Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytochemicals as Invaluable Sources of Potent Antimicrobial Agents to Combat Antibiotic Resistance

Simple Summary Many microorganisms develop resistance to drugs through different mechanisms, and this process is called antimicrobial resistance. It is highly essential to discover new antimicrobials to kill pathogenic microbes that have developed antimicrobial resistance. Natural sources, including plants, have been serving as a great source of medicinally important compounds for the past several decades. In this article, we have discussed the antimicrobial properties of plant-derived compounds against drug-resistant human pathogens, including bacteria, fungi, and viruses. Abstract Plants have been used for therapeutic purposes against various human ailments for several centuries. Plant-derived natural compounds have been implemented in clinics against microbial diseases. Unfortunately, the emergence of antimicrobial resistance has significantly reduced the efficacy of existing standard antimicrobials. The World Health Organization (WHO) has declared antimicrobial resistance as one of the top 10 global public health threats facing humanity. Therefore, it is the need of the hour to discover new antimicrobial agents against drug-resistant pathogens. In the present article, we have discussed the importance of plant metabolites in the context of their medicinal applications and elaborated on their mechanism of antimicrobial action against human pathogens. The WHO has categorized some drug-resistant bacteria and fungi as critical and high priority based on the need to develope new drugs, and we have considered the plant metabolites that target these bacteria and fungi. We have also emphasized the role of phytochemicals that target deadly viruses such as COVID-19, Ebola, and dengue. Additionally, we have also elaborated on the synergetic effect of plant-derived compounds with standard antimicrobials against clinically important microbes. Overall, this article provides an overview of the importance of considering phytogenous compounds in the development of antimicrobial compounds as therapeutic agents against drug-resistant microbes.
Leishmania infantum (JPCM5) Transcriptome, Gene Models and Resources for an Active Curation of Gene Annotations

Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5′- and 3′-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteins.
Kalman Filters : A Tutorial

A Kalman filter is a stochastic, recursive estimator, which estimates the state of a system based on the knowledge of the system input, the measurement of the system output, and a model of the relation between input and output. The Kalman filter equations are well known, but often little effort is spent to explain or understand how the Kalman filter really works, and what its assets and limitations are. This paper introduces the Kalman filter in a very intuitive way, and looks at its properties: what information can be extracted from it, and what are its limitations. This intuitive understanding should help to develop successful practical applications. The paper also points at further reading.
Evaluation of Physicochemical Properties of Trigona sp. Stingless Bee Honey from Various Districts of Johor

Johor as one of the states of Malaysia is a good geographic location for meliponiculture activity. In this study, ten samples of stingless bee honey from each regions of Johor and one sample obtained from Institute Bioproduct Development, Universiti Teknologi Malaysia, Skudai were analyzed for the physicochemical properties of stingless bee honey. The physicochemical analyses were including moisture, total soluble solids, ash, pH, free acidity, conductivity, hydroxymethylfurfural (HMF) content, protein, carbohydrate, fat, dietary fibre, total phenolic content (TPC), total flavonoid content (TFC), and DPPH radical scavenging activity. Trigona sp. sample from Kluang have the highest value of phenolic content (778.23 ± 2.011 mg GAE/100 g) while Trigona sp. sample from Mersing have the highest value of flavonoid content (194.98 ± 0.350 mg RE/100 g). Among eleven samples tested for radical scavenging activity, Trigona sp. sample from Kota Tinggi have the highest scavenging activity (23.37 ± 0.36 mg/ml), but the value of HMF content exceeded the limit of Malaysian standard for stingless bee honey. All parameters were significantly different (p < 0.01) except for ash. This study showed a strong correlation between moisture and acidity (r = 0.601). However, low correlation was obtained between TPC and TFC with DPPH radical scavenging activity (r = -0.235, 0.011). The data obtained from this study could help for a better subsequent of Malaysian stingless bee honey industry.
Impact of Prosopis velutina Wooton on the Composition and Diversity of Native Woody Species in a Semi-Arid Zone along the Molopo River, South Africa

Invasive alien species represent one of the main threats to biodiversity and species extinction. This is the case for the genus Prosopis, among which Prosopis velutina is the most invasive and common tree species along the Molopo River in the North-West Province, impacting native plant communities. However, its impact on the composition and diversity of native woody species remains poorly investigated in the area. Thus, this study aimed to assess the impact of P. velutina on native woody plant composition and diversity across three sites along the Molopo River. At each site, five quadrats of 20 × 20 m2 were randomly established in invaded and adjacent uninvaded stands. A comparative methodological approach was adopted, and the woody plants in invaded and uninvaded stands with similar site conditions were sampled. The results showed that native woody species density differed significantly (p < 0.05) between invaded and uninvaded stands, except for Bray sites, where there was a marginal difference (p = 0.6). The overall native woody species density decreased by 79.7% in the invaded stand. However, non-metric multidimensional scaling (nMDS) and analysis of similarity (ANOSIM) indicated significant differences in native tree composition between invaded and uninvaded stands at all sites. In all three sites, all ecological indices had significantly lower values in invaded stands compared to uninvaded stands. The decrease in all ecological indices in invaded over uninvaded stands indicated that P. velutina invasion reduced the diversity of native woody plant species. Due to the incessant spread of P. velutina, it may become a long-term dominant species with an increasing impact on the native vegetation. Therefore, the findings of this study call for urgent management and appropriate control measures against the ongoing spread of this invader within the riparian zones of the Molopo River in North-West Province.
Association between Clinical Periodontal Features and Glycated Hemoglobin in Patients with Diabetes and Controlled Periodontitis: A Cross-Sectional Study

Diabetes and periodontitis are the most prevalent chronic diseases, and they influence each other’s progression. Only a few studies have shown the association between diabetes and mild periodontitis. We aimed to investigate the relationship between well-controlled periodontitis and glycated hemoglobin (HbA1c) in patients with diabetes. This retrospective study investigated 150 Japanese patients with type 2 diabetes treated with supportive periodontal therapy (SPT). Medical histories of diabetes and periodontal therapy were collected, and a multiple linear regression analysis was performed to determine their association. The patients included 67 (44.7%) males and 83 (55.3%) females, with a mean age of 68.1 (standard deviation = 10.5) years. Forty-four (29.3%) patients were treated for diabetes, and the mean HbA1c was 6.7% (0.7). Oral status was 23.3 (5.1) for the number of teeth, 2.5 mm (0.4) for mean probing pocket depth (PPD), and 163.9 mm2 (181.3) for the periodontal inflamed surface area (PISA). The multiple regression analysis showed a significant association between mean PPD (β = 0.38, p = 0.03) and HbA1c in patients with mild diabetes but not in severe cases. These results suggest that the diagnostic indices for periodontitis used to assess the association between periodontitis and HbA1c would be determined based on the severity of periodontitis and type 2 diabetes.
The impact of Nordic walking compared to non-sporting activities on socialization and well-being

Nordic walking is practiced in a natural environment and in a collective setting. This sport involves both technical and physical effort and is presented by the federations as an ideal activity to regain a better state of health and an optimal level of well-being. However, no study has demonstrated the impact of this activity, the group, and its environment on the well-being of the participants. This study compares the evolution of socialization and well-being between the practice of Nordic walking and the practice of non-sporting activities in the form of a longitudinal study involving 100 volunteers. The results show that, at the end of the season, Nordic walkers benefit from a better progression of their well-being. Moreover, the practice of a nature sport throughout a season allows participants to improve both the connections between them (socialization) and the level of perceived well-being.
Does Tourism Lead to Environmental Impact? Cross-National Static and Dynamic Evidence from the Ecological Footprint

At present, public consciousness on respecting and safeguarding the environment is declining rapidly. On that note, this study assumes that growing tourism has negative environmental implications. To satisfy tourism demand, overconsumption, and overexploitation through the development of tourism-related facilities have generated waste that destroy ecosystem functions. Ecological footprint is used to study the environmental impact of tourism activities by including the role of governance in our model. The outcome reveals that the environment is significantly affected by tourism pressure and good governance is essential for environmental protection.
Epigenetic Rewiring of Metastatic Cancer to the Brain: Focus on Lung and Colon Cancers

Simple Summary The epigenetic state within cells represents a layer for controlling homeostasis and cell differentiation. In cancer, this fine-tuned program is disrupted, resulting in cancer progression and, eventually, dissemination to distant organs. Here, we examine the epigenetic states of brain metastasis from colorectal and lung cancers and we compare those signatures with the ones detected in primary tumors. Our aim is to decipher which are the tumor type-specific regions whose deregulation is involved in metastatic dissemination to the brain and which signaling potentially confers an advantage to tumor cells to colonize the brain milieu. This information will shed light on the epi-mechanisms underpinning CRC and LuC cell dissemination to the brain and provide preliminary clues about the potential clinical value of epigenetics for brain metastasis diagnosis and therapeutic targeting. Abstract Distant metastasis occurs when cancer cells adapt to a tissue microenvironment that is different from the primary organ. This process requires genetic and epigenetic changes in cancer cells and the concomitant modification of the tumor stroma to facilitate invasion by metastatic cells. In this study, we analyzed differences in the epigenome of brain metastasis from the colon (n = 4) and lung (n = 14) cancer and we compared these signatures with those found in primary tumors. Results show that CRC tumors showed a high degree of genome-wide methylation compared to lung cancers. Further, brain metastasis from lung cancer deeply activates neural signatures able to modify the brain microenvironment favoring tumor cells adaptation. At the protein level, brain metastases from lung cancer show expression of the neural/glial marker Nestin. On the other hand, colon brain metastases show activation of metabolic signaling. These signatures are specific for metastatic tumors since primary cancers did not show such epigenetic derangements. In conclusion, our data shed light on the epi/molecular mechanisms that colon and lung cancers adopt to thrive in the brain environment.
The Consequences of Militarized Policing for Human Rights: Evidence from Mexico

What are the consequences of the militarization of public safety? Governments increasingly rely on militaries for policing, but the systematic study of this phenomenon’s consequences for human rights has been neglected. NGO and journalistic accounts point to widespread violations by the military, but these snapshots do not necessarily present evidence of systematic abuse. Based on unique data on military deployments and human rights complaints in Mexico, we conduct a systematic, country-wide study of the consequences of constabularization for human rights. Following matching and difference-in-difference strategies, we find that it leads to a 150% increase in complaints against federal security forces. We also leverage deployments for disaster-relief operations and complaints against non-security institutions to show that the increase is not due to underlying conditions or higher reporting in the military’s presence. The findings have important implications for our understanding of quality of democracy and the democratic ideals of civilian policing.
THE FUTURE OF ENGLISH LANGUAGE TEACHING AND LEARNING THROUGH “MERDEKA BELAJAR - KAMPUS MERDEKA” (MBKM): A SYSTEMATIC REVIEW

This publication systematically reviews literature on MBKM (Merdeka Belajar – Kampus Merdeka). As MBKM is relatively a new program, its prospects and challenges in its implementation in English language teaching are regarded important to be scholarly-reviewed. In this study, the total of 17 scholarly-published journals were systematically reviewed. The journals included in this study were those published in 2020 and 2021 which set “Merdeka Belajar – Kampus Merdeka” and/or “MBKM” as keywords. The searching was conducted on www.google. co.id. Based on analysis, it is found that all journals appreciate the MBKM programs as promising and innovative. Furthermore, the scholarly-published journals explore the MBKM programs through philosophical basis, its implementation, challenges, and how they are perceived. In addition, the 8 programs and 4 policies are mainly set as the findings. In this publication, the future of English language teaching and learning through 8 programs and 4 policies of “Merdeka Belajar – Kampus Merdeka” is addressed.
Effects of Historical Urbanization in the Brussels Capital Region on Surface Air Temperature Time Series: A Model Study

Abstract The authors examine the local impact of change in impervious surfaces in the Brussels capital region (BCR), Belgium, on trends in maximum, minimum, and mean temperatures between 1960 and 1999. Specifically, data are combined from remote sensing imagery and a land surface model including state-of-the-art urban parameterization—the Town Energy Balance scheme. To (i) isolate effects of urban growth on near-surface temperature independent of atmospheric circulations and (ii) be able to run the model over a very long period without any computational cost restrictions, the land surface model is run in a stand-alone mode coupled to downscaled 40-yr ECMWF reanalysis data. BCR was considered a lumped urban volume and the rate of urbanization was assessed by estimating the percentage of impervious surfaces from Landsat images acquired for various years. Model simulations show that (i) the annual mean urban bias (AMUB) on minimum temperature is rising at a higher rate (almost 3 times more) than on maximum t.
Design of sliding mode control for neutral delay systems with perturbation in control channels

This paper considers the problem of sliding mode control for a class of uncertain neutral delay systems. There are uncertainties not only in the state matrices, but also in the control matrix that results from perturbation in the control channels. By means of a sliding surface dependent on both the current states and delayed states, a sliding mode controller is designed such that the asymptotic stability of closed‐loop systems can be ensured. The design of both the sliding surface and the sliding mode controller can be obtained via convex optimization. It is shown that the state trajectories are driven onto the specified sliding surface in finite time and remain there for subsequent time. Finally, a numerical simulation example is provided. Copyright © 2011 John Wiley & Sons, Ltd.
Very large inverse problems in atmosphere and ocean modelling

For the very large nonlinear dynamical systems that arise in a wide range of physical, biological and environmental problems, the data needed to initialize a numerical forecasting model are seldom available. To generate accurate estimates of the expected states of the system, both current and future, the technique of ‘data assimilation’ is used to combine the numerical model predictions with observations of the system measured over time. Assimilation of data is an inverse problem that for very large‐scale systems is generally ill‐posed. In four‐dimensional variational assimilation schemes, the dynamical model equations provide constraints that act to spread information into data sparse regions, enabling the state of the system to be reconstructed accurately. The mechanism for this is not well understood. Singular value decomposition techniques are applied here to the observability matrix of the system in order to analyse the critical features in this process. Simplified models are used to demonstrate how information is propagated from observed regions into unobserved areas. The impact of the size of the observational noise and the temporal position of the observations is examined. The best signal‐to‐noise ratio needed to extract the most information from the observations is estimated using Tikhonov regularization theory. Copyright © 2005 John Wiley & Sons, Ltd.
Equivalence of ADM Hamiltonian and Effective Field Theory approaches at fourth post-Newtonian order for binary inspirals with spins

The next-to-next-to-leading order spin1-spin2 potential for an inspiralling binary, that is essential for accuracy to fourth post-Newtonian order, if both components in the binary are spinning rapidly, has been recently derived independently via the ADM Hamiltonian and the Effective Field Theory approaches, using different gauges and variables. Here we show the complete physical equivalence of the two results, thereby we first prove the equivalence of the ADM Hamiltonian and the Effective Field Theory approaches at next-to-next-to-leading order with the inclusion of spins. The main difficulty in the spinning sectors, which also prescribes the manner in which the comparison of the two results is tackled here, is the existence of redundant unphysical spin degrees of freedom, associated with the spin gauge choice of a point within the extended spinning object for its representative worldline. After gauge fixing and eliminating the unphysical degrees of freedom of the spin and its conjugate at the level of the action, we arrive at curved spacetime generalizations of the Newton-Wigner variables in closed form, which can also be used to obtain further Hamiltonians, based on an Effective Field Theory formulation and computation. Finally, we make use of our validated result to provide gauge invariant relations among the binding energy, angular momentum, and orbital frequency of an inspiralling binary with generic compact spinning components to fourth post-Newtonian order, including all known sectors up to date.
Short-Term Dynamics of Model Errors

Abstract The natural instability of the atmosphere is at the origin of the rapid amplification of errors coming from the uncertainty on the initial conditions and from the imperfect representation (the model) of the atmospheric dynamics. In this paper, the short-term dynamics of model error is examined in the context of low-order chaotic dynamical systems. A mathematical model describing the dynamics of this error is first derived where some of the key ingredients of its erratic behavior are incorporated, namely, the variability of the local Lyapunov exponents and of the model error source term along the dominant unstable direction. The analysis of this simplified equation indicates that depending on the nature of the model error sources (here limited to a white noise or an Ornstein–Uhlenbeck process), the mean square error initially follows either a linear or a quadratic evolution, the latter being generic. The numerical analysis of the Lorenz 1984 low-order atmospheric system, in which the model error s.
A Method for Remote Sensing the Emissivity, Fractional Cloud Cover and Cloud Top Temperature of High-Level, Thin Clouds

Abstract A methodology for retrieving the emissivity, cloud cover and cloud top temperature of high-level, thin clouds is developed and described. In the thermal infrared windows, the outgoing radiances from the earth's atmosphere contain information about cloud emissivity and cloud top temperature. This information is clearly demonstrated in the brightness temperature difference curves of two window channels. For the purpose of illustration, two window channels centered at 810 and 930 cm−1 are chosen to construct the brightness temperature difference curves for a range of cloud top temperatures. These curves vary for different cloud top temperatures, and along each of these curves the emissivity changes. The brightness temperature difference method is used in a simulation study to demonstrate the feasibility of retrieving the cloud top temperature and emissivity by the utilization of measurements in two window channels. As expected, a perfect retrieval is found imperfect measurements and ideal atmospheri.