Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance of Akaike Information Criterion and Bayesian Information Criterion in Selecting Partition Models and Mixture Models

Abstract In molecular phylogenetics, partition models and mixture models provide different approaches to accommodating heterogeneity in genomic sequencing data. Both types of models generally give a superior fit to data than models that assume the process of sequence evolution is homogeneous across sites and lineages. The Akaike Information Criterion (AIC), an estimator of Kullback–Leibler divergence, and the Bayesian Information Criterion (BIC) are popular tools to select models in phylogenetics. Recent work suggests that AIC should not be used for comparing mixture and partition models. In this work, we clarify that this difficulty is not fully explained by AIC misestimating the Kullback–Leibler divergence. We also investigate the performance of the AIC and BIC at comparing amongst mixture models and amongst partition models. We find that under nonstandard conditions (i.e. when some edges have small expected number of changes), AIC underestimates the expected Kullback–Leibler divergence. Under such conditions, AIC preferred the complex mixture models and BIC preferred the simpler mixture models. The mixture models selected by AIC had a better performance in estimating the edge length, while the simpler models selected by BIC performed better in estimating the base frequencies and substitution rate parameters. In contrast, AIC and BIC both prefer simpler partition models over more complex partition models under nonstandard conditions, despite the fact that the more complex partition model was the generating model. We also investigated how mispartitioning (i.e., grouping sites that have not evolved under the same process) affects both the performance of partition models compared with mixture models and the model selection process. We found that as the level of mispartitioning increases, the bias of AIC in estimating the expected Kullback–Leibler divergence remains the same, and the branch lengths and evolutionary parameters estimated by partition models become less accurate. We recommend that researchers are cautious when using AIC and BIC to select among partition and mixture models; other alternatives, such as cross-validation and bootstrapping, should be explored, but may suffer similar limitations [AIC; BIC; mispartitioning; partitioning; partition model; mixture model].
Parental Narcissism Leads to Anxiety and Depression in Children via Scapegoating

Abstract The clinical literature on narcissistic families has often described the presence of a family scapegoat. To date, however, no research has empirically explored this phenomenon. This study investigated the relationship between perceived parental vulnerable and grandiose narcissism and scapegoating, and the impact of these on the symptoms of anxiety and depression in emerging adults, in a sample of 504 Australian adults (M age = 22.38, SD age = 3.63; 59.72% female, 38.09% male). A path model was tested, with perceived parental vulnerable and grandiose narcissism as predictors, scapegoating as a mediator, and participants’ anxiety and depression as outcomes, controlling for demographic variables and participants’ vulnerable and grandiose narcissism. Results indicated that higher perceived paternal grandiose narcissism had a direct effect on anxiety and depression, whereas perceived maternal vulnerable narcissism, perceived paternal vulnerable narcissism, and perceived maternal grandiose narcissism had indirect effects on anxiety and depression via scapegoating. Effect sizes were generally small to medium. These findings show that scapegoating is an important variable linking parental narcissism with negative psychological outcomes such as anxiety and depression in emerging adults.
Wall shear stress–related plaque growth of lipid-rich plaques in human coronary arteries: an near-infrared spectroscopy and optical coherence tomography study

Abstract Aims Low wall shear stress (WSS) is acknowledged to play a role in plaque development through its influence on local endothelial function. Also, lipid-rich plaques (LRPs) are associated with endothelial dysfunction. However, little is known about the interplay between WSS and the presence of lipids with respect to plaque progression. Therefore, we aimed to study the differences in WSS-related plaque progression between LRPs, non-LRPs, or plaque-free regions in human coronary arteries. Methods and results In the present single-centre, prospective study, 40 patients who presented with an acute coronary syndrome successfully underwent near-infrared spectroscopy intravascular ultrasound (NIRS-IVUS) and optical coherence tomography (OCT) of at least one non-culprit vessel at baseline and completed a 1-year follow-up. WSS was computed applying computational fluid dynamics to a three-dimensional reconstruction of the coronary artery based on the fusion of the IVUS-segmented lumen with a CT-derived centreline, using invasive flow measurements as boundary conditions. For data analysis, each artery was divided into 1.5 mm/45° sectors. Plaque growth based on IVUS-derived percentage atheroma volume change was compared between LRPs, non-LRPs, and plaque-free wall segments, as assessed by both OCT and NIRS. Both NIRS- and OCT-detected lipid-rich sectors showed a significantly higher plaque progression than non-LRPs or plaque-free regions. Exposure to low WSS was associated with a higher plaque progression than exposure to mid or high WSS, even in the regions classified as a plaque-free wall. Furthermore, low WSS and the presence of lipids had a synergistic effect on plaque growth, resulting in the highest plaque progression in lipid-rich regions exposed to low shear stress. Conclusion This study demonstrates that NIRS- and OCT-detected lipid-rich regions exposed to low WSS are subject to enhanced plaque growth over a 1-year follow-up. The presence of lipids and low WSS proves to have a synergistic effect on plaque growth.
Optimal and Suboptimal Algorithms for the Quadratic Assignment Problem

A recent article by Steinberg [6] describes a suboptimal procedure for solving what he calls the backboard wiring problem. This problem in the more general form in which it was discussed by Koopmans and Beckmann [2] was called the quadratic assignment problem. Their generalization consists in minimizing not just a backboard wire sum but the sum of a backboard wire sum and a sum for an ordinary assignment problem. ' In the notation of [6], assuming as we may without loss that r = n, the problem becomes: given any n X n matrix A and any n X n matrices C and D for which cii = dii = 0 1 < i _ n, find a permutation p of 1, 2, n for which L(p), where
Ensemble averaging: What can we learn from skewed feature distributions?

Many studies have shown that observers can accurately estimate the average feature of a group of objects. However, the way the visual system relies on the information from each individual item is still under debate. Some models suggest some or all items sampled and averaged arithmetically. Another strategy implies “robust averaging,” when middle elements gain greater weight than outliers. One version of a robust averaging model was recently suggested by Teng et al. (2021), who studied motion direction averaging in skewed feature distributions and found systematic biases toward their modes. They interpreted these biases as evidence for robust averaging and suggested a probabilistic weighting model based on minimization of the virtual loss function. In four experiments, we replicated systematic skew-related biases in another feature domain, namely, orientation averaging. Importantly, we show that the magnitude of the bias is not determined by the locations of the mean or mode alone, but is substantially defined by the shape of the whole feature distribution. We test a model that accounts for such distribution-dependent biases and robust averaging in a biologically plausible way. The model is based on well-established mechanisms of spatial pooling and population encoding of local features by neurons with large receptive fields. Both the loss functions model and the population coding model with a winner-take-all decoding rule accurately predicted the observed patterns, suggesting that the pooled population response model can be considered a neural implementation of the computational algorithms of information sampling and robust averaging in ensemble perception.
Inference on the Order of a Normal Mixture

Finite normal mixture models are used in a wide range of applications. Hypothesis testing on the order of the normal mixture is an important yet unsolved problem. Existing procedures often lack a rigorous theoretical foundation. Many are also hard to implement numerically. In this article, we develop a new method to fill the void in this important area. An effective expectation-maximization (EM) test is invented for testing the null hypothesis of arbitrary order m 0 under a finite normal mixture model. For any positive integer m 0 ⩾ 2, the limiting distribution of the proposed test statistic is . We also use a novel computer experiment to provide empirical formulas for the tuning parameter selection. The finite sample performance of the test is examined through simulation studies. Real-data examples are provided. The procedure has been implemented in R code. The p-values for testing the null order of m 0 = 2 or m 0 = 3 can be calculated with a single command. This article has supplementary materials available online.
Toxoplasma gondii Exposure Prevalence in Little Spotted Kiwi (Apteryx owenii)

Abstract: Toxoplasma gondii has been reported as a cause of morbidity and mortality in New Zealand's native avifauna, including the ground-dwelling Kiwi (Apteryx spp.). To better understand the extent of T. gondii infection in Little Spotted Kiwi (Apteryx owenii), a prevalence survey of kiwi living inside a 200-ha predator-proof mainland ecosanctuary (Zealandia Te Māra a Tāne, Wellington, New Zealand) was undertaken. Antibodies to T. gondii were detected by a latex agglutination test (LAT) with a cutoff positive titer of ≥1:64, and T. gondii DNA was detected by PCR. In total, 16/19 (84.2%) birds tested were positive for T. gondii by LAT (10/11), PCR (10/19), or both (4/11). Antibody titers ranged from 1:32 to ≥1:2,048. These results suggest widespread exposure of T. gondii in this population of Little Spotted Kiwi and, in conjunction with earlier reports of toxoplasmosis causing mortality in kiwi, raise important questions as to the effect this parasite may be having on this rare endemic species. Further information on the epidemiology of T. gondii infections within free-living and managed kiwi populations is urgently needed.
Palliative Care in Patients With Hematological Malignancies. We Have a Long Way to Go…

Background: Patients with hematological malignancies have significant and diverse palliative care needs but are not usually referred to specialist palliative care services in a timely manner, if at all. Objective: To identify the characteristics of patients with hematological malignancies referred to the palliative care service in a tertiary hospital in Mexico City. Patients: Retrospective study including consecutive patients with hematological malignancies referred to palliative care services at Mexico’s National Cancer Institute. Results: Between 2011 and 2019, 5,017 patients with hematological malignancies were evaluated for first time at Mexico’s National Cancer Institute. Of these, 9.1% (n = 457) were referred to palliative care. Most were male (53.4%), with a median age of 58 years. The most frequent diagnosis was non-Hodgkin lymphoma (54.9%). The primary indication for referral to palliative care was for cases wherein chemotherapy was no longer an option (disease refractory to treatment, 42.8%). The median time of referral to the palliative care service occurred 11.2 months after the first evaluation at the National Cancer Institute and death occurred on median 1.1 months after the first palliative care evaluation. Conclusion: Patients with hematological neoplasms are infrequently referred to Palliative Care at the Institute (9.1%). We found no clear referral criteria for Palliative Care referral and note that hematologists’ optimism regarding a cure can delay referrals. Clearly, we have a long way to go in improving the number of patients referred, and we still saw frequent referrals near the end of life, but the high rate of outpatient referrals is encouraging.
Radio frequency discharge modeling: Moment equations approach

A fluid model based on the three moments of the Boltzmann equation is presented to study rf discharges. With rate constants obtained from a zero‐dimensional Boltzmann equation solver, the model is shown to reproduce excitation wave forms seen in experiments. Several other critical features previously reported by particle‐in‐cell simulations such as mechanisms of heating and relation between electron power deposition and ionization have also been reproduced. A parametric study for a 13.56‐MHz argon discharge with varying rf bias and pressure has been used to derive scaling laws for the discharge.
Far-infrared and submillimeter-wavelength observations of star-forming dense cores. I. Spectra

Far-infrared and submillimeter photometry of 10 low-mass star formation regions containing embedded IRAS sources is presented. These new observations define the peak of the spectral energy distributions of these objects and provide more precise estimates of their bolometric luminosities. Two new sources, L1527 and L483, are among the reddest known low-mass objects, with spectral energy distribution peaks at 100-200 microns and extremely steep IRAS slopes. These cold sources have spectra which are similar to blackbodies of 30-40 K but have significant excess emission on the Wien side. Models of the spectral energy distributions using a spherically symmetric core structure indicate that these sources have visual extinctions greater than 1000 mag. However, models with these large extinctions predict too little near-infrared emission. A nonspherically symmetric distribution of circumstellar material may play a role in the generation of the extra near-infrared emission. 64 refs.
Imaging spectrophotometry of ionized gas in NGC 1068. I - Kinematics of the narrow-line region

The kinematics of collisionally excited forbidden N II 6548, 6583 across the inner 1 arcmin diameter of the nearby Seyfert galaxy NGC 1068 is mapped using an imaging Fabry-Perot interferometer and low-noise CCD. The stack of monochromatic images, which spatially resolved the high-velocity gas, was analyzed for kinematic and photometric content. Profiles agree well with previous long-slit work, and their complete spatial coverage makes it possible to constrain the gas volume distribution. It is found that the narrow-line region is distributed in a thick center-darkened, line-emitting cylinder that envelopes the collimated radio jet. Three distinct kinematic subsystems, of which the cylinder is composed, are discussed in detail. Detailed behavior of the emission-line profiles, at the few points in the NE quadrant with simple kinematics, argues that the ionized gas develops a significant component of motion perpendicular to the jet axis. 67 refs.
Therapy with pembrolizumab in treatment‐naïve patients with nonmetastatic, mismatch repair deficient colorectal cancer

Therapy with immune checkpoint inhibitors (ICI) is effective in patients with metastatic mismatch‐repair deficient (dMMR) colorectal cancer (CRC); however, data on treatment with neoadjuvant ICI in patients with locally advanced CRC are limited. From March 2019 to June 2020, five Danish oncological centers treated 10 patients with a treatment‐naïve dMMR CRC with preoperative pembrolizumab, 9 with a nonmetastatic, unresectable colon cancer and 1 with a locally advanced rectum cancer. All 10 patients were evaluated regularly at a multidisciplinary team (MDT) meeting, and they all had a radical resection after a median of 8 cycles (range 2‐13) of pembrolizumab. A microscopic evaluation of the resected tumors revealed no remaining tumor cells in five patients, while five still had tumor cells present. The patients were given no additional therapy. No recurrences were reported after a median follow‐up of 26 months (range 23‐38.5 months). Biopsies from Danish patients with CRC are routinely screened for dMMR proteins. In 2017, data from the Danish Colorectal Cancer Group showed that 19% (565/3000) of the patients with colon cancer and 1.5% (19/1279) of those with rectum cancer had an dMMR tumor. Among the patients with MMR determination, 26% (99/384) patients had a T4 dMMR colon cancer; thus, the 10 patients treated with neoadjuvant pembrolizumab comprised about 9% of the patients with a T4 dMMR colon cancer (9/99) and 5% of patients with dMMR rectal cancer (1/19). Therapy with pembrolizumab was feasible and effective. Larger prospective trials are needed to confirm our findings.
Nanoparticle-containing lyophilized dry powder inhaler formulations optimized using central composite design with improved aerodynamic parameters and redispersibility

Abstract Objectives: The aim of this study was to improve the aerodynamic behavior and redispersibility of a lyophilized dry powder inhaler (DPI) formulation containing nanoparticles. Methods: Paclitaxel (PTX)-human serum albumin (HSA) nanoparticles were used as a model, and DPIs containing the nanoparticles were produced by lyophilization using different carriers and carrier ratios. A central composite design was employed to optimize the formulation. L-leucine and mannitol were chosen as independent variables, and mass median aerodynamic diameter (MMAD), emitted fraction, fine particle fraction (FPF), nanoparticle size, polydispersity index (PDI), zeta potential were selected as dependent variables. Results: The water content of DPIs was less than 5% for all DPIs. The cytotoxicity of the DPIs, determined using A549 cells, was due to PTX alone. Particle sizes of 204.3 ± 1.65 nm and 94.3–1353.0 nm were obtained before and after lyophilization, respectively. The developed method resulted in a reduction in the MMAD from 8.148 µm to 5.274 µm, an increase in the FPF from 17.63% to 33.60%, and an increase in the emitted fraction from 77.68% to 97.03%. The physico-chemical characteristics of the optimized formulation were also assessed. Conclusions: In conclusion, this study demonstrates that lyophilization can be used to produce nanoparticle-containing DPI formulations with improved redispersibility and aerodynamic properties. Graphical Abstract
Bilateral radiation retinopathy 17 years following radiotherapy for nasopharyngeal carcinoma: A diagnostic and therapeutic challenge during COVID-19 lockdown

A 40-year-old male presented with reduced vision in the right eye for one week. He had a history of nasopharyngeal carcinoma for which 34-Gy radiation was administered. The best-corrected visual acuity (BCVA) was 20/40 in the right eye and 20/20 in the left eye. Anterior segment examination suggested a bilateral early posterior subcapsular cataract. Fundoscopy revealed bilateral localized telangiectasia and macular edema in the right eye. Diagnosis of bilateral extremely delayed onset radiation retinopathy with right eye macular edema was made. Three doses of intravitreal bevacizumab injection were administered in the right eye. The patient was lost to follow-up due to COVID-19 and presented with recurrence.
Information Fusion Based Decoupling Control for Multivariable Nonlinear System

A decoupling control method based on information fusion estimation for a nonlinear system is presented in the paper. For each main channel and its coupled channels of the system, according to the information fusion theorem, the estimation of the system future state is obtained by fusing the information of the desired output trajectory of the system. Furthermore, approximate optimal control rule is obtained by fusing the system future state information and the control energy soft constraint information. Then an information fusion based decoupling control (IFBDC) system is established for the nonlinear coupled multiple-input multiple-output systems. This system cannot only control every channel to track reference signals, but also control any channel to be decoupled with other channels. Finally, a robot manipulator system is given to investigate the effectiveness of the decoupling control strategy, analyze its key parameters, and analyze the computational cost. The simulation results show that the IFBDC method is characterized by adjustable decoupling degree and high control quality.
Overflow characteristics of circular-crested weirs

Circular-crested weirs are one of simplest types of hydraulic structures used for discharge measurement and regulation of open channel flow. In the present study, the flow over a circular-crested weir was simulated with an irrotational vortex to determine the weir discharge coefficient and velocity values over the crest. Two dimensionless parameters including circulation and curvature coefficient were defined and determined experimentally. The results show that these parameters could be presented by power equations. To develop and evaluate the proposed method, physical models of circular-crested weirs, containing various radii, heights and slopes, were investigated. It was found that this method produces the main features of weir flow reasonably well.
Complete mitochondrial genome of Macromia manchurica Asahina, 1964 (Odonata: Macromiidae)

Abstract We describe the first time sequencing and assembly of the complete mitochondrial genome of Macromia manchurica Asahina, 1964 (Odonata; Macromiidae; Macromia). The mitochondrial genome of M. manchurica was found to be 15,560 bp. It contains thirteen protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and AT-rich region. The overall base composition of A. japonicus is A-38.6%, C-17.0%, G-12.5%, and T-31.9%. A phylogenetic analysis of 14 species within the order Odonata and order Ephemeroptera suggested that Macromia amphigena is most closely related to M. manchurica.
Decreased DNA Damage and Improved p53 Specificity of RITA Analogs

Abstract Reactivation of p53 tumor-suppressor function by small molecules is an attractive strategy to defeat cancer. A potent p53-reactivating molecule RITA, which triggers p53-dependent apoptosis in human tumor cells in vitro and in vivo, exhibits p53-independent cytotoxicity due to modifications by detoxification enzyme Sulfotransferase 1A1 (SULT1A1), producing a reactive carbocation. Several synthetic modifications to RITA's heterocyclic scaffold lead to higher energy barriers for carbocation formation. In this study, we addressed the question whether RITA analogs NSC777196 and NSC782846 can induce p53-dependent apoptosis without SULT1A1-dependent DNA damage. We found that RITA analog NSC782846, but not NSC777196, induced p53-regulated genes, targeted oncogene addiction, and killed cancer cells upon p53 reactivation, but without induction of DNA damage and inhibition RNA pol II. Our results might demonstrate a method for designing more specific and potent RITA analogs to accelerate translation of p53-targeting compounds from laboratory bench to clinic.