Miracle-dz/UniFAR-FTUs huggingface dataset:
Weakly nonlinear shape oscillations of inviscid drops

Abstract Nonlinear axisymmetric shape oscillations of an inviscid liquid drop in a vacuum are investigated theoretically for their relevance for transport processes across the drop surface. The weakly nonlinear approach is adopted as the theoretical method. For the two-lobed mode of deformation $m=2$, known nonlinear effects are an asymmetry of the times the drop spends in the oblate and prolate deformed states, and an oscillation frequency smaller than the linear one found by Rayleigh. The present analysis shows that, for $m=2$, the frequency decrease with increasing surface deformation of the droplet is a third-order effect. For higher deformation modes, the frequency decrease shows in the second-order approximation already. The analysis is carried out for modes of initial deformation up to $m=4$, but not limited to that. The nonlinearity is due to two different contributions: the coupling of different modes of deformation; and the forces from capillary pressure acting on different drop cross-sectional areas in different phases of the oscillation. For the two-lobed mode of deformation, at an aspect ratio of 1.5, the two effects reduce the oscillation frequency by 5 %. The present analysis represents the quasi-periodicity of nonlinear drop oscillations found by other authors in numerical simulations. The results show that drops in nonlinear oscillations at strong deformation may never reach the spherical shape, thus exhibiting a resultant increase of their surface area.
Nonlinear fluid damping of elastically mounted pitching wings in quiescent water

Abstract We experimentally study the nonlinear fluid damping of a rigid but elastically mounted pitching wing in the absence of a free-stream flow. The dynamics of the elastic mount are simulated using a cyber-physical system. We perturb the wing and measure the fluid damping coefficient from damped oscillations over a large range of pitching frequencies, pitching amplitudes, pivot locations and sweep angles. A universal fluid damping scaling is proposed to incorporate all these parameters. Flow fields obtained using particle image velocimetry are analysed to explain the nonlinear behaviours of the fluid damping.
Influence of chaff and chaff lines on weed seed survival and seedling emergence in Australian cropping systems – ERRATUM

Chaff lining and chaff tramlining are harvest weed seed control (HWSC) systems that involve the concentration of chaff material containing weed seed into narrow (20 to 30 cm) rows between or on the harvester wheel tracks during harvest. These lines of chaff are left intact in the fields through subsequent cropping seasons in the assumption that the chaff environment is unfavorable for weed seed survival. The chaff row environment effect on weed seed survival was examined in field studies, and chaff response studies determined the influence of increasing amounts of chaff on weed seedling emergence. The objectives of these studies were to determine the influences of (1) chaff lines on the summer–autumn seed survival of selected weed species and (2) chaff type and amount on rigid ryegrass seedling emergence. There was frequently no difference (P> 0.05) in seed survival of four weed species (rigid ryegrass, wild oat, annual sowthistle, and turnip weed) when seeds were placed beneath or beside chaff lines. In one instance, wild oat seed survival was increased (P< 0.05) when seed were placed beneath compared to beside a chaff line. The pot studies determined that increasing amounts of chaff consistently resulted in decreasing numbers of rigid ryegrass seedlings emerging through chaff material. The suppression of emergence broadly followed a linear relationship in which there was approximately a 2.0% reduction in emergence with every 1,000 kg ha–1 increase in chaff material. This relationship was consistent across wheat, barley, canola, and lupin chaff types, indicating that the physical presence of the chaff was more important than chaff type. These studies suggested that chaff lines may not affect the survival over summer–autumn of the contained weed seeds but that the subsequent emergence of weed seedlings will be restricted by high amounts of chaff (>40,000 kg ha–1).
Scattering of entropy waves into sound by isolated aerofoils

Abstract This article presents a modelling approach to predict the low-frequency sound generated by entropy fluctuations interacting with isolated aerofoils. A model of the acoustic field is obtained based on a linearisation of the compressible Euler equations about a steady, potential, compressible mean flow. Mean flow variations of velocity and density are accounted for in the source term, but are neglected in the sound propagation. Using a Lorentz-type transformation, the problem is reduced to solving a Helmholtz equation. This equation is recast in integral form and a solution is obtained using a compact Green's function method. This approach places no restrictions on the entropy wavelength, while assuming that the acoustic wavelength is large compared to the profile chord and spacing. The source term is further simplified by assuming that the steady flow is a small perturbation to a uniform flow. The model is illustrated using a symmetric aerofoil and its performance is assessed against numerical simulations of the compressible Euler equations. Good agreement is found for all the frequencies of validity of the theory and for all the range of subsonic Mach numbers. The solution for a symmetric aerofoil interacting with plane entropy waves corresponds to the combination of a dipole along the horizontal axis and a monopole. The dipole originates from the unsteady drag experienced by the aerofoil owing to the fluctuations of density and the monopole from the strong local acceleration of the flow at the leading edge. The monopole term becomes negligible for low Mach numbers.
Intramembrane protease SPP defines a cholesterol-regulated abundance control of the mevalonate pathway enzyme SQS

Intramembrane proteolysis regulates important processes such as signaling and transcriptional and posttranslational abundance control of proteins with key functions in metabolic pathways. This includes transcriptional control of mevalonate pathway genes, thereby ensuring balanced biosynthesis of cholesterol and other isoprenoids. Our work shows that, at high cholesterol levels, signal peptide peptidase (SPP) cleaves squalene synthase (SQS), an enzyme that defines the branching point for allocation of isoprenoids to the sterol and non-sterol arms of the mevalonate pathway. This intramembrane cleavage releases SQS from the membrane and targets it for proteasomal degradation. Regulation of this mechanism is achieved by the E3 ubiquitin ligase TRC8 that, in addition to ubiquitinating SQS in response to cholesterol levels, acts as an allosteric activator of SPP-catalyzed intramembrane cleavage of SQS. Cellular cholesterol levels increase in the absence of SPP activity. Hence, SPP-TRC8 mediated abundance control of SQS acts as a regulation step within the mevalonate pathway.
The SARS-CoV-2 Reproduction Number R0 in Cats

Domestic cats are susceptible to SARS-CoV-2 virus infection and given that they are in close contact with people, assessing the potential risk cats represent for the transmission and maintenance of SARS-CoV-2 is important. Assessing this risk implies quantifying transmission from humans-to-cats, from cats-to-cats and from cats-to-humans. Here we quantified the risk of cat-to-cat transmission by reviewing published literature describing transmission either experimentally or under natural conditions in infected households. Data from these studies were collated to quantify the SARS-CoV-2 reproduction number R0 among cats. The estimated R0 was significantly higher than 1, hence cats could play a role in the transmission and maintenance of SARS-CoV-2. Questions that remain to be addressed are the risk of transmission from humans-to-cats and cats-to-humans. Further data on household transmission and data on virus levels in both the environment around infected cats and their exhaled air could be a step towards assessing these risks.
Growth and immunolocalisation of the brown alga Ectocarpus in a microfluidic environment

PDMS chips have proven to be suitable environments for the growth of several filamentous organisms. However, depending on the specimen, the pattern of growth and cell differentiation has been rarely investigated. We monitored the developmental pattern of the brown alga Ectocarpus inside a PDMS lab-on-chip. Two main methods of inoculation of the lab-on-chip were tested, i.e. by injection of spores or by insertion of sporophyte filaments into the chamber. Growth rate, growth trajectory, cell differentiation, and branching were the main development steps that were monitored for 20 days inside 25 μm or 40 μm parallel channels under standard light and temperature conditions. They were shown to be similar to those observed in non-constrained in-vitro conditions. Labelling of Ectocarpus cell wall polysaccharides – both with calcofluor for cellulose, and by immunolocalisation for alginates with monoclonal antibodies–showed expected patterns when compared to open space growth using either epifluorescence or confocal microscopy. Overall this article describes the experimental conditions for observing and studying the basic unaltered processes of brown algal growth using microfluidic technology, which provides the basis for future biochemical and biological research.
Nighttime Temperatures and Sunlight Intensities Interact to Influence Anthocyanin Biosynthesis and Photooxidative Sunburn in “Fuji” Apple

Light and low temperatures induce anthocyanin accumulation, but intense sunlight causes photooxidative sunburn. Nonetheless, there have been few studies of anthocyanin synthesis under different sunlight intensities and low nighttime temperatures. Here, low nighttime temperatures followed by low light intensity were associated with greater anthocyanin accumulation and the expression of anthocyanin biosynthesis genes in “Fuji” apple peel. UDP-glucose flavonoid-3-O-glucosyltransferase (UFGT) activity was positively associated with anthocyanin enrichment. Ascorbic acid can be used as an electron donor of APX to scavenge H2O2 in plants, which makes it play an important role in oxidative defense. Exogenous ascorbate altered the anthocyanin accumulation and reduced the occurrence of high light–induced photooxidative sunburn by removing hydrogen peroxide from the peel. Overall, low light intensity was beneficial for the accumulation of anthocyanin and did not cause photooxidative sunburn, whereas natural light had the opposite effect on the apple peel at low nighttime temperatures. This study provides an insight into the mechanisms by which low temperatures induce apple coloration and high light intensity causes photooxidative sunburn.
Clinical and Epidemiological Characterization of Acute Chagas Disease in Casanare, Eastern Colombia, 2012–2020

Background: Chagas disease (CD), caused by the protozoan Trypanosoma cruzi, is considered a public health problem in Latin America. In Colombia, it affects more than 437,000 inhabitants, mainly in Casanare, an endemic region with eco-epidemiological characteristics that favor its transmission. The objective of this study was to describe the clinical and epidemiological characteristics of the cases of acute CD in Casanare, eastern Colombia, in the period 2012–2020. Methods: In the present study, 103 medical records of confirmed cases of acute CD were reviewed. The departmental/national incidence and fatality were compared by year; the climatological data of mean temperature, relative humidity, and precipitation per year were reviewed and plotted at IDEAM (Colombian Meteorology Institute) concerning the number of cases of acute CD per month, and it was compared with the frequency of triatomines collected in infested houses by community surveillance. Univariate, bivariate, and multivariate analyses were performed, comparing symptoms and signs according to transmission routes, complications, and age groups. Results: The incidence was 3.16 cases per 100,000 inhabitants, and the fatality rate was 20% in the study period. The most frequent symptoms included: fever 98.1%, myalgia 62.1%, arthralgia 60.2%, and headache 49.5%. There were significant differences in the frequency of myalgia, abdominal pain, and periorbital edema in oral transmission. The main complications were pericardial effusion, myocarditis, and heart failure in the group over 18 years of age. In Casanare, TcI Discrete Typing Unit (DTU) has mainly been identified in humans, triatomines, and reservoirs such as opossums and dogs and TcBat in bats. An increase in the number of acute CD cases was evidenced in March, a period when precipitation increases due to the beginning of the rainy season. Conclusions: The results corroborate the symptomatic heterogeneity of the acute phase of CD, which delays treatment, triggering possible clinical complications. In endemic regions, clinical suspicion, diagnostic capacity, detection, and surveillance programs should be strengthened, including intersectoral public health policies for their prevention and control.
Current Perspective on the Membrane-Damaging Action of Thermostable Direct Hemolysin, an Atypical Bacterial Pore-forming Toxin

Thermostable direct hemolysin (TDH) is the major virulence determinant of the gastroenteric bacterial pathogen Vibrio parahaemolyticus. TDH is a membrane-damaging pore-forming toxin (PFT). TDH shares remarkable structural similarity with the actinoporin family of eukaryotic PFTs produced by the sea anemones. Unlike most of the PFTs, it exists as tetramer in solution, and such assembly state is crucial for its functionality. Although the structure of the tetrameric assembly of TDH in solution is known, membrane pore structure is not available yet. Also, the specific membrane-interaction mechanisms of TDH, and the exact role of any receptor(s) in such process, still remain unclear. In this mini review, we discuss some of the unique structural and physicochemical properties of TDH, and their implications for the membrane-damaging action of the toxin. We also present our current understanding regarding the membrane pore-formation mechanism of this atypical bacterial PFT.
The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa

Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.
Brain and Retinal Abnormalities in the 5xFAD Mouse Model of Alzheimer's Disease at Early Stages

One of the major challenges in treating Alzheimer's disease (AD) is its early diagnosis. Increasing data from clinical and animal research indicate that the retina may facilitate an early diagnosis of AD. However, a previous study on the 5xFAD (a fast AD model), showing retinal changes before those in the brain, has been questioned because of the involvement of the retinal degeneration allele Pde6brd1. Here, we tested in parallel, at 4 and 6 months of age, both the retinal and the brain structure and function in a 5xFAD mouse line that carries no mutation of rd1. In the three tested regions of the 5xFAD brain (hippocampus, visual cortex, and olfactory bulb), the Aβ plaques were more numerous than in wild-type (WT) littermates already at 4 months, but deterioration in the cognitive behavioral test and long-term potentiation (LTP) lagged behind, showing significant deterioration only at 6 months. Similarly in the retina, structural changes preceded functional decay. At 4 months, the retina was generally normal except for a thicker outer nuclear layer in the middle region than WT. At 6 months, the visual behavior (as seen by an optomotor test) was clearly impaired. While the full-field and pattern electroretinogram (ERG) responses were relatively normal, the light responses of the retinal ganglion cells (measured with multielectrode-array recording) were decreased. Structurally, the retina became abnormally thick with few more Aβ plaques and activated glia cells. In conclusion, the timeline of the degenerative processes in the retina and the brain is similar, supporting the use of non-invasive methods to test the retinal structure and function to reflect changes in the brain for early AD diagnosis.
Impact of Warning Pop-Up Messages on the Gambling Behavior, Craving, and Cognitions of Online Gamblers: A Randomized Controlled Trial

Background: Many features of Internet gambling may impact problem severity, particularly for vulnerable populations (availability, anonymity, a convenience and ease of play, digital forms of payment, and a higher level of immersion). To prevent the risks associated with excessive gambling and to inform gamblers, we need responsible gambling strategies. Gambling-related warning messages are one possible strategy that can help minimizing gambling-related harm. Methods: Our experimental study aimed to evaluate the effectiveness of self-appraisal and informative pop-up messages compared to a control condition (blank pop-up messages), for both at-risk (ARG) and low risk/non-problem Internet gamblers (LR/NPG) according to their favorite type of game, in a semi naturalistic setting and with a 15-day follow-up. During the experimental session, participants were invited to gamble on their favorite website with their own money in the laboratory. Effectiveness was investigated through the impact of pop-ups on gambling behavior (money wagered and time spent), craving, cognitive distortions, and gambling experience, taking into account message recall. We analyzed data from 58 participants, playing preferentially either to skill and chance bank games (sports betting, horse race betting) and skill and chance social games (poker). Results: We observed a significant decrease in the illusion of control for ARG in the informative pop-up condition at the 15-day follow-up. A significant effect of self-appraisal pop-ups compared to blank pop-up messages was also demonstrated only for sport and horse bettors, with a decrease on time spent gambling and an increase of gambling-related expectancies at the follow-up. Finally, we also observed that a majority of the participants were disturbed and irritated by pop-ups during their gambling session. Conclusions: The results of our study demonstrated the limited impact of pop-up warning messages on gambling behavior and cognition in Internet gamblers according to the type of game and the status of gamblers. The limited impact of warning messages on gambling behavior and the inconvenience of the pop-ups for Internet gamblers lead us to only consider warning messages as one piece of a larger responsible gambling strategy. Trial Registration Number: NCT01789580 on February 12, 2013.
Low-Frequency TMS Results in Condition-Related Dynamic Activation Changes of Stimulated and Contralateral Inferior Parietal Lobule

Non-invasive brain stimulation is a promising approach to study the causal relationship between brain function and behavior. However, it is difficult to interpret behavioral null results as dynamic brain network changes have the potential to prevent stimulation from affecting behavior, ultimately compensating for the stimulation. The present study investigated local and remote changes in brain activity via functional magnetic resonance imaging (fMRI) after offline disruption of the inferior parietal lobule (IPL) or the vertex in human participants via 1 Hz repetitive transcranial magnetic stimulation (rTMS). Since the IPL acts as a multimodal hub of several networks, we implemented two experimental conditions in order to robustly engage task-positive networks, such as the fronto-parietal control network (on-task condition) and the default mode network (off-task condition). The condition-dependent neural after-effects following rTMS applied to the IPL were dynamic in affecting post-rTMS BOLD activity depending on the exact time-window. More specifically, we found that 1 Hz rTMS applied to the right IPL led to a delayed activity increase in both, the stimulated and the contralateral IPL, as well as in other brain regions of a task-positive network. This was markedly more pronounced in the on-task condition suggesting a condition-related delayed upregulation. Thus together, our results revealed a dynamic compensatory reorganization including upregulation and intra-network compensation which may explain mixed findings after low-frequency offline TMS.
Phosphoinositide Recognition Sites Are Blocked by Metabolite Attachment

Membrane readers take part in trafficking and signaling processes by localizing proteins to organelle surfaces and transducing molecular information. They accomplish this by engaging phosphoinositides (PIs), a class of lipid molecules which are found in different proportions in various cellular membranes. The prototypes are the PX domains, which exhibit a range of specificities for PIs. Our meta-analysis indicates that recognition of membranes by PX domains is specifically controlled by modification of lysine and arginine residues including acetylation, hydroxyisobutyrylation, glycation, malonylation, methylation and succinylation of sidechains that normally bind headgroups of phospholipids including organelle-specific PI signals. Such metabolite-modulated residues in lipid binding elements are named MET-stops here to highlight their roles as erasers of membrane reader functions. These modifications are concentrated in the membrane binding sites of half of all 49 PX domains in the human proteome and correlate with phosphoregulatory sites, as mapped using the Membrane Optimal Docking Area (MODA) algorithm. As these motifs are mutated and modified in various cancers and the responsible enzymes serve as potential drug targets, the discovery of MET-stops as a widespread inhibitory mechanism may aid in the development of diagnostics and therapeutics aimed at the readers, writers and erasers of the PI code.