Miracle-dz/UniFAR-FTUs huggingface dataset:
yEvo: experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in Saccharomyces cerevisiae

Abstract Antifungal resistance in pathogenic fungi is a growing global health concern. Nonpathogenic laboratory strains of Saccharomyces cerevisiae are an important model for studying mechanisms of antifungal resistance that are relevant to understanding the same processes in pathogenic fungi. We have developed a series of laboratory modules in which high school students used experimental evolution to study antifungal resistance by isolating azole-resistant S. cerevisiae mutants and examining the genetic basis of resistance. We have sequenced 99 clones from these experiments and found that all possessed mutations previously shown to impact azole resistance, validating our approach. We additionally found recurrent mutations in an mRNA degradation pathway and an uncharacterized mitochondrial protein (Csf1) that have possible mechanistic connections to azole resistance. The scale of replication in this initiative allowed us to identify candidate epistatic interactions, as evidenced by pairs of mutations that occur in the same clone more frequently than expected by chance (positive epistasis) or less frequently (negative epistasis). We validated one of these pairs, a negative epistatic interaction between gain-of-function mutations in the multidrug resistance transcription factors Pdr1 and Pdr3. This high school–university collaboration can serve as a model for involving members of the broader public in the scientific process to make meaningful discoveries in biomedical research.
Analysis of Nanostar Reshaping Kinetics for Optimal Substrate Fabrication

Gold nanostars (NS) are emerging as a versatile tool in surface-enhanced Raman scattering (SERS) applications because of their wide localized surface plasmon resonance (LSPR) tunability, simple synthesis procedure, and high SERS enhancement. These particles are commonly used in solutions with a stabilizing coating shell (e.g., thiolated molecules or silver shell). However, coatings cannot be used for the fabrication of SERS substrates as the NS have to interact with the substrate planar surface. Without coating, NS have been observed to change over time, leading to a hypochromic shift of the LSPR. To understand this shift, we synthesized surfactant-free gold NS with different spike morphologies and investigated their reshaping morphology and kinetics. Using TEM, the NS sharp spike features were observed to reshape over time. The kinetics of this process were analyzed and determined by monitoring the LSPR, which was observed to follow an exponential decay over time. We used an empirical fit for the LSPR-shift data as a function of time, which permits to predict the LSPR at a specific time based only on the initial LSPR (independently of the initial spike morphology). We show the effect of the LSPR on the SERS signal for the NS and how the SERS signal correlated to our prediction. Finally, we evaluated our approach by fabricating SERS substrates with immobilized NS and collecting the reflectance spectra. We were able to predict the substrate LSPR and aim for an optimal LSPR with an average 3% deviation. These new insights on NS reshaping can permit the fabrication of NS-based substrates with desirable optical/plasmonic properties. Graphical Abstract
Bianchi I model: an alternative way to model the present-day Universe

Although the new era of high-precision cosmology of the cosmic microwave background (CMB) radiation improves our knowledge to understand the infant as well as the present-day Universe, it also leads us to question the main assumption of the exact isotropy of the CMB. There are two pieces of observational evidence that hint towards there being no exact isotropy. These are: first, the existence of small anisotropy deviations from isotropy of the CMB radiation and secondly, the presence of large angle anomalies, although the existence of these anomalies is currently a huge matter of debate. These hints are particularly important since isotropy is one of the two main postulates of the Copernican principle on which the Friedmann Robertson Walker (FRW) models are built. This almost-isotropic CMB radiation implies that the universe is almost an FRW universe, as is proved by previous studies. Assuming that the matter component forms the deviations from isotropy in the CMB density fluctuations when matter and radiation decouples, we here attempt to find possible constraints on the FRW-type scale and Hubble parameter by using the Bianchi type I (BI) anisotropic model which is asymptotically equivalent to the standard FRW. To obtain constraints on such an anisotropic model, we derive average and late-time shear values that come from the anisotropy upper limits of the recent Planck data based on a model independent shear parameter of Maartens, Ellis & Stoeger and from the theoretical consistency relation. These constraints lead us to obtain a BI model which becomes an almost-FRW model in time, and which is consistent with the latest observational data of the CMB.
Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island

Abstract As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30–50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, that is, Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000–3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B-cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.
Some Results on Linear Models of Nonlinear Systems

Linear time-invariant approximations of nonlinear systems are used in many a pplications. Such approximations can be obtained in many ways. For example,using system identification and the prediction-error method, it is always possible to estimate a linear model without considering the fact that the input and output measurements in general come from a nonlinear system. The main objective of this thesis is to explain some properties of such estimated models.More specifically, linear time-invariant models that are optimal approximations in the mean-square error sense are studied. Although this is a classic field of research, relatively few results exist about the properties of such models when they are based on signals from nonlinear systems. In this thesis, some interesting, but in applications usually undesirable, properties of linear approximations of nonlinear systems are pointed out. It is shown that the linear model can be very sensitive to small nonlinearities. Hence, the linear approximation of an almost linear system can be useless for some applications, such as robust control design.In order to improve the models, conditions are given on the input signal implying various useful properties of the linear approximations. It is shown, for instance, that minimum phase filtered white noise in many senses is a good choice of input signal. Furthermore, some special properties of Gaussian signals are discussed. These signals turn out to be especially useful for approximations of generalized Hammerstein or Wiener systems. Using a Gaussian input, it is possible to estimate the denominator polynomial of the linear part of such a system without compensating for the nonlinearities. In addition, some theoretical results about almost linear systems and about separable input processes are presented. Linear models, both with and without a noise description, are studied.
Hand-Held Haptic Navigation Devices for Actual Walking

In this survey, we give an overview of hand-held haptic navigation devices specifically designed for and tested with pedestrians. We distinguish devices for indoor use and for outdoor use as the implementation is usually quite different. Outdoor devices make use of Global Positioning Systems (GPS) tracking built-in in smartphones; indoor devices use a variety of sensors, and tracking and localization systems and these are usually restricted to a small part of a building. Overall, the high success rates reported in the studies show that vibrotactile stimulation via a hand-held user interface is suitable for navigation instructions, as in all experiments (almost) all participants reached their goal. An issue for several of the indoor devices is that walking speeds were (much) lower than normal walking speeds and path efficiency was relatively low. However, these issues might be overcome with some training as in most studies there was hardly any practice time. Several of the outdoor devices seem quite close to taking the last step before commercial use. In the Discussion, we evaluate the suitability of the devices for persons with visual and/or hearing impairments. Especially devices that provide very specific instructions, such as, ‘go straight’ or ‘go right,’ seem valuable for this population.
Spontaneous quantum Hall effect in quarter-doped Hubbard model on honeycomb lattice and its possible realization in doped graphene system

We show that a magnetic insulating state with nonzero spin chirality is realized in a quarter-doped Hubbard model on honeycomb lattice as a result of the nesting property of the Fermi surface. This state is topological nontrivial and has a quantized Hall conductance of . We find that such a state is robust against next-nearest-neighboring hopping and we propose that it can be realized in a quarter-doped graphene system. We also show that the quarter-doped Hubbard model on honeycomb lattice is equivalent to a 3/4-filled Hubbard model on triangular lattice in the weak coupling limit, in which a similar effect was predicted previously.
Prevalence of Current PTSD Symptoms Among a Sample of Black Individuals Aged 15 to 40 in Canada: The Major Role of Everyday Racial Discrimination, Racial Microaggresions, and Internalized Racism

Objective Most Black individuals in Canada report having experienced racial discrimination. Although previous studies have shown that there is a strong relationship between racial discrimination and posttraumatic stress disorder (PTSD), no studies in Canada have documented this association among Black individuals. The present study documents (1) the prevalence of PTSD among Black individuals using data from the Black Communities Mental Health project and (2) risk factors associated with PTSD, including racial microaggressions, everyday racial discrimination, and internalized racism. Method A total of 860 participants (75.6% of women) aged 15 to 40 years old (M = 24.96, SD = 6.29) completed questionnaires assessing PTSD, experience of traumatic events, racial microaggressions, everyday racial discrimination, and internalized racism. Results Findings showed that 95.1% of participants reported exposure to at least one traumatic event during their lifetime. In total, 67.11% of participants reported probable PTSD with no significant difference between men and women (68.2% and 67.8%, χ2 = 0.132, p = 0.72). Participants born in Canada were more likely to experience significant PTSD symptoms, compared to those born abroad (70.92% and 53.14%, χ2 = 19.69, p < 0.001). A multivariable linear regression model of PTSD symptoms was computed using sociodemographic variables and exposure to traumatic events as independent variables, which explained 25.9% of the variance. In addition to these variables, a second model included racial microaggressions, everyday racial microaggressions, and internalized racism, which explained 51.8% of the variance. The model showed that traumatic events (b = 0.6; p = 0.02), racial microaggressions (b = 0.5; p < 0.001), everyday discrimination (b = 0.2; p = 0.03) and internalized racism (b = 0.5; p < 0.001) were positively associated with PTSD symptoms. Conclusions This article highlights the detrimental consequences of racial discrimination against Black people in Canada. Prevention and mental health programs aimed at mitigating its consequences on the lives of Black people and other racialized populations must be implemented.
Ultrasound‐guided‐electromyography in plegic muscle: Usefulness of nerve stimulation

In traumatic nerve lesions (TNLs), motor unit potentials (MUPs) may be difficult to detect in early injury. Ultrasound‐guided electromyography (US‐EMG) can aid in identifying areas of muscle activation, but its sensitivity can be improved. In this study we compare the sensitivity of US‐EMG alone with US‐EMG after peripheral nerve stimulation (NC‐US‐EMG) to better identify active muscle regions.
Rarefied Gas Dynamics

1. Boltzmann equation and gas-surface interaction 2. Problems for a gas in a slab: general aspects and preliminary example 3. Problems for a gas in a slab or a half-space: discussion of some solutions 4. Propagation phenomena and shock waves in rarefied gases 5. Perturbation methods in more than one dimension 6. Polyatomic gases, mixtures, chemistry and radiation 7. Solving the Boltzmann equation by numerical techniques 8. Evaporation and condensation phenomena.
Effect of compassion‐focused therapy on self‐criticism and self‐soothing: A meta‐analysis

Abstract Objective Compassion is oriented towards perceiving and relieving suffering. Hence, its development is beneficial for mental health. Many interventions aimed at cultivating compassion in patients have been empirically supported. This meta‐analysis analyses the effectiveness of compassion‐focused therapy (CFT) in decreasing self‐criticism, a vulnerability factor that has been related to several mental health problems, and in increasing self‐soothing. Methods A literature search was conducted in the PsycInfo, Web of Science, Medline and Scopus databases, through which 7 controlled trials (N = 640) and 7 observational studies (N = 207) were retrieved. Results The results of the meta‐analysis determine that CFT decreases the level of self‐criticism and increases the ability to experience soothing. The size of the effect varies depending on the design of the study and the subscale of the test used to measure self‐criticism (Forms of Self‐Criticizing/Attacking and Self‐Reassuring Scale). Conclusions CFT has proven to be an effective intervention for reducing self‐criticism. However, given that the number of studies is small and that only half of them are controlled trials, the results must be interpreted cautiously. More randomized controlled trials comparing CFT with other therapies are needed to determine the effect of this intervention on self‐criticism with more scientific evidence.
Risk Factors and Preventive Measures for Anastomotic Leak in Colorectal Cancer

Anastomotic leak (AL) represents one of the most detrimental complications after colorectal surgery. The patient-related factors and surgery-related factors leading to AL have been identified in previous studies. Through early identification and timely adjustment of risk factors, preventive measures can be taken to reduce potential AL. However, there are still many problems associated with AL. The debate about preventive measures such as preoperative mechanical bowel preparation (MBP), intraoperative drainage, and surgical scope also continues. Recently, the gut microbiota has received more attention due to its important role in various diseases. Although the underlying mechanisms of gut microbiota on AL have not been validated completely, new strategies that manipulate intrinsic mechanisms are expected to prevent and treat AL. Moreover, laboratory examinations for AL prediction and methods for blood perfusion assessment are likely to be promoted in clinical practice. This review outlines possible risk factors for AL and suggests some preventive measures in terms of patient, surgery, and gut microbiota.
A GENERALIZATION OF NOETHERIAN RINGS

In this paper, we introduce the concept of $AFG$ rings. $R$ is said to be a left $AFG$ ring in case the left annihilator of every nonempty subset of $R$ is a finitely generated left ideal. Some characterizations of $AFG$ rings and applications are obtained
SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells

Abstract Motivation Cell type-specific activities of cis-regulatory elements (CRE) are central to understanding gene regulation and disease predisposition. Single-cell RNA 5′end sequencing (sc-end5-seq) captures the transcription start sites (TSS) which can be used as a proxy to measure the activity of transcribed CREs (tCREs). However, a substantial fraction of TSS identified from sc-end5-seq data may not be genuine due to various artifacts, hindering the use of sc-end5-seq for de novo discovery of tCREs. Results We developed SCAFE—Single-Cell Analysis of Five-prime Ends—a software suite that processes sc-end5-seq data to de novo identify TSS clusters based on multiple logistic regression. It annotates tCREs based on the identified TSS clusters and generates a tCRE-by-cell count matrix for downstream analyses. The software suite consists of a set of flexible tools that could either be run independently or as pre-configured workflows. Availability and implementation SCAFE is implemented in Perl and R. The source code and documentation are freely available for download under the MIT License from https://github.com/chung-lab/SCAFE. Docker images are available from https://hub.docker. com/r/cchon/scafe. The submitted software version and test data are archived at https://doi.org/10.5281/zenodo.7023163 and https://doi.org/10.5281/zenodo.7024060, respectively. Supplementary information Supplementary data are available at Bioinformatics online.
STARS AND IONIZED GAS IN THE S0 GALAXY NGC 7743: AN INCLINED LARGE-SCALE GASEOUS DISK

We used deep, long-slit spectra and integral-field spectral data to study the stars, ionized gas kinematics, and stellar population properties in the lenticular barred galaxy NGC 7743. We show that ionized gas at distances larger than 1.5 kpc from the nucleus settles in the disk, which is significantly inclined toward the stellar disk of the galaxy. Making different assumptions about the geometry of the disks and including different sets of emission lines in the fitting, under the assumption of thin, flat-disk circular rotation, we obtain the full possible range of angles between the disks to be 34° ± 9° or 77° ± 9°. The most probable origin of the inclined disk is the external gas accretion from a satellite orbiting the host galaxy, with a corresponding angular momentum direction. The published data on the H i distribution around NGC 7743 suggest that the galaxy has a gas-rich environment. The emission-line ratio diagrams imply the domination of shock waves in the ionization state of the gaseous disk, whereas the contribution of photoionization from recent star formation seems to be negligible. In some parts of the disk, a difference between the velocities of the gas emitting from the forbidden lines and Balmer lines is detected. This may be caused by the mainly shock-excited inclined disk, whereas some fraction of the Balmer-line emission is produced by a small amount of gas excited by young stars in the main stellar disk of NGC 7743. In the circumnuclear region (R < 200 pc), some evidence of the active galactic nucleus jet's interaction with an ambient interstellar medium was found.
THE EFFECT OF A TIME-VARYING ACCRETION DISK SIZE ON QUASAR MICROLENSING LIGHT CURVES

Microlensing perturbations to the magnification of gravitationally lensed quasar images are dependent on the angular size of the quasar. If quasar variability at visible wavelengths is caused by a change in the area of the accretion disk, it will affect the microlensing magnification. We derive the expected signal, assuming that the luminosity scales with some power of the disk area, and estimate its amplitude using simulations. We discuss the prospects for detecting the effect in real-world data and for using it to estimate the logarithmic slope of the luminosity's dependence on disk area. Such an estimate would provide a direct test of the standard thin accretion disk model. We tried fitting six seasons of the light curves of the lensed quasar HE 0435−1223 including this effect as a modification to the Kochanek et al. approach to estimating time delays. We find a dramatic improvement in the goodness of fit and relatively plausible parameters, but a robust estimate will require a full numerical calculation in order to correctly model the strong correlations between the structure of the microlensing magnification patterns and the magnitude of the effect. We also comment briefly on the effect of this phenomenon for the stability of time-delay estimates.
Matter-Neutrino Resonance Above Merging Compact Objects

Accretion disks arising from neutron star- neutron star mergers or black hole- neutron star mergers produce large numbers of neutrinos and antineutrinos. In contrast to other astrophysical scenarios, like supernovae, in mergers the antineutrinos outnumber the neutrinos. This antineutrino dominance gives neutrinos from merger disks the opportunity to exhibit new oscillation physics, specifically a matter-neutrino resonance. We explore this resonance, finding that consequences can be a large transition of $\nu_e$ to other flavors, while the $\bar{\nu}_e$s return to their initial state. We present numerical calculations of neutrinos from merger disks and compare with a single energy model. We explain both the basic features and the conditions for a transition.
Development of non-adherent cell-enclosing domes with enzymatically cross-linked hydrogel shell

Non-adherent cells, such as hematopoietic cells and lymphocytes, are important research subjects in medical and biological fields. Therefore, a system that enables the handling of non-adherent cells in solutions in the same manner as that of adhering cells during medium exchange, exposure to chemicals, washing, and staining in imaging applications would be useful. Here, we report a ‘Cell Dome’ platform in which non-adherent cells can be enclosed and grown in the cavities of about 1 mm diameter and 270 μm height. The domes consist of an alginate-based hydrogel shell of 90 μm thickness. Cell Domes were formed on glass plates by horseradish peroxidase-mediated cross-linking. Human leukaemia cell line K562 cells enclosed in Cell Domes were stable for 29 days with every 2–3 days of medium change. The enclosed cells grew in the cavities and were stained and differentiated with reagents supplied from the surrounding medium. Additionally, K562 cells that filled the cavities (a 3D microenvironment) were more hypoxic and highly resistant to mitomycin C than those cultured in 2D. These findings demonstrate that the ‘Cell Dome’ may be a promising tool for conveniently culturing and evaluating non-adherent cells.