Miracle-dz/UniFAR-FTUs huggingface dataset:
A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools

Introduction Tuberculosis (TB) is among the deadliest diseases worldwide, and its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, nonadherence to treatment and circulation of previously resistant isolates of Mycobacterium tuberculosis. In this study, we evaluated the performance and functionalities of web-based tools, including Mykrobe, TB-profiler, PhyResSE, KvarQ, and SAM-TB, for detecting resistance in 88 Ecuadorian isolates of Mycobacterium tuberculosis drug susceptibility tested previously. Statistical analysis was used to determine the correlation between genomic and phenotypic analysis. Our results showed that with the exception of KvarQ, all tools had the highest correlation with the conventional drug susceptibility test (DST) for global resistance detection (98% agreement and 0.941 Cohen’s kappa), while SAM-TB, PhyResSE, TB-profiler and Mykrobe had better correlations with DST for first-line drug analysis individually. We also identified that in our study, only 50% of mutations characterized by the web-based tools in the rpoB, katG, embB, pncA, gyrA and rrs regions were canonical and included in the World Health Organization (WHO) catalogue. Our findings suggest that SAM-TB, PhyResSE, TB-profiler and Mykrobe were efficient in determining canonical resistance-related mutations, but more analysis is needed to improve second-line detection. Improving surveillance programs using whole-genome sequencing tools for first-line drugs, MDR-TB and XDR-TB is essential to understand the molecular epidemiology of TB in Ecuador. Importance Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis, most commonly affects the lungs and is often spread through the air when infected people cough, sneeze, or spit. However, despite the existence of effective drug treatment, patient adherence, long duration of treatment, and late diagnosis have reduced the effectiveness of therapy and increased drug resistance. The increase in resistant cases, added to the impact of the COVID-19 pandemic, has highlighted the importance of implementing efficient and timely diagnostic methodologies worldwide. The significance of our research is in evaluating and identifying a more efficient and user-friendly web-based tool to characterize resistance in Mycobacterium tuberculosis by whole-genome sequencing, which will allow more routine application to improve TB strain surveillance programs locally.
Research Online

This paper provides exploratory evidence on corporate governance (CG) and corporate social responsibility (CSR) interfaces. Although there remains a voluminous literature on CG and CSR, very little effort has been put forward to explore the nature of this relationship. Using interviews with senior executives of New Zealand Stock Exchange (NZX) listed firms, this research assesses CG and CSR practices, identifies barriers for CG and CSR adoption, and investigates the nature of the relationship between CG and CSR. The results indicate a moderate level of CG and CSR practices, with lack of resources and cost-time balance as common barriers for CG and CSR adoption. However, despite these barriers, we note that the majority of executives appreciate the increasing convergence between CG and CSR and believe that a more robust CG framework will lead to more sustainable CSR practices. These findings have important implications for managers and policymakers interested in understanding the CG-CSR nexus and promoting responsible business practices.
The Concept of Information Support for Bi-oresource and Ecosystem Research in the North-West Pacific: Theory and Practical Implementation

The first part of the article provides an overview of the theoretical evidence, the main provisions, and the implementation strategy of information support for bioresource and ecosystem research in the north-west Pacific, which has been conducted over the past 20 years in the Russian Far East Research Institute TINRO-Center. In short, the concept consists of a combination of the following four assertions: 1) For the steady and sustainable development of the Russian Far East, the entire Russian Federation and the Asia-Pacific Region in general, environmental, food, economic, and other security is required, which cannot be achieved without the rational use of bioresources based on the ecosystem approach to the management of aquatic bioresources. 2) For the inventory, appraisal, monitoring, forecasting of the state of and management the natural water resources when applying this approach, statistically relevant quantitative information is required on the greatest possible number of constituents of marine biocenosis of the north-western Pacific for the longest possible period of time, which is only available at the TINRO-Center. 3) This valuable data should be organized into databases, based on which geo-information and other electronic information systems are prepared, and based on these map atlases and reference books on natural water resources, using automated workplaces created especially for this. 4) The resulting unique information support will be of great value not only for practical purposes, but also for science, both applied and fundamental. Next comes a summary of the many years of work on the practical implementation of this concept and the key achievements in this field obtained by the TINRO-Center by the end of 2015 are reviewed. At the end, some plans for the near future are outlined.
Antioxidant and antibacterial activities of selected marine algae and Egyptian aromatic herbs regarding to their phytochemical characteristics and mass spectrometry evaluation

1 Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta 34517, Egypt. 2 National institute of Oceanography and Fisheries, NIOF, Cairo, Egypt. 3 Department of Microbiology, Faculty of Science, Omer Almokhtar University, Libya. 4 Environmental Sciences Department, Faculty of Science, Damietta University, New Damietta, Egypt. * Corresponding Author: m_okbah@yahoo.com
Sedentary lifestyle of university students is detrimental to the thoracic spine in men and to the lumbar spine in women

Background Sitting for long periods of time and lack of physical activity in young adults can cause postural deterioration leading to rapid onset of fatigue and increase the risk of back pain. We were interested in whether there are gender differences in spinal curvature among university students with a predominantly sedentary lifestyle. Methods 20 sedentary female (age 20 ± 0.73 years) and 39 sedentary male university students (age 20 ± 1.08 years) participated in this study. Their thoracic and lumbar curvatures were assessed while standing and sitting using a Spinal Mouse. Results In standing, 80.0% of the females and 69.2% of the males had a neutral position of the thoracic spine (33.25° and 35.33°, respectively). However, more males, 30.8%, than females, 10.0%, had hyperkyphosis (54.27° and 47.0°, respectively). Hypokyphosis was found in 10.0% of the females (18.50°) and none in the males. Similarly, 90.0% of the females and 97.4% of the males had neutral position of the lumbar spine (-33.11° and -29.76°, respectively). Increased hyperlordosis was found in 10.0% of the females and 2.6% of the males (-41.0° and -50.0°, respectively). Hypolordosis was not detected in either females or males. In sitting, on the other hand, 70.0% of the females and only 33.3% of the males had a neutral position of the thoracic spine (30.20° and 30.62°, respectively). Increased hyperkyphosis was found in 46.2% of the males (59.76°) and none of the females. 30.0% of the females and 23.1% of the males had light hypokyphosis (47.50° and 46.67°, respectively). Similarly, 70.0% of the females and only 38.5% of the males had a neutral position of the lumbar spine (7.0° and 6.6°, respectively). 35.9% of the males and only 5.0% of the females had a light hypokyphosis (16.14° and 16.0°, respectively). Slightly increased hyperkyphosis was identified in 25.6% of the males and 25.0% of the females (23.9° and 22.5°, respectively). Conclusion There are significant gender differences in spinal curvature. While in the thoracic spine it was to the detriment of the males when both standing and sitting, in the lumbar spine it is related to the females only when standing. It is therefore necessary to eliminate these spinal deviations in young adults induced by prolonged sitting during university courses by appropriate recovery modalities.
Genetic Diversity and Phylogenetic Analysis of Lepidopteran Species by Molecular Barcoding Using Co I Gene Sequences

Lepidoptera is one of the largest orders of insects that include moths and butterflies. Most of the Lepidopterans are morphologically similar, therefore the identification of these insects is tedious using morphotaxonomy and that is detrimental in designing a better strategy to control and conserve them. These are extremely important group of ‘model’ organisms and are used to investigate many areas of biological research, including such diverse fields as navigation, pest control, embryology, mimicry, evolution, genetics, population dynamics and biodiversity conservation. The knowledge of Lepidopteran genomics will create new methods of insect pest management and will contribute to sustainable agriculture, protection of the environment and the maintenance of biodiversity. In this study we amplified cytochrome oxidase I gene of Junonia atlites for species identification and constructed phylogenetic tree for recognizing evolutionary relationship.
Influences of community engagement and health system strengthening for cholera control in cholera reporting countries

The 2030 Global Task Force on Cholera Control Roadmap hinges on strengthening the implementation of multistranded cholera interventions, including community engagement and health system strengthening. However, a composite picture of specific facilitators and barriers for these interventions and any overlapping factors existing between the two, is lacking. Therefore, this study aims to address this shortcoming, focusing on cholera-reporting countries, which are disproportionately affected by cholera and may be cholera endemic. A scoping methodology was chosen to allow for iterative mapping, synthesis of the available research and to pinpoint research activity for global and local cholera policy-makers and shareholders. Using the Arksey and O’Malley framework for scoping reviews, we searched PubMed, Web of Science and CINAHL. Inclusion criteria included publication in English between 1990 and 2021 and cholera as the primary document focus in an epidemic or endemic setting. Data charting was completed through narrative descriptive and thematic analysis. Forty-four documents were included, with half relating to sub-Saharan African countries, 68% (30/44) to cholera endemic settings and 21% (9/44) to insecure settings. We identified four themes of facilitators and barriers to health systems strengthening: health system cooperation and agreement with external actors; maintaining functional capacity in the face of change; good governance, focused political will and sociopolitical influences on the cholera response and insecurity and targeted destruction. Community engagement had two themes: trust building in the health system and growing social cohesion. Insecurity and the community; cooperation and agreement; and sociopolitical influences on trust building were themes of factors acting at the interface between community engagement and health system. Given the decisive role of the community–health system interface for both sustained health system strengthening and community engagement, there is a need to advocate for conflict resolution, trust building and good governance for long-term cholera prevention and control in cholera reporting countries.
Current status and analysis of the development of SLAM technology applied to mobile robots

Mobile robots are tasked with jobs that assist or replace human work. With the development of technology, mobile robots have had a significant impact on human productive life. As for mobile robots, the core technology is the location awareness of itself. Therefore, this paper analyses the current development state of simultaneous localization and mapping (SLAM) technology applied to mobile robots. First, the overall process and key technologies were explained in detail. Subsequently, the classical algorithms developed in SLAM technology so far are classified based on the characteristics of information-aware devices in terms of methods as well as a more detailed description and comparative analysis of the algorithms. Finally, this paper analyses the current development status of SLAM and the remaining problems from the key performance indicators of SLAM technology, and interprets the future development trend of SLAM technology applied to mobile robots.
UvA-DARE (Digital Academic Repository) RT-based memory detection: Item saliency effects in the single-probe and the multiple-probe protocol

RT-based memory detection may provide an efﬁcient means to assess recognition of concealed information. There is, however, considerable heterogeneity in detection rates, and we explored two potential moderators: item saliency and test protocol. Participants tried to conceal low salient (e.g., favourite colour) and high salient items (e.g., ﬁrst name) and were tested with either the single-probe protocol or the multiple-probe protocol. Experiment 1 was a laboratory study with knowledgeable individuals only ( n = 47). Experiment 2 was an Internet study ( n = 283) that also included unknowledgeable individuals. High salient items were better detected than low salient items in the laboratory, but not the Internet study (in which the item saliency manipulation was less successful). The multiple-probe protocol outperformed the single-probe protocol in both studies. We conclude that pronounced differences in item saliency affect the validity of RT-based memory detection, and we recommend the multiple-probe protocol for RT-based memory detection. © 2015 Society for Applied Research in Memory and Cognition. Published by Elsevier Inc. All rights reserved.
Mechanical positive feedback and biochemical negative feedback combine to generate complex contractile oscillations in cytokinesis

Contractile force generation by the cortical actomyosin cytoskeleton is essential for a multitude of biological processes. The actomyosin cortex behaves as an active material that drives local and large-scale shape changes via cytoskeletal remodeling in response to biochemical cues and feedback loops. Cytokinesis is the essential cell division event during which a cortical actomyosin ring generates contractile force to change cell shape and separate two daughter cells. Our recent work with active gel theory predicts that actomyosin systems under the control of a biochemical oscillator and experiencing mechanical strain will exhibit complex spatiotemporal behavior, but cytokinetic contractility was thought to be kinetically simple. To test whether active materials in vivo exhibit spatiotemporally complex kinetics, we used 4-dimensional imaging with unprecedented temporal resolution and discovered sections of the cytokinetic cortex undergo periodic phases of acceleration and deceleration. Quantification of ingression speed oscillations revealed wide ranges of oscillation period and amplitude. In the cytokinetic ring, activity of the master regulator RhoA pulsed with a timescale of approximately 20 seconds, shorter than that reported for any other biological context. Contractility oscillated with 20-second periodicity and with much longer periods. A combination of in vivo and in silico approaches to modify mechanical feedback revealed that the period of contractile oscillation is prolonged as a function of the intensity of mechanical feedback. Effective local ring ingression is characterized by slower speed oscillations, likely due to increased local stresses and therefore mechanical feedback. Fast ingression also occurs where material turnover is high, in vivo and in silico. We propose that downstream of initiation by pulsed RhoA activity, mechanical positive feedback, including but not limited to material advection, extends the timescale of contractility beyond that of biochemical input and therefore makes it robust to fluctuations in activation. Circumferential propagation of contractility likely allows sustained contractility despite cytoskeletal remodeling necessary to recover from compaction. Our work demonstrates that while biochemical feedback loops afford systems responsiveness and robustness, mechanical feedback must also be considered to describe and understand the behaviors of active materials in vivo.
Bmc Medical Research Methodology Open Access the Development of Quadas: a Tool for the Quality Assessment of Studies of Diagnostic Accuracy Included in Systematic Reviews

Background: In the era of evidence based medicine, with systematic reviews as its cornerstone, adequate quality assessment tools should be available. There is currently a lack of a systematically developed and evaluated tool for the assessment of diagnostic accuracy studies. The aim of this project was to combine empirical evidence and expert opinion in a formal consensus method to develop a tool to be used in systematic reviews to assess the quality of primary studies of diagnostic accuracy.
Short-Term Meditation Training Alters Brain Activity and Sympathetic Responses at Rest, but not during the meditation

Numerous studies have shown that meditation has a number of positive effects on the physical and psychological well-being of practitioners. As a result, meditation has become widely practiced not only as a religious practice but also as a self-regulation technique to achieve specific measurable goals. This raises the question of how quickly physiological changes can be noticed in individuals for whom meditation is not the main focus of their lives but rather a wellbeing keeping technique. Another question is whether it is possible to observe changes occurring directly during meditation and use bio- or neuro-feedback to enhance such meditation training and achieve tangible results. In our study, the experimental group of individuals with no previous meditation experience underwent eight weeks of training in Taoist meditation (2 sessions lasting 1 hour each week), under the guidance of a certified instructor. Participants in the control group attended offline group meetings during the same period, where they listened to audio books. All participants performed meditation testing before and after the intervention, following audio instructions. During the meditation practice, participants’ EEG, photoplethysmogram, respiratory rate, and skin conductance were recorded. The meditation training, but not the control group activity, resulted in topically organized changes of the resting state brain activity and heart rate variability. Specifically, we observed an increase in EEG power in multiple frequency bands (delta, theta, alpha, beta) and changes in the heart rate variability indicators associated with sympathetic system activation. However, no significant changes were observed when we compared the physiological indicators during the actual meditation process performed prior and post the 8-week training. We interpret these changes as signs of increased alertness and possibly accelerated resting metabolic rate. Importantly, these changes were observed after only 16 hours of meditation training performed during the 8-week period of time. The absence of difference in the band-specific power profiles between the experimental and control groups during the process of meditation conceptually complicates the development of assistive devices aimed at “guiding” the novice meditators during the actual meditation. Our results suggest that the focus in creating such digital assistants should rather be shifted towards monitoring neurophysiological activity during the time intervals outside of the actual meditation. The apparent changes occur not only in the EEG derived parameters but are also detectable based on the markers of autonomous nervous system activity that can be readily registered with a range of wearable gadgets which renders hope for a rapid translation of our results into practical applications.
On the perception of urgency in audition: sound design of an early warning alarm

Earthquake early warning (EEW) systems play a critical role in providing advance notice to potentially affected regions, enabling individuals and communities to take immediate safety actions. The efficacy of EEW alarms greatly depends on the timely perception of urgency by the recipients. This paper presents a possible early warning infrastructure which also takes into account the possibility of adapting the alarm to the sensed soundscape in order to define a trade-off between an alarm's urgency and its tolerability in residential and public spaces, aiming to strike a balance between providing timely warnings and minimizing unnecessary panic. The impact of sound alarms on the perception of urgency when the signal is immersed in different soundscapes is thus evaluated and discussed. Preliminary results demonstrate the need of designing an adaptive alarm as a function of the soundscape where it is immersed.
Non-Player Character Decision-Making With Prolog and Ontologies

This paper proposes a new approach to non-player character (NPC) decision-making in games using a Prolog and ontologies declarative approach, addressing limitations of traditional techniques such as flexibility and maintainability. We implement a more complex Unity version of the Wumpus World to show our method’s effectiveness and its potential to facilitate game AI design and prototyping. Our approach can achieve the same results as the classical methods without having to hard-code all the transitions between each possible game situation.