Miracle-dz/UniFAR-FTUs huggingface dataset:
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy revisited

Objective The aim of this study was to evaluate the correlation between the various NOTCH3 mutations and their clinical and genetic profile, along with the presentation of a novel mutation in a patient. Methods Here, we describe the phenotype of a patient with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) harboring a novel mutation. We also performed an extensive literature research for NOTCH3 mutations published since the identification of the gene and performed a systematic review of all published cases with NOTCH3 mutations. We evaluated the mutation pathogenicity in a great number of patients with detailed clinical and genetic evaluation and investigated the possible phenotype-genotype correlations. Results Our patient harbored a novel mutation in the NOTCH3 gene, the c.3084 G > C, corresponding to the aminoacidic substitution p.Trp1028Cys, presenting with seizures as the first neurologic manifestation. We managed to find a correlation between the pathogenicity of mutations, severity of the phenotype, and age at onset of CADASIL. Significant differences were also identified between men and women regarding the phenotype severity. Conclusions The collection and analysis of these scarce data published since the identification of NOTCH3 qualitatively by means of a systematic review and quantitatively regarding genetic profile and pathogenicity scores, highlight the significance of the ongoing trend of investigating phenotypic genotypic correlations.
Krylov Subspace and Multigrid Methods Applied to the Incompressible Navier-Stokes Equations

We consider numerical solution methods for the incompressible Navier-Stokes equations discretized by a finite volume method on staggered grids in general coordinates. We use Krylov subspace and multigrid methods as well as their combinations. Numerical experiments are carried out on a scalar and a vector computer. Robustness and efficiency of these methods are studied. It appears that good methods result from suitable combinations of GCR and multigrid methods.
Exploring the fringe- belt phenomenon in a Sino- Portuguese environment: the case of Macao

The fringe- belt concept has been recognized as an effective means of investigating the growth and transformation of urban physical form. Hitherto case studies of fringe belts have been mainly conducted in fairly homogeneous cultural environments. In this paper the fringe- belt concept is investigated in a city characterized by a Sino- Western admixture of cultures. The investigation of three fringe belts in Macao Peninsula reveals major factors influencing their formation and modification processes, especially in relation to socio- economic conditions, land reclamation from the sea and industrial development. Understanding the characteristics of fringe belts has implications for the appreciation and management of urban landscapes.
Pulse spectral evolution of GRBs: implication as standard candle

Using an \emph{empirical} description of a prompt GRB pulse, we analyze the individual pulses of all Fermi/GBM GRBs with known redshifts, till July 2009. This description is simultaneous in time and energy and allows one to determine the peak energy of Band spectrum at zero fluence ($E_{peak,0}$). We demonstrate, for the first time, that the $E_{peak,0}$ bears a very strong correlation with the isotropic energy of the individual pulses, and hence, each pulse can be used as a luminosity indicator. As a physical description is needed in order to use GRB pulses for cosmological purposes, we explore other physical spectral models. As pulses are the building blocks of a GRB, we choose another sample of Fermi/GBM GRBs having bright, long and single/ separable pulse(s) and fit the time-resolved spectra of the individual pulses with the Band model and a model consisting of a blackbody and a power-law. Both these models give acceptable fits. We find that the peak energy/ temperature always decreases exponentially with fluence in the later part of a pulse. We investigate multiple spectral components in the initial rising part and provide a comprehensive empirical description of the spectral and timing behaviour of prompt GRB pulses. This work strongly extends the possibility of using GRB pulses as standard candles and the spectral parameters as proxy for redshift.
THE GEMINI NICI PLANET-FINDING CAMPAIGN: DISCOVERY OF A MULTIPLE SYSTEM ORBITING THE YOUNG A STAR HD 1160

We report the discovery of two low-mass companions to the young A0V star HD 1160 at projected separations of 81 ± 5 AU (HD 1160 B) and 533 ± 25 AU (HD 1160 C) by the Gemini NICI Planet-Finding Campaign. Very Large Telescope images of the system taken over a decade for the purpose of using HD 1160 A as a photometric calibrator confirm that both companions are physically associated. By comparing the system to members of young moving groups and open clusters with well-established ages, we estimate an age of 50+50− 40 Myr for HD 1160 ABC. While the UVW motion of the system does not match any known moving group, the small magnitude of the space velocity is consistent with youth. Near-IR spectroscopy shows HD 1160 C to be an M3.5 ± 0.5 star with an estimated mass of 0.22+0.03− 0.04 M☉, while NIR photometry of HD 1160 B suggests a brown dwarf with a mass of 33+12− 9 MJup. The very small mass ratio (0.014) between the A and B components of the system is rare for A star binaries, and would represent a planetary-mass companion were HD 1160 A to be slightly less massive than the Sun.
Progenitor model of cosmic ray knee

The primary energy spectrum of cosmic rays exhibits a knee at about 3 PeV where a change in the spectral index occurs. Despite many efforts, the origin of such a feature in the spectrum is not satisfactorily solved yet. Here it is proposed that the steepening of the spectrum beyond the knee may be a consequence of the mass distribution of the progenitor of the cosmic ray source. The proposed speculative model can account for all the major observed features of cosmic rays without invoking any fine tuning to match flux or spectra at any energy point. The prediction of the proposed model regarding the primary composition scenario beyond the knee is quite different from most of the prevailing models of the knee, and thereby can be discriminated from precise experimental measurement of the primary composition.
NetSHy: network summarization via a hybrid approach leveraging topological properties

Biological networks can provide a system level understanding of underlying processes. In many contexts, networks have a high degree of modularity, i.e., they consist of subsets of nodes, often known as subnetworks or modules, which are highly interconnected and may perform separate functions. In order to perform subsequent analyses to investigate the association between the identified module and a variable of interest, a module summarization, that best explains the module's information and reduces dimensionality is often needed. Conventional approaches for obtaining network representation typically rely only on the profiles of the nodes within the network while disregarding the inherent network topological information. In this article, we propose NetSHy, a hybrid approach which is capable of reducing the dimension of a network while incorporating topological properties to aid the interpretation of the downstream analyses. In particular, NetSHy applies principal component analysis (PCA) on a combination of the node profiles and the well-known Laplacian matrix derived directly from the network similarity matrix to extract a summarization at a subject level. Simulation scenarios based on random and empirical networks at varying network sizes and sparsity levels show that NetSHy outperforms the conventional PCA approach applied directly on node profiles, in terms of recovering the true correlation with a phenotype of interest and maintaining a higher amount of explained variation in the data when networks are relatively sparse. The robustness of NetSHy is also demonstrated by more consistent correlation with the observed phenotype as the sample size decreases. Lastly, a genome wide association study (GWAS) is performed as an application of a downstream analysis, where NetSHy summarization scores on the biological networks identify more significant single nucleotide polymorphisms (SNP) than the conventional network representation.
The role of perceived expertise and trustworthiness in research study and clinical trial recruitment: Perspectives of clinical research coordinators and African American and Black Caribbean patients

This study investigates the role of source credibility on minority participant recruitment, particularly African American and Black Caribbean patients. A total of nine focus groups (N = 48 participants) were conducted with both patient groups and clinical research coordinators (CRCs). Using the elaboration likelihood model as a guiding framework for analysis, this study found that the credibility of research coordinators (or other professionals who recruit for research studies and clinical trials) was instrumental in shaping attitudes of prospective participants. The perspectives of patients and CRCs aligned closely, with few exceptions. For both groups, professionalism and professional displays (clothing, institutional artifacts) enhanced perceived expertise, a core component of credibility. Trustworthiness, another important component of credibility, was fostered through homophily between recruiter and patient, expressions of goodwill and assuaging anxiety about CRCs financial motivations for recruitment. Additionally, CRCs believed that credibility was supported when CRCs could emphasize transparency and truthfulness in communication. The importance of these findings for the development of empirically-based training programs to improve communication practices in recruitment contexts is discussed.
The ATLAS3D project - II. Morphologies, kinemetric features and alignment between photometric and kinematic axes of early-type galaxies

We use the ATLAS3D sample of 260 early-type galaxies to study the apparent kinematic misalignment angle, Ψ, defined as the angle between the photometric and kinematic major axes. We find that 71 per cent of nearby early-type galaxies are strictly aligned systems (Ψ≤ 5°), an additional 14 per cent have 5° <Ψ≤ 10° and 90 per cent of galaxies have Ψ≤ 15°. Taking into account measurement uncertainties, 90 per cent of galaxies can be considered aligned to better than 5°, suggesting that only a small fraction of early-type galaxies (˜10 per cent) are not consistent with the axisymmetry within the projected half-light radius. We identify morphological features such as bars and rings (30 per cent), dust structures (16 per cent), blue nuclear colours (6 per cent) and evidence of interactions (8 per cent) visible on ATLAS3D galaxies. We use KINEMETRY to analyse the mean velocity maps and separate galaxies into two broad types of regular and non-regular rotators. We find 82 per cent of regular rotators and 17 per cent of non-regular rotators, with two galaxies that we were not able to classify due to the poor data quality. The non-regular rotators are typically found in dense regions and are massive. We characterize the specific features in the mean velocity and velocity dispersion maps. The majority of galaxies do not have any specific features, but we highlight here the frequency of the kinematically distinct cores (7 per cent of galaxies) and the aligned double peaks in the velocity dispersion maps (4 per cent of galaxies). We separate galaxies into five kinematic groups based on the kinemetric features, which are then used to interpret the (Ψ-ɛ) diagram. Most of the galaxies that are misaligned have complex kinematics and are non-regular rotators. In addition, some show evidence of the interaction and might not be in equilibrium, while some are barred. While the trends are weak, there is a tendency that large values of Ψ are found in galaxies at intermediate environmental densities and among the most massive galaxies in the sample. Taking into account the kinematic alignment and the kinemetric analysis, the majority of early-type galaxies have velocity maps more similar to that of the spiral discs than to that of the remnants of equal-mass mergers. We suggest that the most common formation mechanism for early-type galaxies preserves the axisymmetry of the disc progenitors and their general kinematic properties. Less commonly, the formation process results in a triaxial galaxy with much lower net angular momentum.
Modeling Bounded Rationality

The notion of bounded rationality was initiated in the 1950s by Herbert Simon; only recently has it influenced mainstream economics. In this book, Ariel Rubinstein defines models of bounded rationality as those in which elements of the process of choice are explicitly embedded. The book focuses on the challenges of modeling bounded rationality, rather than on substantial economic implications. In the first part of the book, the author considers the modeling of choice. After discussing some psychological findings, he proceeds to the modeling of procedural rationality, knowledge, memory, the choice of what to know, and group decisions. In the second part, he discusses the fundamental difficulties of modeling bounded rationality in games. He begins with the modeling of a game with procedural rational players and then surveys repeated games with complexity considerations. He ends with a discussion of computability constraints in games. The final chapter includes a critique by Herbert Simon of the author's methodology and the author's response.
Acute melanization of silkworm hemolymph by peptidoglycans of the human commensal bacterium Cutibacterium acnes

Cutibacterium acnes is a pathogenic bacterium that cause inflammatory diseases of the skin and intervertebral discs. The immune activation induced by C. acnes requires multiple cellular responses in the host. Silkworm, an invertebrate, generates melanin by phenoloxidase upon recognizing bacterial or fungal components. Therefore, the melanization reaction can be used as an indicator of innate immune activation. A silkworm infection model was developed for evaluating the virulence of C. acnes, but a system for evaluating the induction of innate immunity by C. acnes using melanization as an indicator has not yet been established. Here we demonstrated that C. acnes rapidly causes melanization of the silkworm hemolymph. On the other hand, Staphylococcus aureus, a gram-positive bacterium identical to C. acnes, does not cause immediate melanization. Even injection of heat-killed C. acnes cells caused melanization of the silkworm hemolymph. DNase, RNase, and protease treatment of the heat-treated C. acnes cells did not decrease the silkworm hemolymph melanization. Treatment with peptidoglycan-degrading enzymes, such as lysostaphin and lysozyme, however, decreased the induction of melanization by the heat-treated C. acnes cells. These findings suggest that silkworm hemolymph melanization may be a useful indicator to evaluate innate immune activation by C. acnes and that C. acnes peptidoglycans are involved in the induction of innate immunity in silkworms.
Role of convective-scale processes in tropical cyclone development, The

An eiglteen level axisymmetric primitive equation tropical cyclone model which incorporates the Arakawa-Schubert (1974) spectral cumulus parameterization is presented. The quasi-equilibrium hypothesis, which involves the solution of an integral equation for the cloud base mass flux distribution, is successfully formulated as an optimization problem to guarantee a nonnegative solution. A linear analysis suggests that in the tropics a large fraction of the available potential energy generated by the release of latent heat is partitioned to gravityinertia wave motion and hence is radiated away to the far field. Therefore, an approximate pure gravity wave radiation boundary condition is derived which minimizes the reflection of gravity-inertia waves by the 1ateral bour,dary of the model. The sersitivity of axisymmetric model storm development to the exact form of the lateral boundary condition, initial moisture distribution, and latent heat release mechanism is tested. It is demonstrated that the development of a hurricane-like circulation can be simulated without parameterized convection as suggested by Rosenthal (1978). Several other sensitivity experiments are conducted to address the roles of radiation and cumulus momentum transport in tropical cyclone development. The numerical results lead to the conclusion that neither of these processes should be neglected in attempts to numerically simulate the life cycle of the tropical cyclone since they appear to contribut2 significantly to the organization and scale of tropical disturbances.
THE IMPACT OF THE SUPERSONIC BARYON–DARK MATTER VELOCITY DIFFERENCE ON THE z ∼ 20 21 cm BACKGROUND

Recently, Tseliakhovich & Hirata showed that during the cosmic Dark Ages the baryons were typically moving supersonically with respect to the dark matter with a spatially variable Mach number. Such supersonic motion may source shocks that inhomogeneously heat the universe. This motion may also suppress star formation in the first halos. Even a small amount of coupling of the 21 cm signal to this motion has the potential to vastly enhance the 21 cm brightness temperature fluctuations at 15 ≲ z ≲ 40, as well as to imprint distinctive acoustic oscillations in this signal. We present estimates for the size of this coupling, which we calibrate with a suite of cosmological simulations of the high-redshift universe using the GADGET and Enzo codes. Our simulations, discussed in detail in a companion paper, are initialized to self-consistently account for gas pressure and the dark matter–baryon relative velocity, vbc (in contrast to prior simulations). We find that the supersonic velocity difference dramatically suppresses structure formation on 10–100 comoving kpc scales, it sources shocks throughout the universe, and it impacts the accretion of gas onto the first star-forming minihalos (even for halo masses as large as 107 M☉). However, prior to reheating by astrophysical sources, we find that the vbc-sourced temperature fluctuations can contribute only as much as ≈10% of the fluctuations in the 21 cm signal. We do find that vbc in certain scenarios could source an component in the power spectrum of the 21 cm background on observable scales via the X-ray (but not ultraviolet) backgrounds produced once the first stars formed. In a scenario in which ∼106 M☉ minihalos reheated the universe via their X-ray backgrounds, we find that the pre-reionization 21 cm signal would be larger than previously anticipated and exhibit more significant acoustic features. Such features would be a direct probe of the first stars and black holes. In addition, we show that structure formation shocks are unable to heat the universe sufficiently to erase a strong 21 cm absorption trough at z ∼ 20 that is found in most models of the sky-averaged 21 cm intensity.
A SECOND NEUTRON STAR IN M4?

We show that the optical counterpart of the X-ray source CX 1 in M4 is a ∼20th magnitude star, located in the color–magnitude diagram on (or very close to) the main sequence of the cluster, and exhibiting sinusoidal variations of the flux. We find the X-ray flux to be also periodically variable, with X-ray and optical minima coinciding. Stability of the optical light curve, lack of UV-excess, and unrealistic mean density resulting from period–density relation for semidetached systems speak against the original identification of CX 1 as a cataclysmic variable. We argue that the X-ray active component of this system is a neutron star (probably a millisecond pulsar).
Separate optogenetic manipulation of Nerve/glial antigen 2 (NG2) glia and mural cells using the NG2 promoter

Nerve/glial antigen 2 (NG2) is a protein marker of NG2 glia and mural cells, and NG2 promoter activity is utilized to target these cells. However, the NG2 promoter cannot target NG2 glia and mural cells separately. This has been an obstacle for NG2 glia‐specific manipulation. Here, we developed transgenic mice in which either cell type can be targeted using the NG2 promoter. We selected a tetracycline‐controllable gene induction system for cell type‐specific transgene expression, and generated NG2‐tetracycline transactivator (tTA) transgenic lines. We crossed tTA lines with the tetO‐ChR2 (channelrhodopsin‐2)‐EYFP line to characterize tTA‐dependent transgene induction. We isolated two unique NG2‐tTA mouse lines: one that induced ChR2‐EYFP only in mural cells, likely due to the chromosomal position effect of NG2‐tTA insertion, and the other that induced it in both cell types. We then applied a Cre‐mediated set‐subtraction strategy to the latter case and eliminated ChR2‐EYFP from mural cells, resulting in NG2 glia‐specific transgene induction. We further demonstrated that tTA‐dependent ChR2 expression could manipulate cell function. Optogenetic mural cell activation decreased cerebral blood flow, as previously reported, indicating that tTA‐mediated ChR2 expression was sufficient to impact cellular function. ChR2‐mediated depolarization was observed in NG2 glia in acute hippocampal slices. In addition, ChR2‐mediated depolarization of NG2 glia inhibited their proliferation but promoted their differentiation in juvenile mice. Since the tTA–tetO combination is expandable, the mural cell–specific NG2‐tTA line and the NG2 glia‐specific NG2‐tTA line will permit us to conduct observational and manipulation studies to examine in vivo function of these cells separately.
Loss of TET2 with reduced genomic 5-hmC is associated with adverse-risk AML

Abstract While considerable information exists on the ten-eleven translocation 2 (TET2) mutational landscape in AML, the information on TET2 expression is limiting. So, we aimed to study the TET2 expression at mRNA and protein levels in AML patients compared to healthy controls. To achieve this, we recruited 70 non-M3, de novo AML patients and 20 healthy controls. The expression of TET2 was checked at mRNA and protein levels by qPCR and ELISA respectively and the TET activity was checked by the 5-hmC assay. TET2 mRNA expression was correlated with clinicopathological parameters and overall survival. We found a significant downregulation of TET2 mRNA and protein and significantly lower DNA 5-hmC levels in AML patients compared to controls. TET2 downregulation was more in patients with high blast counts and patients of the adverse-risk ELN category. We also found a significant upregulation of DNMT1 and DNMT3a suggesting a hypermethylation phenotype in de novo AML.