Photosynthesis needs to run efficiently under permanently changing illumination. To achieve this, highly dynamic acclimation processes optimize photosynthetic performance under a variety of rapidly changing light conditions. Such acclimation responses are acting by a complex interplay of reversible molecular changes in the photosynthetic antenna or photosystem assemblies which dissipate excess energy and balance uneven excitation between the two photosystems. This includes a number of non-photochemical quenching processes including state transitions and photosystem II remodeling. In the laboratory such processes are typically studied by selective illumination set-ups. Two set-ups known to be effective in a highly similar manner are (i) light quality shifts  or (ii) dark-light shifts . Both set-ups result in similar effects on the plastoquinone redox state, but their equivalence in induction of photosynthetic acclimation responses remained still open. Here, we present a comparative study in which dark-light and light-quality shifts were applied to samples of the same growth batches of plants. Both illumination set-ups caused comparable effects on the phosphorylation of LHCII complexes and, hence, on the performance of state transitions, but generated different effects on the degree of state transitions and the formation of PSII super-complexes. The two light set-ups, thus, are not fully equivalent in their physiological effectiveness potentially leading to different conclusions in mechanistic models of photosynthetic acclimation. Studies on the regulation of photosynthetic light acclimation, therefore, requires to regard the respective illumination test set-up as a critical parameter that needs to be considered in the discussion of mechanistic and regulatory aspects in this subject. The reaction centers possess slightly different absorption maxima of 680 nm for PSII and 700 nm for PSI. Enrichment of either wavelength in the incident light, thus, can cause imbalances in photosystems excitation which in turn reduces the efficiency in photosynthetic energy conversion  and photosystem I (PSI) work electrochemically in series. Efficient electron transport from the donor at PSII, water, to the final acceptor at PSI, NADPnversion . Many abnversion .6f complex, an electron transport complex functionally placed between PSII and PSI, is the slowest and, therefore, rate-limiting step of the photosynthetic electron transport. It, thus, represents an ideal sensor for environmental fluctuations  from the top leaves of the canopy . Far-redtuations . Indeed,tuations .State transitions represent a short-term regulation mechanism for excitation energy redistribution in which the relative antenna cross section of PSII and PSI is modulated through selective phosphorylation of the light harvesting complex of PSII (LHCII) . Upon prOur understanding of the mechanistic steps triggering state transitions is highly complicated by the fact that the linear electron transfer function is not reflected in the structure of the photosynthetic apparatus. The thylakoid membrane system in which the photosystems reside possesses a highly organized three-dimensional structure and can be distinguished into grana membranes with tightly appressed membrane stacks and the interconnecting stroma lamellae. The precise structure of the thylakoid membrane system is still under investigation , howeverThe structure of the thylakoid membrane system is not fixed but highly dynamic. Phosphorylation of LHCII complexes and/or PSII core proteins within the grana stacks induces a  de-stacking of the membrane structure probably by introducing negative charges on both sides of the membrane stack that repel each other . It is i2S2M2 complex  complexes with each having one strongly (S) and one moderately (M) bound LHCII trimer generating the C complex . In vivoembranes . Upon a nsitions . In addinsitions .Phosphorylation of PSII core and LHCII trimers is a major determinant of the highly complex arrangement of the photosynthetic apparatus and the thylakoid membrane structure, but the precise sequence of events is far from being clear. We recently could demonstrate that light-quality shifts that either reduce or oxidize the photosynthetic electron transport chain do have pronounced effects not only on STN7 activity and state transitions but also on the formation and the release of PSII super-complexes . These cResearch on processes involved in state transitions typically is done in the laboratory on plants grown under defined light conditions that induce either reduction or oxidation of the PQ pool, respectively. These conditions may be induced by technically slightly different test set-ups, but not much attention has been given yet to such details. We were wondering whether illumination set-ups with small different technical settings but with comparable effects on the PQ pool redox state do induce equivalent physiological effects on photosynthetic acclimation. To this end, we compared light-quality shifts and dark-white light shifts in their effectiveness on state transitions, photosynthetic antenna phosphorylation and PSII super-complex formation.Arabidopsis thaliana var. Columbia-O (Col-0) plants were grown on soil for 14 days under long day (LD) conditions (16 h light/8 h dark) at 50 μmol m–2 s–1 white light  at 23°C and 60% humidity before subsequent light treatments. Plants subjected to long-term light-quality treatment (6 days under continuous PSI- or PSII-light) were grown for 5 days in LD conditions followed by 3 days of continuous WL (to adapt the plants to the continuous illumination) matching a final age of 14 days. Plant material was grown in several parallel pots allowing to split plant sets for individual light treatments after a common initial growth phase. All growth experiments and their subsequent physiological and molecular characterizations were done with at least three independent biological replicates.After 14 days of pre-cultivation under LD conditions (if not indicated otherwise) plants were subjected to various illumination set-ups for the indicated time periods. White light (WL) treatments were performed under the identical light sources as used for pre-cultivation. The technological set-up for PSI- and PSII-light treatments was identical to that described in stn7 mutants grown under DL conditions subjected to indicated shifts in illumination were detected using a pulse amplitude modulation (PAM)-based fluorometer . The measurements aimed to analyze the general dynamics in the Chl fluorescence changes induced by the indicated light shifts with a special emphasis on the process of state transitions. As reference a standard state transition experiment using the internal monochromatic light sources  of the Junior-PAM device was performed. To this end plants in their growth pots were placed under the Junior-PAM detector in a way that Chl fluorescence detection was yielding sufficient intensity, but without using a clamp for the leaf that could influence gas exchange. The distance between the fiber optics probe and the leaf surface was adjusted to 5 mm. After 1 h of dark acclimation F0 and Fm were determined for calculation of Fv/Fm (Fv = Fm − F0) using the Junior-PAM internal measuring light and saturation pulses. Then, actinic light  was switched on for 30 min for induction of state 2. At steady state fluorescence in state 2 (Fs2) a saturation pulse was given for detection of Fm2′. Then, far-red light  was added for further 30 min to induce state 1. When reaching a steady state fluorescence in state 1 (Fs1) another saturation pulse was given for detection of Fm1′. Reversibility of the light-induced acclimation responses was checked in each replicate by switching off the far-red LED allowing for returning to state 2. Determination of Chl fluorescence transients and state transitions induced by growth light sources were done essentially in the same manner as described for the LED-driven reference experiment, but using shifts between the growth lights instead of the internal LEDs. In light quality shift experiments state 2 was induced in 1 h dark-acclimated plants by 50 min illumination with PSII-light, while state 1 was induced by subsequent illumination with PSI-light for 30 min. Reversibility of state transitions in these conditions was checked by a switch back to PSII-light for each replicate. Dark-light shift experiments were performed analogously starting with 1 h dark-acclimation, followed by a 50 min illumination period with white light to induce state 2, followed by a 30 min shift to darkness to induce state 1. Again, reversibility of state transitions was checked by another 30 min of illumination with white light. Calculations of state transition parameters for all light set-ups are given in legend of Time course and degree of Chl fluorescence transients of 14-to-21-day-old WT plants and ®) and the enhanced chemiluminescence (ECL) assay. Indicated amounts of samples were separated by either denaturing SDS-PAGE or BN-PAGE and transferred to nitrocellulose membrane (®PROTAN Whatman) by semi-dry-western blotting using standard protocols  or an anti-phospho-threonine antibody  and state transitions (qT). The impact of photoinhibition-dependent quenching (qI) was regarded as negligible since only weak actinic light was used for excitation in these experiments.Recent studies reported 77K fluorescence emission spectra indicating that both, light-quality and dark-white light shifts, induce a significant lateral movement of the mobile LHCII antenna between PSII and PSI resulting in considerable changes of the respective antenna cross sections. The state transition deficient nsitions . The 77Kstn7 mutant resulted in a completely different response pattern  subjected to standard LEDs providing monochromatic blue and far-red light as typically used in PAM-derived Chl fluorescence measurements (for detection of state transitions) . Illuminstn7 mutant displayed Chl fluorescence changes in response to the light shifts which were highly similar to those in the LED-based system. In sum, the obtained data indicate that shifts between the PSI- and PSII-growths are able to effectively induce state transitions.Subjecting WT plants to shifts between PSII- and PSI-growth lights resulted in Chl fluorescence changes highly comparable to the LED based system . The flustn7 mutant resulted in a significant drop in fluorescence after shift to darkness. The mutant was unable to return to the starting level in Chl fluorescence, thus the slow sigmoidal return observed in WT can be regarded as a transition to state 1. A shift back to white light induced a fluorescence rise that was considerably smaller than in WT followed by rapid quenching comparable to the WT control.Next, we performed corresponding experiments using dark-white light shifts for manipulation of photosynthetic electron transport . Dark-acFr) that describes the relative difference of fluorescence in state 2 and state 1 upon changes between either PSI- or PSII-light . Then we subtracted the values of the mutant from WT assuming that the remaining values provide an approximation for the contribution of state transitions to the fluorescence changes in the growth light systems  and non-photochemical quenching (NPQ) processes. Since these processes occur in parallel their relative contribution to the overall Chl fluorescence quenching is difficult to quantify, but for determination of state transition dependent quenching (qT) an established protocol exists. This quantification of qT requires saturation light pulses that close the PSII reaction centers and indicate their relative antenna size in either state 1 or state 2 . HoweverII-light . In ordelues see  excludinArabidopsis thaliana plants were grown for 2 weeks and subjected to various illumination protocols using light-quality (PSI- or PSII-light) or dark-white light (WL) shifts -PAGE as reported earlier . StrongeArabidopsis thaliana plants grown under corresponding light conditions were analyzed for their assembly states. To this end plant material was harvested under the respective condition, thylakoids were isolated, membranes were solubilized and blue native (BN) PAGE (2S2M1 and C2S2M2 complexes) (vice versa).In order to study such potentially different effects of light-quality and dark-light shifts on PSII super-complexes, thylakoid membrane complexes from BN) PAGE  was perfBN) PAGE . For tesBN) PAGE . While iBN) PAGE . Controlmplexes) . Since implexes) . This inmplexes) . Dark-limplexes) . Such a mplexes) . In sum,mplexes)  that mosmplexes)  suggesti2S2M1 and C2S2M2 complexes) when compared to the subsequent PSI-light acclimation   . Therefodomonas) . Our datArabidopsis  which is in contrast to PSII-light illumination –4, whichChlamydomonas reinhardtii where state 1 and state 2 represent two different metabolic states  a shift from dark to light conditions represents a shift from heterotrophic to autotrophic life style (Another difference between the two light systems relates to the metabolic state of the plants in state 1. The original observations describing state 1–state 2 transitions trace back to two studies on photosynthesis in algae; both done in the light . The oric states . In Arabfe style  while a fe style . For thefe style . This spfe style  being infe style . This stfe style , suggestfe style , 2. Whetfe style  with LHCfe style  suggestsfe style .In sum, our study reveals that growth light set-ups with highly similar physiological effects and only minor technically different properties may still induce differences in photosynthetic acclimation responses which can be of importance for our understanding of the studied processes. The question of comparability of results between different illumination set-ups may become even more urgent with the advent of LED based illumination systems that are increasingly used now for plant growth . A recenThe original contributions presented in the study are included in the article/TP designed the research. EH, ML, and SO performed the research. All authors discussed the data and contributed to the writing of the article.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Patients with ischemic cardiomyopathy (ICMP) are at high risk for malignant arrhythmias, largely due to electrophysiological remodeling of the non-infarcted myocardium. The electrophysiological properties of the non-infarcted myocardium of patients with ICMP remain largely unknown.To assess the pro-arrhythmic behavior of non-infarcted myocardium in ICMP patients and couple computational simulations with machine learning to establish a methodology for the development of disease-specific action potential models based on clinically measured action potential duration restitution (APDR) data.p < 0.01). In cell-level simulations, APD alternans were induced in ICMP models at a longer cycle length compared to SNLV models (385–400 vs 355 ms). In tissue-level simulations, ICMP models were more susceptible for sustained functional re-entry compared to SNLV models.We enrolled 22 patients undergoing left-sided ablation (10 ICMP) and compared APDRs between ICMP and structurally normal left ventricles (SNLVs). APDRs were clinically assessed with a decremental pacing protocol. Using genetic algorithms (GAs), we constructed populations of action potential models that incorporate the cohort-specific APDRs. The variability in the populations of ICMP and SNLV models was captured by clustering models based on their similarity using unsupervised machine learning. The pro-arrhythmic potential of ICMP and SNLV models was assessed in cell- and tissue-level simulations. Clinical measurements established that ICMP patients have a steeper APDR slope compared to SNLV (by 38%, Myocardial remodeling in ICMP patients is manifested as a steeper APDR compared to SNLV, which underlies the greater arrhythmogenic propensity in these patients, as demonstrated by cell- and tissue-level simulations using action potential models developed by GAs from clinical measurements. The methodology presented here captures the uncertainty inherent to GAs model development and provides a blueprint for use in future studies aimed at evaluating electrophysiological remodeling resulting from other cardiac diseases. Ischemic cardiomyopathy (ICMP) patients are at high risk for malignant arrhythmias , largelyThe first goal of this study is to characterize the EP remodeling of the arrhythmogenic substrate in ICMP patients, and specifically changes in electrical restitution. Action potential duration restitution (APDR) is an important EP property that contributes to tissue-level EP dynamics, and is critical in arrhythmogenesis . The stein silico. Incorporating the APDR of non-infarcted myocardium in Virtual Heart models of ICMP patients is of critical importance: First, current cardiac action potential models have been derived from pre-clinical data  risk assessment , localizcal data , and do cal data , as wellcal data . Third, Specifically, our aims are: (1) to clinically characterize the APDR of the surviving LV myocardium of ICMP patients and compare it to the APDR of structurally normal left ventricles (SNLV); (2) to develop the methodology to construct action potential models based on clinically obtained cohort-specific APDRs using a custom-developed genetic algorithm (GA); (3) to compare the emerging EP dynamic behaviors between ICMP and SNLV in cell- and tissue-level computer simulations using the GA-derived action potential models; and (4) to capture the uncertainty in the GA-derived action potential models and in the resulting cell-level and tissue-level EP behavior by combining computer simulations with unsupervised machine learning. The results of this study have important implications because they improve our understanding on the EP substrate of ICMP patients and provide a methodology for calibration of cardiac action potential models account for the uncertainty related to model development from clinical data. Such models can be used for the development of personalized risk-stratification and guidance of ablative strategies, contributing to the ongoing efforts towards precision medicine in cardiology.To assess the activation-repolarization dynamics in ICMP compared to that of SNLV, we performed programmed electrical stimulation in patients undergoing left-sided catheter ablation procedures. We used the corresponding unipolar electrograms (UniEGMs) to obtain APDR curves with the help of a customized signal processing approach. We then utilized the clinically obtained APDRs to construct populations of action potential models of ICMP and SNLV patients, employing a custom-developed GA. We used unsupervised machine learning to capture the uncertainty in model development from clinical data. We then used the developed action potential models to characterize the dynamic pro-arrhythmic substrate of ICMP patients.We prospectively enrolled consecutive patients undergoing left-sided catheter ablation procedures at the Johns Hopkins Hospital. Criteria for inclusion were patients older than 18 years old undergoing any clinically indicated left-sided catheter ablation procedure that had either ICMP or SNLV. We required that all participants had echocardiographic assessment within 1 year of the procedure day. The presence of ICMP was ascertained by a positive history for coronary artery disease and decreased left ventricular systolic function on echocardiogram, with wall motion abnormalities consistent with the distribution of coronary artery disease. Exclusion criteria were: patients younger than 18 years old, pregnancy, presentation with electrical storm, presence of cardiomyopathy other than ischemic, need for inotropic support prior to the procedure, need for mechanical circulatory support before or during the procedure and patients with congenital heart diseases. All patients gave informed consent to participate in the study. Enrollment target was a total of 20 patients (10 ICMP and 10 SNLV patients).We evaluated activation-repolarization dynamics in the non-infarcted myocardium of ICMP patients and the myocardium of patients with SNLV by pacing at a fixed cycle length at progressively decreasing cycle lengths, 20 min after completion of the clinical ablation procedure. Specifically, we placed either a multi-electrode mapping catheter , or a standard 4-mm tip ablation catheter with 2 mm inter-electrode spacing  in an area (remote from scar in ICMP patients) with a bipolar signal voltage amplitude >1.5 mV. For each patient only one of either an ablation or a multi-electrode catheter was used for data collection. A multi-electrode catheter was used if the operating electrophysiologist had deemed it necessary for clinical/procedural purposes. We then paced at a fixed cycle length the patient from a catheter placed in the RV apex for 20 beats at cycle lengths decrementing from 600 to 350 ms with a step of 50 ms. These pacing maneuvers were performed with intervals of 15 s to a few minutes, allowing for blood pressure recovery in case the blood pressure dropped with fast pacing. We recorded UniEGM from the mapping or ablation catheter during burst pacing . Signals were recorded from all electrodes at a fixed catheter location in the left ventricle and catheter stability during recordings was confirmed fluoroscopically. The sampling frequency of the recorded signal was 977 Hz. The recorded signal was filtered using a high-pass filter at 0.05 Hz, a low-pass filter at 150 Hz and a notch filter at 60 Hz .min dV/dt) of the UniEGM ventricular activation component and the steepest positive slope (max dV/dt) of the UniEGM ventricular repolarization component. ARIs obtained from experimental and clinical measurements have been extensively validated as a surrogate measure of APD  at each pacing cycle length and location using the activation-recovery interval (ARI) method on the recorded UniEGMs. We analyzed the electrograms from each recording site of the multi-electrode catheter separately. The ARIs at each cycle length was assessed using the Wyatt method . ARI wase of APD .To maximize accuracy and reproducibility of ARI measurement, we extracted ARI from the recorded UniEGMs using a custom-made, semi-automatic approach that combined: (a) signal post-processing to attenuate experimental noise and improve ARI detection accuracy ; and (b)R2 > 50% were used in analysis.To assess the APDR intercept and slope of the myocardium of patients with ICMP and SNLV, for each recording, we plotted the ARI of each beat against its preceding diastolic interval (DI), constructing a clinically obtained APDR curve. We excluded from analysis the first three beats and the last beat of each pacing burst, to remove UniEGM waveforms that were not at steady-state. A logarithmic curve was fitted to the measured ARI and its preceding DI. Since ARI approximates APD , the intp-values are two-sided, and the statistical significance criterion was set at an alpha of 0.05. We performed all statistical analysis using Stata version 14.2 .Baseline characteristics are presented stratified by ICMP/SNLV status. Continuous variables are presented as median (inter-quartile range) and categorical variables as count (percentage). Comparisons between baseline characteristics in the ICMP and SNLV groups are performed using the Wilcoxon rank-sum test for continuous variables and the Pearson’s Chi-squared or Fisher’s exact test for categorical variables. ARI and DI for each pacing cycle length is reported as mean ± SEM. To compare APDR intercept and slope between ICMP and SNLV groups we used linear mixed-effects models. We used this approach to account for the fact that for each patient we had multiple measurements (multiple simultaneous recordings per patient). ICMP/SNLV status was introduced as a fixed effect in the model and patient number as a random effect. With this approach each electrode recording was nested within each patient and each patient was classified by the ICMP/SLNLV status. Robust variance-covariance matrix estimators were used. We performed sensitivity analysis by repeating the mixed model analysis after excluding patients with atrial fibrillation, patients taking any membrane active anti-arrhythmic medication , the patient with the highest and lowest APDR slope, women (since we were unable to enroll women in the ICMP cohort), and restitution curves that had a regression coefficient of determination <60, 70, 80, and 90%. The effect of patient diagnosis [premature ventricular complex (PVC) vs VT] and catheter selection  was examined, by introducing these as fixed effect co-variates in the mixed model analysis. All The APDRs obtained as described above are surrogates of cellular activation-repolarization dynamics. In order to develop ICMP and SNLV action potential models we used average APDR derived from the ICMP and SNLV cohorts. Next, we used these APDRs to construct populations of action potential models of ICMP and SNLV patients that capture APDR properties. Those action potential models were, in turn, used to characterize the contribution of APDR to the emerging tissue-level EP behavior and arrhythmogenesis in ICMP.We used GA to construct the action potential models. GAs are biologically inspired metaheuristics that are appropriate for fitting action potential models to experimental measurements, since action potential models have parameter spaces that are highly nonlinear, frequently discontinuous, with multiple local minima. To proceed with action potential model development from the clinical data using GA, we needed a baseline action potential model with small number of variables and parameters that would allow for computationally tractable execution of the GA. For this, the endocardial formulation of the Bueno-Orovio-Fenton-Cherry (BOFC) action potential model was selected . The BOFWe designed and optimized a GA that incorporates the clinically obtained APDR curves in the BOFC model using the local-iterative approach . A complOptimization problems of non-linear differential equations, such as the ones that describe cardiac action potential, do not have unique solutions, given a finite amount of data. Consequently, GAs yield a population of suitable derived models. These derived models may have different emergent behaviors when used in tissue-level simulations. Executing simulations with all derived models would capture the variability with respect to emergent behaviors but would be computationally not tractable. To circumvent this, we used an unsupervised machine learning approach to explore the entire population of derived models and group models based on the degree of dissimilarity with respect to their parameter values.We explored the hierarchical organization and evaluated for the presence of clustering in the population of derived models yielded by our GA using agglomerative hierarchical clustering (AHC) , an unsuTo characterize the pro-arrhythmic substrate of ICMP patients, we performed cell-level and tissue-level simulations using the best fit and each of the most dissimilar action potential models derived from our GA. In cell-level simulations a single cell was paced using a decremental dynamic restitution protocol to explore the onset of APD alternans. The cell was paced for 10 beats at cycle lengths starting at 620 ms and decrementing to 260 ms with a step of 5 ms. We used the last two beats of each 10-beat burst for APD assessment. We defined APD at the 10% of the peak action potential voltage (APD90). We constructed bifurcation plots of APD over cycle length and we marked the cycle length where APD alternans occurred. APD alternans were defined if the difference of the APD between two consecutive beat was greater or equal to 2 ms for two consecutive pacing cycle lengths. Earlier onset of APD alternans  suggests a more proarrhythmic behavior.To characterize the contribution of ICMP APDR to the dynamic EP behaviors emerging at the tissue level, we performed tissue-level simulations using the best fit and each of the most dissimilar action potential models derived by our GA. These simulations were performed on a 2 cm × 2 cm × 0.25 mm isotropic cardiac tissue slab. The cells were pre-paced of the slab for 100 beats at a cycle length of 600 ms to achieve steady-state. First, we performed a restitution protocol on tissue-level simulations using the same settings with what we describe in cell-level simulations. The purpose of this was to compare the APDR of the GA-derived models in tissue-level simulations with that of the cell-level simulations. We then performed a S1S2 cross-field stimulation protocol to assess for inducibility of sustained functional re-entry. Specifically, we delivered S1 as a single stimulus at the lower edge of the slab (area of stimulation: 2 cm × 0.5 mm × 0.25 mm) and S2 in a rectangular area in the lower left corner of the slab (area of stimulation: 1 cm × 1 cm × 0.25 mm). We tested S1S2 coupling intervals starting from 500 ms and decreasing to 50 ms by a step of 5 ms. The model was defined as inducible for a given S1S2 coupling interval, if sustained functional re-entry was induced and persisted for >2 s in simulation. As we conduction velocity was not assessed in our cohort, we executed the above-described tissue-level simulations over a wide range of conductivity values (from 0.001 to 0.012 in steps of 0.0005 Siemens/m). This conductivity range corresponds to the clinically observed conduction velocity range of 17–74 cm/s. For each conductivity value, we defined the range of S1–S2 coupling intervals that the cross-field simulation resulted in sustained functional re-entry. A wider range of coupling intervals that result in sustained functional re-entry suggests a more proarrhythmic behavior.p < 0.001) and left ventricular end-diastolic diameter was significantly higher  in ICMP patients compared to SNLV. All ICMP patients and 9/12 SNLV underwent ablation for VT or PVC. 3/12 patients with SNVL underwent AF ablation procedure. VT was the indication of the ablation procedure more frequently in ICMP patients compared to SNLV . All ICMP patients and 50% with SNLV were on beta blockers. Four ICMP patients and one with SNLV were on amiodarone. A similar percentage of ICMP and SNLV patients had APDR data collected using a multi-electrode ablation catheter vs an ablation catheter . Mean ARI over mean DI in ICMP patients and SNVL is presented in p = 0.002] and a significantly lower intercept . Variance decomposition analysis demonstrated that APDR slope of ICMP patients had higher within-subject and between-subject variance compared to SNLV . Sensitivity analysis revealed that ICMP patients have a significantly steeper APDR slope compared to those with SNLV even after exclusion of patients with AF, patients taking any membrane-active antiarrhythmic medication, patients with the highest and lowest APDR slope, and women , or VT/PVC status . Patients that underwent VT ablation had on average similar APDR intercept and slope with patients that underwent PVC ablation.The APDR curve fitted to the clinical data was significantly steeper in ICMP patients compared to SNLV. In mixed model analysis, ICMP patients had a significantly higher APDR slope [steeper by 30.8 ± 10 (38%), The GA converged at 174 generations during SNLV model derivation and at 227 generations during ICMP model derivation . The actw1− (16.6 and 16.7 fold-change),τsi (3.2 and 6.1 fold-change), k_s (3.7 and 4.0 fold-change), and τs2 . These parameters control the inactivating gate of the slow inward current (si), respectively.The parameters of the best fit model for SNLV and ICMP GA-derived models are presented in 1.9-fold . The parIn single cell simulations, GA-derived ICMP models developed APD alternans at a slower pacing cycle length compared to SNLV , the proarrhythmic behavior of the models was similar to that of cell- and tissue-level simulations using the best-fit derived model (described in the section above). Specifically, in cell-level simulations, the ICMP models developed APD alternans earlier (385–400 ms) compared to the SNLV models 355 ms, .In tissue-level simulations the ICMP models developed sustained functional re-entry over a wider range of S1S2 coupling intervals for all conductivity values, compared to SNLV . The resclinical finding is that APDR of the non-infarcted LV myocardium of ICMP patients is clinically and statistically significantly steeper compared to SNLV. This suggests that the non-infarcted myocardium of ICMP patients, despite having normal (>1.5 mV) bipolar voltage amplitude on EGMs, is remodeled and has different EP properties from SNLV. The increased within-subject variance of APDR slope in ICMP patients suggests heterogeneous substrate with respect to repolarization dynamics. Furthermore, the magnitude and statistical significance of the difference of APDR slope between ICMP and SNLV was robust in sensitivity analysis and independent of the PVC/VT status of the patients. This suggests that the underlying disease process and cardiac remodeling is what determines APDR, rather than the presenting arrhythmic phenotype.The goal of this study was to characterize the electrical restitution properties of the non-infarcted myocardium in ICMP patients, establish a methodology that enables development of action potential models that incorporate cohort-specific APDR, and capture the uncertainty inherent to the process of model development from clinical data. Our main in silico finding is that GA-derived ICMP models exhibited a more pro-arrhythmic behavior in cell-level and tissue-level simulations compared to SNLV. This is the first study to show that EP measurements performed with equipment routinely available in the electrophysiology laboratory can be used to develop action potential models. The parameters of the GA-derived ICMP models were up to 1.9-fold different compared to SNLV. The steeper APDR slope present in ICMP has a critical effect in tissue-level emergent EP behavior, promoting the development of sustained functional re-entry. Although conduction velocity was not assessed in the patient cohort, we performed tissue-level analysis over a wide range of conductivity values making our results generalizable to different tissue conductivity states. These results highlight the importance of developing action potential models using clinically derived EP properties such as APDR, since generic action potential models do not capture clinically assessed EP properties of healthy or diseased myocardium.Our main A novel finding is that despite the variability present in the population of GA-derived models, GA-derived models can be clustered in a hierarchical cluster tree and the emergent pro-arrhythmic behavior of the highest-level (most dissimilar) clusters are similar in cell and tissue-level simulations. This suggests that: (a) there is significant redundancy built in the GA-derived models; and (b) our model development approach was reliable with small variability and uncertainty in the population of derived models. Despite variability in individual parameter values and the exact results produced by simulations using different GA-derived models, the emergent behaviors that are relevant in arrhythmogenesis were preserved.n = 42) (n = 24) and SNLV (n = 12). Similar to our results, there was no difference in baseline APD between SNLV and SHD patients, when pacing at 600 ms. The reported baseline APD was similar to ours (277 ± 5 ms for SHD and pacing cycle length of 600 ms). However, in our study the restitution curves of SNLV and ICMP separated at longer DIs compared to There are no prior studies comparing APDR of non-infarcted LV myocardium of ICMP patients to SNLV. Our results are consistent with what has been previously reported in studies assessing APDR of the RV myocardium in patients with SHD. Our ARI measurements in the LV of ICMP patients are similar to what has been previously reported using monophasic action potential (MAP) catheters in the RV of patients with SHD  . Koller n = 18)  . Althougcurrents ; (b) actcurrents ; and (c) failure . Experim failure ; (b) sel failure ; and (c) failure .There are no other studies to date that have fitted action potential models (other than the Mitchel-Shaffer model) to APDR of ventricular myocardium of SNLV and ICMP patients. We will not discuss fitting of the Mitchel-Schaffer model , since iOur study helps overcome critical barriers to incorporating the EP remodeling of ICMP patients in cardiac action potential models. First, there is a paucity of studies assessing the APDR of the non-infarcted LV myocardium in ICMP patients. In this study we provide absolute values of APD and APDR slope of the non-infarcted myocardium of the LV of ICMP patients. We also demonstrate a wide within- and between-subject variance in APD/APDR values of the non-infarcted LV myocardium in ICMP patients. This variance reflects the heterogeneous substrate in ICMP patients and can be used in variability and uncertainty quantification studies of organ-scale simulations performed for VT localization and ablation planning in ICMP patients.Second, there are no established methods for incorporating clinically assessed APDR in models of cardiac EP. Previous clinical studies have adapted the Mitchell-Schaffer model to reproduce clinically assessed APDR by either manually adjusting model parameters , or by uLast, there is a significant uncertainty associated with the process of model development form experimental data. This stems from the facts that: (1) there is uncertainty with respect to variability in experimental measurements; and (2) optimization problems involving non-linear differential equations do not yield unique solutions. Stochastic optimization approaches have been used in pre-clinical studies to derive populations of models that reproduce experimental APDR . There iThere are no studies assessing whether the invasively acquired slope of the APDR is related to the risk for hard clinical outcomes such as the onset of ventricular arrhythmias and cardiac death. Previous studies assessing ECG-derived APDR surrogates report increased risk for ventricular arrhythmias or death in patients with ICMP  and non-In this study we developed action potential models using average, cohort-specific, clinically obtained APDR, but this pipeline could be used for development of action potential models to patient-specific APDR and even region-specific APDR (within the same patient), capturing the spatial dispersion of APDR. APDR heterogeneity is a critical substrate for arrhythmogenesis and degeneration of VT to VF  and it iCoupling machine learning with computer-based simulations is an emerging approach as it provides means to comprehensively analyze the wealth of high-dimensional, complex data produced by simulations . In thisThis is important because simulations using the parameter space centroids of clusters produce the average dynamics of the population of derived models rather than the dynamics of the non-unique “best-fit” model. If the emergent dynamics of interest are the same between the best-fit model and the most dissimilar clusters, this suggests a reliable model development with small variability and uncertainty in the population of derived models. Alternatively, if the emergent dynamics of interest are different between the best-fit derived models and/or different clusters, this suggests that either the model derivation method was inadequate or that there is more than one emergent dynamic behavior in the derived model population. If there are concerns of inadequate model development, then a more detailed sensitivity analysis and tuning of the model development algorithm is warranted. Otherwise, the presence of more than one emergent dynamic behaviors among different clusters demonstrates the variability and uncertainty present in the derived model population with respect to the emergent behaviors of interest. Should such derived models be used in Virtual Heart modeling studies for different hypothesis testing, then simulations should be executed using the centroids of clusters with different emergent behaviors. This will result in the uncertainty present in the population of derived models to be captured in the Virtual Heart modeling study.in-vivo difference in cellular EP. Phenomena such as post-repolarization refractoriness cannot be explicitly captured. Development of action potential models that capture true cellular EP would require cellular EP measurements and maneuvers (This study has several limitations. First, we developed action potential models using cell-level simulations, whereas the clinical measurements represent a tissue-level behavior. Development of action potential models using tissue-level simulations might yield different parameter results. However, considering the large population of individuals and generations that we used in the GA, model development using tissue-level simulations would be computationally not tractable. To address this limitation, we performed tissue-level simulations to assess the APDR of GA-derived models. Both for SNLV and ICMP models, APDR in tissue-level was similar to that of cell-level simulations. Second, we did not incorporate action potential morphology specific to SNLV and ICMP patients in the model development process. We rather used the same action potential morphology template, derived from the baseline BOFC model, to constrain the model development process see . Incorpoaneuvers  that werIn silico, we demonstrated that ICMP APDR contributes to a more pro-arrhythmic tissue-level behavior. We coupled virtual heart modeling with machine learning to establish a robust and reproducible methodology to incorporate easily obtainable clinical EP measurements to cardiac action potential models and capture the uncertainty inherent to the model development process. We demonstrated that action potential models derived from ICMP patients capture the pro-arrhythmic potential of the underlying disease in simulations. Importantly, we showed that despite the variability in the derived action potential model population, even the most dissimilar clusters formed by this population exhibit the same emergent pro-arrhythmic behavior in cell- and tissue-level simulations. The methods that we present here can be used for model development in any disease state that affects ventricular repolarization and restitution, contributing to the emergent field of precision medicine. Virtual heart models incorporating disease-specific EP properties have the potential to result in improved risk stratification and therapeutic planning and this is the focus of our future research.This is the first study to characterize the electrical restitution properties of the non-infarcted LV myocardium of ICMP patients. We clinically characterized the pro-arrhythmic substrate of ICMP patients and demonstrated that it has a steeper APDR compared to SNLV, indicating the presence of EP remodeling in the non-infarcted LV myocardium. The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The studies involving human participants were reviewed and approved by the Johns Hopkins IRB. The patients/participants provided their written informed consent to participate in this study.KA did substantial contributions to the conception and design of the work, the acquisition, analysis and interpretation of the data for the work, and drafting the work. RB, PB, HA, and NT did substantial contributions to the design of the work and data interpretation and revising it critically for important intellectual content. TB, JC, SJ, JM, SS, HT, and HA did substantial contribution to data acquisition, analysis, and interpretation. All authors provided the approval for publication of the content and agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work were appropriately investigated and resolved.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The Institutional Review Board approved this study. Mortality data were obtained from the Population Register Center with a follow-up coverage of 100%.This study includes data on 293 patients who underwent TAVR with newer generation devices  and 3-year mortality   or STS score .8 A few studies investigated whether BNP/pro-BNP may increase the predictive ability of current risk-scoring methods in patients undergoing cardiovascular interventions but not all studies were able to demonstrate this effect when BNP/pro-BNP was added to the EuroSCORE or STS scores.14 In the present study, baseline BNP levels were predictive of 30-day and 3-year mortality when adjusted for other independent clinical risk factors. However, when adjusted for the STS score and the EuroSCORE II, only BNP dichotomized according to its cutoff value of 690 pg/ml was predictive of 3-year mortality. We speculate that the relatively small size of this series might lead to type II error.The present study confirmed that BNP was an independent predictor of early and late mortality after TAVR when adjusted for other significant variables.The present findings showed that baseline BNP levels were predictive of early and mid-term mortality after TAVR with newer generation devices. However, the incremental prognostic value of BNP in TAVR over current risk scores may be limited and should be further assessed in larger studies.There are no conflicts of interest.


Acute lung injury (ALI) often causes severe trauma that may progress to significant morbidity and mortality. ALI results from a combination of the underlying clinical condition of the patient  with a secondary insult such as viral pneumonia or a blood transfusion. While the secondary insult may be variable, the rapidly progressive disease process leading to pulmonary failure is typically mediated by an overwhelming innate immunological or inflammatory reaction driven by excessive complement and neutrophil-mediated inflammatory responses. We recently developed a ‘two-hit’ ALI rat model mediated by lipopolysaccharide followed by transfusion of incompatible human erythrocytes resulting in complement activation, neutrophil-mediated ALI and free DNA in the blood indicative of neutrophil extracellular trap formation. The objective of this study was to evaluate the role of peptide inhibitor of complement C1 (RLS-0071), a classical complement pathway inhibitor and neutrophil modulator in this animal model. Adolescent male Wistar rats were infused with lipopolysaccharide followed by transfusion of incompatible erythrocytes in the presence or absence of RLS-0071. Blood was collected at various time points to assess complement C5a levels, free DNA and cytokines in isolated plasma. Four hours following erythrocyte transfusion, lung tissue was recovered and assayed for ALI by histology. Compared to animals not receiving RLS-0071, lungs of animals treated with a single dose of RLS-0071 showed significant reduction in ALI as well as reduced levels of C5a, free DNA and inflammatory cytokines in the blood. These results demonstrate that RLS-0071 can modulate neutrophil-mediated ALI in this novel rat model. Acute lung injury (ALI) is often a complication of severe trauma that can progress to acute respiratory distress syndrome (ARDS) resulting in significant morbidity and mortality . To dateIn the case of TRALI, which represents one of the leading causes of transfusion-related mortality, this disease process is complex and not fully understood, however a ‘two-hit’ model is currently believed to most accurately exemplify the clinical situation with the first hit mediated by the underlying clinical condition of the patient and the second hit triggered by a component in the transfused unit , 11. VarOur laboratory has recently developed a novel two-hit rat model of ALI in which Wistar rats are infused with lipopolysaccharide (LPS) to stimulate neutrophils followed 30 minutes later with a transfusion of 30% incompatible erythrocytes to activate the classical complement pathway . Four hoOver the last few years, our laboratory has developed a novel family of anti-inflammatory molecules known as Peptide Inhibitors of Complement C1 (PIC1) that inhibit the classical pathway of complement inhibit neutrophil-mediated myeloperoxidase (MPO) and NET activity –20 and eAnimal Research: Animal research was approved by the Eastern Virginia Medical School (EVMS) IACUC. For euthanasia of rats, animals deeply anesthetized with a cocktail of ketamine/acepromazine were subsequently subject to isoflurane inhalation followed by decapitation by guillotine. Adolescent male Wistar rats (200–250 g) were purchased from Hilltop Lab Animals  with indwelling jugular catheters. Care and handling of the animals were in accord with NIH guidelines.Human subjects research: Human subjects research was approved by the EVMS IRB, protocol #02-06-EX 0216. Written consent was obtained. A healthy human volunteer (type AB+) donating whole blood was used as the source of purified human erythrocytes.10 cells/ml did not reveal any viable contaminating human granulocytes.Human erythrocytes from an AB+ donor were acquired the day before the animal experiments and processed as described previously . BrieflySalmonella enterica serotype enteritidis, 2 mg/kg  ) was administered intravascularly through the indwelling jugular catheter as the ‘first-hit’. This was followed 30 minutes later by 30% ABO mismatched erythrocyte transfusion as the ‘second-hit’  and at 5, 60, and 240 minutes after erythrocyte transfusion . Plasma Scoring of lung injury was performed by the following methodology: fixed lung tissue was stained with hematoxylin and eosin (H&E) and images were visualized with a microscope  at a magnification of 20X at room temperature. Images of randomized microscopy fields were acquired with a digital camera  and were converted to black and white images and the pixels were quantified by ImageJ (NIH) analysis. The ratio of black to white pixels was then determined. A minimum of 10 images were analyzed per slide for each animal.C5a levels were measured from plasma samples by ELISA, according to the manufacturer’s instructions  as previously described . BrieflyFree DNA was measured by PicoGreen in rat plasma samples as previously described . BrieflyPlasma samples were analyzed for cytokines and chemokines by the Cytokine Core  using xMAP bead-based immunoassay technology specific for rat. Plasma samples were analyzed for the following experimental groups: sham, 1-hit, 2-hit, 2-hit + 10 mg/kg prophylactic dose RLS-0071, 2-hit + 160 mg/kg prophylactic dose RLS-0071, 2-hit + 40 mg/kg rescue dose RLS-0071 at 30 seconds, and 2-hit + 160 mg/kg rescue dose RLS-0071 at 30 seconds. For each cytokine reported, two replicates were run for each animal. Data are means and standard error of the means.Data are represented as mean and standard error of the mean. A Generalized Linear Model was used for analyzing the level of lung damage between experimental groups. The comparisons between experimental groups in C5a, DNA, and cytokines were conducted using bootstrap approach or Welch’s ANOVA. The multiple comparisons in C5a and DNA were two-sided and analyzed by using bootstrap approach and Games-Howell methods. The comparisons in cytokines variables were one-sided using 2-hit as the control group and performed using Dunnett’s test. All statistical tests were performed using R 3.5.2 and SPSS 26 . P value ≤ 0.05 was considered statistically significant.Our previously developed two-hit ALI model is initiated by infusion of LPS (first hit) into Wistar rats followed 30 minutes later with transfusion of 30% incompatible erythrocytes (second hit) and sacrifice of the animals 4 hours later . Lungs oTo determine the level of lung tissue protection by RLS-0071 in this model, grading of H&E sections for cell wall thickening for the different treatment groups was performed. Images of randomized microscopy fields were converted to black and white and quantified by ImageJ (NIH) analysis. The ratio of black to white pixels was then determined as a measure of lung damage: as lung damage increases, the alveolar walls thicken, shrinking the alveolar space (white space), resulting in a decrease in white pixels and increase in black pixels. Consistent with the lack of tissue damage directly visualized by microscopic observation of the H&E sections, sham animals and animals receiving the LPS first-hit only had low lung injury scores whereas animals receiving the 2-hit insult demonstrated a much higher injury score as previously demonstrated  21]. An. An21]. We had previously demonstrated that the complement system is activated in this rat model as measured by blood levels of C5a taken at various time points after the second hit . AnimalsNeutrophil extracellular traps (NETs) released from activated neutrophils have been previously shown to play a pathogenic role in a variety of autoimmune, metabolic and inflammatory diseases . NETs haIn severe cases of ALI, alveolar macrophages and epithelial cells may release significant amounts of pro-inflammatory cytokines that exacerbate the disease process leading to acute respiratory disease syndrome (ARDS). This so-called ‘cytokine storm’ has been well documented for virally-induced ALI, in particular the aggressive inflammatory response associated with severe outcomes in COVID-19 . Given tThe objective of this study was to determine if the anti-inflammatory molecule RLS-0071 was able to mitigate ALI in a novel 2-hit rat model that we have described previously . The LPSALI ensues following activation of the complement cascade and innate immune response by an external trigger such as a viral infection  or transfusion and is influenced by the underlying health status of the patient. Complement activation occurs within seconds leading to neutrophil recruitment to the lung tissue and activation of these cells to produce NETs as well as recruit and activate macrophages which in turn produce inflammatory cytokines. This temporal amplification of the immune response leads to a hyperinflammation state that may progress to ALI/ARDS and death . The potThis study demonstrates that a single dose of RLS-0071 given prophylactically or as a rescue therapy can modulate neutrophil-mediated ALI in this novel 2-hit rat model preventing ALI and inflammatory cytokine release. The ability of RLS-0071 to mitigate ALI in this two-hit model has potential for utility as a clinical therapeutic for virally induced ALI or TRALI. Additionally, it may have efficacy in other acute neutrophil-mediated pulmonary exacerbations characterized by a dysregulated immune response such as COPD or steroid-refractory neutrophilic asthma.S1 Data(XLSX)Click here for additional data file.


O(n2) instead of the O(n6) time complexity of the naive implementation of Sankoff-style algorithm for input RNA sequence of length n.Effective embedding is actively conducted by applying deep learning to biomolecular information. Obtaining better embeddings enhances the quality of downstream analyses, such as DNA sequence motif detection and protein function prediction. In this study, we adopt a pre-training algorithm for the effective embedding of RNA bases to acquire semantically rich representations and apply this algorithm to two fundamental RNA sequence problems: structural alignment and clustering. By using the pre-training algorithm to embed the four bases of RNA in a position-dependent manner using a large number of RNA sequences from various RNA families, a context-sensitive embedding representation is obtained. As a result, not only base information but also secondary structure and context information of RNA sequences are embedded for each base. We call this ‘informative base embedding’ and use it to achieve accuracies superior to those of existing state-of-the-art methods on RNA structural alignment and RNA family clustering tasks. Furthermore, upon performing RNA sequence alignment by combining this informative base embedding with a simple Needleman–Wunsch alignment algorithm, we succeed in calculating structural alignments with a time complexity of  Unstructured data, such as biological sequences and networks, require an embedding operation that encodes the unstructured data into a high-dimensional numerical vector space. This is a necessary step for processing unstructured data in downstream analysis using computational models such as neural networks. In the deep learning field, embedding using the pre-training framework with a large set of unlabelled data has been shown to be effective for the downstream supervised learning task even when smaller size of labelled data is available. When embedding an RNA sequence, each nucleotide  is usually encoded to a numerical representation so that the RNA sequence is embedded into a numerical vector. An effective embedding method further attempts to encode contextual information into the numerical vector representation . Word2vec, an effective word embedding technique  are not large enough to obtain an effective embedding when dna2vec is applied to base-by-base DNA sequence embedding.Recently, DNA, RNA and amino acid sequences have been attempted to be effectively embedded using deep representation learning, especially techniques developed in the field of natural language processing . These sechnique  that vecTwo recently developed state-of-the-art embedding methods, namely, embeddings from language models (ELMo) and bidirectional encoder representations from transformers (BERT), are used to generate context-sensitive distributed word representations ,7. In thIn this study, we propose RNABERT for the effective embedding of RNA bases by adopting the pre-training BERT algorithm to non-coding RNA (ncRNA). We apply informative base embedding to encode the characteristics of each RNA family and structure. To see whether this informative base embedding technique successfully captures these characteristics, we apply RNABERT to two basic RNA sequence analysis tasks: structural alignment and clustering. Then, we evaluate the quality of the informative base embedding results by structural alignment of RNA sequences and by RNA family clustering.O(n6) for the length n of input RNA sequences, and accelerating the Sankoff algorithm is an unsolved hard problem (O(n2) using the dynamic programming technique. Hence, we aim to apply the informative base embedding to determine the position-dependent and secondary structure-dependent score matrix in calculating alignments so that the structural alignment is obtained using a simple Needleman–Wunsch algorithm instead of the computationally expensive Sankoff-style algorithm.The first important problem in RNA sequence analysis is the structural alignment of RNA sequences, which calculates the alignment of not only RNA sequences but also their secondary structures. The most influential method for the structural alignment of RNA sequences is the Sankoff algorithm, which simultaneously performs secondary structure prediction and alignment . However problem . While S problem  and Dyna problem  calculat problem  determinBuilding an appropriate clustering algorithm for ncRNAs is an effective step towards unsupervised analysis of ncRNA sequences without their family labels ,16, as hFor our goals of RNA structural alignment of lower computational complexity and accurate RNA family clustering, we construct an informative base embedding method, RNABERT, for RNA sequences that takes into account the context and secondary structure of RNA sequences through two training tasks: MLM and structural alignment learning (SAL). In RNABERT, pre-training is performed using a large number of unlabelled ncRNA sequences. RNABERT introduces a novel pre-training task, SAL, in addition to the usual MLM task to more explicitly incorporate RNA secondary structure information into the base embedding for structural alignments. The SAL task employs pre-training using seed alignments obtained from the Rfam database  so that The architecture of the RNABERT model consists of three components: token and position embedding, a transformer layer and pre-training tasks. The input to RNABERT is an RNA sequence. First, the token embedding randomly generates a 120-dimensional numerical vector that encodes four RNA bases  and assigns the same vector to each base in the input RNA sequence. Second, the position embedding generates a 120-dimensional vector that encodes the position information of each base in the input RNA sequence. Third, the element-wise sum of token embedding and position embedding for each base in the input RNA sequence is fed to the transformer layer. The transformer layer component consists of a stack of six transformer layers, each of which is composed of a multi-head self-attention mechanism followed by a feedforward neural network. The final output from the transformer layer is an informative base embedding, denoted The self-attention mechanism  is a cenThe self-attention mechanism is described as mapping a query and a set of key-value pairs to an output sequence, where the query, key, and value are all matrices: query MLM is a task that masks a part of the input RNA sequence and predicts the masked part using the surrounding bases. The MLM task performs a base embedding so that the masked part can be restored, which enables context-sensitive embedding. First, 15% of the bases are randomly selected in a given RNA sequence for training. Next, one of the following three actions is performed on the selected base in the input: 80% of the selected bases are replaced with a token indicating an unspecified base  for the input RNA sequence of length n.A pairwise RNA sequence alignment based on the base embedding is calculated using the Needleman–Wunsch algorithm using the n and m. The similarity RNA family clustering is performed as the second evaluation test to confirm the quality of the informative base embedding. A similarity measure between two RNA sequences with respect to soft symmetric alignment  is definThe similarity O(n6) for RNA sequences of length n. PMcomp takes base-pairing probability matrices generated using McCaskill’s algorithm as the input and incorporates the energy information of each sequence into these matrices to quickly find common secondary structures and alignments (O(n4) is achieved by simplifying the dynamic programming method utilizing the fact that the base-pairing probability matrix is actually sparse. SPARSE (O(n3). R-Coffee is a multiple RNA alignment package that takes a similar strategy with our study by utilizing an alignment-scoring scheme that incorporates secondary structure information (O(n2). As R-Coffee makes use of the base-pairing probability calculated with McCaskill’s algorithm, it is considered as a type of structural alignment algorithm. TOPAS is a network-based scheme for pairwise structural alignment of RNAs that can handle pseudoknots (O(n4) in the worst case. TOPAS employs graph data structures to represent the RNA secondary structure including pseudoknots and designs an efficient algorithm to calculate an alignment of two graph structures by matching two nodes in two different graphs. Finally, MAFFT v7  and F1 score, which are calculated as follows. The number of true positives (TP)  is the number of positions Clustering accuracy was measured with the Rfam family as the true reference class. Three indices, namely, the adjusted Rand index (ARI), homogeneity, and completeness, were used to evaluate the clustering performance. The ARI is a measure of how well two types of clustering results match. ARI takes a real number from -1 to 1: if the value of ARI is -1, the two clustering results do not match at all, while a value of 1 indicates that they completely match. In this study, the ARI reflects how close the predicted clustering result is to the true reference class composed of the Rfam family.The ARI is derived from the Rand index (RI), defined as follows:For the pre-training of the MLM task, 76 237 human-derived small ncRNAs with lengths ranging from 20 to 440 bases from RNAcentral  were utiIn the training of the SAL task, two types of datasets, named TrainSet-A and TrainSet-B, were devised. In both datasets, the pairwise structural alignment extracted from Rfam alignment  was usedFor the structural alignment benchmark, we utilized the BRAliBase2.1 k2 database  used in To evaluate the clustering accuracy of RNABERT, the test dataset was collected from the BRAliBase2.1 database. The multiple alignment of each ncRNA family provided by the database was treated as a true reference cluster, and each ncRNA sequence in the multiple alignment was treated as a member sequence. All reference clusters with a sequence identity of <40% were selected. The dataset contained 37 RNA sequences and 12 RNA families. The RNA sequences used in the RNA family clustering test did not overlap with those used for the pre-training of the SAL task.The RNABERT model was implemented using PyTorch for deep learning. All experiments were run on Linux Red Hat 4.8.5–2  Xeon(R) Gold 6148). Optuna  was usedt-distributed stochastic neighbour embedding (t-SNE)  , which i (t-SNE) , left an (t-SNE) , right. Table O(n2) for two sequences of length n. We achieved high-speed computation by implementing the deep learning algorithm using Python and PyTorch while implementing the Needleman–Wunsch algorithm in C++. Note that the loading time of the transformer model into the GPU was excluded from the time measurement of pairwise alignment by RNABERT. The typical amount of time needed to load the transformer model onto GPU was around 4.376 s. In addition, the maximum memory consumption for the RNA structural alignment was around 35.2G bytes in RNABERT.In terms of computation time, RNABERT was faster than the existing state-of-the-art algorithms and even faster than the sequence-based  alignment algorithm MAFFT. The alignment computation of RNABERT consists of three sub-procedures: the first procedure (transformer) obtains the embedding of each base, the second procedure calculates the match score between the two input sequences, and the third procedure calculates the alignment by the Needleman–Wunsch algorithm. The first two procedures can be accelerated by GPU computation, and the Needleman–Wunsch algorithm is a simple algorithm that requires a computation time of Figure Table Several well-known sequence motifs in the snoRNA and tRNA families were identified by observing the attention maps. Attention maps, which indicate the ratios of contribution to the MLM task, were extracted from the final transformer layer of RNABERT, and sequence motifs were detected from the attention maps. The ‘UUCGA’ sequence motif shown in Figure In this study, we performed two tasks to obtain informative base embeddings. The MLM task is a fundamental step in the original BERT algorithm, whereas SAL is a novel RNA sequence-specific task introduced in this study. To determine whether these tasks effectively incorporate RNA secondary structure information into base embeddings, we performed two tests, RNA clustering and sequence alignment.O(n2) for two sequences of length n.Sankoff-style algorithm provides high structural alignment accuracy, but these algorithms are usually very complex in both time and space. Unlike the many structural alignment algorithms based on the Sankoff algorithm, RNABERT does not explicitly consider RNA folding and boasts a high structural alignment accuracy. This is considered to be evidence that the base embedding encodes the secondary structure information specific to RNAs. Furthermore, while RNABERT achieves the same accuracy as Sankoff-style algorithms, it is much faster because it uses a simple sequence-based alignment algorithm. In fact, the time complexity of the RNABERT algorithm is only SPARSE  achievesPerformance evaluation was done for two types of training datasets, TrainSet-A and TrainSet-B. TrainSet-A contains the same RNA families as the benchmark test dataset while TrainSet-B has no RNA family overlap with the test dataset. When TrainSet-A was used, RNABERT exhibited a superior accuracy than state-of-the-art existing structural alignment methods. When TrainSet-B was used, the performance of RNABERT was still sufficiently high and comparable to the one using TrainSet-A. This result shows that RNABERT has succeeded in proposing a new scoring scheme for sequence-based alignment algorithms to accomplish RNA structural alignment and has sufficient generalization ability. It has to be noted that with the development of high-throughput sequencing, hundreds of thousands of ncRNAs have been detected, but many have not been annotated yet. In fact, 86% (24 972 896) of the 28 895 596 ncRNAs present in RNAcentral do not have gene ontology (GO) annotations. Therefore, fast and accurate structural alignment of unknown sequences of existing RNA families is still practically valuable and RNABERT could contribute to the annotation of such novel transcripts.The base embeddings obtained by RNABERT are applicable to various fields in RNA informatics. One immediate problem is the multiple structural alignment of RNA sequences. RNABERT can be expected to accomplish this task by combining existing sequence-based multiple alignment algorithms such as MUSCLE  and MAFFructures ,41,42. Shttps://github.com/mana438/RNABERT.git.The codes, pre-trained RNABERT model, and all datasets used in this study are available at lqac012_Supplemental_FileClick here for additional data file.


As the pressure of the diabatic nanofluid and/or non-continuum-flows rises, average-mean-free-path diminishes and thus, the Knudsen-number lowers heading to a zero-slip wall-boundary condition with the compressible-viscous-flow regime in the nanoscale-tubes leading to Sanal-flow-choking due to the sonic-fluid-throat effect. At the Sanal-flow-choking condition the total-to-static pressure ratio  is a unique function of the heat-capacity-ratio of the real-world flows. The innovation of the nanoscale Sanal-flow-choking model is established herein through the entropy relation, as it satisfies all the conservation-laws of nature. The physical insight of the boundary-layer-blockage persuaded nanoscale Sanal-flow-choking in diabatic flows presented in this article sheds light on finding solutions to numerous unresolved scientific problems in physical, chemical and biological sciences carried forward over the centuries because the mathematical-model describing the phenomenon of Sanal-flow-choking is a unique scientific-language of the real-world-fluid flows. The 3D-boundary-layer-blockage factors presented herein for various gases are universal-benchmark-data for performing high-fidelity in silico, in vitro and in vivo experiments in nanotubes.Evidences are escalating on the diverse neurological-disorders and asymptomatic cardiovascular-diseases associated with COVID-19 pandemic due to the Sanal-flow-choking. Herein, we established the proof of the concept of nanoscale Sanal-flow-choking in real-world fluid-flow systems using a closed-form-analytical-model. This mathematical-model is capable of predicting exactly the 3D-boundary-layer-blockage factor of  Sanal flow choking leads to asymptomatic aneurysm5, hemorrhagic-stroke6, acute myocardial infarction7 and other neurological-disorders12 on Earth and Human spaceflight if the vessel geometry is having divergence, bifurcation, stenosis and/or occlusion regions. Although the interdisciplinary science of nanotechnology has been advanced significantly over the last few decades, there were no closed-form analytical models to predict the three-dimensional (3D) boundary-layer-blockage (BLB) factor of nanotubes until the theoretical discovery of Sanal flow choking phenomenon5. Herein, the proof of the concept of nanoscale Sanal flow choking in diabatic flows (flows involving the transfer of heat) is established and the exact values of the 3D-BLB factors of various gases passing through a cylindrical nanotube are reported. The accurate prediction of the 3D-BLB factor in the sonic-fluid-throat region  of a nanotube presented herein for each gas is a universal benchmark data for performing high-fidelity in silico, in vitro and in vivo experiments for the lucrative design optimization of nanoscale fluid flow systems in gravity and microgravity environments. It also aims for discovering the high-efficacy drug for prohibiting the undesirable Sanal flow choking in the blood circulatory system causing asymptomatic cardiovascular diseases and neurological-disorders. Note that these asymptomatic cardiovascular and neurological disorders are experienced in Earth12 and Human spaceflight12. Note that high heat capacity ratio (HCR) of the fluid can delay the undesirable Sanal flow choking and streamtube flow choking that cause shock wave12 and detonation15 in real-world fluid flow systems because high HCR increases the critical total-to-static pressure ratio (CPR) for flow choking. The series of studies conducted by Kumar et al.15 reveal that the systolic-to-diastolic blood pressure ratio (BPR) is the risk factor of Sanal flow choking causing asymptomatic cardiovascular diseases and neurological-disorders15. Kumar et al.15 established conclusively that the heat capacity ratio is the controlling parameter of fluid viscosity and its turbulence for negating the undesirable Sanal flow choking due to the BLB factor13. Therefore, the accurate estimation of the 3D BLB factor of diabatic flows in a cylindrical nanotube is a meaningful research objective for performing high-fidelity in silico, in vitro and in vivo experiments for various applications in physical, chemical, and biological sciences, which we have carried out herein through mathematical methodology as the mathematics is the unique language of the universe.Evidences are escalating on the diverse neurological disorders associated with COVID-19 pandemicSanal-flow-choking13 and streamtube-flow-choking15  for high precision applications23. The design of such systems are currently a subject of great interest in aerospace, chemical, material, biomedical, and allied industries. This is particularly true for the design optimization of nanoscale aerospace systems in the international space station (ISS) and the micro-nanoscale-thrusters25 operating at both gravity and microgravity environments where the flow field exhibit both the continuum and non-continuum fluid properties. In such physical situations multiscale and hybrid modeling approaches are encouraged25.The theoretical discovery of the 12 reported that hemorrhagic-strokes in multiple regions of the cerebral artery causing neurological disorders are due to biofluid/Sanal flow choking  including capillaries, vasa vasorum and/or nanoscale vessels in both hypertension or hypotension subjects at a critical blood pressure ratio15. At the threshold of the Sanal-flow-choking condition, a minor oscillation in the blood pressure ratio (BPR = SBP/DBP) for both hyper and hypo subjects is likely to aggravate the risk of the brain hemorrhage in Covid-19 patients, which is corroborated with the clinical report presented by Razavi et al.26 from Mazandaran University of Medical Science, Iran. Brain computed tomography of this Covid 19 patient , with no history of hypertension or anticoagulation therapy, revealed a massive intracerebral hemorrhage (ICH) in the right hemisphere, accompanied by intraventricular and subarachnoid hemorrhage. It is crystal clear from this case report that this Covid-19 patient experiences gas embolism as his temperature exceeds 37 °C, the evaporation temperature of blood of a healthy subject7 and the BPR of the patient exceeds the CPR for nanoscale Sanal flow choking15. Note that blood vessels in the brain circulatory system with sudden expansion, divergence or bifurcation regions without any apparent occlusions , which gives an explicit clue of the type of flow, viz., the continuum or non-continuum. Note that numerous modeling efforts have been reported in the open literature for nanoscale flow simulation without authentic code verification using any benchmark data and/or any closed-form analytical solution38. The fact is that generating benchmark data for compressible viscous flow from the nanoscale system is a challenging task or quite impractical by using conventional in vitro methods and/or in vivo animal models. And it is anticipated that the classical assumptions on the hydrodynamic model will ride into hitches as the composite flow system reaches nanometer (nm) size19.39 and mortality. A few authors utilized maximum likelihood method and Bayesian paradigm41. Shafiq and Sindhu44, carried out various studies pertaining to nanofluid flow with specific attention on the unsteady boundary layer flow of an incompressible Williamson fluid over a permeable radiative stretched surface45. Hayat47, Khan53 Muhammad56, and their collaborators62 put considerable efforts for modeling the entropy generation with constant density in creeping nanofluid and ferrofluid flow with slip condition. Entropy optimized Darcy-Forchheimer flow with magnetohydrodynamic over a stretched surface59, influences of skin friction coefficient47, stagnation point flow of a viscoelastic nanofluid towards a stretching surface with nonlinear radiative effects58, and the influence of carbon nanotubes in the Marangoni convection boundary layer flow of the viscous fluid were considered in their studies46. All these studies62 would be useful for in silico simulation of creeping incompressible nanofluid flows. The authors can extend their modeling efforts by incorporating the compressibility effect for reaching the physical situation of nanoscale Sanal flow choking for solving the real-world fluid flow problems with credibility. Obviously, due to the lack of universal benchmark data for an authentic verification of the in silico results, the conclusions drawn using sophisticated models, by various investigators across the globe, viz., direct simulation Monte Carlo (DSMC), molecular dynamics (MD), Burnett equation, and the hydrodynamic models, will not be endorsed by the high precision industries for the highly expensive nanoscale aerospace systems design for practical applications. Admittedly, an exact prediction of the BLB factor is inevitable for in silico, in vitro and in vivo flow choking experiments and data verification for drug discovery. Note that nanoscale drug delivery devices can be tailored for site-specific therapeutic activity38.Of late, various modeling studies have been reported on Covid-19 pandemic and neurological outcome31 reported that in vitro data well matched with the predicted results using the hydrodynamic Navier Stokes method with the first-order slip condition for the range of average pore diameters from 169–220 nm. Singh and Myong63 reported that neither continuum models nor free-molecular models could be invoked for fluid flow cases when the Knudsen number falls in the intermediate range between the continuum (Kn ≤ 0.01) and free-molecular flow regimes (Kn ≥ 10). When the Knudsen number becomes large (Kn > 0.01), the conventional assumptions of no-slip boundary condition, thermodynamic equilibrium, and linear stress–strain relationship fail. When the pressure of the nanofluid rises, the average-mean-free-path diminishes and thus, the Knudsen number lowers heading to a zero-slip wall-boundary condition with the compressible viscous flow regime creating streamline pattern in the nanoscale fluid flow system. Therefore, the Sanal flow choking and supersonic flow development leading to the shock-wave generation due to the sonic-fluid-throat effect at the zero-slip-length is a valid physical situation in the real-world fluid flows where CD shaped nanoscale streamtubes persists  that the time dependent mass flow rate predicted using their enhanced computational fluid dynamics (CFD) simulation matches well with full molecular dynamics (MD) simulation and highlighted that the traditional CFD results of such cases are incompetent. Of late (2020), Zhao et al.65 reported that the soundness of the traditional theories at the microscale and nanoscale has been taken into question. Authors reported that the thermal fluctuations are spontaneously occurring within molecular dynamics (MD) simulations. The study conclusions of the previous researchers47 lead to say that in real-world scientific experiments of complex nano-microscale systems the robustness of in silico model needs to be tested by featuring the actual fluid characteristics in a non-trivial geometry at the nanoscale. Singh and Myong63 reported that for improved modeling efforts, the joint effect of material properties, the scale and shape of the flowing medium on fluid flow must be taken into account, which is lacking now and hence we are addressing it herein through the closed-form analytical models satisfying the Sanal flow choking condition in diabatic nanoscale fluid flow systems. Based on this rationale, herein, the proof of the concept of fluid-throat persuaded Sanal-flow-choking in the nanoscale diabatic fluid flow system is established conclusively through an infallible closed-form analytical model. This model is capable to predict the three-dimensional (3D) boundary layer displacement thickness of diabatic flows in nanotubes, which is described in the subsequent section. The novelty of the closed-form analytical model reported herein stem from the authenticity that at the Sanal flow choking condition for diabatic nanoflows, all conservation laws of nature are satisfied in the unique sonic-fluid-throat location. Therefore, data generated from this closed-form analytical model can be taken as universal benchmark data for in silico, in vitro and in vivo experiments with confidence.Holland et al.The nanoscale Sanal flow choking occurs in real-world flows at a critical total-to-static pressure ratio irrespective of the boundary layer blockage in the nanotube. Figure Sanal flow choking5 is a compressible viscous flow effect, which occurs in any duct with uniform port geometry, due to the boundary layer blockage persuaded internal flow choking at a critical-total-to-static pressure ratio (CPR), as all real-world-fluids experience the Sanal flow choking phenomenon5. The CPR for flow choking (Eq. 1 of composite fluids would vary based on the lowest heat capacity ratio (HCR) of the evolved species at the constriction region (fluid-throat) of the streamtube Sanal floogy Eqs.  representhermal choking8 (Rayleigh flow effect69) condition. It gives the desirable inflow condition in terms of Mach number for achieving Sanal flow choking in a nanoscale diabatic fluid flow system, which is regulated by the material property viz., HCR (γ). The solution curve of Eq.  of gases decreases due to the decreases in CPR of the nanoscale flow system as dictated by Eq.  is known. Note that Maxial alters due to the flow turbulence and as on today there is no closed-form analytical solution for predicting Maxial at the unchoked fluid flow condition, which is a challenging research topic. Note that Eq.  with molecular precision at the condition prescribed by the Sanal-flow-choking for diabatic fluid flows. The data generated using Eq.  as benchmark data for comparison at the Sanal flow choking condition for real-world flows. The solution curve of Eq.  of the evolving gases for satisfying the condition set for the Sanal flow choking for real-world multiphase, multi-species nanoscale fluid-flow systems4.69 termed as Eq.  in micro-nanoscale hybrid thrusters  are  are Sanasee Fig. g with coVigneshwaran’s Table  with credibility.le Table  gives thnanoscale biological fluid flow system must always maintain the flow Mach number less than one as dictated by Eq. (7) for prohibiting asymptomatic cardiovascular diseases and neurological disorders due to Sanal flow choking. Equation  is  is nanosions Eq. –(7c) are69, are highlighted herein for demonstrating the various influencing parameters and the conflicting requirements to prohibit the Sanal flow choking in the nanoscale fluid flow system. Equation , de, de7c), Equation  reveals ion Fig. a–g. Therion Fig.  must be memory effect, aneurysm, and hemorrhagic stroke as the case may be. This is a grey area in nano medicine70, which needs to be examined in detail through fluid-structural interactive multiphase, multispecies models, which is beyond the scope of this article. The Sanal flow choking for the diabatic condition presented herein is valid for all the real-world fluid flow problems for designing various nanoscale fluid flow systems and sub systems due to the fact that the model is untied from empiricism and any types of errors of discretization. Using Eqs. (deflagration to detonation transition (DDT)15 with the given inlet flow Mach number and the lowest value of the HCR of the leading gas coming from the upstream port of the chemical system15. In a nutshell, the best choice of increasing the solid fuel loading in the nanoscale thruster design without inviting any undesirable detonation and catastrophic failures, is to increase the HCR of the working fluid. Further discussion on the nanoscale propulsion system design is beyond the scope of this article.Note that in a vascular system the boundary layer induced flow choking leads to the shock-wave generation and pressure-overshoot leading to ing Eqs.  and 2)  memory ei <  < 1) originated from the upstream port of the system could accelerate to the supersonic flow leading to an undesirable phenomenon of pressure-overshoot due to shock wave generation as a result of the Sanal flow choking. Through the proposed mathematical methodology, we could disprove the general belief of the impossibilities of internal flow choking in such real-world nanoscale fluid flow systems at the creeping inflow conditions. There was a general belief in the scientific community over the centuries that the subsonic/creeping flow would not be augmented up to supersonic flow without passing through a geometric throat, which we have disproved herein through the closed-form analytical model. Note that if the total-to-static pressure ratio at the fluid-throat is lower than the LCDI the detonation would not occur even if the blockage factor is relatively high in nanoscale fluid flow systems. The physical insight of the nanoscale Sanal flow choking and streamtube flow choking14 presented in this article sheds light on finding solutions to numerous unresolved scientific problems carried forward over the centuries. We concluded that the 3D-boundary-layer-blockage factors presented herein are universal-benchmark-data for performing high-fidelity in silico, in vitro and in vivo experiments in nanotubes with different working fluids with credibility. Briefly, discovery of nanoscale Sanal flow choking and streamtube flow choking in real-world flow offers disruptive technologies at the cutting edge to resolve century-long unresolved problems in physical, chemical and biological sciences.We have established herein that, due to the evolving boundary layer and the corresponding area blockage in the upstream port of any internal nanofluid flow system with sudden expansion or divergent region, the creeping diabatic nanoflow (M


Amine acid transformation is an important chemical process in biological systems. As a well-developed and acknowledged tool, chiral aldehyde catalysis provides good catalytic activation and stereoselective control abilities in the asymmetric reaction of N-unprotected amino acid esters and amino acid esters analogs, in which the key to success is the design of the catalysts derived from chiral BINOL aldehyde, which is based on the face control of enolate intermediates. In this review, one of the co-catalytic systems that combined with a transition metal to form a multiplex catalytic system and the well-established multiplex stereocenters of chiral aldehyde catalysis have been reviewed. Finally, a novel organocatalysis is prospected. In the last decades, the use of aldehyde catalysis is one of the most important and prevalent transformations in organic chemistry . It has Except for the research works, some literature reviews have referred to these areas. For example, Subrata Shaw and James D. White summarized recent advances in asymmetric catalysis using chiral salen–metal complexes. It puts an emphasis on asymmetric phase-separative resolution of amino acids. Sun Li et al. reviewed new options for asymmetric organocatalytic reactions of aldehyde catalysis. They described Zhao and his coworkers developed a novel asymmetric Mannich reaction by introducing chiral aldehydes. This review summarizes articles covering the period up to 2018. Based on the previous review works, combining with the latest research articles, the aspects about chiral aldehyde catalysis that used transition-metal catalysis or asymmetric 1,6-conjugated addition and Mannich reactions are reviewed and summarized.α-functionalization of primary amine and derivatives has an important impact in synthesis chemistry and is widely applied in the preparation of natural products and pharmaceuticals. Guo and his colleagues successfully synthesized a chiral BINOL aldehyde catalyst in 2014, which could directly catalyze the asymmetric α-functionalization reaction of the α-functional group of the N-unprotected amino ester  via imine activation (α-C-H bond of an amine can activate chiral BINOL aldehyde to form enamine through the corresponding 2-aza-allylic anion intermediates and deprotonation. Then the active imine carbon anion was formed and subsequently attacked electrophilic reagent. Finally, α-functional chiral primary amine was generated by the reversible in situ dissociation or amine exchange of imine. Although the enantioselectivity was improved by the utility of chiral BINOL aldehyde, the amino acid substrate could not be effectively extended, and the dosage of aldehyde catalyst is high. The development of efficient catalysts for amine acid transformation remains an elusive task. Inspired by this well-established enamine activation mode, synthetic chemists adopted this concept in the laboratory. Several biomimetic chiral BINOL aldehyde analogs or chiral pyridoxal analogs have been developed and employed in Mannich reactions (α-C–H bond of N-unprotected amines. It was based on the face control of the enolate intermediates. Chiral formyl BINOL aldehyde is an efficient nonpyridoxal-dependent catalyst that can promote the direct asymmetric α-functionalization of N-unprotected glycine esters. The successful usage of 2-formyl chiral BINOL aldehyde catalyst showed a high activity and stereoselectivity. It also expands the substrate including glycine esters, glycine amide, and glycine-derived dipeptides.The asymmetric tivation . In thiseactions , aldol reactions , cyclizaeactions , and Copeactions . In 2018eactions . The cateactions . Formyl α-allylation reaction of N-unprotected amino acid esters and allyl acetates, exhibiting a good yield and enantioselectivity. With the expansion of the application of chiral aldehyde catalyst, new catalytic technologies are emerging. Guo and his coworkers have disclosed chiral 3-formyl BINOL aldehyde catalyst of anti–1,6-conjugate addition and syn-Mannich reaction that was inspired by the intermediate ketimine in transamination. Another chiral 2-formyl BINOL aldehyde catalyst gave the syn-selective conjugate addition and anti-Mannich products. The good yields obtained both the syn- and anti-products of transformations with high diastereo- and enantioselectivity.Despite chiral aldehyde catalysis has become a powerful asymmetric synthesis strategy in amine chemistry, the development of catalysts for amine chemistry remains a great challenge. Inspired by a level of reactivity that could be achievable with the combinations of organic and transition-metal catalysts, Lei Chen and his coworkers provided a good strategy for the combination of chiral aldehyde catalysts with transition metals . In 2019The novel chiral 3-formyl BINOL aldehyde catalyst was displayed in the study of the Mannich reaction of 1,6-conjugated addition of amino acids (as shown in Chiral aldehyde catalysis promotes new methods to activate simple amines. However, no matter in the binary or ternary catalytic systems in asymmetric synthesis, the structurally diverse chiral aldehyde catalysts that were hardly achieved hampered the development of this field. Therefore, different aldehyde catalytic systems have been established. Professor Bing-Feng Shi has reported a system that synthesis of chiral aldehyde catalysts by Pd-catalyzed atroposelective C–H naphthylation . Jumpei In summary, the role of asymmetric catalysis by chiral aldehyde has grown rapidly in chemical reactions of amino acids. One limit is the reaction types. One more important limitation is how to get structurally diverse chiral aldehyde. Compared with binary catalytic systems, chiral aldehyde catalysts in ternary catalytic system not only acts as organic catalysts to activate amino acid and its derivatives through the formation of Schiff bases but also acts as ligands to promote the nucleophilic attack process. Importantly, compatibility also needs to be considered. Although the asymmetric catalysis involving chiral aldehyde has been grown in recent years, they are still rare. It is believed that the organic reactions catalyzed by chiral aldehydes are very important kind of asymmetric catalytic reactions, although some difficulties remain and new challenges will emerge. It is also believed that more researchers would involve and new and efficient chiral aldehyde catalysts will be developed.


Illness perceptions (IP) has been associated with self-management and health outcomes in individuals with chronic diseases such as heart disease and diabetes; however, there is less research on the relationship between IP and health outcomes in individuals with multiple chronic conditions (MCC). Older adults with MCC are more likely to experience poor outcomes such as hospitalizations and poor self-rated health yet, there is less understanding of the processes associated with these outcomes. The purpose of this study was to (1) explore the relationship between IP and self-rated health among older adults with MCC (2) explore the relationship between IP and the number of hospitalization within the past year among older adults with MCC. Understanding these relationships may be instrumental to designing targeted interventions to improve health outcomes for this population. 116 participants (ages 65-90) completed the illness perception of multimorbidity scale, modified general health subscale of the SF-36 questionnaire, and self-reported number of hospitalizations within the past year. Ordinal logistic regression was used for analysis. Older adults who reported negative IP were likely to report worse self-rated health and this relationship remained significant after controlling for age and number of chronic conditions {-0.032 (95% CI (-0.050 to 0.014) p< 0.05}. There was no significant relationship between IP and the number of hospitalization within the past year. The study results study suggest that IP is associated with self-rated health in older adults with MCC. IP may be useful to design targeted interventions to improve self-rated health in this population.