Miracle-dz/UniFAR-FTUs huggingface dataset:
A Systematic Review of the Potential Effects of Lippia sidoides on Dental Plaque and Periodontal Diseases

Abstract Lippia sidoides is a typical shrub from Brazil that has been used in traditional medicine. This is a systematic review on the effect of L. sidoides for controlling dental plaque, gingivitis, and periodontitis. A database search through May 2021 in Medline/PubMed, SCOPUS, BVS, and Web of Science identified 711 reports of which 17 met our inclusion criteria. Five randomized controlled trials and three animal studies were included that compared L. sidoides-based products (toothpaste, mouthrinse, and gel) to cetylpyridinium chloride, chlorhexidine, and placebo products. Among the human studies, a significant antiplaque effect after treatment with L. sidoides-based products was observed in three studies and an antigingivitis effect in two studies, similar to chlorhexidine-based products. One study found superior dental plaque reduction compared to cetylpyridinium chloride mouthrinse. Only one study testing a L. sidoides gel found no antiplaque effect. Among the animal studies, an L. sidoides mouthrinse significantly reduced calculus in two studies, inflammatory infiltrate in one study, and plaque bacteria and gingivitis in one study. An L. sidoides gel significantly reduced alveolar bone loss and inflammatory response in one study in which mice were submitted to ligature-induced periodontal disease. In general, L. sidoides-based products were effective in reducing dental plaque and calculus formation, as well as clinical signs of gingivitis. As most studies present methodological limitations, these results should be interpreted carefully. Further clinical trials with greater methodological accuracy and control of biases are necessary for the use of L. sidoides-based products in humans to be viable in clinical practice.
Determining the rotational orientation of directional deep brain stimulation electrodes using magnetoencephalography

Objective. The aim of the present study was to evaluate the effect of different electrode configurations on the accuracy of determining the rotational orientation of the directional deep brain stimulation (DBS) electrode with our previously published magnetoencephalography (MEG)-based method. Approach. A directional DBS electrode, along with its implantable pulse generator, was integrated into a head phantom and placed within the MEG sensor array. Predefined bipolar electrode configurations, based on activation of different directional and omnidirectional contacts of the electrode, were set to generate a defined magnetic field during stimulation. This magnetic field was then measured with MEG. Finite element modeling and model fitting approach were used to calculate electrode orientation. Main results. The accuracy of electrode orientation detection depended on the electrode configuration: the vertical configuration (activation of two directional contacts arranged one above the other) achieved an average accuracy of only about 41 ∘. The diagonal configuration (activation of the electrode tip and a single directional contact at the next higher level of the electrode) achieved an accuracy of 13∘, while the horizontal electrode configuration (activation of two adjacent directional contacts at the same electrode level) achieved the best accuracy of 6∘. The accuracy of orientation detection of the DBS electrode depends on the change in spatial distribution of the magnetic field with the rotation of the electrode along its own axis. In the vertical configuration, rotation of the electrode has a small effect on the magnetic field distribution, while in the diagonal or horizontal configuration, electrode rotation has a significant effect on the magnetic field distribution. Significance. Our work suggests that in order to determine rotational orientation of a DBS electrode using MEG, horizontal configuration should be used as it provides the most accurate results compared to other possible configurations.
The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation

In Drosophila, two chromosomes require special mechanisms to balance their transcriptional output to the rest of the genome. These are the male-specific lethal complex targeting the male X-chromosome, and Painting of fourth targeting chromosome 4. The two systems are evolutionarily linked to dosage compensation of the X-chromosome and the chromosomes involved display specific chromatin structures. Here we explore the role of histone H3 tri-methylated at lysine 36 (H3K36me3) and the associated methyltransferases in these two chromosome-specific systems. We show that the loss of Set2 impairs the MSL complex mediated dosage compensation; however, the effect is not recapitulated by H3K36 replacement and indicates an alternative target of Set2. Unexpectedly, balanced transcriptional output from the 4th chromosome requires intact H3K36 and depends on the additive functions of NSD and the Trithorax group protein Ash1. We conclude that H3K36 methylation and the associated methyltransferases are important factors to balance transcriptional output of the male X-chromosome and the 4th chromosome. Furthermore, our study highlights the pleiotropic effects of these enzymes.
Thermal Conductivity Enhancement Phenomena in Ionic Liquid-Based Nanofluids (Ionanofluids)

The dispersion of nanoparticles into ionic liquids leads to enhancement of their thermal conductivity. Several papers report on various enhancement values, whereas the comparison between these values with those from theoretical calculations is not always performed. These thermal conductivity enhancements are desired due to their beneficial impact on heat transfer performance in processes requiring the utilisation of heat transfer fluids. Moreover, on the one hand, the theoretical modelling of these enhancements might lead to an easier, cheaper, and faster heat transfer unit design, which could be an enormous advantage in the design of novel industrial applications. On the other hand, it significantly impacts the enhancement mechanism. The aim of this work is to discuss the enhancement of thermal conductivity caused by the dispersion of nanoparticles in ionic liquids, including the analysis of their errors, followed by its theoretical modelling. Furthermore, a comparison between the data reported herein with those available in the literature is carried out following the reproducibility of the thermal conductivity statement. The ionic liquids studied were 1-butyl-3-methylimidazolium dicyanamide, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, 1-ethyl-3-methylimidazolium ethylsulfate, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide, and 1-hexyl-3-methylimidazolium hexafluorophosphate, while carbon nanotubes, boron nitride, and graphite were selected as nanoparticles to be dispersed in the investigated ionic liquids to design novel heat transfer fluids.
Proceedings of the Society for Computation in Linguistics Proceedings of the Society for Computation in Linguistics

Stabler (2013)’s top-down parser for Minimal-ist grammars has been used to account for a variety of off-line processing preferences, with measures of memory load sensitive to subtle structural details. This paper expands the model’s empirical coverage to ergative languages by looking at the processing asymmetries reported for Basque relative clauses. Our results show that the model predicts a subject over object preference as identified in the relevant psycholinguistic literature.
Building and Designing Expressive Speech Synthesis

You all know the test for artificial intelligence—the Turing test. A human judge has a conversation with a human and a computer. If the judge can’t tell the machine apart from the human, the machine has passed the test. I now propose a test for computer voices—the Ebert test. If a computer voice can successfully tell a joke and do the timing and delivery as well as Henny Youngman, then that’s the voice I want. — Roger Ebert .
Results from a conservation initiative for parrotfishes in the Colombian Caribbean

Parrotfish (Family Scaridae) are a family of herbivorous fishes crucial to coral reef health, particularly for Caribbean reefs due to their declining coral cover. However, despite parrotfish are fully protected in some countries, they are still heavy fished in most of their Caribbean range. The consequences of this targeted fishery in the Colombian Caribbean are not fully understood due to a lack of local conservation and management resources. This research aimed to evaluate and enhance the conservation status and protection of parrotfish among local communities in the National Natural Park Corales del Rosario and San Bernardo. Underwater visual census surveys (UVC) were undertaken to evaluate reef fish community structure, and participatory education campaigns and activities were carried out with local communities to raise awareness about parrotfish ecology and their functional role in conserving Caribbean coral reef ecosystems of Colombia. UVC showed parrotfish to be dominant in the fish community, yet there was evidence of exploitation of large adults by selective fishing. Conflicts exist between the community and environmental authorities because fishing regulations are not clear, and the level of enforcement is insufficient. Parrotfish are sold to tourists, as ‘red snapper’ to fulfil high seafood demand since commercially valuable fish are now scarce. However, following intensive awareness-raising activities developed as part of this study, the community has started to recognize the vital ecological role of parrotfish in coral reef systems, and are suggesting a redrafting of fishing legislation by the environmental authorities, in order to recognise and incorporate the traditional fishing rights of human communities living within the MPA. Lobbying for the protection of parrotfish and inclusion of local communities in decision-making will take time, but this research represents the crucial first steps towards sustainable practice and cooperative alliances in the Colombian Caribbean.
Klebsiella pneumoniae hijacks the Toll-IL-1R protein SARM1 in a type I IFN-dependent manner to antagonize host immunity

Many bacterial pathogens antagonize host defence responses by translocating effector proteins into cells. It remains an open question how those pathogens not encoding effectors counteract anti-bacterial immunity. Here, we show that Klebsiella pneumoniae hijacks the evolutionary conserved innate immune protein SARM1 to control cell intrinsic immunity. Klebsiella exploits SARM1 to regulate negatively MyD88 and TRIF-governed inflammation, and the activation of the MAP kinases ERK and JNK. SARM1 is required for Klebsiella induction of IL10 by fine-tuning the p38-type I IFN axis. SARM1 inhibits the activation of Klebsiella-induced absent in melanoma 2 inflammasome to limit IL1β production, suppressing further inflammation. Klebsiella exploits type I IFNs to induce SARM1 in a capsule and LPS O-polysaccharide-dependent manner via TLR4-TRAM-TRIF-IRF3-IFNAR1 pathway. Absence of SARM1 reduces the intracellular survival of K. pneumonaie in macrophages whereas sarm1 deficient mice control the infection. Altogether, our results illustrate a hitherto unknown anti-immunology strategy deployed by a human pathogen.
A Mediterranean-like fat blend protects against the development of severe colitis in the mucin-2 deficient murine model

The Mediterranean diet (MD) is a health-promoting, moderate fat diet (∼ 40% energy). It is not known if the blend of fats found in the MD contribute to the beneficial protective effects. We compared the MD fat blend (high monounsaturated, 2:1 n-6:n-3 polyunsaturated and moderate saturated fat) to isocaloric diets composed with corn oil (CO, n-6 polyunsaturated-rich), olive oil (high monounsaturated-rich) or milk fat (MF, saturated-rich) on spontaneous colitis development in Muc2-/- mice. The MD resulted in lower clinical and histopathological scores, and induced tolerogenic CD103+CD11b+ dendritic, Th22 and IL-17+IL-22+ cells important for intestinal barrier repair. MD also reduced attendant insulin resistance and a shift to a higher health-promoting gut microbes including Lactobacillus B. animalis and Muribaculaceae, whereas CO showed higher prevalence of mucin-degraders (Akkermansia muciniphila) and colitis promoters (Enterobacteriaceae). Our findings suggest that the MD fat blend could be recommended as a maintenance diet for colitis.
Cytokinin Regulates Energy Utilization in Botrytis cinerea

The hormone cytokinin (CK) is a plant developmental regulator. Previous research has highlighted the involvement of CK in plant defense. ABSTRACT The plant hormone cytokinin (CK) is an important developmental regulator. Previous work has demonstrated that CKs mediate plant immunity and disease resistance. Some phytopathogens have been reported to secrete CKs and may manipulate CK signaling to improve pathogenesis. In recent work, we demonstrated that CK directly inhibits the development and virulence of fungal phytopathogens by attenuating the cell cycle and reducing cytoskeleton organization. Here, focusing on Botrytis cinerea, we report that CK possesses a dual role in fungal biology, with role prioritization being based on sugar availability. In a sugar-rich environment, CK strongly inhibited B. cinerea growth and deregulated cytoskeleton organization. This effect diminished as sugar availability decreased. In its second role, we show using biochemical assays and transgenic redox-sensitive fungal lines that CK can promote glycolysis and energy consumption in B. cinerea, both in vitro and in planta. Glycolysis and increased oxidation mediated by CK were stronger in low sugar availability, indicating that sugar availability could indeed be one possible element determining the role of CK in the fungus. Transcriptomic data further support our findings, demonstrating significant upregulation to glycolysis, oxidative phosphorylation, and sucrose metabolism upon CK treatment. Thus, the effect of CK in fungal biology likely depends on energy status. In addition to the plant producing CK during its interaction with the pathogen for defense priming and pathogen inhibition, the pathogen may take advantage of this increased CK to boost its metabolism and energy production, in preparation for the necrotrophic phase of the infection. IMPORTANCE The hormone cytokinin (CK) is a plant developmental regulator. Previous research has highlighted the involvement of CK in plant defense. Here, we report that CK has a dual role in plant-fungus interactions, inhibiting fungal growth while positively regulating B. cinerea energy utilization, causing an increase in glucose utilization and energy consumption. The effect of CK on B. cinerea was dependent on sugar availability, with CK primarily causing increases in glycolysis when sugar availability was low, and growth inhibition in a high-sugar environment. We propose that CK acts as a signal to the fungus that plant tissue is present, causing it to activate energy metabolism pathways to take advantage of the available food source, while at the same time, CK is employed by the plant to inhibit the attacking pathogen.
Data-driven approaches for genetic characterization of SARS-CoV-2 lineages

The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), has been sequenced at an unprecedented scale, leading to a tremendous amount of viral genome sequencing data. To understand the evolution of this virus in humans, and to assist in tracing infection pathways and designing preventive strategies, we present a set of computational tools that span phylogenomics, population genetics and machine learning approaches. To illustrate the utility of this toolbox, we detail an in depth analysis of the genetic diversity of SARS-CoV-2 in first year of the COVID-19 pandemic, using 329,854 high-quality consensus sequences published in the GISAID database during the pre-vaccination phase. We demonstrate that, compared to standard phylogenetic approaches, haplotype networks can be computed efficiently on much larger datasets, enabling real-time analyses. Furthermore, time series change of Tajima’s D provides a powerful metric of population expansion. Unsupervised learning techniques further highlight key steps in variant detection and facilitate the study of the role of this genomic variation in the context of SARS-CoV-2 infection, with Multiscale PHATE methodology identifying fine-scale structure in the SARS-CoV-2 genetic data that underlies the emergence of key lineages. The computational framework presented here is useful for real-time genomic surveillance of SARS-CoV-2 and could be applied to any pathogen that threatens the health of worldwide populations of humans and other organisms.
Stochastic effects during the establishment of β-lactam resistant E. coli mutants indicate conditions for collective resistance

For antibiotic resistance to arise, new resistant mutants must establish in a bacterial population before they can spread via natural selection. Comprehending the stochastic factors that influence mutant establishment is crucial for a quantitative understanding of antibiotic resistance emergence. Here, we quantify the single-cell establishment probability of four Escherichia coli strains expressing β-lactamase alleles with different activity against the antibiotic cefotaxime, as a function of antibiotic concentration in both unstructured (liquid) and structured (agar) environments. We show that concentrations well below the minimum inhibitory concentration (MIC) can substantially hamper establishment, particularly for highly resistant mutants. While the pattern of establishment suppression is comparable in both tested environments, we find greater variability in establishment probability on agar. Using a simple branching model, we investigate possible sources of this stochasticity, including environment-dependent lineage variability. Lastly, we use the single-cell establishment probability to predict each strain’s MIC in the absence of social interactions. We observe substantially higher measured than predicted MIC values, particularly for highly resistant strains, which indicates cooperative effects among resistant cells at large cell numbers, such as in standard MIC assays.
Structural basis of human protein disulfide isomerase flexibility revealed by single-molecule FRET

Protein disulfide isomerase (PDI) is a ubiquitous redox-regulated enzyme, which interacts with hundreds of client proteins intracellularly and extracellularly. It comprises two redox-sensitive domains, each hosting the conserved catalytic motif CxxC, two redox-insensitive protein-binding domains, and three linkers. Snapshots of oxidized and reduced PDI have been obtained by X-ray crystallography. However, how PDI’s structure dynamically changes in response to the redox microenvironment and ligand binding remain unknown. Here, we used multiparameter confocal single-molecule Förster resonance energy transfer (smFRET) and multiple FRET pairs to track the movements of the two catalytic domains with high temporal resolution. Our studies document that, at equilibrium, PDI visits three structurally distinct conformational ensembles, two “open” (O1 and O2) and one “closed” (C), whose distribution is dictated by the redox environment. Despite undergoing large conformational changes, the ensembles interconvert remarkably fast, on the sub-millisecond timescale, indicative of a shallow free-energy landscape. Using mutational analyses, we further demonstrate that the two active sites are structurally nonequivalent and that ligands targeting the active sites of reduced PDI shift the equilibrium towards closed conformations of the enzyme. This work introduces a new structural framework that helps rationalize the multifaced role of PDI in biology and may assist drug development.
Association between psychological distress trajectories from adolescence to midlife and mental health during the pandemic: evidence from two British birth cohorts

Abstract Background This paper examined whether distinct life-course trajectories of psychological distress from adolescence to midlife were associated with poorer mental health outcomes during the pandemic. Methods We present a secondary analysis of two nationally representative British birth cohorts, the 1958 National Child Development Study (NCDS) and 1970 British Cohort Study (BCS70). We used latent variable mixture models to identify pre-pandemic longitudinal trajectories of psychological distress and a modified Poisson model with robust standard errors to estimate associations with psychological distress, life satisfaction and loneliness at different points during the pandemic. Results Our analysis identified five distinct pre-pandemic trajectories of psychological distress in both cohorts. All trajectories with prior symptoms of psychological distress irrespective of age of onset, severity and chronicity were associated with a greater relative risk of poorer mental health outcomes during the pandemic and the probability of poorer mental health associated with psychological distress trajectories remained fairly constant. The relationship was not fully attenuated when most recent pre-pandemic psychological distress and other midlife factors were controlled for. Conclusions Whilst life-course trajectories with any prior symptoms of psychological distress put individuals at greater risk of poor mental health outcomes during the pandemic, those with chronic and more recent occurrences were at highest risk. In addition, prior poor mental health during the adult life-course may mean individuals are less resilient to shocks, such as pandemics. Our findings show the importance of considering heterogeneous mental health trajectories across the life-course in the general population in addition to population average trends.
Understanding Retail Investors: Evidence from China

Using comprehensive account-level data from 2016 to 2019, we examine retail investor trading behavior in the Chinese stock market. We separate millions of retail investors into five groups by their account sizes and document strong heterogeneity in their trading dynamics and performance. Retail investors with smaller account sizes cannot predict future price movements correctly, in the sense that they buy future losers and sell future winners. These investors fail to process public news and display behavioral biases such as overconfidence and gambling preferences. In sharp contrast, retail investors with larger account balances predict future returns correctly, incorporate public news in their trading, and gain more in stocks which are more attractive to investors with behavioral biases. For liquidity provision, the smaller retail investors follow daily momentum strategies, demanding immediate liquidity, while they become contrarian over weekly horizons, and they contribute positively towards firm-level liquidity. On the contrary, larger retail investors ae contrarian at daily horizons, providing immediate liquidity, but their potentially informed trades demand liquidity over longer terms.
Refugee reception, extreme-right voting, and compositional amenities: evidence from Italian municipalities

We use data from Italy to study the political and social impact of a refugee reception policy (SPRAR) directly managed by local governments, whose features recall the conditions of the contact theory (Allport, 1954). Instrumental variables estimates indicate that municipalities that opened a refugee center between the 2013 and 2018 national elections experienced a change in the vote shares of extreme-right parties approximately 7 percentage points lower compared to towns that did not open a refugee center. We document that the positive impact of SPRARs on “compositional amenities” (i.e., local schools) and population growth allows explaining the negative impact on anti-immigrants’ prejudice. Finally, we provide evidence of spillovers in prejudice reduction in neighboring municipalities without a SPRAR.