Miracle-dz/UniFAR-FTUs huggingface dataset:
Forest Disturbance Mapping with Microwave Remote Sensing

Abstract It is pre-requisite to conserve and protect the forest cover, therefore mapping of the forest distribution and monitoring of their temporal changes are also necessary. In the field of forestry, radar datasets have a high potential due to its ability to derive/extract information from the surface, sub-surface and even from the depth. The current work tries to utilize the capability of C-band radar datasets provided by Sentinel 1A/B mission to derive the required information for sensing the disturbances in the forest areas. Application of SAR or microwave remote sensing for forest disturbance mapping with dual-polarization is partially developed and have been attempted by limited researchers to process and interpret the derived results. Microwave datasets can map the areas with frequent cloud-cover due to its cloud penetrating capabilities in day-night operation mode. The present work tries to identify and locate the disturbances in forest areas to organize better understanding of detailed information for further analysis with the help of open archive microwave datasets incoherent to optical datasets.
Anticariogenic Casein Phosphopeptides

Proteins and peptides containing clusters of phosphoseryl residues have been shown to stabilize amorphous calcium phosphate in solution, and have been implicated in the regulation of biomineralisation processes. Casein phosphopeptides (CPP) containing the cluster sequence -Ser(P)-Ser(P)-Ser(P)-Glu-Glu- have been demonstrated to significantly reduce the level of dental caries (tooth decay) in animal and human experiments and also to repair early stages of decay. Through their multiple phosphoseryl residues the peptides bind to forming nanoclusters of amorphous calcium phosphate (ACP) in metastable solution, preventing their growth to the critical size required for nucleation and phase transformation. Conformational and binding studies have shown that all the phosphoseryl residues are important in interaction with ACP. The CPP localise ACP at the tooth surface providing a reservoir of calcium and phosphate ions thereby helping to maintain a state of supersaturation with respect to tooth enamel. The CPP-ACP, unlike fluoride, can be added to sugar-containing foods as well as oral care products for the control of dental caries.
Frobenius cowreaths and Morita contexts

Abstract We prove a uniqueness type theorem for (weak, total) integrals on a Frobenius cowreath in a monoidal category. When the cowreath is, moreover, pre-Galois, we construct a Morita context relating the subalgebra of coinvariants and a certain wreath algebra. Then we see that the strictness of the Morita context is related to the Galois property of the cowreath and the existence of a weak total integral on it. We apply our results to quasi-Hopf algebras.
CHAPTER 13:Ferritin and Its Role in Iron Homeostasis

Nature uses ferritins (protein cages around iron biominerals) to concentrate iron and consume pro-oxidants. Fe2+ released from dissolved ferritin mineral forms cofactors for iron proteins. Ferritin mineral substrates Fe2+, O2 or H2O2 are pro-oxidants, making ferritins one of the antioxidant response proteins encoded in ARE genes. The two ferritin cage sizes are 12 subunit mini-ferritins (prokaryote Dps proteins) and 24 subunit maxi-ferritins (eukaryotes and prokaryotes); subunits fold into 4α-helix bundles and self-assemble into cages featuring multiple sites for iron chemistry. The four known activities of ferritin proteins are: 1. Fe2+ entry/exit (via ion channels); 2. multi-site, enzymatic (ferroxidase) oxidation of Fe2+ by O2 or H2O2; 3. post-enzymatic hydrolysis yielding Fe2O3·H2O precursors (eukaryotic nucleation channels); 4. protein-controlled reductive dissolution of ferritin mineral. Fe2+ is both the precursor and the product of ferritin chemistry and also regulates ferritin biosynthesis (mRNA translation) by binding ferritin IRE-RNA. An inhibitor protein IRP dissociates while an enhancer protein eIF-4F associates with the Fe2+/IRE-RNA complex. When newly synthesized ferritin protein converts Fe2+ to caged ferritin mineral, elevated ferritin protein synthesis stops, shutting down the iron feedback loop. Ferritin proteins hold considerable promise as nano-vessels for sensor and drug delivery, for nano-material syntheses and nano-catalysis. The ferritin future is huge.
Diagnostic work up of anemic patients: role of iron deficiency

Abstract Objectives Diagnosing disturbances in iron metabolism can be challenging when accompanied by inflammation. New diagnostic tools such as the “Thomas-plot” (TP) (relation of soluble transferrin receptor [sTfR]/log ferritin to reticulocyte hemoglobin content [RET-He]) were established to improve classification of anemias. Aim of this retrospective study was to assess the added diagnostic value of the TP in anemia work up. Methods Patients from December 2016 to September 2018 with a complete blood count, iron status, RET-He and sTfR were manually classified into the four quadrants of the TP on basis of conventional iron markers. Manual and algorithm-based classifications were compared using cross tabulations, Box–Whisker-Plots as well as Receiver-Operating-Characteristics (ROC) to calculate the diagnostic accuracy using Area under the Curve (AUC) analysis. Results A total of 3,745 patients with a conventional iron status, including 1,721 TPs, could be evaluated. In 70% of the cases the manual classification was identical to the TP, in 10% it was deviant. 20% could not clearly be classified, mostly due to inflammatory conditions. In the absence of an inflammatory condition, ferritin was a reliable parameter to define iron deficiency (ID) (AUC 0.958). In the presence of inflammation, the significance of the ferritin index (AUC 0.917) and of the RET-He (AUC 0.957) increased. Conclusions The TP can be useful for narrowing down the causes of anemia in complex cases. Further studies with focus on special patient groups, e.g., oncological or rheumatic patients, are desirable.
On typeless species and the perils of fast taxonomy

C H A R L E S M O R P H Y D . S A N T O S 1, D A L T O N S . A M O R I M 2, B R U N A K L A S S A 1, D I E G O A . F A C H I N 2, S I L V I O S . N I H E I 3, C L A U D I O J . B . D E C A R VA L H O 4, R A F A E L A L . F A L A S C H I 5, C Á T I A A . M E L L O P A T I U 6, M Á R C I A S . C O U R I 6, S A R A H S . O L I V E I R A 7, V E R A C . S I L VA 8, G U I L H E R M E C . R I B E I R O 1, R E N A T O S . C A P E L L A R I 9 and C A R L O S J O S É E . L A M A S 5
Trends in Life Insurance Demand and Lapse Literature

Abstract The article analyzes the interconnectedness and gaps between two interrelated streams of literature, evolving in different time periods, by employing bibliometric tools. The research on the factors of life insurance demand started in the late 1960s and early 1970s, while more intensive works on the drivers of lapses in life insurance appeared during the 2000s. We map the research fields using our own criteria to create clusters and visualize the flow of knowledge within and between the clusters employing citation network analysis (CNA). We contribute by providing the most comprehensive systematic review that integrates both fields, additionally encapsulating studies on the demand for policy loans. The article detects the most important drivers of life insurance policyholder behavior during his/her lifetime and opens new horizons for future research.
GENTAMICIN : MYTHS AND TRUTHS

Aminoglycosides, as the name implies contain amino sugars linked with an aminocyclitol ring by glycosidic bonds. They are poly-cations, and their polarity is responsible for the pharmacokinetic properties shared by all members of the group. None of these drugs is adequately absorbed after oral administration, inadequate concentrations are found in cerebrospinal fluid, and are all excreted relatively rapidly by the normal kidney. Gentamicin is a broad spectrum antibiotic derived from the species of actinomycete Micromonospora. It was first studied and described by Weinstein and co-workers in 1963; isolated, purified and characterized by Roselot et al. It has a broader spectrum of activity than Kanamycin and is currently widely used. Mechanism of action Gentamicin, like all other aminoglycosides, diffuses through the aqueous channels produced by p o r i n s i n t h e o u t e r m e m b r a n e o f g r a m negative bacteria and enters the periplasmic s p a c e . I t i s t h e n transferred into the inner
Non-invasive temperature measurement of turbulent flows of aqueous solutions and gases in pipes

Abstract Accurate and responsive non-invasive temperature measurements are enablers for process monitoring and plant optimization use cases in the context of Industry 4.0. If their performance is proven for large classes of applications, such measurement principles can replace traditional invasive measurements. In this paper we describe a two-step model to estimate the process temperature from a pipe surface temperature measurement. This static case model is compared to and enhanced by computational fluid dynamic (CFD) calculations to predict transient situations. The predictions of the approach are validated by means of controlled experiments in a laboratory environment. The experimental results demonstrate the efficacy of the model, the responsiveness of the pipe surface temperature, and that state of the art industrial non-invasive sensors can achieve the performance of invasive thermowells. The non-invasive sensors are then used to demonstrate the performance of the model in industrial applications for cooling fluids and steam.
Socioeconomic inequalities trends in child health comparing within and between group inequalities: Food insecurity and malnutrition in Zimbabwe

Background Food insecurity and malnutrition in children are pervasive public health concerns in Zimbabwe. Several studies previously done, only identified determinants of food insecurity and malnutrition with very little efforts have been done in assessing related inequalities and decomposing the inequalities across household characteristics in Zimbabwe. This study explored socioeconomic inequalities trends in child health using the decomposition approach to compare within and between group inequalities. Methods The study used Demographic Health Survey (DHS) data sets of 2010\11 and 2015. Food insecurity in children was determined based on the WHO dietary diversity score. Minimum dietary diversity was defined by a cut- off point of >4 therefore, in this study children with less than 3 of the 13 food groups were defined as food insecure. Malnutrition was assessed using weight for age Z-score, with children whose weight-for-age Z-score below minus two standard deviations (-2 SD) from the median considered malnourished. Concentration indices were computed to understand if malnutrition was dominant among the poor or rich. The study used the Theil index and decomposed the index by population subgroups (geographical clusters and socioeconomic status). Results Over the study period, malnutrition prevalence increased by 1.03 percentage points (p.p), while food insecurity prevalence decreased by 4.35p.p. Prevalence of malnutrition and food insecurity increased among poor rural children. Theil indices for nutrition status show socioeconomic inequality gaps to have widened, while food security status socioeconomic inequality gaps contracted for the period under review. Conclusion: Within-group inequalities are driving most of the socioeconomic inequalities in nutritional status and food security status among children in Zimbabwe. To address the socioeconomic inequalities, there is need to tackle the four pillars (availability, accessibility, utilization and stability of food supply) of food and nutrition security.
Daily rewiring of a neural circuit generates a predictive model of environmental light

Daily physical remodeling of neurons changes the internal sense of daytime and nighttime. Behavioral responsiveness to external stimulation is shaped by context. We studied how sensory information can be contextualized, by examining light-evoked locomotor responsiveness of Drosophila relative to time of day. We found that light elicits an acute increase in locomotion (startle) that is modulated in a time-of-day–dependent manner: Startle is potentiated during the nighttime, when light is unexpected, but is suppressed during the daytime. The internal daytime-nighttime context is generated by two interconnected and functionally opposing populations of circadian neurons—LNvs generating the daytime state and DN1as generating the nighttime state. Switching between the two states requires daily remodeling of LNv and DN1a axons such that the maximum presynaptic area in one population coincides with the minimum in the other. We propose that a dynamic model of environmental light resides in the shifting connectivities of the LNv-DN1a circuit, which helps animals evaluate ongoing conditions and choose a behavioral response.
ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures

The recently developed Hi-C technique has been widely applied to map genome-wide chromatin interactions. However, current methods for analyzing diploid Hi-C data cannot fully distinguish between homologous chromosomes. Consequently, the existing diploid Hi-C analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to inaccurate modeling of diploid genome architecture. Here, we present ASHIC, a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genomes. We developed two models under this Bayesian framework: the Poisson-multinomial (ASHIC-PM) model and the zero-inflated Poisson-multinomial (ASHIC-ZIPM) model. The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simultaneously infer allelic 3D structures. Through simulation studies, we demonstrated that our methods outperformed existing approaches, especially under low coverage and low SNP density conditions. Additionally, we applied ASHIC-ZIPM to a published diploid mouse Hi-C data and studied the active/inactive X chromosomes and the H19/Igf2 imprinting region. In both cases, our method produced fine-resolution diploid chromatin maps and 3D structures, and provided insights into the allelic chromatin organizations and functions. To summarize, our work provides a statistically rigorous framework for investigating fine-scale allele-specific chromatin conformations. The ASHIC software is publicly available at https://github.com/wmalab/ASHIC.
Decoding of attentional state using high-frequency local field potential is as accurate as using spikes

Local field potentials (LFPs) in visual cortex are reliably modulated when the subject’s focus of attention is cued into versus out of the receptive field of the recorded sites, similar to modulation of spiking activity. However, human psychophysics studies have used an additional attention condition, neutral cueing, for decades. The effect of neutral cueing on spiking responses was examined recently and found to be intermediate between cued and uncued conditions. However, whether LFPs are also precise enough to represent graded states of attention is unknown. We found that LFPs during neutral cueing were intermediate between cued and uncued conditions, and, for a single electrode, attention was more discriminable using high frequency (>30 Hz) LFP power than spikes. Surprisingly, spikes did not outperform LFPs even when discriminability was computed using multiple electrodes. These results constrain the spatial scale attention operates over and highlight the usefulness of LFPs in studying attention.
Heading-Time Genes of the Rice Varieties Grown in South-West-Warm Region in Japan

Many genetic studies have so far revealed a number of genes responsible for heading-time of rice. However, the knowledge about these respective genes has yet been of little use for actual breeding program. For saving this situation, it is necessary to detect and identify the genes controlling the heading-time of presently grown varieties, to clarify the relationships among known, detected and identified genes, and thus to systematize the information about heading-time genes. From these points of view, gene analysis of the heading time of Japanese rice varieties was undertaken with the aid of 7 tester lines named EG lines, which are different from one another in the genotype for three late-heading-time genes E1. E2 and E3.
A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV

Multiple infection (when a single cell can become super-infected with multiple copies of virus) can effect evolutionary processes in HIV infection, such as the generation and spread of different mutations. Synaptic transmission (where multiple copies of virus can be transferred during a single cell-to-cell interaction) leads to an increase in infection multiplicity. Here, we analyze the effect of multiple infection on the evolution of an HIV infection using a hybrid stochastic-deterministic algorithm. This algorithm allows us to stochastically simulate a large number of cells and large number of cell subpopulations in a computationally efficient way. Specifically, we classify each cell subpopulation as “large” or “small” based on some size threshold (for which we provide an analytical lower bound), and then simulate the small populations stochastically, while simultaneously using the deterministic equations for the large populations. We first demonstrate to what extent deterministic models are incomplete in predicting mutant dynamics, and then use the hybrid method to study aspects of mutant evolution. Focusing on the mutant populations at the time of peak infection, we find that overall, multiple infection promotes the existence of mutant strains of virus, both in terms of faster generation and overall number. It also increases the variance in mutant numbers and results in a larger probability to observe rare strains, such as triple mutants. In the context of multiple infection, synaptic transmission is superior at generating mutants, as it increases the number of transcription events that occur. This effect is observed for neutral and advantageous mutants, even in the presence of interference. For disadvantageous mutants, purely synaptic or purely free virus transmission pathways result in an increased number of mutants, but in the presence of complementation, purely synaptic transmission maximizes mutant production and spread.
Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology

Eukaryotic genes are combinatorially regulated by a diversity of factors, including specific DNA-binding proteins called transcription factors (TFs). Physical interactions between regulatory factors have long been known to mediate synergistic behaviour, commonly defined as deviation from additivity when TFs or sites act in combination. Beyond binding-based interactions, the possibility of synergy emerging from functional interactions between TFs was theoretically proposed, but its governing principles have remained largely unexplored. Theoretically, the interplay between the binding of TFs and their effects over transcription has been challenging to integrate. Experimentally, probing kinetic synergy is easily confounded by physical interactions. Here we circumvent both of these limitations by focusing on a scenario where only one TF can be specifically bound at any given time, which we build using a synthetic biology approach in a mammalian cell line. We develop and analyze a mathematical model that explicitly incorporates the details of the binding of the TFs and their effects over transcription. The model reveals that synergy depends not only on the biochemical activities of the TFs, but also on their binding kinetics. We find experimental evidence for this result in a reporter-based system where fusions of mammalian TFs with engineered zinc fingers bind to a single, shared site. A complex synergy landscape emerges where TF activity, concentration and binding affinity shape the expression response. Our results highlight the relevance of an integrated understanding of TF function in eukaryotic transcriptional control.
Evolution Without Variation and Selection

A central tenet of evolutionary theory is that it requires variation upon which selection can act. We describe a means of attaining cumulative, adaptive, open-ended change that requires neither variation nor selective exclusion, and that can occur in the absence of generations (i.e., no explicit birth or death). This second evolutionary process occurs through the assimilation, restructuring, and extrusion of products into the environment by identical, interacting Reflexively Autocatalytic and Food set-generated (RAF) networks. Since there is no self-assembly code, it is more haphazard than natural selection, and there is no discarding of acquired traits (a signature characteristic of natural selection). We refer to this more primitive process evolutionary process as Self–Other Reorganisation because it involves internal self-organising and self-maintaining processes within entities, as well as interaction between entities. In the extreme, it can work with just one entity but it differs from learning because it can operate in groups of entities and produce adaptive change across generations. We suggest that this more primitive process is operative during the initial stage of an evolutionary process, and that it is responsible for both the origin and early evolution of both organic life, and human culture. In cultural evolution, this ‘evolution without variation’ process can increase homogeneity amongst members of a group and thereby foster group identity and cohesion.
Human belief state-based exploration and exploitation in an information-selective reversal bandit task

Humans often face sequential decision-making problems, in which information about the environmental reward structure is detached from rewards for a subset of actions. For example, a medicated patient may consider partaking in a clinical trial on the effectiveness of a new drug. Taking part in the trial can provide the patient with information about the personal effectiveness of the new drug and the potential reward of a better treatment. Not taking part in the trial does not provide the patient with this information, but is associated with the reward of a (potentially less) effective treatment. In the current study, we introduce a novel information-selective reversal bandit task to model such situations and obtained choice data on this task from 24 participants. To arbitrate between different decision-making strategies that participants may use on this task, we developed a set of probabilistic agent-based behavioural models, including exploitative and explorative Bayesian agents, as well as heuristic control agents. Upon validating the model and parameter recovery properties of our model set and summarizing the participants’ choice data in a descriptive way, we used a maximum likelihood approach to evaluate the participants’ choice data from the perspective of our model set. In brief, we provide evidence that participants employ a belief state-based hybrid explorative-exploitative strategy on the information-selective reversal bandit task, lending further support to the finding that humans are guided by their subjective uncertainty when solving exploration-exploitation dilemmas.