Miracle-dz/UniFAR-FTUs huggingface dataset:
Wolbachia Effect on Drosophila melanogaster Lipid and Carbohydrate Metabolism

Simple Summary A study to investigate the effect that different Wolbachia pipientis strains have on the carbohydrate and lipid metabolism, starvation resistance and feeding behavior of Drosophila melanogaster females has been performed. The data obtained demonstrate that Wolbachia most likely change their hosts’ metabolism in different aspects, including the effect on energy metabolism, fitness and behavior, to ensure the host’s competitive advantage over uninfected insects, which contributes to the spread of the bacteria in the population. Abstract The effect of maternally inherited endosymbiotic bacteria Wolbachia on triglyceride and carbohydrate metabolism, starvation resistance and feeding behavior of Drosophila melanogaster females was studied. Eight D. melanogaster lines of the same nuclear background were investigated; one had no infection and served as the control, and seven others were infected with different Wolbachia strains pertaining to wMel and wMelCS groups of genotypes. Most of the infected lines had a higher overall lipid content and triglyceride level than the control line and their expression of the bmm gene regulating triglyceride catabolism was reduced. The glucose content was higher in the infected lines compared to that in the control, while their trehalose levels were similar. It was also found that the Wolbachia infection reduced the level of tps1 gene expression (coding for enzyme for trehalose synthesis from glucose) and had no effect on treh gene expression (coding for trehalose degradation enzyme). The infected lines exhibited lower appetite but higher survival under starvation compared to the control. The data obtained may indicate that Wolbachia foster their hosts’ energy exchange through increasing its lipid storage and glucose content to ensure the host’s competitive advantage over uninfected individuals. The scheme of carbohydrate and lipid metabolism regulation under Wolbachia’s influence was suggested.
Assessment and Selection of Cyanobacterial Strains for CO2 Mineral Sequestration: Implications for Carbonation Mechanism

Abstract CO2 mineral carbonation induced by microalgae is an emerging approach to carbon capture, utilization, and storage (CCUS). Freshwater cyanobacteria are common microalgae in nature that can raise the pH of eutrophic waters and drive the precipitation of carbonate. Still, limited studies have been conducted to evaluate and select appropriate cyanobacteria strains for CCUS. Here we present experimental investigations to compare the capacity of different freshwater cyanobacterial strains in converting CO2 to carbonates. We compare five cyanobacterial strains by monitoring their growth curves. We examine three metrics, the maximum pH of the solution, hydroxide production capacity, and extracellular polymeric substances (EPS) secretion capacity, to assess the capacity for carbon sequestration. Our results indicate that among the five strains, Microcystis aeruginosa shows the highest pH and EPS content per unit cell number, marking the most significant capacity for CO2 carbonation. We observe carbonate precipitates as hydromagnesite and dypingite. We suggest the negatively charged, hydrophilic EPS can effectively promote the precipitation of magnesium carbonate and inhibit the precipitation of calcium carbonate. Overall, our approach provides a framework for assessing and selecting cyanobacterial strains for CO2 carbonation, advancing the understanding of the mechanism of microalgae-induced CO2 Mg-carbonation from the perspective of EPS surface properties.
Identifying mRNAs Residing in Myelinating Oligodendrocyte Processes as a Basis for Understanding Internode Autonomy

In elaborating and maintaining myelin sheaths on multiple axons/segments, oligodendrocytes distribute translation of some proteins, including myelin basic protein (MBP), to sites of myelin sheath assembly, or MSAS. As mRNAs located at these sites are selectively trapped in myelin vesicles during tissue homogenization, we performed a screen to identify some of these mRNAs. To confirm locations, we used real-time quantitative polymerase chain reaction (RT-qPCR), to measure mRNA levels in myelin (M) and ‘non-myelin’ pellet (P) fractions, and found that five (LPAR1, TRP53INP2, TRAK2, TPPP, and SH3GL3) of thirteen mRNAs were highly enriched in myelin (M/P), suggesting residences in MSAS. Because expression by other cell-types will increase p-values, some MSAS mRNAs might be missed. To identify non-oligodendrocyte expression, we turned to several on-line resources. Although neurons express TRP53INP2, TRAK2 and TPPP mRNAs, these expressions did not invalidate recognitions as MSAS mRNAs. However, neuronal expression likely prevented recognition of KIF1A and MAPK8IP1 mRNAs as MSAS residents and ependymal cell expression likely prevented APOD mRNA assignment to MSAS. Complementary in situ hybridization (ISH) is recommended to confirm residences of mRNAs in MSAS. As both proteins and lipids are synthesized in MSAS, understanding myelination should not only include efforts to identify proteins synthesized in MSAS, but also the lipids.
The daily locomotor activity profile of Zebrafish Danio rerio is affected when exposed to polluted water from Lerma River (Guanajuato, Mexico)

ABSTRACT Environmental pollution is a threat to circadian rhythms of behaviour and physiology of organisms. The daily rhythm of swimming activity in zebrafish Danio rerio was studied to evaluate the toxicity of water from Lerma River, in Mexico, as it passed through the city of Salamanca, Guanajuato. Swimming activity along 3 days of acute exposure to polluted water, and then, the activity of the enzyme acetylcholinesterase and the oxidative stress in homogenized tissue was tested. Exposure to polluted water drastically reduces magnitude and alters the daily pattern of swimming activity. Cosinor analysis shows effect on mesor and robustness of rhythms, Tissue analysis showed a negative effect on AChE or an increase on oxidative stress. The analysis of water ions Al, P, F−, PO4 3-, SO4 2- in concentrations above the established in the official references. We discuss that daily swimming activity in zebra fish is useful to test water quality in polluted environments.
The Hidden Structure of Photons

We deduce that the speed of light is constant in all inertial frames of reference because both time and space are discretized. To provide a theoretical basis for this discreteness, we postulate our space to be an ocean of the “Gamma elements” having extremely small size and energy (or mass) density. The relativistic relationship between time and space with respect to the constant speed of light is then determined by the process of light propagation in this medium. The theory finds light energy propagating as “elemental waves” with the phase velocity, c. Here a photon is no longer a particle traveling with the velocity, c, but a Gamma element transforming into a Planck element, an energized state carrying an angular momentum, h, with a frequency, v, substantially behaving like a particle with the energy, Eph = hν, traveling with the velocity, c. The lifetime of each Planck element is on the order of the elemental time, tp. A possible mechanism for this transformation is proposed by the use of the quantum field process involving a vector boson transforming between a massive state (Planck element) and a massless, charged state (Gamma element.) We note that the vacuum state in the quantum field theory is approximately equivalent to the Gamma element state. A visualized space-time and photon models are presented and the Compton experiment and the double slit experiment are re-validated by the theory. Owing to the relativistic effect, in particular, the Compton scattering variables, the wavelength change of the incident Gamma rays and the velocity acquired by the electron by the scaterring, are shown to be the same whether the scattering is by the single photon particle or by the series of Planck elements. The difference is the rate at which the energy of the incident Gamma ray is assumed to be delivered, which will then manifest the difference in the acceleration of the electron. This difference may be explored to verify the theory by experiments.
Achievable precision and accuracy in EPR dosimetry of tooth enamel

The utility of combining various methodologies is examined to remove systematically or correct for the major instrumental effects which introduce uncertainties in EPR dosimetry of tooth enamel. The result is a relatively high precision method that can be successfully transferred between laboratories. Only an ideal case was considered in this study whereby the actual native signal prior to irradiation was used as the empirical zero in each individual dose response. To prove its general value, the overall methodology was applied to seven teeth of differing quality, prepared using different methodologies, and measured in three laboratories using different EPR spectrometers. Using this approach to characterise the utility of both the methodology and instrumentation resulted in 5 ± 5 mGy (1σ) spectral intensity reproducibility at the 100 mGy dose level for the seven samples analysed. Similarly, at the 1100 mGy level, spectral intensity reproducibility was found to be equivalent to 13 ± 5 mGy (1σ) for the same seven samples. Assuming linearity of dose response in the 0-1100 mGy dose range and using dose responses at 100 mGy and 1100 mGy levels, gave an overall extrapolated x intercept (dose estimate) offset of -13 ± 19 mGy (1σ).
The Evolution of Mitochondrial Genomes between Two Cymbidium Sister Species: Dozens of Circular Chromosomes and the Maintenance and Deterioration of Genome Synteny

Plant mitochondrial genomes (mitogenomes) exhibit fluid genome architectures, which could lead to the rapid erosion of genome synteny over a short evolutionary time scale. Among the species-rich orchid family, the leafy Cymbidium lancifolium and leafless Cymbidium macrorhizon are sister species with remarkable differences in morphology and nutritional physiology. Although our understanding of the evolution of mitochondria is incomplete, these sister taxa are ideal for examining this subject. In this study, the complete mitogenomes of C. lancifolium and C. macrorhizon, totaling 704,244 bp and 650,751 bp, respectively, were assembled. In the 2 mitogenomes, 38 protein-coding genes, 18 cis- and 6 trans-spliced introns, and approximately 611 Kb of homologous sequences are identical; overall, they have 99.4% genome-wide similarity. Slight variations in the mitogenomes of C. lancifolium and C. macrorhizon in repeat content (21.0 Kb and 21.6 Kb, respectively) and mitochondrial DNA of plastid origin (MIPT; 38.2 Kb and 37.5 Kb, respectively) were observed. The mitogenome architectures of C. lancifolium and C. macrorhizon are complex and comprise 23 and 22 mini-circular chromosomes, respectively. Pairwise comparisons indicate that the two mitogenomes are largely syntenic, and the disparity in chromosome numbers is likely due to repeat-mediated rearrangements among different chromosomes. Notably, approximately 93.2 Kb C. lancifolium mitochondrial sequences lack any homology in the C. macrorhizon mitogenome, indicating frequent DNA gains and losses, which accounts mainly for the size variation. Our findings provide unique insights into mitogenome evolution in leafy and leafless plants of sister species and shed light on mitogenome dynamics during the transition from mixotrophy to mycoheterotrophy.
The Relationship between Anxiety, Subjective and Objective Sleep, Chronotype and Circadian Rhythms with Depressive Symptoms in Insomnia Disorder

Insomnia is a highly prevalent sleep disorder with strong bidirectional associations with depressive symptoms. The circadian preference for eveningness has been shown to be associated with depressive symptoms in insomnia and other mental health conditions. However, there is a lack of studies in insomnia investigating whether objective measures, such as dim light melatonin onset (DLMO) or polysomnographic (PSG) sleep, are associated with depressive symptoms. Therefore, we investigated the associations between subjective measures (questionnaires assessing anxiety, sleep quality and circadian preference, and sleep diary) and depressive symptoms and whether the addition of objective measures (DLMO, PSG parameters) would strengthen the associations with depressive symptoms. In 115 insomnia disorder patients we found that anxiety was strongly associated with depressive symptoms in a model including circadian preference, dysfunctional beliefs of sleep, and self-reported previous depressive symptoms (R2 = 0.496, p < 0.001). The addition of sleep diary measures did not strengthen the model. We also found that the addition of objective measures (DLMO, PSG parameters) did not improve the subjective associations with depressive symptoms. Our data suggest that objective circadian markers are less important in the prediction of depressive symptoms in insomnia compared to subjective measures.
SOLVABILITY OFGENERAL DIFFERENTIAL ALGEBRAIC EQUATIONS

In the last few years there has been considerable research on differential algebraic equations (DAEs) f(t, x, x) 0 where fx' is identically singular. Most of this effort has focused on computing a solution that is assumed to exist. That is, the DAE is assumed solvable. More recently there have been existence results developed using differential geometry. Forcomplexhigherindex systems these characterizations canbehard to verify in practice. In this paper the computational verification of solvability is investigated. This first requires developing an alternative set of sufficient conditions for solvability which are more amenable to computation. Verification of these conditions using readily available numerical and symbolic software is then discussed. An example from robotics where classical graph theoretical approaches give an incorrect answer is worked to illustrate the usefulness of the sufficient condition and the computational approach.
Monitoring Seasonal Fluctuation and Long‐Term Trends for the Greenland Ice Sheet Using Seismic Noise Auto‐Correlations

One important feature of the Greenland Ice Sheet (GrIS) change is its strong seasonal fluctuation. Taking advantage of deployed seismographic stations in Greenland, we apply cross‐component auto‐correlation of seismic ambient noise to measure in‐situ near surface relative velocity change (dv/v) in different regions of Greenland. Our results demonstrate that dv/v measurements for most stations have less than 3 months lag times in comparison to the surface mass change. These various lag times may provide us constraints for the thickness of the subglacial till layer over different regions in Greenland. Moreover, in southwest Greenland, we observe a change in the long‐term trend of dv/v for three stations, which might be consistent with the mass change rate (dM/dt) due to the “2012–2013 warm‐cold transition. ” These observations suggest that seismic noise auto‐correlation technique may be used to monitor both seasonal and long‐term changes of the GrIS.
New experimental investigation of the structure of Be 10 and C 16 by means of intermediate-energy sequential breakup

Be10 and C16 spectroscopy has been investigated by analyzing their breakup events on CH2 and CD2 targets. Breakup fragments have been detected by means of the CHIMERA detector. In particular, we investigated cluster decays of Be10 in He4+He6 and of C16 in He6+Be10 and He4+He6+He6. From the relative energy analysis of breakup fragments, we investigate the spectroscopy of excited states of projectile nuclei. In the Be10 case we observe known states at 9.51, 10.16, 10.6, and 11.8 MeV. Further, we suggest the existence of a new state at 13.5 MeV, possibly 6+ as indicated from angular correlation analysis. The relative energy (Erel+Eth) spectrum of C16, reconstructed starting from He6+Be10 correlations, shows a peak at about 20.6 MeV, probably related to the existence of an high-lying excited state. Non-vanishing yields are also seen in the triple coincidences He4+He6+He6.
Synthesis of Novel Benzenesulfonamide-Bearing Functionalized Imidazole Derivatives as Novel Candidates Targeting Multidrug-Resistant Mycobacterium abscessus Complex

Infections caused by drug-resistant (DR) Mycobacterium abscessus (M. abscessus) complex (MAC) are an important public health concern, particularly when affecting individuals with various immunodeficiencies or chronic pulmonary diseases. Rapidly growing antimicrobial resistance among MAC urges us to develop novel antimicrobial candidates for future optimization. Therefore, we have designed and synthesized benzenesulfonamide-bearing functionalized imidazole or S-alkylated derivatives and evaluated their antimicrobial activity using multidrug-resistant M. abscessus strains and compared their antimycobacterial activity using M. bovis BCG and M. tuberculosis H37Ra. Benzenesulfonamide-bearing imidazole-2-thiol compound 13, containing 4-CF3 substituent in benzene ring, showed strong antimicrobial activity against the tested mycobacterial strains and was more active than some antibiotics used as a reference. Furthermore, an imidazole-bearing 4-F substituent and S-methyl group demonstrated good antimicrobial activity against M. abscessus complex strains, as well as M. bovis BCG and M. tuberculosis H37Ra. In summary, these results demonstrated that novel benzenesulfonamide derivatives, bearing substituted imidazoles, could be further explored as potential candidates for the further hit-to-lead optimization of novel antimycobacterial compounds.
Application of Electrochemical Biosensors for Determination of Food Spoilage

Food security is significantly affected by the mass production of agricultural produce and goods, the growing number of imported foods, and new eating and consumption habits. These changed circumstances bring food safety issues arising from food spoilage to the fore, making food safety control essential. Simple and fast screening methods have been developed to detect pathogens and biomarkers indicating the freshness of food for safety. In addition to the traditional, sequential, chemical analytical and microbiological methods, fast, highly sensitive, automated methods suitable for serial tests have appeared. At the same time, biosensor research is also developing dynamically worldwide, both in terms of the analytes to be determined and the technical toolkit. Consequently, the rapid development of biosensors, including electrochemical-based biosensors, has led to significant advantages in the quantitative detection and screening of food contaminants. These techniques show great specificity for the biomarkers tested and provide adequate analytical accuracy even in complex food matrices. In our review article, we summarize, in separate chapters, the electrochemical biosensors developed for the most important food groups and the food safety issues they can ensure, with particular respect to meat and fish products, milk and dairy products, as well as alcoholic and non-alcoholic beverages.
Effectivity of Using Model Reference Adaptive System in the Field of Complex Numbers for Parameter Identification

The model reference adaptive system (MRAS) is generally described in the field of real numbers. Therefore, the MRAS cannot be directly applicable to the system described by complex numbers such as three-phase ac motors.In order to apply the MRAS to the discrete-time linear time-invariant system whose coefficients and variables are complex numbers, the authors expand the theory of the MRAS into the field of complex numbers. The hyperstability theory in the field of complex numbers is used to give the asymptotic stability of the suggested algorithm.The effectiveness of the suggested algorithm is proved by simulation results for the parameter identification. The results show that the convergence time of the parameters using the proposed method can be reduced to one tenth compared with that using the MRAS in the field of real numbers.
Understanding number sequences leads to understanding mathematics concepts

abstract Ninety-six first grade students in an urban school system were tested in October and May on reading, mathematics, and their understanding of sequences of letters and numbers. A time lag analysis was subsequently conducted. In such analyses, cross-correlations between the first measurement of one variable and the second measurement of another are compared. The larger of the correlations indicates the direction of the relationship; i.e., which variable is most likely to be causal. Correlations of the fall scores on the number sequences with spring scores on the mathematics concepts scale were significant, while correlations of the fall mathematics concepts scores with spring number sequence scores were negligible. This indicates that understanding such complex sequences has a directional effect on understanding mathematics concepts. Fall–spring cross-correlations for the letter sequences and reading test, although significant, did not differ, and hence provided no indication of the direction of the relationship. Potential explanations were discussed.
Beyond the Rainbow: A Review of Advanced Lineage Tracing Methodologies for Interrogating the Initiation, Evolution, and Recurrence of Brain Tumors

The mammalian forebrain is perhaps the pinnacle of evolution and one of the most complex structures in known existence. The origin of this complexity and diversity partly lies in dynamic behavior of progenitors during embryonic neural development, all of which is under the control of regulatory mechanisms that ensure all the elements end up in the right place at the right time. Historically, dye-base, histochemical, enzymatic, or fluorescent lineage tracing techniques have been used deconvolute developmental dynamics in tissues and cells. Technical limitations resulted from a restrictive number of fluorophores, the half-life of the dyes, or the ability to deconvolute mixed population. These limitations often impede larger scale lineage tracing using these methods in spatial and temporal contexts. Genetic barcoding techniques have been used for decades to explore clonal investigations and have now evolved with high-throughput sequencing methods to allow for impressive insights into population and even organism-level lineage relationships. In this review, we will discuss the progression of lineage tracing methodologies and how they are applied to answer questions around molecular and cellular mechanisms of gliogenesis and neurogenesis. We will also discuss recent advances in computational biology, single-cell sequencing, and in situ-based lineage tracing methodologies. Incorporation of these methods into toolset of lineage tracing promise to enable a higher resolution, multimodal view of neural lineages during development and disease processes that highjack developmental signaling such as brain tumor development and recurrence – where traditional developmental hierarchies become more plastic and less predictable. Given the dismal prognosis of high-grade brain tumors like glioblastoma multiforme, a better understanding of the lineage relationships leading to disease heterogeneity and recurrence is desperately needed to formulate efficacious approaches to treatment. Here we discuss a historical foundation on, as well as the future of, lineage tracing at the intersection of development and disease.