences of the sequence of interest to work with, which consumes a substantial amount of the researcher’s time dedicated to find and retrieve the sequence files. Access to GenBank through JAVA HTTPS protocols was established to request and receive the sequence files associated with the input accessions. SeqDown was shown to be very efficient in terms of the retrieval time of the sequences as compared to the other internet browsers and was found to be 15.27% faster than Mozilla Firefox. SeqDown also provides the feature to retrieve coding DNA sequences and protein sequences present in a single chromosome. Sequence retrieval from most biological databases doesn’t show the proper naming of their files and the user has to deal with the redundantly named sequence files. This leads to an incorrect and time consuming analysis and this problem can be solved with SeqDown.
Exploring collections of 3D models using fuzzy correspondences

Large collections of 3D models from the same object class (e.g., chairs, cars, animals) are now commonly available via many public repositories, but exploring the range of shape variations across such collections remains a challenging task. In this work, we present a new exploration interface that allows users to browse collections based on similarities and differences between shapes in user-specified regions of interest (ROIs). To support this interactive system, we introduce a novel analysis method for computing similarity relationships between points on 3D shapes across a collection. We encode the inherent ambiguity in these relationships using fuzzy point correspondences and propose a robust and efficient computational framework that estimates fuzzy correspondences using only a sparse set of pairwise model alignments. We evaluate our analysis method on a range of correspondence benchmarks and report substantial improvements in both speed and accuracy over existing alternatives. In addition, we demonstrate how fuzzy correspondences enable key features in our exploration tool, such as automated view alignment, ROI-based similarity search, and faceted browsing.
Potensi Senyawa Turunan Xanton dari Kulit Buah Manggis (Garcinia mangostana L.) Sebagai Inhibitor Protein Mycobacterium tuberculosis: Studi In Silico

Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis infection that attacks the lungs. Tuberculosis is a dangerous disease that can cause death. In overcoming it, a safe and effective treatment is needed so that this disease can be cured. The purpose of this study was to determine the potential activity of the active compounds derived from xanthones contained in the mangosteen rind as an inhibitor of Mycobacterium tuberculosis protein with the comparison compound Isoniazid. The active compounds used in this study were α-mangostin, β-mangostin, γ-mangostin, garsinon, gartanin, and 8-deoxygartanin. This research uses the molecular docking method with Yasara, MarvinSketch, PubChem, PDB, and Plants 1.1 software. The results showed that the Gibss energy produced by each test ligand had a difference value, either lower or higher than the native ligand protein of Mycobacterium tuberculosis. Lipinski screening was done to make it easier to determine a molecule or compound based on its permeability and absorption properties. The results showed that gartanin and 8-deoxygartanin complied with Lipinski's rules. Prediction of pharmacokinetic properties and toxicity was carried out using the pkCSM website and can be concluded that gartanin and 8-deoxygartanin compounds have good pharmacokinetic properties and low toxicity.
Linking State-owned Nature-based Tourism Assets for Local Small Enterprise Development in South Africa

Tourism is often discussed as a pathway to local economic development especially in the Global South. Although much discussion surrounds upliftment via job creation and the direct income generated from tourism enterprises, there is increasing focus on the benefits of tourism supply chains for local communities. Existing research demonstrates the potential role of tourism supply chains to uplift local businesses, particularly small medium and micro-enterprises (SMMEs). Nevertheless, there are many barriers which face local SMMEs in accessing tourism supply chains particularly in the Global South. This can create conflict between these assets and local communities. This paper seeks to investigate the relationship between a major state-owned tourism asset in South Africa, the Addo Elephant National Park, and SMME development in the surrounding communities. Using qualitative interviews with stakeholders within the Addo Elephant National Park, local tourism businesses as well as local SMMEs, the challenges faced by these enterprises in entering the tourism supply chain are highlighted as well as the tenuous linkages between local SMMEs and state-owned tourism assets. The data provides important insight into the disconnect between local small enterprise development and public procurement processes within the South African tourism sector.
The lacustrine sediment record of Oberwinkler Maar (Eifel, Germany): Chironomid and macro‐remain‐based inferences of environmental changes during Oxygen Isotope Stage 3

The lacustrine record of Oberwinkler Maar (Eifel, Germany) is the northernmost continuous record documenting the Weichselian Pleniglacial in central Europe – a period characterized by multiple abrupt climate oscillations known as the Dansgaard/Oeschger cycles. Here, the results of a high‐resolution study of chironomid remains are presented, with a focus on the earlier part of Oxygen Isotope Stage (OIS) 3 (60–50 kyr BP) covering four stadial/interstadial cycles. During the stadials, the chironomid fauna of the former lake was dominated by many cold‐stenothermic chironomid taxa, indicating a cold, oligotrophic lake. The concentrations of chironomid remains were lower during the interstadials, and featured a higher number of warm‐indicating taxa. This could have been the result of a higher summer temperature at the study site, but also of bottom‐water anoxia, an increase in trophic state or a combination of all these factors. During the stadial intervals, a taxon that is restricted to (sub‐)arctic environments is present in our record, suggesting a change in the temperature regime rather than in‐lake processes as the driving mechanism for the changes in the chironomid record. Although, consistently, there was a response of the lake ecosystem to climate changes, the amplitude of this response was not constant. This study provides unique and independent evidence of the impact of Dansgaard/Oeschger climate variability on the European continent during the earlier part of OIS‐3.
Semantic Lifting and Reasoning on the Personalised Activity Big Data Repository for Healthcare Research

The fast growing markets of smart health monitoring devices and mobile applications provide opportunities for common citizens to have capability for understanding and managing their health situations. However, there are many challenges for data engineering and knowledge discovery research to enable efficiently dealing with the data that are collected from heterogonous devices and applications with big volumes and velocity. This paper presents a research work in MyHealthAvatar project, which developed a comprehensive semantic driven knowledge discovery framework based on the integrated data from multiple data resources. The framework applies cloud-based hybrid database architecture of NoSQL and RDF repositories with introductions of semantic oriented data mining and knowledge lifting algorithms. The major aim of the research is to enhance the knowledge management and discovery capabilities and efficiency to support further accurate health risk analysis and lifestyle summarization.
Comment on “New evidence of magmatic diapirs in the intermediate crust under the Dead Sea, Israel” by Nitzan Rabinowitz, Jean Steinberg, and Yossi Mart

The Dead Sea transform fault and the Dead Sea basin, in particular, were the subject of many geophysical studies. Any new geophysical study should improve our understanding of the seismotectonic setting of this region. The current view of the Dead Sea basin is that of a classical pull-apart basin with a passive north-south extension along a fault jog [Kashai and Crocker, 1987]. The extension is confined to the crust, and the upper mantle beneath the basin does not appear elevated [ten Brink et al., 1993]. Rabinowitz et al. [1996] suggest a major change in our view of the structure of the Dead Sea basin, which bears important implications for issues such as the rifling mechanism, the development of pull-apart basins, and seismotectonics. Using travel time seismic tomography from local earthquakes, Rabinowitz et al. [1996] identified for the first time a series of magmatic diapirs underlying the western side of the basin and largely aligned along the north-south direction. The diapirs ascend from the lower crust up to depth of 8 km below the surface but produce no domal effect at the surface. Here we comment on the methodology presented by Rabinowitz et al. [1996]. We further compare their results to known geological and geophysical information from the Dead Sea. We conclude that the diapirs must be either model artifacts or misinterpreted known salt diapirs, but they are not lower crustal magmatic diapirs.
Geographic information science: emerging research on the societal implications of the geospatial web

This review examines emerging research on the geoweb, particularly recent efforts to assess the social, political and disciplinary shifts associated with it. The rise of the geoweb is associated with shifts in the processes and power relations of spatial data creation and use, reconfigurations in previously bounded disciplinary knowledge sets, and shifts in the subjectivities and social relations that are produced through the geoweb’s technologies, data, and practices. This early research on the societal implications of the geoweb is drawing productively upon conceptual frameworks from critical GIS, public participation GIS, and spatial data infrastructure research, but must also theorize beyond these existing bodies of work.
Does Mother's Migrant Status Affect Child Fostering in sub-Saharan Africa?: Evidence from Two Informal Settlements in Nairobi, Kenya

• Fostering is common throughout sub-Saharan Africa, where it may be used to cement kinship ties, provide educational opportunities, and shift the financial burden of child-raising from biological parents to others. The role of mother‟s migration in fostering, however, is relatively unknown. • Few studies on fostering in Kenya: cross-national studies suggest approximately 7% of children (McDaniel & Zulu 1996) throughout Kenya; no research on fostering rates among those living in Nairobi • Both migration and fostering decisions often take place within kinship networks and are strategies that help families survive over time. We know relatively little, however, about how mothers make decisions about fostering in relation to migration.
Development of Postgraduate Psychiatric Nursing Students’ Clinical Competency Questionnaire

Introduction: As to the significance of clinical competency, the competency concept should be up-to-date periodically until clinical competency is evaluated based on it. This study aimed to develop and evaluate psychometric properties of a new tool to measure the postgraduate psychiatric nursing students' competencies. Methods: The current study was conducted with a sequential exploratory mixed-method, in Iran, in 2019 -2022. The qualitative part was conventional content analysis, and the quantitative part was a methodology study. The questionnaire was developed by the item generation via individual semi-structured interviews with 21 participants sampled purposefully, and a literature systematic review. In the quantitative phase, psychometric analysis was performed based on consensus-based standards for the selection of health status measurement instruments (COSMIN) criteria, and using face, content, and construct (i.e., convergent, known group, and exploratory factor analysis done on 199 postgraduate psychiatric nursing students by available sampling) validity. t-test analysis was used to compare the clinical competence ratings of two groups of experienced and inexperienced postgraduate psychiatric nursing students. Additionally, dependability was examined for internal consistency, stability over a one-month period, and measurement error. The sampling technique used for content validity was deliberate. Then, the responsiveness (through minimally detectable changes), and interpretability (through minimal important changes) were calculated. Results: The questionnaire consisted of 43 items. Construct validity assessment via exploratory factor analysis (EFA) showed that 67.53% of the cumulative variance was explained by two factors: "Education and nursing care" (23 items) and "Evidence based psychiatric nursing interventions" (20 items). The convergent validity with one golden standard instrument was 0.49. The difference of the clinical competency scores of the two groups of experienced and novice was significant (p<0.001). The internal consistency of the entire instrument, and the first and second factors analyzed using alpha Cronbach (α) were respectively 0.947, 0.897, and 0.891. Stability was confirmed by the ICC agreement 0.956 for interrater (CI 0.907-0.980). Standard error of measurement was 3.14. The competency score of students based on their demographic information was not significant (p>0.05). Conclusion: The 43-item postgraduate psychiatric nursing students' clinical competency questionnaire is a valid and reliable newly developed instrument. Further studies are recommended to be conducted to assess competency with the largest sample size to promote instrument.
Modelling vegetated dune landscapes

This letter presents a self‐organising cellular automaton model capable of simulating the evolution of vegetated dunes with multiple types of plant response in the environment. It can successfully replicate hairpin, or long‐walled, parabolic dunes with trailing ridges as well as nebkha dunes with distinctive deposition tails. Quantification of simulated landscapes with eco‐geomorphic state variables and subsequent cluster analysis and PCA yields a phase diagram of different types of coastal dunes developing from blow‐outs as a function of vegetation vitality. This diagram indicates the potential sensitivity of dormant dune fields to reactivation under declining vegetation vitality, e.g. due to climatic changes. Nebkha simulations with different grid resolutions demonstrate that the interaction between the (abiotic) geomorphic processes and the biological vegetation component (life) introduces a characteristic length scale on the resultant landforms that breaks the typical self‐similar scaling of (un‐vegetated) bare‐sand dunes.
A Framework for the Assessment of the Scotian Shelf and Southern Grand Banks Atlantic Halibut Stock Cadre d'évaluation du stock de flétan de l'Atlantique du plateau néo-écossais et du sud des Grands Bancs

The literature and data on Atlantic halibut was reviewed with the primary goal of supporting the first quantitative age-structured assessment of the Scotian Shelf and southern Grand Banks Atlantic halibut stock. The Canadian and foreign landings back to 1970 were used in the assessment. The catch at length was estimated using observer and port sampling data from 1988 for the longline fishery and from 1984 for the otter trawl fishery. The long-term average discard rate was used to estimate the total catch back to 1970. The total catch in the longline fishery was further divided into males and females based on observer data. A length-based, age-structured model was fitted to the length compositions in the catch and to the catch rate and length composition of halibut caught in the Scotia-Fundy groundfish Research Vessel survey (1970-2009) and halibut survey (1998-2009). Simulation testing, model fit and model comparisons indicate that the catch at length (CAL) model was good for estimating stock size and the impact of the fishery. Model estimates indicate a high population biomass and recruitment in the 1970s, increased biomass, but poor recruitment in the 1980s, low biomass and recruitment in the 1990s, and increasing biomass and recruitment in the 2000s. The spawning stock biomass in 2009 was estimated at 6527t (2592t females only). Exploitation rates were about 0.2 for the longline and otter trawl fisheries in 1970, but rapidly increased to 0.4 or greater in the late 1980s and early 90s as the population decreased. Current fishing mortality is about 0.2 for the longline fishery, but in recent years there was increased pressure on females with fishing mortality of 0.30 compared to 0.14 for males in 2009. Fishing mortality from the otter trawl fishery has been low since the mid 1990s and in 2009 was estimated at 0.02. Candidate biological reference points were estimated from the catch at length (CAL) and virtual population analysis (VPA) models using the approach outline by Sissenwine-Shepherd (1987). Both assessment models gave similar results (BMSY=4900t, FMSY=0.36). Based on assessment model results, 3NOPs4VWX5Zc Atlantic halibut population is in a productive period due to high recruitment. The SSB is estimated to be in the healthy zone; above the BMSY. Current fishing mortality (0.2) is well below FMSY (0.36). Although catch projections were not made, recent high recruitment would be expected to result in higher SSB at the current fishing mortality rate in the near term. The proposed framework for assessing Atlantic halibut takes advantage of length frequency and catch rate data from multiple datasets and is both robust and effective in estimating stock status, the impact of the fishery, and the provision of management advice. Maritimes Region Framework and Assessment: Atlantic Halibut Stock
Dynamic Cost Volumes with Scalable Transformer Architecture for Optical Flow

We introduce DCV-Net, a scalable transformer-based architecture for optical flow with dynamic cost volumes. Recently, FlowFormer [Huang et al., 2022], which applies transformers on the full 4D cost volumes instead of the visual feature maps, has shown significant improvements in the flow estimation accuracy. The major drawback of FlowFormer is its scalability for high-resolution input images, since the the complexity of the attention mechanism on the 4D cost volumes scales to O ( N 4 ) , with N being the number of visual feature tokens. We propose a novel architecture where we obtain the FlowFormer type enrichment of matching cost representations, but using light-weight attention on the visual feature maps with quadratic ( O ( N 2 ) ) complexity. Firstly, we generate sequential updates to the visual feature representations and, consequently, the cost volumes using lightweight attention layers. Secondly, we interleave this sequence of cost volumes with iterations of flow refinement, thereby modeling the update operator to handle dynamic cost volumes. Our architecture, with two orders of computational complexity lower than that of FlowFormer , demonstrates strong cross-domain generalization on the Sintel and KITTI datasets. We outperform FlowFormer on the KITTI dataset and achieve highly competitive flow estimation accuracies on the Sintel dataset.
Assimilation of satellite altimeter data into an open ocean model

Geosat sea surface height data are assimilated into an eddy-resolving quasi-geostrophic open ocean model using the adjoint technique. The method adjusts the initial conditions for all layers and is successful on the timescale of a few weeks. Time-varying values for the open boundaries are prescribed by a much larger quasi-geostrophic model of the Antarctic Circumpolar Current (ACC). Both models have the same resolution of approximately 20×20 km (1/3°×1/6°), have three layers, and include realistic bottom topography and coastlines. The open model box is embedded in the African sector of the ACC. For continuous assimilation of satellite data into the larger model the nudging technique is applied. These results are used for the adjoint optimization procedure as boundary conditions and as a first guess for the initial condition. For the open model box the difference between model and satellite sea surface height that remains after the nudging experiment amounts to a 19-cm root-mean-square error (rmse). By assimilation into the regional model this value can be reduced to a 6-cm rmse for an assimilation period of 20 days. Several experiments which attempt to improve the convergence of the iterative optimization method are reported. Scaling and regularization by smoothing have to be applied carefully. Especially during the first 10 iterations, the convergence can be improved considerably by low-pass filtering of the cost function gradient. The result of a perturbation experiment shows that for longer assimilation periods the influence of the boundary values becomes dominant and they should be determined inversely by data assimilation into the open ocean model.
LTCS-Report Finding New Diamonds: Temporal Minimal-World Query Answering over Sparse ABoxes (Extended Version)

Lightweight temporal ontology languages have become a very active ﬁeld of research in recent years. Many real-world applications, like processing electronic health records (EHRs), inherently contain a temporal dimension, and require eﬃcient reasoning algorithms. Moreover, since medical data is not recorded on a regular basis, reasoners must deal with sparse data with potentially large temporal gaps. In this paper, we introduce a temporal extension of the tractable language ELH (cid:150) , which features a new class of convex diamond operators that can be used to bridge temporal gaps. We develop a completion algorithm for our logic, which shows that entailment remains tractable. Based on this, we develop a minimal-world semantics for answering metric temporal conjunctive queries with negation. We show that query answering is combined ﬁrst-order rewritable, and hence in polynomial time in data complexity.
Food strategy: Antioxidants Synergistic effect of natural plant extracts

This study is based on the exploitation of plant extracts and the subsequent conversion of knowledge into a tactile application in the food industry in order to promote sustainable solutions to various challenges, in particular the excessive use of synthetic products (food, food supplements, cosmetics, etc.). The latter has long been linked to many questions in terms of risks to human health (cancer diseases among others). While creating positive synergies with the various sectors (pharmaceutical, food, cosmetics, etc.) and the discovery of new paths (nutraceuticals, etc.), energy and cost aspects are of interest. Economical, effective, and natural are three basic valleys of research and applications, products or even molecules with antioxidant effects and their combinations in order to preserve the food system in particular and other sectors and integrate biodiversity into value chains.