Miracle-dz/UniFAR-FTUs huggingface dataset:
Second Order, Linear, and Unconditionally Energy Stable Schemes for a Hydrodynamic Model of Smectic-A Liquid Crystals

In this paper, we consider the numerical approximations for a hydrodynamical model of smectic-A liquid crystals. The model, derived from the variational approach of the modified Oseen--Frank energy, is a highly nonlinear system that couples the incompressible Navier--Stokes equations and a constitutive equation for the layer variable. We develop two linear, second order time marching schemes based on the Invariant Energy Quadratization method for nonlinear terms in the constitutive equation, the projection method for the Navier--Stokes equations, and some subtle implicit-explicit treatments for the convective and stress terms. Moreover, we prove the well-posedness of the linear system and their unconditionally energy stabilities rigorously. Various numerical experiments are presented to demonstrate the stability and the accuracy of the numerical schemes in simulating the dynamics under shear flow and the magnetic field.
“I tend to forget bad things”: Immigrant and refugee young men’s narratives of distress

Distress among young immigrant and refugee men has drawn increasing research attention in recent years. Nuanced understandings of distress are needed to inform mental health and public health programming. The purpose of this research was to examine distress from the perspectives of young immigrant and refugee men living in Greater Vancouver, British Columbia, Canada. Thirty-three young men (aged 15–22 years) from diverse immigrant and refugee backgrounds participated in interviews, which were conducted between 2014 and 2015. Data were examined using narrative analysis and theories of masculinities. Three narratives were identified—norming distress, acknowledging distress as ongoing, and situating distress. The findings reveal that the narratives offer different frames through which distress was rendered a norm, or acknowledged and situated in relation to the participants’ relationships and to masculine discourses that shaped their expressions of distress. The findings can inform initiatives aimed at providing spaces for diverse young men to acknowledge their distress and to receive support for mental health challenges.
Assessment of morphological and functional changes in the mouse testis and epididymal sperms following busulfan treatment.

BACKGROUND Busulfan, a cytotoxic drug, which is currently used as a chemotherapeutic agent, has many side effects on different body organs. In this research, the effects of busulfan on sperm parameters and microstructure of mouse testis were investigated. METHODS Busulfan was injected intrapretoneally at 10, 20, 30, 40 and 50 mg/kg and testes were removed after 4, 6 and 8 weeks, weighed and processed for light microscopic examination. Transverse and cross section diameters of testes, seminiferous tubules diameters, percentage of different types of tubules, epithelium thickness, spermatogenic cell numbers and capsule thickness as well as the sperm parameters in epididymis were measured. RESULTS There was a significant decline in sperm numbers and marked changes in testes structures. Almost 8 weeks after the injection of drug, some of the changes are reversed. Accordingly, the changes in percent of normal tubules without sperm, abnormal tubules and capsule thickness were increased until 6 weeks of drug administration, the changes declined thereafter. CONCLUSION In general, busulfan caused a decrease in all analyzed parameters (except capsule thickness, normal tubules without sperm and abnormal tubules), probably due to the arrest of spermatogenesis. Our results also revealed that some of the changes are reversible and dose dependent.
DotU and VgrG, Core Components of Type VI Secretion Systems, Are Essential for Francisella LVS Pathogenicity

The Gram-negative bacterium Francisella tularensis causes tularemia, a disease which requires bacterial escape from phagosomes of infected macrophages. Once in the cytosol, the bacterium rapidly multiplies, inhibits activation of the inflammasome and ultimately causes death of the host cell. Of importance for these processes is a 33-kb gene cluster, the Francisella pathogenicity island (FPI), which is believed to encode a type VI secretion system (T6SS). In this study, we analyzed the role of the FPI-encoded proteins VgrG and DotU, which are conserved components of type VI secretion (T6S) clusters. We demonstrate that in F. tularensis LVS, VgrG was shown to form multimers, consistent with its suggested role as a trimeric membrane puncturing device in T6SSs, while the inner membrane protein DotU was shown to stabilize PdpB/IcmF, another T6SS core component. Upon infection of J774 cells, both ΔvgrG and ΔdotU mutants did not escape from phagosomes, and subsequently, did not multiply or cause cytopathogenicity. They also showed impaired activation of the inflammasome and marked attenuation in the mouse model. Moreover, all of the DotU-dependent functions investigated here required the presence of three residues that are essentially conserved among all DotU homologues. Thus, in agreement with a core function in T6S clusters, VgrG and DotU play key roles for modulation of the intracellular host response as well as for the virulence of F. tularensis.
Implication of Major Adverse Postoperative Events and Myocardial Injury on Disability and Survival: A Planned Subanalysis of the ENIGMA-II Trial

BACKGROUND: Globally, >300 million patients have surgery annually, and ⩽20% experience adverse postoperative events. We studied the impact of both cardiac and noncardiac adverse events on 1-year disability-free survival after noncardiac surgery. METHODS: We used the study cohort from the Evaluation of Nitrous oxide in Gas Mixture of Anesthesia (ENIGMA-II) trial, an international randomized trial of 6992 noncardiac surgical patients. All were ≥45 years of age and had moderate to high cardiac risk. The primary outcome was mortality within 1 postoperative year. We defined 4 separate types of postoperative adverse events. Major adverse cardiac events (MACEs) included myocardial infarction (MI), cardiac arrest, and myocardial revascularization with or without troponin elevation. MI was defined using the third Universal Definition and was blindly adjudicated. A second cohort consisted of patients with isolated troponin increases who did not meet the definition for MI. We also considered a cohort of patients who experienced major adverse postoperative events (MAPEs), including unplanned admission to intensive care, prolonged mechanical ventilation, wound infection, pulmonary embolism, and stroke. From this cohort, we identified a group without troponin elevation and another with troponin elevation that was not judged to be an MI. Multivariable Cox proportional hazard models for death at 1 year and assessments of proportionality of hazard functions were performed and expressed as an adjusted hazard ratio (aHR) and 95% confidence intervals (CIs). RESULTS: MACEs were observed in 469 patients, and another 754 patients had isolated troponin increases. MAPEs were observed in 631 patients. Compared with control patients, patients with a MACE were at increased risk of mortality (aHR, 3.36 [95% CI, 2.55–4.46]), similar to patients who suffered a MAPE without troponin elevation (n = 501) (aHR, 2.98 [95% CI, 2.26–3.92]). Patients who suffered a MAPE with troponin elevation but without MI had the highest risk of death (n = 116) (aHR, 4.29 [95% CI, 2.89–6.36]). These 4 types of adverse events similarly affected 1-year disability-free survival. CONCLUSIONS: MACEs and MAPEs occur at similar frequencies and affect survival to a similar degree. All 3 types of postoperative troponin elevation in this analysis were associated, to varying degrees, with increased risk of death and disability.
Serological screening for celiac disease in symptomatic 12 to 36 month-old children.

CONTEXT The correct diagnosis of celiac disease in environmentally deprived children is frequently hindered by the common presence of other causes for the classical celiac disease symptoms: malnutrition, failure to thrive and frequent diarrheas. OBJECTIVES To determine the prevalence of celiac disease in a group of 12 to 36 month-old children using immunoglobulin antibodies against gliadin (IgG and IgA-AGA), against endomysium (IgA-EMA), and against human tissue transglutaminase (IgA-tTG) as screening method. METHODS A total of 214 children (114 boys), aged 12 to 36 months, on gluten-containing diet, were admitted to the study. IgG and IgA-AGA, IgA-tTG and IgA-EMA tests were performed in all sera. Biopsy was obtained from all children showing positive result in one or more of the serologic tests, excluding those in which IgG-AGA had been the only positive result. In those cases, polymerase chain reaction (PCR) HLA genotyping for the identification of celiac disease predisposing alleles was applied. HLA genotyping was also performed to confirm the diagnosis in children identified as celiac by means of positive serologic testing and compatible biopsy results. RESULTS Normal results were obtained in 131 children. Ten children out of 68 identified as positive exclusively on the IgG-AGA test disclosed the presence of celiac disease predisposing alleles on PCR and underwent jejunal biopsy with normal results. All serologic tests were positive in four children. A fifth child showed positive IgG and IgA-AGA and IgA-tTG results but disclosed a negative IgA-EMA test. Jejunal biopsy of these five children revealed characteristic lesions of celiac disease. CONCLUSION A prevalence of 2.3% was found among symptomatic 12- to 36-month-old children that had not been previously diagnosed as celiac.
Genetic Structure of the Tree Peony (Paeonia rockii) and the Qinling Mountains as a Geographic Barrier Driving the Fragmentation of a Large Population

Background Tree peonies are great ornamental plants associated with a rich ethnobotanical history in Chinese culture and have recently been used as an evolutionary model. The Qinling Mountains represent a significant geographic barrier in Asia, dividing mainland China into northern (temperate) and southern (semi–tropical) regions; however, their flora has not been well analyzed. In this study, the genetic differentiation and genetic structure of Paeonia rockii and the role of the Qinling Mountains as a barrier that has driven intraspecific fragmentation were evaluated using 14 microsatellite markers. Methodology/Principal Findings Twenty wild populations were sampled from the distributional range of P. rockii. Significant population differentiation was suggested (FST value of 0.302). Moderate genetic diversity at the population level (HS of 0.516) and high population diversity at the species level (HT of 0.749) were detected. Significant excess homozygosity (FIS of 0.076) and recent population bottlenecks were detected in three populations. Bayesian clusters, population genetic trees and principal coordinate analysis all classified the P. rockii populations into three genetic groups and one admixed Wenxian population. An isolation-by-distance model for P. rockii was suggested by Mantel tests (r = 0.6074, P<0.001) and supported by AMOVA (P<0.001), revealing a significant molecular variance among the groups (11.32%) and their populations (21.22%). These data support the five geographic boundaries surrounding the Qinling Mountains and adjacent areas that were detected with Monmonier's maximum-difference algorithm. Conclusions/Significance Our data suggest that the current genetic structure of P. rockii has resulted from the fragmentation of a formerly continuously distributed large population following the restriction of gene flow between populations of this species by the Qinling Mountains. This study provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of this species and for improving the genetic basis for breeding its cultivars.
Osteogenic potential of adipogenic predifferentiated human bone marrow‐derived multipotent stromal cells for bone tissue‐engineering

In the present study, we evaluated the benefits of an adipogenic predifferentiation, the pathway most closely related to osteoblastogenesis, on the pro‐osteogenic potential of human adult multipotent bone marrow stromal cells (hBMSCs), both in vitro and in vivo. Adipogenic differentiation of hBMSCs for 14 days resulted in a heterogeneous cell population from which the most adipogenic‐committed cells were eliminated by their lack of readhesion ability. Our results provided evidence that the select adherent adipogenic differentiated hBMSCs (sAD+ cells) express a gene profile characteristic of both adipogenic and osteogenic lineages. In vitro, when cultured in osteogenic medium, sAD+ differentiated along the osteogenic lineage faster than undifferentiated hBMSCs. In vivo, in an ectopic mouse model, sAD+ exhibited a significantly higher bone formation capability compared with undifferentiated hBMSCs. We sought, then, to investigate the underlying mechanisms responsible for such beneficial effects of adipogenic predifferentiation on bone formation and found that this outcome was not linked to a better cell survival post‐implantation. The secretome of sAD+ was both proangiogenic and chemoattractant, but its potential did not supersede the one of undifferentiated hBMSCs. However, using co‐culture systems, we observed that the sAD+ paracrine factors were pro‐osteogenic on undifferentiated hBMSCs. In conclusion, adipogenic priming endows hBMSCs with high osteogenic potential as well as pro‐osteogenic paracrine‐mediated activity. This preconditioning appears as a promising strategy for bone tissue engineering technology in order to improve the hBMSC osteogenic potency in vivo.
Moved to Opportunity: The Long-Run Effect of Public Housing Demolition on Labor Market Outcomes of Children

This paper provides new evidence on the effects of moving out of disadvantaged neighborhoods on the long-run economic outcomes of children. My empirical strategy is based on public housing demolitions in Chicago which forced households to relocate to private market housing using vouchers. Specifically, I compare adult outcomes of children displaced by demolition to their peers who lived in nearby public housing that was not demolished. Displaced children are 9 percent more likely to be employed and earn 16 percent more as adults. These results contrast with the Moving to Opportunity (MTO) relocation study, which detected effects only for children who were young when their families moved. To explore this discrepancy, this paper also examines a housing voucher lottery program (similar to MTO) conducted in Chicago. I find no measurable impact on labor market outcomes for children in households that won vouchers. The contrast between the lottery and demolition estimates remains even after re-weighting the demolition sample to adjust for differences in observed characteristics. Overall, this evidence suggests lottery volunteers are negatively selected on the magnitude of their children’s gains from relocation. This implies that moving from disadvantaged neighborhoods may have substantially larger impact on children than what is suggested by results from voucher experiments where parents elect to participate. JEL Classification: I38, J18, J38.
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

Summary: Structural and physiochemical descriptors extracted from sequence data have been widely used to represent sequences and predict structural, functional, expression and interaction profiles of proteins and peptides as well as DNAs/RNAs. Here, we present iFeature, a versatile Python‐based toolkit for generating various numerical feature representation schemes for both protein and peptide sequences. iFeature is capable of calculating and extracting a comprehensive spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. It also allows users to extract specific amino acid properties from the AAindex database. Furthermore, iFeature integrates 12 different types of commonly used feature clustering, selection and dimensionality reduction algorithms, greatly facilitating training, analysis and benchmarking of machine‐learning models. The functionality of iFeature is made freely available via an online web server and a stand‐alone toolkit. Availability and implementation: http://iFeature.erc. monash.edu/; https://github.com/Superzchen/iFeature/. Supplementary information: Supplementary data are available at Bioinformatics online.
Anatomical and Physiological Plasticity in Leymus chinensis (Poaceae) along Large-Scale Longitudinal Gradient in Northeast China

Background Although it has been widely accepted that global changes will pose the most important constrains to plant survival and distribution, our knowledge of the adaptive mechanism for plant with large-scale environmental changes (e.g. drought and high temperature) remains limited. Methodology/Principal findings An experiment was conducted to examine anatomical and physiological plasticity in Leymus chinensis along a large-scale geographical gradient from 115° to 124°E in northeast China. Ten sites selected for plant sampling at the gradient have approximately theoretical radiation, but differ in precipitation and elevation. The significantly increasing in leaf thickness, leaf mass per area, vessel and vascular diameters, and decreasing in stoma density and stoma index exhibited more obvious xerophil-liked traits for the species from the moist meadow grassland sites in contrast to that from the dry steppe and desert sites. Significant increase in proline and soluble sugar accumulation, K+/Na+ for the species with the increasing of stresses along the gradient showed that osmotic adjustment was enhanced. Conclusion/Significance Obvious xerophytic anatomical traits and stronger osmotic adjustment in stress conditions suggested that the plants have much more anatomical and physiological flexibilities than those in non-stress habitats along the large-scale gradient.
Activating mutations in the ABCC8 gene in neonatal diabetes mellitus.

BACKGROUND The ATP-sensitive potassium (K(ATP)) channel, composed of the beta-cell proteins sulfonylurea receptor (SUR1) and inward-rectifying potassium channel subunit Kir6.2, is a key regulator of insulin release. It is inhibited by the binding of adenine nucleotides to subunit Kir6.2, which closes the channel, and activated by nucleotide binding or hydrolysis on SUR1, which opens the channel. The balance of these opposing actions determines the low open-channel probability, P(O), which controls the excitability of pancreatic beta cells. We hypothesized that activating mutations in ABCC8, which encodes SUR1, cause neonatal diabetes. METHODS We screened the 39 exons of ABCC8 in 34 patients with permanent or transient neonatal diabetes of unknown origin. We assayed the electrophysiologic activity of mutant and wild-type K(ATP) channels. RESULTS We identified seven missense mutations in nine patients. Four mutations were familial and showed vertical transmission with neonatal and adult-onset diabetes; the remaining mutations were not transmitted and not found in more than 300 patients without diabetes or with early-onset diabetes of similar genetic background. Mutant channels in intact cells and in physiologic concentrations of magnesium ATP had a markedly higher P(O) than did wild-type channels. These overactive channels remained sensitive to sulfonylurea, and treatment with sulfonylureas resulted in euglycemia. CONCLUSIONS Dominant mutations in ABCC8 accounted for 12 percent of cases of neonatal diabetes in the study group. Diabetes results from a newly discovered mechanism whereby the basal magnesium-nucleotide-dependent stimulatory action of SUR1 on the Kir pore is elevated and blockade by sulfonylureas is preserved.
Reproductive Ecology and Severe Pollen Limitation in the Polychromic Tundra Plant, Parrya nudicaulis (Brassicaceae)

Pollen limitation is predicted to be particularly severe in tundra habitats. Numerous reproductive patterns associated with alpine and arctic species, particularly mechanisms associated with reproductive assurance, are suggested to be driven by high levels of pollen limitation. We studied the reproductive ecology of Parrya nudicaulis, a species with relatively large sexual reproductive investment and a wide range of floral pigmentation, in tundra habitats in interior montane Alaska to estimate the degree of pollen limitation. The plants are self-compatible and strongly protandrous, setting almost no seed in the absence of pollinators. Supplemental hand pollinations within pollinator exclusion cages indicated no cage effect on seed production. Floral visitation rates were low in both years of study and particularly infrequent in 2010. A diversity of insects visited P. nudicaulis, though syrphid and muscid flies composed the majority of all visits. Pollen-ovule ratios and levels of heterozygosity are consistent with a mixed mating system. Pollen limitation was severe; hand pollinations increased seed production per plant five-fold. Seed-to-ovule ratios remained low following hand pollinations, indicating resource limitation is likely to also be responsible for curtailing seed set. We suggest that pollen limitation in P. nudicaulis may be the result of selection favoring an overproduction of ovules as a bet-hedging strategy in this environmental context of highly variable pollen receipt.
Electrical Properties Tomography Based on B1 Maps in MRI: Principles, Applications and Challenges

<italic>Objective:</italic> The purpose is to provide a comprehensive review of the electrical properties tomography (EPT) technique, which was introduced to image the electrical properties (EPs) of tissue noninvasively by exploiting the measured <inline-formula><tex-math notation="LaTeX">$B_{{1}}$</tex-math></inline-formula> field data of MRI. <italic>Methods</italic>: We reviewed the principle of EPT, reconstruction methods, biomedical applications such as tumor imaging, and existing challenges. As a key application of EPT, the estimation of specific absorption rate (SAR) due to MRI was discussed in the background of elevated risk of tissue heating at high field. <italic>Results and Conclusion</italic>: Since the originally proposed local, homogeneous Helmholtz equation-based reconstruction algorithm, advanced EPT algorithms have emerged to address the challenges of EPT, including reconstruction error near tissue boundaries, noise sensitivity, inaccurate <inline-formula><tex-math notation="LaTeX">$B_{{1}}$</tex-math> </inline-formula> phase estimation, and elimination of the unmeasurable <inline-formula><tex-math notation="LaTeX"> $B_{{\rm{z}}}$</tex-math></inline-formula> component, along with demonstrations of <italic>in vivo</italic> experiments. EPT techniques have been applied to investigate EPs of both healthy and pathological tissues <italic>in vivo</italic> and factors contributing to various EP value, including sodium, water content, etc. More studies are anticipated to consolidate the current findings. EPT-based subject-specific SAR estimation has led to <italic>in vivo </italic> demonstration of its feasibility and prediction of temperature increase of phantom during MRI scans merely using measured <inline-formula><tex-math notation="LaTeX">$B_{{1}}$</tex-math></inline-formula> data. <italic> Significance</italic>: EPT has the advantage of high resolution and practical feasibility in a clinical setup for imaging the biomedically interesting EPs of tissue in the radiofrequency range. EPT-based SAR estimation is another promising topic for predicting tissue heating of individual subjects during a specific MRI scan.