Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein nonadditive expression and solubility in Arabidopsis hybrids and allotetraploids

Interspecific hybridization in plants often leads to allopolyploids including most important crops such as wheat, cotton, and canola, while many other crops such as corn and sorghum are grown as hybrid. Both allopolyploids and hybrids show hybrid vigor or heterosis. The phenomenon has been widely applied in agriculture and extensively studied at the genetic and gene expression levels. However, proteomic changes in hybrids and polyploids remain poorly understood. Here, we report comparative analysis of soluble and insoluble proteomes in Arabidopsis intraspecific and interspecific hybrids or allotetraploids formed between A. thaliana and A. arenosa. Both allotetraploids and intraspecific hybrids displayed nonadditive expression (unequal to the sum of the two parents) of the proteins, most of which were involved in biotic and abiotic stress responses. In the allotetraploids, homoeolog-expression bias was not observed among all proteins examined but could occur among 17-20% of the nonadditively expressed proteins, consistent with the transcriptome results. Among expression-biased homoeologs, there were more A. thaliana-biased than A. arenosa-biased homoeologs,. Analysis of the insoluble and soluble proteomes revealed more soluble proteins in the hybrids than their parents but not in the allotetraploids. Most proteins in ribosomal biosynthesis and in the thylakoid lumen, membrane, and stroma were in the soluble fractions, indicating a role of protein stability in photosynthetic activities for promoting growth. These results collectively support roles of nonadditive expression of stress-responsive proteins and increased solubility of photosynthetic proteins in Arabidopsis hybrids and allotetraploids, which may promote hybrid vigor. Plain Language Summary We analyzed fractionated proteomes to test protein abundance and solubility in Arabidopsis hybrids and polyploids. Many proteins in stress-responses are nonadditively expressed in intraspecific hybrids or allotetraploids. There are more soluble proteins of ribosomal biosynthesis and photosynthetic activities in the hybrids than in their parents but not in allotetraploids. Expression levels are equal among most protein homoeologs in the allotetraploids but are biased for ~20% of nonadditively expressed proteins. Nonadditive protein expression and solubility may play a role in heterosis.
OsNLP3/4-OsRFL module regulates nitrogen-promoted panicle architecture in rice

Rice panicles, a major component of yield, are regulated by phytohormones and nutrients. How mineral nutrients promote panicle architecture remains largely unknown. Here, we report that NIN-LIKE PROTEIN3 and 4 (OsNLP3/4) are crucial positive regulators of rice panicle architecture in response to nitrogen (N). Loss-of- function mutants of either OsNLP3 or OsNLP4 produced smaller panicles with reduced primary and secondary branches and fewer grains compared with wild type, whereas their overexpression plants showed the opposite phenotypes. Notably, the OsNLP3/4-regulated panicle architecture was positively correlated with N availability. OsNLP3/4 directly bind to the promoter of OsRFL and activate its expression to promote inflorescence meristem development. Furthermore, OsRFL activates OsMOC1 expression by binding to its promoter. Our findings reveal the novel N- responsive OsNLP3/4-OsRFL-OsMOC1 module that integrates N availability to regulate panicle architecture, shedding light on how nutrient signals regulate panicle architecture and providing candidate targets for the improvement of crop yield.
Not one size fits all: influence of EEG type when training a deep neural network for interictal epileptiform discharge detection

Objective Deep learning methods have shown potential in automating interictal epileptiform discharge (IED) detection in electroencephalograms (EEGs). While it is known that these algorithms are dependent on the type of data used for training, this has not been explored in EEG analysis applications. We study the difference in performance of deep learning algorithms on routine and ambulatory EEG data. Methods We trained the same neural network on three datasets: 166 routine EEGs (VGGC–R), 75 ambulatory EEGs (VGGC–A) and a combination of the two data types (VGGC-C, 241 EEGs total). Networks were tested on 34 routine EEGs and 33 ambulatory recordings, where all 2 s non-overlapping epochs were labeled with a probability that expressed the likelihood of containing an epileptiform discharge. Performance was quantified as sensitivity, specificity and the rate of false detections (FPR). Results The VGGC-R led to 84% sensitivity at 99% specificity on the routine EEGs, but its sensitivity was only 53% on ambulatory EEGs, with a FPR > 3 FP/min. The VGGC-C and VGGC-A yielded sensitivities of 79% and 60%, respectively, at 99% specificity on ambulatory data, but their sensitivity was less than 60% for routine EEGs. Conclusion We show that performance of deep nets for IED detection depends critically on the type of recording. The VGGC-R should be used for routine recordings and the VGGC-C should be used for ambulatory recordings for IED detection. Significance The type of data used to train algorithms should be optimized according to their application, as this has a significant impact on algorithm performance.
Resonant transmission of light through finite arrays of slits

Finite-size effects associated with the phenomenon of extraordinary optical transmission are theoretically addressed. We analyze the N dependence of the transmission resonances appearing in one-dimensional periodic arrays of N slits. For the transmission resonances located close to the period of the array, it is found that the evolution is controlled by the width of the slits. This parameter completely governs the electromagnetic coupling between slits that, in turn, is the key actor in the formation of the collective surface electromagnetic mode responsible for the enhanced transmission. On the contrary, the transmission process associated with the excitation of waveguide resonances inside the slits is almost independent of the number of slits perforated on the metallic film.
Title: Emotional memories are enhanced when reactivated in slow wave sleep, but impaired when reactivated in REM Abbreviated Title: Sleep can enhance or impair emotional memories

Sleep supports memory consolidation. However, it is not completely clear how different sleep stages contribute to this process. While rapid eye movement sleep (REM) has been traditionally implicated in the processing of emotionally charged material, recent studies indicate a role for slow wave sleep (SWS) in strengthening the memories of emotional stimuli. Here, to directly examine which sleep stage is primarily involved in emotional memory consolidation, we used targeted memory reactivation (TMR) in REM and SWS during a daytime nap. We also examined neural oscillations associated with TMR-related changes in memory. Contrary to our hypothesis, reactivation of emotional stimuli during REM led to impaired memory. Meanwhile, reactivation of emotional stimuli in SWS improved memory and was strongly correlated with the product of times spent in REM and SWS (%SWS × %REM). When this variable was taken into account, reactivation significantly enhanced memory, with larger reactivation benefits compared to reactivation in REM. Notably, sleep spindle activity was modulated by emotional valence, and delta/theta activity was correlated with the memory benefit for both emotional and neutral items. Finally, we found no evidence that emotional memories benefited from TMR more than did neutral ones. Our results provide direct evidence for a complementary role of both REM and SWS in emotional memory consolidation, and suggest that REM may separately facilitate forgetting. In addition, our findings expand upon recent evidence indicating a link between sleep spindles and emotional processing.
Interference between turbulent and molecular diffusion

The problem of the interference between turbulent and molecular diffusion is investigated. A decorrelating mechanism leading to a depletion of turbulent transport was discussed by Saffman (J. Fluid Mech., 8 (1960) 273). We identify another effect associated with anticorrelated regions which leads to enhancement of transport. The competition between these two effects makes it possible to have either constructive or destructive interference, depending on specific flow correlations. We show that the same arguments apply to the interference between turbulent transport and a large-scale mean flow.
Glucose oxidase as an alternative to antibiotic growth promoters improves the immunity function, antioxidative status, and cecal microbiota environment in white-feathered broilers

This study aimed to demonstrate the effects of glucose oxidase (GOD) on broilers as a potential antibiotic substitute. A total of four hundred twenty 1-day-old male Cobb500 broilers were randomly assigned into five dietary treatments, each with six replicates (12 chicks per replicate). The treatments included two control groups (a basal diet and a basal diet with 50 mg/kg aureomycin) and three GOD-additive groups involving three different concentrations of GOD. Analysis after the t-test showed that, on day 21, the feed:gain ratio significantly decreased in the 1,200 U/kg GOD-supplied group (GOD1200) compared to the antibiotic group (Ant). The same effect was also observed in GOD1200 during days 22–42 and in the 600 U/kg GOD-supplied group (GOD600) when compared to the control group (Ctr). The serum tests indicated that, on day 21, the TGF-β cytokine was significantly decreased in both GOD600 and GOD1200 when compared with Ctr. A decrease in malondialdehyde and an increase in superoxide dismutase in GOD1200 were observed, which is similar to the effects seen in Ant. On day 42, the D-lactate and glutathione peroxidase activity changed remarkably in GOD1200 and surpassed Ant. Furthermore, GOD upregulated the expression of the jejunal barrier genes (MUC-2 and ZO-1) in two phases relative to Ctr. In the aureomycin-supplied group, the secretory immunoglobulin A significantly decreased in the jejunum at 42 days. Changes in microbial genera were also discovered in the cecum by sequencing 16S rRNA genes at 42 days. The biomarkers for GOD supplementation were identified as Colidextribacter, Oscillibacter, Flavonifractor, Oscillospira, and Shuttleworthia. Except for Shuttleworthia, all the abovementioned genera were n-butyrate producers known for imparting their various benefits to broilers. The PICRUSt prediction of microbial communities revealed 11 pathways that were enriched in both the control and GOD-supplied groups. GOD1200 accounted for an increased number of metabolic pathways, demonstrating their potential in aiding nutrient absorption and digestion. In conclusion, a diet containing GOD can be beneficial to broiler health, particularly at a GOD concentration of 1,200 U/kg. The improved feed conversion ratio, immunity, antioxidative capacity, and intestinal condition demonstrated that GOD could be a valuable alternative to antibiotics in broiler breeding.
COVID-19 and Cancer Diseases—The Potential of Coriolus versicolor Mushroom to Combat Global Health Challenges

Coriolus versicolor (CV) is a common species from the Polyporaceae family that has been used in traditional Chinese herbal medicine for over 2000 years. Among well-described and most active compounds identified in CV are polysaccharopeptides, such as polysaccharide peptide (PSP) and Polysaccharide-K (PSK, krestin), which, in some countries, are already used as an adjuvant agent in cancer therapy. In this paper, research advances in the field of anti-cancer and anti-viral action of CV are analyzed. The results of data obtained in in vitro and in vivo studies using animal models as well as in clinical research trials have been discussed. The present update provides a brief overview regarding the immunomodulatory effects of CV. A particular focus has been given to the mechanisms of direct effects of CV on cancer cells and angiogenesis. A potential use of CV compounds in anti-viral treatment, including therapy against COVID-19 disease, has also been analyzed based on the most recent literature. Additionally, the significance of fever in viral infection and cancer has been debated, providing evidence that CV affects this phenomenon.
The Smallest Eigenvalue of a Large Dimensional Wishart Matrix

For each s : 1,2. let n: r? (s) be a posit ive integer such that n/s --+ y > 0 as s --+ cc. Let V" be an n X s matrix whose entries are i.i. d. N(0, 1) random variables and let M": (I/s)V"V:. The random matrix V,V: is commonly referred to as the Wishart matrix W(1,, s). It is well known [Mar0enko and Pastur (1967), Wachter (1978)] that the empirical distribution function 4 of the eigenvalues of M, t.F"(r) = (I/n) x (number of eigenvalues of M " < *)l converges almost r.rr"ly ur r -+ oo to a nonrandom probability distribution function { having a density with positive support on [(1 tF)',(l + ,F>t], and when yi r, { yields additional mass on {0}. It is also known fGeman (1980)] that the maximum eigenvalue I(** of M" converges a.s. to (1 + ,F)'as s -+ oo. [The statement of thi. r"rult in Geman (1980) has all the M, constructed from one doubly infinite array of i.i. d. random variables. However, it is obvious from the proof that no relation on the entries of V" for different s is needed. ] These results are established under assumptions more general on the entries of % than Gaussian distributed, involving conditions on the moments of these random variables. The present paper will prove the following
Optimal state-space partition for control of discrete-event systems with static specifications

The sensors distinguish among elements of the observation space, which is a partition of the state space, and the controller assigns a control pattern to each observation value. We study the coarsest partition to satisfy the static specification. If the sensors are reliable, then we can reduce the sensor cost by implementing the coarsest partition as the observation space. We show that, unfortunately, the coarsest partition does not uniquely exist in general. We then present a necessary and sufficient condition for the unique existence of the coarsest partition.
SHOCK PROPAGATION IN POLYDISPERSE BUBBLY FLOWS

The effect of distributed bubble size on shock propagation in homogeneous bubbly liquids is computed using a continuum two-phase model. An ensemble-averaging technique is employed to derive the statistically averaged equations and a finite-volume method is used to solve the model equations. The bubble dynamics are incorporated using a Rayleigh-Plesset-type equation which includes the effects of heat transfer, liquid viscosity and compressibility. For the case of monodisperse bubbles, it is known that relaxation oscillations occur behind the shock due to the bubble dynamics. The present computations for the case of polydisperse bubbles show that bubble size distributions lead to additional damping of the shock dynamics. If the distribution is sufficiently broad, the statistical effect dominates over the physical damping associated with the single bubble dynamics. This smooths out the oscillatory shock structure.
An Explorative Study of the Causal Pathogenesis of Green Liver Discoloration in Organically Reared Female Bronze Turkeys (Meleagris gallopavo) Considering the Infectious Risk Factors

Simple Summary Organically raised turkeys investigated in a recent study showed a high prevalence of green liver discoloration. The condition is commonly associated with bone alterations and is potentially caused by opportunistic bacteria. This study was performed to determine possible infectious risk factors and reduce disease prevalence. The prevalence of green livers has decreased between both studies, and there was no explicable significant correlation with bacterial or parasitological findings. However, there was a significant correlation between green livers and the immunosuppressive turkey hemorrhagic enteritis virus at the early fattening stage. Hens with virus detection had impaired physical health. At the late fattening stage, there was a significant correlation between green livers and joint/bone lesions, as described in previous literature. It can be assumed that the hemorrhagic enteritis virus affects the pathogenesis of green liver discoloration at the early fattening stage. Therefore, an adequate vaccination schedule should be implemented in poultry farms to reduce the prevalence of discoloration and improve animal health. However, further standardized investigations to determine and evaluate possible infectious risks regarding green liver discoloration are necessary. Abstract A recent study revealed that organically raised Bronze turkeys showed a high prevalence of green liver discoloration. This alteration is commonly associated with the Turkey Osteomyelitis Complex and potentially caused by opportunistic bacteria. Therefore, 360 organically fattened Bronze turkeys were examined post-mortem throughout two fattening trials with two examinations each to determine possible infectious risk factors and reduce disease prevalence. Clinical and pathoanatomical examinations were performed on every hen. Histopathological, bacteriological, parasitological, and virological examinations were performed on at least six hens without and, if applicable, six hens with green livers on each examination date. Overall, 9.0% of all hens had a green liver without a correlation with bacterial or parasitological findings but multiple health impairments. The discoloration correlated significantly with the detection of immunosuppressive turkey hemorrhagic enteritis virus at the early stage and macro- and histological joint/bone lesions at the late fattening stage, indicating the presence of two different predisposing pathogeneses. Flocks not being vaccinated against hemorrhagic enteritis but having a virus-positive sample showed the highest prevalence of green liver discoloration and developed worse in various parameters. In conclusion, an adequate vaccination schedule and the prevention of field infections may lead to a decreased risk of performance reduction and improved animal health.
Set-based concept selection in multi-objective problems: optimality versus variability approach

This paper presents a novel approach to support the selection of conceptual solutions to multi-objective problems. The proposed method involves a comparison between concepts, based on the performances of sets of solutions that represent them. The set-based comparison of concepts is consistent with the so-called Toyota set-based concurrent engineering process. Such an approach discourages early exploitation of solutions and promotes extended exploration of the design space by means of sets of solutions. Both optimality and variability of concepts are considered, and their measures are devised to pose the selection problem as an auxiliary multi-objective problem. The auxiliary objectives are to maximise optimality and to maximise the variability. This highlights the inherent multi-objectivity of concept selection and supports decision-making under the possible contradictory nature of optimality and variability of concepts. Both academic and engineering problems are used to demonstrate the approach and to expose the inherent subjectivity of the measures, which are dependent on the selection of a window of interest by the decision-makers.
Discovery of Highly Dynamic Matter Enhancements along the Polar Axis and Equatorial Plane in the Luminous Blue Variable Binary HD 5980

HD 5980 is a W-R+O eclipsing binary in the Small Magellanic Cloud that has attracted considerable attention since it underwent a luminous blue variable (LBV)-type outburst in 1994. Since then, intense spectroscopic and photometric monitoring have revealed the presence of periodic variability on a timescale of 6-7 hr that cannot be explained by our current understanding of the system. In this paper, we present the first results from our polarimetric observations around secondary eclipse when the assumed Wolf-Rayet (W-R) star passes in front of the assumed LBV component (phase ϕ = 0.36). These data confirm the presence of stochastic polarimetric variability on a typical timescale of ~30 minutes, reaching a very high amplitude of almost 1% on our last of five nights. At that time, we also found that the mass loss, which is responsible for the polarimetric variability, presented fluctuations in axial symmetry ranging from very rapid density enhancements along the orbital plane to polar ejections. We propose that either a fast rotator model for the W-R star or the presence of a close orbiting neutron star could qualitatively explain the observed polarimetric, spectroscopic, and photometric behavior. The evidence presented in this paper is crucial for an understanding of the erratic behavior of this important binary and should be taken into account in any consistent model of the system.
Quantitative flow ratio-guided versus angiography-guided operation for valve disease accompanying coronary heart disease

Background Valve replacement combined with coronary artery bypass graft (CABG) operation (VR + CABG) is usually associated with higher mortality and complication rates. Currently, angiography remains the most commonly used approach to guide CABG. The aim of this study is to investigate whether a quantitative flow ratio (QFR)-guided strategy can improve the clinical outcomes of VR + CABG. Methods Patients (n = 536) treated by VR + CABG between January 2018 and December 2021 were retrospectively assessed. In 116 patients, all lesions were revascularized entirely based on QFR (the QFR-guided group), whereas in 420 patients, all lesions were revascularized entirely based on angiography (the angiography-guided group). To minimize selection bias between the 2 groups, propensity score matching was performed at a ratio of 1:2. The primary endpoint of the study was the rate of major adverse cardiac and cerebrovascular events (MACCE) at 1-year, which was defined as a composite of cardiac mortality, myocardial infarction (MI), any repeat revascularization, and stroke. Results No statistically significant differences were observed in the baseline clinical characteristics between the QFR-guided and angiography-guided groups after propensity score matching. The mean age of all patients was 66.2 years [standard deviation (SD) = 8.3], 370 (69%) were men, the mean body-mass index of the population was 24.8 kg/m2 (SD = 4.5), 129 (24%) had diabetes, and 229 (43%) had angina symptoms. When compared with the angiography-guided group, the QFR-guided group had a significantly shorter operative time (323 ± 60 min vs. 343 ± 71 min, P = 0.010), extra corporal circulation time (137 ± 38 min vs. 155 ± 62 min, P = 0.004), clamp time (73 ± 19 min vs. 81 ± 18 min, P < 0.001), and less intraoperative bleeding volume (640 ± 148 ml vs. 682 ± 166 ml, P = 0.022). Compared with the angiography-guided group, the 1-year MACCE was significantly lower in the QFR-guided group (6.9% vs. 14.7%, P = 0.036, hazard ratio = 0.455, 95% confidence interval: 0.211–0.982). Conclusion Our results raise the hypothesis that among patients who undergo VR + CABG, QFR-guided strategy is associated with optimized surgical procedure and a superior clinical outcome, as evidenced by a lower rate of MACCE at 1-year compared with conventional angiography-guided strategy.
On Robust Model Selection Within the Cox Model

Summary Model selection methods have shown to be useful in the process of econometric modelling. The paper studies robust Akaike–Schwarz type information criteria of model choice within the Cox model. The criteria are based on a smooth modification of the partial likelihood function. Apart from asymptotic results, a Monte Carlo study is presented, which shows the finite sample behaviour of the procedure under discrepancies from the Cox model. Analysis of a real unemployment data case is also included.