Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-scale analyses of angiosperm Flowering Locus T genes reveal duplication and functional divergence in monocots

FLOWERING LOCUS T (FT) are well-known key genes for initiating flowering in plants. Delineating the evolutionary history and functional diversity of FT genes is important for understanding the diversification of flowering time and how plants adapt to the changing surroundings. We performed a comprehensive phylogenetic analysis of FT genes in 47 sequenced flowering plants and the 1,000 Plant Transcriptomes (1KP) database with a focus on monocots, especially cereals. We revealed the evolutionary history of FT genes. The FT genes in monocots can be divided into three clades (I, II, and III), whereas only one monophyletic group was detected in early angiosperms, magnoliids, and eudicots. Multiple rounds of whole-genome duplications (WGD) events followed by gene retention contributed to the expansion and variation of FT genes in monocots. Amino acid sites in the clade II and III genes were preferentially under high positive selection, and some sites located in vital domain regions are known to change functions when mutated. Clade II and clade III genes exhibited high variability in important regions and functional divergence compared with clade I genes; thus, clade I is more conserved than clade II and III. Genes in clade I displayed higher expression levels in studied organs and tissues than the clade II and III genes. The co-expression modules showed that some of the FT genes might have experienced neofunctionalization and subfunctionalization, such as the acquisition of environmental resistance. Overall, FT genes in monocots might form three clades by the ancient gene duplication, and each clade was subsequently subjected to different selection pressures and amino acid substitutions, which eventually led to different expression patterns and functional diversification. Our study provides a global picture of FT genes’ evolution in monocots, paving a road for investigating FT genes’ function in future.
How does goal framing effect influence household low-carbon behavior: The roles of environmental self-efficacy and global–local identity

Introduction: Compared to carbon emission reduction from production, reduction from households is more required. This study explores the mechanism and boundary conditions of the effect of goal framing on household low-carbon behavior by drawing on the framing effect and social cognitive theory. The central questions posed in this research are whether, how, and under what circumstances goal framing affects household low-carbon behavior. Methods: We tested the hypotheses in two studies. Study 1 investigated the main effect of whether the framing effect of climate change has a different influence on household low-carbon behavior. Study 2 further confirmed the main effect of this study and verified the mediating role of environmental self-efficacy and the moderating role of global–local identity. Results: Across two experiments, we discovers: 1) Goal framing of climate change messages affects household low-carbon behavior. In particular, loss framing elicits a greater persuasive impact on household low-carbon behavior than gain framing. 2) Environmental self-efficacy plays a mediating role between the framing effect and household low-carbon behavior. Specifically, loss framing of climate change messages is more likely to increase residents' environmental self-efficacy than gain framing, which increases their household low-carbon behavior. 3) Residents' global-local identity moderates the effect of the framing messages on household low-carbon behavior. Among residents with a local identity, loss framing has a more powerful influence on household low-carbon behavior compared to gain framing. Among residents with a global identity, a significant difference between the effects of loss and gain framing on household low-carbon behavior is not found. Discussion: The theoretical and managerial implications of the study are also discussed.
LGBMDF: A cascade forest framework with LightGBM for predicting drug-target interactions

Prediction of drug-target interactions (DTIs) plays an important role in drug development. However, traditional laboratory methods to determine DTIs require a lot of time and capital costs. In recent years, many studies have shown that using machine learning methods to predict DTIs can speed up the drug development process and reduce capital costs. An excellent DTI prediction method should have both high prediction accuracy and low computational cost. In this study, we noticed that the previous research based on deep forests used XGBoost as the estimator in the cascade, we applied LightGBM instead of XGBoost to the cascade forest as the estimator, then the estimator group was determined experimentally as three LightGBMs and three ExtraTrees, this new model is called LGBMDF. We conducted 5-fold cross-validation on LGBMDF and other state-of-the-art methods using the same dataset, and compared their Sn, Sp, MCC, AUC and AUPR. Finally, we found that our method has better performance and faster calculation speed.
Negative regulation of floral transition in Arabidopsis by HOS15-PWR-HDA9 complex

Arabidopsis HOS15/PWR/HDA9 repressor complex, which is similar to the TBL1/NcoR1/HDAC complex in animals, plays a well-known role in epigenetic regulation. PWR and HDA9 have been reported to interact with each other and modulate the flowering time by repressing AGL19 expression, whereas HOS15 and HDA9, together with the photoperiodic evening complex, regulate flowering time through repression of GI transcription. However, the role of the HOS15/PWR/HDA9 core repressor complex as a functional unit in the regulation of flowering time is yet to be explored. In this study, we reported that the loss-of-function hos15-2/pwr/hda9 triple mutant accumulates higher transcript levels of AGL19 and exhibits an early flowering phenotype similar to those of hos15, pwr, and hda9 single mutants. Interestingly, the accumulation of HOS15 in the nucleus was drastically reduced in pwr and hda9 mutants. As a result, HOS15 could not perform its role in histone deacetylation or interaction with H3 in the nucleus. Furthermore, HOS15 is also associated with the same region of the AGL19 promoter known for PWR-HDA9 binding. The acetylation level of the AGL19 promoter was increased in the hos15-2 mutant, similar to the pwr and hda9 mutants. Therefore, our findings reveal that the HOS15/PWR/HDA9 repressor complex deacetylates the promoter region of AGL19, thereby negatively regulating AGL19 transcription, which leads to early flowering in Arabidopsis.
Investigating the diagnostic efficiency of a computer-aided diagnosis system for thyroid nodules in the context of Hashimoto’s thyroiditis

Objectives This study aims to investigate the efficacy of a computer-aided diagnosis (CAD) system in distinguishing between benign and malignant thyroid nodules in the context of Hashimoto’s thyroiditis (HT) and to evaluate the role of the CAD system in reducing unnecessary biopsies of benign lesions. Methods We included a total of 137 nodules from 137 consecutive patients (mean age, 43.5 ± 11.8 years) who were histopathologically diagnosed with HT. The two-dimensional ultrasound images and videos of all thyroid nodules were analyzed by the CAD system and two radiologists with different experiences according to ACR TI-RADS. The diagnostic cutoff values of ACR TI-RADS were divided into two categories (TR4 and TR5), and then the sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) of the CAD system and the junior and senior radiologists were compared in both cases. Moreover, ACR TI-RADS classification was revised according to the results of the CAD system, and the efficacy of recommended fine-needle aspiration (FNA) was evaluated by comparing the unnecessary biopsy rate and the malignant rate of punctured nodules. Results The accuracy, sensitivity, specificity, PPV, and NPV of the CAD system were 0.876, 0.905, 0.830, 0.894, and 0.846, respectively. With TR4 as the cutoff value, the AUCs of the CAD system and the junior and senior radiologists were 0.867, 0.628, and 0.722, respectively, and the CAD system had the highest AUC (P < 0.0001). With TR5 as the cutoff value, the AUCs of the CAD system and the junior and senior radiologists were 0.867, 0.654, and 0.812, respectively, and the CAD system had a higher AUC than the junior radiologist (P < 0.0001) but comparable to the senior radiologist (P = 0.0709). With the assistance of the CAD system, the number of TR4 nodules was decreased by both junior and senior radiologists, the malignant rate of punctured nodules increased by 30% and 22%, and the unnecessary biopsies of benign lesions were both reduced by nearly half. Conclusions The CAD system based on deep learning can improve the diagnostic performance of radiologists in identifying benign and malignant thyroid nodules in the context of Hashimoto’s thyroiditis and can play a role in FNA recommendations to reduce unnecessary biopsy rates.
Multisystem in ﬂ ammatory syndrome in children (MIS-C) and “ Near MIS-C ” : A continuum?

Conclusion: MIS-C presents a diagnostic challenge due to the nonspeci ﬁ c symptoms, lack of pathognomonic ﬁ ndings, and potentially fatal complications. More research is needed to fully understand its pathogenesis, clinical presentation spectrum, and diagnostic criteria. Based on our experience, we favor the hypothesis that MIS-C has a continuum of severity that necessitates revisiting and unifying the current de ﬁ nitions.
Frontal waves in a strait

The slow downstream (x) variation of a dense and inviscid bottom current (u) in a parabolic strait with a sill at y = 0 is investigated. Vanishing potential vorticity is assumed and the density interface in the 1 1/2-layer model intersects the bottom at y = y1 and y = y2 < y1, where the vanishing layer thickness (h) provides the free dynamical boundary condition. For time-dependent finite-amplitude waves, the nonlinear hyperbolic equations obtained here give the wave velocity and indicate the sense in which lateral wave steepening occurs. The long-wave perturbations of y1(x,t), y2(x,t) are stationary if $ \[ \frac{y_1 }{y_2 } = 1 - \frac{2}{1 + \sqrt {6{g}'\mu / f^2} } \] $ where g′ is the reduced gravity, μ = ∂2M/∂y2 is the parabolic curvature of the bottom elevation (M), and f is the Coriolis parameter. This controls the upstream–downstream flow, and the downstream nonlinearity generates ‘short’ waves which may initiate lateral mixing with the adjacent (less dense) water mass. It is also shown that short waves are exponentially amplified with a maximum growth rate (about 1/day) depending only on g′μ/f2. When g′μ/f2 = 1 (a narrow strait) the instability is suppressed, but for small g′μ/f2≪1 the growth rate is comparable to the flat bottom case μ = 0, studied by Griffiths, Killworth & Stern (J. Fluid Mech. Vol. 117, 1982, p. 343.).
A representation and classification method for collective investor attention in the financial market

Introduction: It is increasingly becoming integral to analyze the collected information effectively. Methods: We propose a representation and classification method for collective investor attention in the financial market, taking the Chinese stock market as an example. The method includes three key steps: 1) converting the hourly search volume of each stock per week to an image representation for describing the changes of collective investor attention; 2) extracting features of each image by utilizing a self-encoding algorithm in deep learning; and 3) clustering generated images by K-means to arrange stocks into different groups. Results: The empirical results show that the portfolio considering the clustering information outperforms the HS300 index. Discussion: The method may not only use deep learning features for stock similarity measurement, but also shed some light on profoundly understanding the mechanisms of the collective investor attention for the financial market.
The Poly I:C maternal immune stimulation model shows unique patterns of brain metabolism, morphometry, and plasticity in female rats

Introduction: Prenatal infections are associated with an increased risk of the onset of schizophrenia. Rodent models of maternal immune stimulation (MIS) have been extensively used in preclinical studies. However, many of these studies only include males, omitting pathophysiological features unique to females. The aim of this study is to characterize the MIS model in female rats using positron emission tomography (PET), structural magnetic resonance imaging (MR), and neuroplasticiy studies. Methods: In gestational day 15, Poly I:C (or Saline) was injected into pregnant Wistar rats to induce the MIS model. Imaging studies: [18F]-fluoro-2-deoxy-D-glucose-PET scans of female-offspring were acquired at post-natal day (PND) 35 and PND100. Furthermore, T2-MR brain images were acquired in adulthood. Differences in FDG uptake and morphometry between groups were assessed with SPM12 and Regions of Interest (ROI) analyses. Ex vivo study: The density of parvalbumin expressing interneurons (PV), perineuronal nets (PNN), and parvalbumin expressing interneurons surrounded by perineuronal nets (PV-PNN) were evaluated in the prelimbic cortex and basolateral amygdala using confocal microscopy. ROIs and neuroplasticity data were analyzed by 2-sample T-test and 2-way-ANOVA analyses, respectively. Results: A significant increase in brain metabolism was found in all animals at adulthood compared to adolescence. MIS hardly modified brain glucose metabolism in females, highlighting a significant hypometabolism in the thalamus at adulthood. In addition, MIS induced gray matter (GM) enlargements in the pituitary, hippocampus, substantia nigra, and cingulate cortex, and GM shrinkages in some thalamic nuclei, cerebelar areas, and brainstem. Moreover, MIS induced white matter shrinkages in the cerebellum, brainstem and corpus callosum, along with cerebrospinal fluid enlargements in the lateral and 4th ventricles. Finally, MIS reduced the density of PV, PNN, and PV-PNN in the basolateral amygdala. Conclusion: Our work showed in vivo the differential pattern of functional and morphometric affectation in the MIS model in females, as well as the deficits caused at the synaptic level according to sex. The differences obtained highlight the relevance of including both sexes in psychiatric research in order to consider their pathophysiological particularities and successfully extend the benefits obtained to the entire patient population.
Solar modulation of galactic cosmic rays.

The modulation of galactic protons and He nuclei during the last solar cycle is analyzed according to Parker's theory. The mechanism of modulation remains essentially the same during several years of low solar activity (1961–1965). The modulation near solar maximum (1959) implies that the scale sizes of the magnetic inhomogeneities in the solar wind are reduced below the values at solar minimum. An adequate description at solar maximum would require further refinements of the theory. The proton-to-He-nucleus ratio outside the solar system is shown to be consistent with the value ≈6, in a kinetic-energy/nucleon representation, for the interval 100–1000 Mev/nucleon.
Chromosome architecture and homologous recombination in meiosis

Meiocytes organize higher-order chromosome structures comprising arrays of chromatin loops organized at their bases by linear axes. As meiotic prophase progresses, the axes of homologous chromosomes align and synapse along their lengths to form ladder-like structures called synaptonemal complexes (SCs). The entire process of meiotic recombination, from initiation via programmed DNA double-strand breaks (DSBs) to completion of DSB repair with crossover or non-crossover outcomes, occurs in the context of chromosome axes and SCs. These meiosis-specific chromosome structures provide specialized environments for the regulation of DSB formation and crossing over. In this review, we summarize insights into the importance of chromosome architecture in the regulation of meiotic recombination, focusing on cohesin-mediated axis formation, DSB regulation via tethered loop-axis complexes, inter-homolog template bias facilitated by axial proteins, and crossover regulation in the context of the SCs. We also discuss emerging evidence that the SUMO and the ubiquitin-proteasome system function in the organization of chromosome structure and regulation of meiotic recombination.
Loneliness as a mediation from social support leading to a decrease of health-related quality of life among PLWHIV

This study focused on the mental health of people living with HIV(PLWHIV) and explored their relationship between loneliness and perceived social support, health related quality of life (HRQoL) with a method of structural equation model. We collected clinical and psychological data from consecutively enrolled PLWHIV. A total of 201 PLWHIVs were enrolled and measured with self-reporting survey instruments of UCLA Loneliness Scale, Self-Rating Depression Scale, Self-Rating Anxiety Scale, Social Support Ratio Scale and Short Form Health Survey-36. The levels of loneliness, depression, anxiety, perceived social support and HRQoL were assessed. PLWHIV enrolled were divided into two groups of loneliness and non-loneliness based on their UCLA Loneliness Scale scores. Multivariable analysis indicated that being married is a protective factor associated with loneliness (OR = 0.226; P = 0.032). We further found the loneliness group had a higher level of depression (P < 0.001) and anxiety (P < 0.001), but lower level of HRQoL (P < 0.001) than the non-loneliness group. We found there was a positive linear correlation between social support and HRQoL among the enrolled PLWHIVs (r2 = 0.0592; P = 0.0005). A structural equation model (SEM) was established to evaluate whether the loneliness played as a mediation role between social support and HRQoL. The model showed loneliness as a mediation from social support leading to a decrease of HRQoL. Our findings showed a potential psychological pathway from social support to HRQoL, suggesting the need for interventions focusing on social support may improve poor HRQoL lead by loneliness.
Association of sub-acute changes in plasma amino acid levels with long-term brain pathologies in a rat model of moderate-severe traumatic brain injury

Introduction Traumatic brain injury (TBI) induces a cascade of cellular alterations that are responsible for evolving secondary brain injuries. Changes in brain structure and function after TBI may occur in concert with dysbiosis and altered amino acid fermentation in the gut. Therefore, we hypothesized that subacute plasma amino acid levels could predict long-term microstructural outcomes as quantified using neurite orientation dispersion and density imaging (NODDI). Methods Fourteen 8–10-week-old male rats were randomly assigned either to sham (n = 6) or a single moderate-severe TBI (n = 8) procedure targeting the primary somatosensory cortex. Venous blood samples were collected at days one, three, seven, and 60 post-procedure and NODDI imaging were carried out at day 60. Principal Component Regression analysis was used to identify time dependent plasma amino acid concentrations after in the subacute phase post-injury that predicted NODDI metric outcomes at day 60. Results The TBI group had significantly increased plasma levels of glutamine, arginine, alanine, proline, tyrosine, valine, isoleucine, leucine, and phenylalanine at days three-seven post-injury. Higher levels of several neuroprotective amino acids, especially the branched-chain amino acids (valine, isoleucine, leucine) and phenylalanine, as well as serine, arginine, and asparagine at days three-seven post-injury were also associated with lower isotropic diffusion volume fraction measures in the ventricles and thus lesser ventricular dilation at day 60. Discussion In the first such study, we examined the relationship between the long-term post-TBI microstructural outcomes across whole brain and the subacute changes in plasma amino acid concentrations. At days three to seven post-injury, we observed that increased plasma levels of several amino acids, particularly the branched-chain amino acids and phenylalanine, were associated with lesser degrees of ventriculomegaly and hydrocephalus TBI neuropathology at day 60 post-injury. The results imply that altered amino acid fermentation in the gut may mediate neuroprotection in the aftermath of TBI.
How can applicants' reactions to scholastic aptitude tests be improved? A closer look at specific and general tests

Since the 1980's, scientific interest in applicants' reactions to admission procedures has been growing. Several theoretical frameworks and evaluation questionnaires were developed. Many researchers have asked potential participants about their attitudes—what is missing, however, are studies of applicants who have actually taken part in the selection procedures. In addition, applicants' reactions to student selection procedures receive less attention than applicants' reactions to personnel selection procedures. Furthermore, tests and testing conditions continue to develop, e.g., through online-based testing and test supervision at home (“proctoring”). Therefore, we used a standardized questionnaire for measuring the overall test evaluation and different dimensions of acceptance including face validity, controllability, and the absence of strain to examine six scholastic aptitude tests. We added items to get deeper insights into situational aspects. According to the results of 2,052 test participants, applicants prefer specific tests and shorter tests. Situational aspects, such as privacy, working conditions, and prior information, have an influence on the perceptions of applicants. Proctored testing is evaluated positively, but taking the test at a test center is still rated more favorably. This study discusses the practical implications.
Boost dynamic protocols for producing mammalian biopharmaceuticals with intensified DoE—a practical guide to analyses with OLS and hybrid modeling

Introduction: For the implementation of robust bioprocesses, understanding of temporal cell behavior with respect to relevant inputs is crucial. Intensified Design of Experiments (iDoE) is an efficient tool to assess the joint influence of input parameters by including intra-experimental changes. Methods: We applied iDoE to the production phase of a monoclonal antibody in a mammalian bioprocess. The multidimensional design space spanned by temperature, dissolved oxygen (DO), timing of change, and growth category was investigated in 12 cultivations. We built ordinary least squares (OLS) and hybrid models (HM) on the iDoE-data, validated them with classical DoE (cDoE)-derived data, and used the models as in silico representation for process optimization. Results: If the complexity of interactions between changing setpoints of inputs is sufficiently captured during planning and modeling, iDoE proved to be valid for characterizing the mammalian biopharmaceutical production phase. For local behavior and flexible composition of optimization goals, OLS regressions can easily be implemented. To predict global and interconnected dynamics while incorporating mass balances, HM holds potential. Discussion: iDoE will boost protocols that optimize inputs for different bioprocess phases. The described key aspects of OLS- and HM-based analyses of iDoE-data shall guide future applications during manufacturing.