Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust Distributional Regression with Automatic Variable Selection

Datasets with extreme observations and/or heavy-tailed error distributions are commonly encountered and should be analyzed with careful consideration of these features from a statistical perspective. Small deviations from an assumed model, such as the presence of outliers, can cause classical regression procedures to break down, potentially leading to unreliable inferences. Other distributional features, such as heteroscedasticity, can be handled by going beyond the mean and modelling the scale parameter in terms of covariates. We propose a method that accounts for heavy tails and heteroscedasticity through the use of a generalized normal distribution (GND). The GND contains a kurtosis-characterizing shape parameter that moves the model smoothly between the normal distribution and the heavier-tailed Laplace distribution — thus covering both classical and robust regression. A key component of statistical modelling is determining the set of covariates that inﬂuence the response variable. While correctly accounting for kurtosis and heteroscedasticity is crucial to this endeavour, a procedure for variable selection is still required. For this purpose, we use a novel penalized estimation procedure that avoids the typical computationally demanding grid search for tuning parameters. This is particularly valuable in the distributional regression setting where the location and scale parameters depend on covariates, since the standard approach would have multiple tuning parameters (one for each distributional parameter). We achieve this by using a “smooth information criterion” that can be optimized directly, where the tuning parameters are ﬁxed at log( n ) in the BIC case.
Anomalous Vapor and Ice Nucleation in Water at Negative Pressures: A Classical Density Functional Theory Study.

In contrast to the abundance of work on the anomalous behavior of water, the relationship between the water's thermodynamic anomalies and kinetics of phase transition from metastable water is relatively unexplored. In this work, we have employed classical density functional theory to provide a unified and coherent picture of nucleation (both vapor and ice) from metastable water at negative pressure conditions. Our results suggest a peculiar nonmonotonic temperature dependence of vapor-liquid surface tension at temperatures where vapor-liquid coexistence is metastable with respect to the ice phase. The vapor nucleation barrier on isochoric cooling also shows a nonmonotonic temperature dependence. We further report that, for low density isochores, the temperature of the minimum vapor nucleation barrier (TΔΩv/min*) does not coincide with the temperature of maximum density (TMD) where metastability is maximum. The difference between the TΔΩv/min* and the TMD, however, decreases with increasing the density of the isochore. The vapor nucleation barrier along isobars shows an interesting crossover behavior in the vicinity of the Widom line on lowering the temperature. Our results on the ice nucleation suggest an anomalous retracing behavior of the nucleation barrier along isotherms at negative pressures and theoretically validate the recent findings that the reentrant ice(Ih)-liquid coexistence line can induce a drastic change in the kinetics of ice nucleation. Thus, this study establishes a direct connection between the metastable water's thermodynamic anomalies and the (vapor and ice) nucleation kinetics. In addition, this study provides deeper insights into the origin of the isothermal compressibility maximum on isochoric cooling.
Magnetized matter effects on dilaton photon mixing

Dilatons ($\phi(x)$) are a class of bosonic scalar particles associated with scaling symmetry and its compensation (under the violations of the same). Due to two photon coupling, they can produce optical signatures in a magnetic field. In vacuum or plain matter they couple to one of the transversely polarized state of the photon. But in a magnetized matter, they couple to both the transversely polarized state of photon (due to emergence of a parity violating part of photon self energy contribution from a magnetized matter). A part of this work is directed towards understanding the issue of mixing of scalar with various polarizations states of photon in a medium ( magnetized or unmagnetized ) due to the constraints from different discrete (CPT) symmetries associated with the interaction. Based on these symmetry aided arguments, the structure of the mixing matrix is found to be $3 \times 3$. Thus there exists non-zero finite probabilities of oscillation between different polarization states of photon to dilaton. Our analytical and numerical analysis show no existence of periodic oscillation length either in temporal or spatial direction for most general values of the parameters in the theory. Possible astrophysical consequences of these results, those can be detected through observations are discussed.
Detailed scanning probe microscopy tip models determined from simultaneous atom-resolved AFM and STM studies of the TiO2(110) surface

The atomic-scale contrast in noncontact atomic force microscopy (nc-AFM) images is determined by the geometry and exact atomic structure of the tip apex. However, the tip state is an experimentally unknown parameter, and the lack of insight into the tip apex often limits the possibilities of extracting precise quantitative and qualitative atomistic information on the surface under inspection. From an interplay between simultaneously recorded nc-AFM and scanning tunneling microscopy (STM) data, and atomistic STM simulations based on multiple scattering theory, we demonstrate how the state of the scanning probe microscopy (SPM) tip in the experiments may be determined. The analysis of a large number of experimental SPM images recorded with different tips reveals that no general correlation exists between the contrast observed in the nc-AFM and the tunneling current (I-t) images on TiO2(110) surface. The exact state of the SPM tip must, therefore, be determined for each specific case, which is normally a very difficult endeavor. However, our analysis of the AFM contrast on TiO2(110) surface allows us to considerably reduce the number of tips to be considered in a full simulation. By carefully evaluating the contrast of a handpicked library of SPM tips, we manage to determine a very accurate model of the SPM tip used in an experiment for the first time. It is envisioned that the approach presented here may eventually be used in future studies to screen for and select a SPM tip with a special functionalization prior to imaging an unknown sample, and in that way facilitate precise modeling and chemical identification of surface species.
Imaging of integer quantum Hall edge state in a quantum point contact via scanning gate microscopy

Integer quantum Hall edge states have been imaged in the constriction region of a quantum point contact fabricated in an InGaAs heterostructure at high magnetic fields using low-temperature scanning gate microscopy (SGM). Features in the SGM images grew wider and deeper as side gates squeezed the constriction. Furthermore, clear plateaus corresponding to the depopulation of edge states were observed. We propose a model for these images based on the variation of the local confinement potential induced by the tip.
The Data-Driven Multivariate Process Monitoring and Diagnosis of Rides in an Amusement Park

To guarantee the safety of rides is vitally important and meaningful to the amusement park industry. A multi-scale principal component analysis (MSPCA) is engaged in the fault detection of a ride for long term, where wavelets capture correlation within a sensor and principal component analysis correlates across sensors. The data measured from a ride in an amusement park are given and fed into the MSPCA model to diagnose whether a fault would occur. For the non-stationary process of a ride on run, it is hard to clarify how healthy the ride is according to the data on once run. A strategy of long-term monitoring and diagnosis is given.
Tracking Performance Bound with Finite Control Energy and Erasure Channel Energy Constraint

This paper studies the tracking performance of the single‐input single‐output (SISO), finite dimensional, linear and time‐invariant (LTI) system under the channel input energy constraint over the Erasure channel. A new performance index is proposed which is minimized over all two‐degree‐of‐freedom stabilizing controllers. The explicit expressions of the lower bound of the performance index and the minimum of the signal‐to‐noise ratio are obtained. The results show that the performance bound is correlated to unstable poles, non‐minimum phase zeros and the packet loss probability. Finally, examples are given to validate the conclusions derived.
Inequality systems and global optimization

Abstract Solvability results for infinite inequality systems involving convex and difference of convex (DC) functions are given. Generalizations of Farkas' lemma are obtained. These results are presented in terms of epigraphs of conjugate functions. Applications are given for characterizing global ϵ-optimality (and optimality) of difference of convex (DC) optimization problems with convex inequality constraints. Solvability results for cone convex inequality systems are also given.
reveals parallel

One-sentence summary: Haplotagging, a novel linked-read sequencing technique that enables whole genome haplotyping in large populations, reveals the formation of a novel hybrid race in parallel hybrid zones of two co-mimicking Heliconius butterfly species through strikingly parallel divergences in their genomes. Abstract Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies ( Heliconius erato and H. melpomene ), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing colour patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations. both alleles (50.6% and 49.4%, respectively; about 1.0 million molecules each on autosomes). Many of these molecules span many kilobases (kbp), up to as much as 415 kbp (N 50 = 42.1 kbp; Supplementary Table 4). These results provide strong evidence that haplotagging can accurately capture and reconstruct haplotypes. Using these data, we phased nearly all heterozygous SNPs (99.74%) using HAPCUT2 10 into large, megabase-spanning phased haplotype blocks (N 50 = 15.5 Mbp; Extended Data fig. 2a; maximum: 61.46 Mbp; Supplementary Table 4; see Supplementary Notes for phasing performances in additional human and mouse samples, including comparison against other LR platforms).
Characteristic boundary conditions for simulations of compressible reacting flows with multi-dimensional, viscous and reaction effects

A generalized formulation of the characteristic boundary conditions for compressible reacting flows is proposed. The new and improved approach resolves a number of lingering issues of spurious solution behaviour encountered in turbulent reacting flow simulations in the past. This is accomplished (a) by accounting for all the relevant terms in the determination of the characteristic wave amplitudes and (b) by accommodating a relaxation treatment for the transverse gradient terms with the relaxation coefficient properly determined by the low Mach number asymptotic expansion. The new boundary conditions are applied to a comprehensive set of test problems including: vortex-convection; turbulent inflow; ignition front propagation; non-reacting and reacting Poiseuille flows; and counterflow cases. It is demonstrated that the improved boundary conditions perform consistently superior to existing approaches, and result in robust and accurate solutions with minimal acoustic wave interactions at the boundary in hostile turbulent combustion simulation conditions.
The Endophytic Root Microbiome Is Different in Healthy and Ralstonia solanacearum-Infected Plants and Is Regulated by a Consortium Containing Beneficial Endophytic Bacteria

Bacterial wilt disease causes heavy yield losses in many crops. Endophytic microbiomes play important roles in control of plant diseases. ABSTRACT Plant bacterial wilt disease caused by Ralstonia solanacearum leads to huge economic losses worldwide. Endophytes play vital roles in promoting plant growth and health. It is hypothesized that the endophytic root microbiome and network structure are different in healthy and diseased plants. Here, the endophytic root microbiomes and network structures of healthy and diseased tobacco plants were investigated. Composition and network structures of endophytic root microbiomes were distinct between healthy and diseased plants. Healthy plants were enriched with more beneficial bacteria and bacteria with antagonistic activity against R. solanacearum. R. solanacearum was most abundant in diseased plants. Microbial networks in diseased plants had fewer modules and edges, lower connectivity, and fewer keystone microorganisms than those in healthy plants. Almost half of the nodes were unique in the two networks. Ralstonia was identified as a key microorganism of the diseased-plant network. In healthy plants, abundant bacteria and biomarkers (Pseudomonas and Streptomyces) and keystone microorganisms (Bacillus, Lysobacter, and Paenibacillus) were plant-beneficial bacteria and showed antibacterial and plant growth-promoting activities. The endophytic strain Bacillus velezensis E9 produced bacillaene to inhibit R. solanacearum. Consortia containing keystone microorganisms and beneficial endophytic bacteria significantly regulated the endophytic microbiome and attenuated bacterial wilt by inducing systemic resistance and producing antibiotic. Overall, the endophytic root microbiome and network structure in diseased plants were different from those in healthy plants. The endophytic root microbiome of diseased plants had low abundances of beneficial bacteria and an unstable network and lacked beneficial keystone microorganisms, which favored infection. Synthetic microbial consortia were effective measures for preventing R. solanacearum infection. IMPORTANCE Bacterial wilt disease causes heavy yield losses in many crops. Endophytic microbiomes play important roles in control of plant diseases. However, the role of the endophytic root microbiome in controlling bacterial wilt disease is poorly understood. Here, differences in endophytic root microbiomes and network structures between healthy and diseased tobacco plants are reported. A synthetic microbial consortium containing beneficial endophytic bacteria was used to regulate the endophytic microbiome and attenuate bacterial wilt disease. The results could be generally used to guide control of bacterial wilt disease.
Plasma-Like Culture Medium for the Study of Viruses

Viral infections attract more and more attention, especially after the emergence of novel zoonotic coronaviruses and the monkeypox virus over the last 2 decades. Research on viruses is based to a great extent on mammalian cell lines that are permissive to the respective viruses. ABSTRACT Viral infections attract more and more attention, especially after the emergence of novel zoonotic coronaviruses and the monkeypox virus over the last 2 decades. Research on viruses is based to a great extent on mammalian cell lines that are permissive to the respective viruses. These cell lines are usually cultivated according to the protocols established in the 1950s to 1970s, although it is clear that classical media have a significant imprint on cell growth, phenotype, and especially metabolism. So, recently in the field of biochemistry and metabolomics novel culture media have been developed that resemble human blood plasma. As perturbations in metabolic and redox pathways during infection are considered significant factors of viral pathogenesis, these novel medium formulations should be adapted by the virology field. So far, there are only scarce data available on viral propagation efficiencies in cells cultivated in plasma-like media. But several groups have presented convincing data on the use of such media for cultivation of uninfected cells. The aim of the present review is to summarize the current state of research in the field of plasma-resembling culture media and to point out the influence of media on various cellular processes in uninfected cells that may play important roles in viral replication and pathogenesis in order to sensitize virology research to the use of such media.
Functional Characterization of 15 Novel Dense Granule Proteins in Toxoplasma gondii Using the CRISPR-Cas9 System

Dense granule proteins (GRAs) play important roles in Toxoplasma gondii pathogenicity. However, the functions of many putative GRAs have not been elucidated. ABSTRACT The analysis of the subcellular localization and function of dense granule proteins (GRAs) is of central importance for the understanding of host-parasite interaction and pathogenesis of Toxoplasma gondii infection. Here, we identified 15 novel GRAs and used C-terminal endogenous gene tagging to determine their localization at the intravacuolar network (IVN), parasitophorous vacuole (PV), or PV membrane (PVM) in the tachyzoites and at the periphery of the bradyzoites-containing cysts. The functions of the 15 gra genes were examined in type I RH strain and 5 of these gra genes were also evaluated in the cyst-forming type II Pru strain. The 15 novel gra genes were successfully disrupted by using CRISPR-Cas9 mediated homologous recombination and the results showed that 13 gra genes were not individually essential for T. gondii replication in vitro or virulence in mice during acute and chronic infection. Intriguingly, deletion of TGME49_266410 and TGME49_315910 in both RH and Pru strains decreased the parasite replication in vitro and attenuated its virulence, and also reduced the cyst-forming ability of the Pru strain in mice during chronic infection. Comparison of the transcriptomic profiles of the 15 gra genes suggests that they may play roles in other life cycle stages and genotypes of T. gondii. Taken together, our findings improve the understanding of T. gondii pathogenesis and demonstrate the involvement of two novel GRAs, TGME49_266410 and TGME49_315910, in the parasite replication and virulence. IMPORTANCE Dense granule proteins (GRAs) play important roles in Toxoplasma gondii pathogenicity. However, the functions of many putative GRAs have not been elucidated. Here, we found that 15 novel GRAs are secreted into intravacuolar network (IVN), parasitophorous vacuole (PV), or PV membrane (PVM) in tachyzoites and are located at the periphery of the bradyzoite-containing cysts. TGME49_266410 and TGME49_315910 were crucial to the growth of RH and Pru strains in vitro. Deletion of TGME49_266410 and TGME49_315910 attenuated the parasite virulence in mice. However, disruption of other 13 gra genes did not have a significant impact on the proliferation and pathogenicity of T. gondii in vitro or in vivo. The marked effects of the two novel GRAs (TGME49_266410 and TGME49_315910) on the in vitro growth and virulence of T. gondii are notable and warrant further elucidation of the temporal and spatial dynamics of translocation of these two novel GRAs and how do they interfere with host cell functions.
Pathologische Gefäßkalzifizierung – klinische Relevanz und molekulare Mechanismen

Zusammenfassung Die kardiovaskuläre Kalzifizierung stellt als pathologische Mineralablagerung in Herzklappen und Arterien einen Prädiktor und Risikofaktor für die kardiovaskuläre Morbidität und Mortalität dar – ein globales Gesundheitsproblem. Die kardiovaskuläre Kalzifizierung ist ein ‚Unmet need‘ in der kardiovaskulären Medizin, da es bisher keine therapeutischen Ansatzpunkte gibt, die diesen Prozess aufhalten oder modifizieren können. Diese Übersichtsarbeit fasst die Manifestationsformen der kardiovaskulären Kalzifizierung mit ihren klinischen Relevanzen zusammen. Dabei wird der Fokus insbesondere auf die arterielle Mikrokalzifizierung der Tunica intima, sowie Makrokalzifizierung der Tunica media und der Aortenklappe gelegt. Die zellulären und molekularen Mechanismen, die die kardiovaskuläre Kalzifizierung regulieren, sind vielfältig und zeigen Parallelen zum Knochenstoffwechsel. Neben den klassischen Signalwegen, wird die Rolle epigenetischer Veränderungen diskutiert. Letztlich werden offene Fragen aufgezeigt, deren Beantwortung wichtig ist, um Therapieansätze zur Prävention und Behandlung kardiovaskulärer Kalzifizierung entwickeln zu können, die die Knochengesundheit nicht beeinflussen.
Treatment Outcomes of Mechanical Thrombectomy in Patients with Acute Posterior Circulation Stroke

Abstract Objective The benefits of mechanical thrombectomy (MT) in patients with acute posterior circulation stroke remain unclear. Currently, there is no evidence from randomized control trials to show the safety and effectiveness of MT in patients with posterior circulation stroke. This study was to evaluate the treatment outcomes of MT in posterior circulation stroke patients enrolling in our hospital during 2010 to 2020. Materials and Methods Between January 2010 and December 2020, 66 patients with acute posterior circulation stroke underwent MT. Data collected and analyzed included demographics, comorbidity, National Institutes of Health Stroke Scale (NIHSS), procedure time, site of occlusion, presence of posterior communicating artery (PCoA), endovascular technique, and modified Rankin Scale (mRS). Good clinical outcome was defined by mRS at 2 or less at 90 days after MT. Statistical Analysis Variables with normal distribution were reported with mean ± standard deviation, meanwhile those with nonnormal distribution were demonstrated with median and range. Fisher's exact test for categorical variables or Mann–Whitney U test for continuous variables was performed. Multivariate logistic regression analysis with binary logistic regression method was used analyze the association between the prognosis factor and good outcome. Statistical significance was defined when p -value less than 0.05. Results The mean age of patients was 65.2 years with male predominance. The median NIHSS was 18.5. Successful recanalization (modified thrombolysis in cerebral infarction 2b-3) was achieved in 61/66 cases (92.42%) and postprocedure symptomatic intracerebral hemorrhage occurred in 5/66 cases (7.60%). Successful recanalization with good clinical outcome was obtained from 30 of 61 cases (49.18%); it was also associated with distal basilar artery occlusion ( p = 0.035) and PCoA patency presence ( p = 0.024). Our study showed the correlation between good treatment outcomes with initial NIHSS less than 20, intravenous recombinant tissue-type plasminogen activator, pre-MT magnetic resonance imaging Q5 brain, and contact aspiration MT technique. Conclusion MT is beneficial to patients with posterior circulation stroke. A good clinical outcome was significantly associated with distal basilar artery occlusion and PCoA patency presence within a group of successful recanalization.