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Supplementary_Table_1 for The Peritoneal Dialysis Telemedicine-assisted Platform Cohort (PDTAP) Study: Design and methods by Tiantian Ma, Zhikai Yang, Shaomei Li, Huaying Pei, Jinghong Zhao, Yi Li, Zibo Xiong, Yumei Liao, Zhanzheng Zhao, Jing Xiao, Ying Li, Qiongzhen Lin, Zhaoxia Zheng, Liping Duan, Gang Fu, Shanshan Guo, Wenbo Hu, Yulin Li, Fuyun Sun, Nan Zhao, Qin Wang, Tianrong Ji, Beiru Zhang, Rui Yu, Li Hao, Guiling Liu, Li Zuo, Huiping Zhao, Caili Wang, Lirong Deng, Hongyu Chen, Li Li, Yulan Shen, Yong Zhang, Lihua Wang, Yan Yan, Zhigang Ma, Yingping Li, Xianchao Zhang, Xuejian Wang, Yirong Liu, Xinying Gao, Zhonggao Xu, Li Zhang, Shutong Du, Cui Zhao, Xiaoli Chen, Hongyi Li, Yingli Yue, Shanshan Chen, Yingchun Ma, Yuanyuan Wei, Jingwei Zhou, Jie Lv, Yingdong Zheng, Sainan Zhu, Minghui Zhao and Jie Dong in Peritoneal Dialysis International

Facing the huge challenges brought by changing market environment, the academic community is constantly looking for factors and combinations that can obtain excess returns on basis of traditional multi-factor stock selection model. Compared with the traditional linear multi-factor model, the machine learning algorithm can capture the more granular market signal by the nonlinear expression of the factor. To mine the stock factor data and optimize the stock selection model, this paper uses the equal weight linear model, machine learning support vector machine and linear regression algorithm for factor analysis. Based on the theory of SVM machine learning algorithm and multi-factor stock selection, this paper establishes and solves the SVR stock market forecasting model by characterizing the data. Then, we give and analyze examples after combining relevant data. The results show that the factors such as PB, PE, ROE, NetProfitGrowRate, OperatingRevenue-GrowRate, EPS and NegMktValue are outstanding. After putting excellent factors into the SVR model, the return rate of the stock portfolio is far greater than that of the traditional equal weight linear model, which indicates that the stock selection model using the machine learning algorithm has higher returns and stable results. This paper provides some guidance for decision makers to formulate stock picking strategies by mining stock factor data.

This paper describes a new methodology capable of analyzing coupled bending and torsional vibrations in non-uniform thin-walled beams. The transfer matrix method (TMM) and the differential transform method (DTM) are combined to create the proposed transfer differential transform method (TDTM) for solving equations coupling bending and torsional vibrations in non-uniform beams. Compared with the finite element method (FEM), the TDTM utilizes a type of changeable mode shape functions so that the number of meshed elements can be reduced greatly when the beam's geometric size is uniform. The equations of motion of the non-uniform thin-walled beams are established using Hamilton's principle. The method considers both the warping and rotary effects of the beam section. The natural frequencies and mode shapes of the bending and torsional components are obtained using the TDTM. The accuracy of solutions can be controlled by the mesh density and the series expansion order of the mode shape whose ranges are also discussed. For illustrative purposes, the natural frequencies and the frequency response curves of a uniform beam and a non-uniform beam are studied respectively and are validated by experiments. The effects of warping and the distance between the centroid of a given section and the corresponding shear center on the vibration properties of the beam are also investigated.

MnO 2 nanorods were synthesized by mechanochemical processing with subsequent heat treatment and their photocatalytic activity was studied on the decolourization of aqueous solution of Rhodamine B at different pH levels. A solid state redox reaction 2KMnO 4 + MnCl 2 → 3MnO 2 + 2KCl + O 2 was activated during mechanical milling. Excess KCl salt was added in the starting powder mixture to prevent agglomeration of MnO 2 nanoparticles. The milling resulted in the production of amorphous MnO 2 nanoparticles with a high surface area of 204 m 2 g −1 . Crystalline MnO 2 nanorods of diameters about 15–20 nm were produced by heating the as-milled powder at 350 °C for 1 h in air. Amorphous MnO 2 nanoparticles showed higher degradation rate of Rhodamine B than crystalline MnO 2 nanorods under simulated sunlight. The degradation rate was higher under acidic conditions. This work demonstrates the potential for cost effective, green and scalable synthesis of MnO 2 nano-catalysts for environmental applications.

Major et al. claimed that the patterns of proton transfer (Re- vs Si-face) and methyl transfer (C12 or C13) in our recent work [Wang et al. ACS Catal. 2017, 7, 5841−5846] on biocatalysis in trichodiene synthase (FSTS) contradict the so-called “well-established” spectrometric data and make “incorrect statements” on their previous work [Major et al. ACS Catal. 2017, 7, 812−818]. This response aims to clarify that the proton/methyl transfer styles are not yet validated experimentally, at least from their citations in the rebuttal paper [Major et al. DOI: 10.1021/acscatal.7b02823] and other studies we have found. Furthermore, the main conclusion (we proposed a general rule) in our previous work indeed is not dependent on those two reaction steps. In addition, we also compare the different views on reaction energetics, chemo-selectivity, and theoretical modeling for FSTS between Major’s and our work, which can serve as a framework for citation by other research groups and academic discussion in the future.

The development of novel isoform/class-selective inhibitors is still of great biological and medical significance to conquer the continuously reported side effects for the histone deacetylase (HDAC) drugs. The first potent HDAC allosteric inhibitor was discovered last year, and this allosteric inhibitor design is thought to be a promising strategy to overcome the current challenges in HDAC inhibitor design. However, the detailed allosteric mechanism and its remote regulatory effects on the catalytic/inhibitor activity of HDAC are still unclear. In this work, on the basis of microsecond-time-scale all-atom molecular dynamics (MD) simulations and picosecond-time-scale density functional theory/molecular mechanics MD simulations on HDAC8, we propose that the allostery is achieved by the intrinsic conformational flexibility of the binding rail (constituted by a highly conserved X-D residue dyad), which steers the loop-loop motion and creates the diverse shapes of the allosteric sites in different HDAC isoforms. Additionally, the rotatability of the binding rail is an inherent structural feature that regulates the hydrophobicity of the linker binding channel and thus further affects the HDAC enzyme inhibitory/catalytic activity by utilizing the promiscuity of X-D dyad. Since the plastic X residue is different among class I HDACs, these new findings provide a deeper understanding of the allostery, which is guidable for the design of new allosteric inhibitors toward the allosteric site and structure modifications on the conventional inhibitors binding into the active pocket by exploiting the intrinsic dynamic features of the conserved X-D dyad.

The Ca2(UO2)(CO3)3 complex has been shown to be the dominant species of uranyl in different aqueous environments, and thermodynamic data of the complexation have been measured accurately recently. However, a detailed understanding of the binding processes with explicit consideration of the water molecules in the presence of common salt ions such as Na+ and Cl– has been lacking. Here we use classical molecular dynamics combined with umbrella sampling to map the complete binding processes and their free-energy profiles leading to formation of the Ca2(UO2)(CO3)3 complex from UO22+, CO32–, and Ca2+ in an aqueous NaCl solution to simulate the seawater conditions. We find that the presence of Na+ ions affects the binding between UO22+ and CO32– as well as between [(UO2)(CO3)3]4– and Ca2+ by changing the coordination mode of carbonate to UO22+. The free energies of binding from our simulations are in good agreement with the experimental data for both pure water and the NaCl solution. Our work shows that free-ene...

The folding mode of substrate FPP in sesquiterpene cyclases/synthases is key to the chemo- and stereoselectivity of the ultimate sesquiterpene products. However, the precise substrate folding modes in most sesquiterpene cyclases are still elusive, and it is challenging for theoretical simulations due to the high flexibility of FPP. Herein, by DFT/MM MD simulations, we obtain the optimal folding mode of FPP in the 1,6-closure trichodiene synthase and illuminate the whole catalytic mechanism for the biosynthesis of trichodiene. Furthermore, a simple and practical rule is proposed to decipher the relationship between the diverse FPP folding modes and chemical selectivity toward 1,6- and 1,10-ring closure, which are common pathways in all sesquiterpene cyclases.

One of the current challenges present in uranium extraction from seawater is the competitive sorption of vanadium. But compared with uranium, much less is known about the solvation and speciation of the vanadate ion in seawater. Herein, we utilize both first principles molecular dynamics and classical molecular dynamics simulations to provide a microscopic insight into the solvation of the HVO 4 2− ion in pure water and in seawater. In pure water, we found that the dianion state is the most probable structure. But in a simulated seawater with 0.55 M NaCl, the NaHVO 4 − ion is most probable, followed by the neutral Na 2 HVO 4 ; averaging over 100-ns trajectory, the coordination number of Na + ions around V was found to be 1.5 within a radius of 4.0 A. We found that the NaHVO 4 − ion can exist in two interchangeable states: a bidentate state where the Na + ion interacts directly with two vanadate oxo groups; a monodentate where the Na + ion interacts with only one vanadate oxo group. From this monodentate state, the Na + ion can further dissociate away with a free-energy barrier of 2.5 kcal/mol. Our work therefore demonstrates that Na + ions are closely associated with the vanadate species in seawater.

A derivative formula, DGBX, which is composed of three herbs (Radix astragali,Radix Angelicae sinensis, andCoptis chinensisFranch), is derived from a famous Chinese herbal formula, Danggui Buxue Tang (DBT) (Radix astragaliandRadix Angelicae sinensis). We aimed to investigate the effects of DGBX on the regulation of the balance between proliferation and apoptosis of hematopoietic stem cells (HSCs) due to the aberrant immune response in a mouse model of aplastic anemia (AA). Cyclosporine (CsA), an immunosuppressor, was used as the positive control. Our results indicated that DGBX could downregulate the production of IFNγin bone marrow cells by interfering with the binding between SLAM and SAP and the expressions of Fyn and T-bet. This herbal formula can also inhibit the activation of Fas-mediated apoptosis, interferon regulatory factor-1-induced JAK/Stat, and eukaryotic initiation factor 2 signaling pathways and thereby induce proliferation and attenuate apoptosis of HSCs. In conclusion, DGBX can relieve the immune-mediated destruction of HSCs, repair hematopoietic failure, and recover the hematopoietic function of HSCs in hematogenesis. Therefore, DGBX can be used in traditional medicine against AA as a complementary and alternative immunosuppressive therapeutic formula.

A slotted waveguide phased array based on a single-ridged waveguide (SRWG) with enhanced scanning angle, wide impedance bandwidth and side lobes bandwidth, as well as low cross-polarization is designed. A transition structure is designed to feed the ridge waveguide with polarization torsion and conversion from the ridge waveguide to a standard rectangular waveguide. A single waveguide is divided into two subarrays to achieve small angle scanning in vertical dimension (yoz plane). An 8 × 8 array is designed and simulated to validate the slot antenna design. The bandwidth for VSWR＜2.0 is 3 GHz at the center frequency of 28 GHz. The realized gain at the center frequency is 24.0 dBi with antenna efficiencies better than 83%. The side lobes are controlled lower than -15dB over the entire working frequency, and the array can achieve a horizontal (xoz plane) scanning angle of ±45 °, and vertical scanning angle of ± 3 °, respectively.

A Ka-band high-gain dual-polarized microstrip antenna for 5G application is presented in this paper. The antenna is designed based on the multi-layer printed circuit board technology, which is cost effective and suitable for mass production. In order to improve the bandwidth and realized gain of the antenna array, a microstrip patch antenna with parasitic patches are designed. Each antenna element is fed by two orthogonal microstrip lines to realize both vertical and horizontal polarizations. The vertical polarization is fed directly by microstrip line, and the horizontal one is fed by coupling slot right below the patch. Besides, a crossover slot is cut in the parasitic patch to improve the isolation of cross polarization. An $8\times 8$ antenna array is designed with dual polarization. The feeding networks for the array are designed in different layers to improve the port isolation. A simulated bandwidth from 26.1 to 30.4 GHz ( $\text{VSWR} \leqslant 2$ ), and a peak realized gain up to 21.35 dBi are achieved for both polarizations. The port isolation is over 26 dB, and the cross polarization is below −25 dB. This antenna is a good candidate for 5G communication systems.

Staphylopine is a newly identified broad-spectrum metallophore for metal acquisition, and it plays important roles in the survival and virulence of Staphylococcus aureus and other pathogens in the metal-scarce environment in hosts. CntK catalyzes the first step of staphylopine synthesis by converting L-histidine to D-histidine to provide an essential building block of staphylopine. Herein, the crystal structures of S. aureus CntK (SaCntK) and its C72S variant are determined at 1.82 and 1.58 A resolution, respectively. SaCntK forms a homodimer and each subunit contains a two-domain α/β structure. Its overall structure resembles diaminopimelate epimerase, although their sequence identities are lower than 22%. SaCntK is specific for histidine, whereas other proteinogenic amino acids, with the exception of arginine, do not show any binding with SaCntK. Structural modeling suggested that residues Asn16, Glu46, Gln47 and Glu208 are responsible for specific substrate binding, and their substitutions significantly reduced the binding of histidine to SaCntK. Structural modeling suggested SaCntK uses a two-base catalytic mechanism, which has been observed in many cofactor-independent racemases. Our study provides critical insights into the structure and functions of CntK in staphylopine synthesis, which makes it helpful for developing potential antibiotics targeting the staphylopine-mediated metal acquisition process in bacteria.

Background: Several clinical practice guidelines noted the potential benefits of urate-lowering therapy (ULT) on cardiovascular disease (CVD) and chronic kidney disease (CKD) progression, however effect of this regimen remains much uncertainty. In this systematic review, we aimed to evaluate the efficacy of ULT on major adverse cardiovascular events(MACEs), all-cause mortality and kidney failure events. Methods: We systematically searched MEDLINE, Embase, and the Cochrane databases for trials published through April 2019. We included prospective, randomized, controlled trials assessing the effects of ULT on cardiovascular or renal outcomes. We extracted published data and did a meta-analysis of urate-lowering therapy on relative risks (RRs) of major adverse cardiovascular events, all-cause mortality, kidney failure events, and adverse events. Summary estimates of RR reductions were calculated with a random effects model. Findings: We identified 28 trials including a total of 9194 participants, of which 5070 participants received ULT, 4104 participants received placebo, usual-care or no treatment. Finally, 1279 MACEs, 377 deaths and 87 kidney failure events were recorded. Among all the population with 3103 (34·18%) participants having chronic kidney disease and 5718 (61·14%) having cardiovascular disease or stroke, ULT reduced the risk of MACEs [risk ratio (RR) 0·80, 95% confidence interval (CI) 0·67-0·95; I2 = 42·7%] and all-cause mortality (RR 0·80, 95% CI 0·66-0·97; I2 =0·0%), but had no effect on kidney failure (RR 1·04, 95%CI 0·43-2·42; I2 =64·4%). There was no significant difference (RR=0·99, 95% CI 0·95 to 1·03; I2 =55·7%) in the risk of adverse events between the participants receiving ULT and the control group. Interpretation: ULT has a beneficial effect on reducing the risk of MACEs and all-cause mortality. However, there is insufficient evidence to support an effect of ULT in reducing risk of kidney failure events. Funding Statement: This work was funded by National Key Research and Development Program of China (2018YFC1314004). JL was supported by the grant from the National Natural Science Foundation of China (no. 81270795), JZ was supported by the National Natural Science Foundation of China (81874401). Dr Badve is supported by a John Chalmers Clinical Research Fellowship with the support of Servier from The George Institute for Global Health. Declaration of Interests: Dr Badve reports grants from the National Health and Medical Research Council of Australia, personal fees from Bayer AG and Amgen Australia, and nonfinancial support from Bayer AG. Other authors listed in this paper declare no competing interests. Ethics Approval Statement: This study is registered with PROSPERO, number CRD42018104227.

Diabetic kidney disease (DKD) is a global pandemic, and microinflammation has been reported as an important pathogenic factor of DKD. Traditional Chinese Medicine (TCM) has been used in the treatment of DKD for thousands of years, and modern Chinese medicine studies have found that herbal medicines with heat-clearing property have a curative anti-inflammation effect in DKD. This article reviews the new clinical and experimental progress made in herbal medicines with heat-clearing property, in the treatment of DKD, as well as their safety aspects.

Uranium from the sea provides a long-time supply guarantee of nuclear fuels for centuries to come, and the neutral Ca2UO2(CO3)3 complex has been shown to be the dominant species of uranium in seawater. However, the solvation and structure of the Ca2UO2(CO3)3 complex in seawater have been unclear. Herein we simulate the Ca2UO2(CO3)3 complex in a model seawater solution via classical molecular dynamics. We find that Na(+) and Cl(-) ions interact very differently with the neutral Ca2UO2(CO3)3 complex in seawater. Especially, one Na(+) ion is closely associated with the Ca2UO2(CO3)3 complex, thereby effectively making the complex have a +1 charge, while Cl(-) ions are much farther away. Hence, this work reveals the important role of Na(+) ions in affecting the solvation of the Ca2UO2(CO3)3 complex in seawater, which has implications in designing ligands to attract the Ca2UO2(CO3)3 complex to the sorbent.

From a national strategic development perspective, statism and state administrative apparatus may be functional and thus desirable in the course of development of some nation-states. Continual monitoring of the development trajectory, however, is necessary to ensure that the respective state is prepared to address a critical question as raised by Nobel Laureate Prof. Joseph Stiglitz: development for what? Basing on literature review and field interview, this paper aims to underscore the basic problems that negatively affect China’s effort to enhance substantive rationality in its present course of development. Singled out are the logic of administration and state cadres’ dominant logic that have a direct bearing on the search for a substantively rational administrative state. Policy and research implications are discussed.

Histone Deacetylases (HDACs) are promising anticancer targets and several selective inhibitors have been created based on the architectural differences of foot-pockets among HDACs. However, the "gate-keeper" of foot-pockets is still controversial. Herein, it is for the first time revealed that a conserved R-E salt bridge plays a critical role in keeping foot-pockets closed in class-II HDACs by computational simulations. This finding is further substantiated by our mutagenesis experiments.

The present study investigated the expression of microRNA (miRNA or miR)-199a-5p in the peripheral blood of patients with primary hypertension, and examined its mechanism of action in vascular endothelial cell injury induced by hypertension. A total of 57 patients with primary hypertension, who were treated at the Affiliated Hospital of Qingdao University (Qingdao, China) between December 2014 and November 2015 were included in the present study. Peripheral blood was collected from all patients. The expression of miR-199a-5p was measured using reverse-transcription quantitative polymerase chain reaction analysis. Human umbilical vein endothelial cells (HUVECs) were divided into negative control, miR-199a-5p mimics and rescue (co-transfected with miR-199a-5p mimics and inhibitor) groups. After transfection, the proliferation and apoptosis of HUVECs were evaluated by a Cell Counting Kit-8 assay, a bromodeoxyuridine incorporation assay and flow cytometry. Western blot analysis was used to determine the expression of proteins involved in autophagy-associated and adenosine monophosphate kinase (AMPK)/unc-51 like autophagy activating kinase 1 (ULK1) signaling pathways. Laser scanning confocal microscopy and electron microscopy were used to observe the autophagy of HUVECs. The expression of miR-199a-5p was elevated in peripheral blood of patients with hypertension, and was correlated with the progression of hypertension. Overexpression of miR-199a-5p inhibited the proliferation and promoted the apoptosis of HUVECs. Upon expression of miR-199a-5p, the transition between microtubule-associated proteins 1A/1B light chain 3B (LC3B)I and LC3BII proteins was inhibited, the expression of p62 protein was upregulated. In addition, miR-199a-5p decreased the numbers of autophagosomes and autolysosomes in HUVECs. The present study demonstrated that expression of miR-199a-5p is positively correlated with the severity of hypertension. Expression of miR-199a-5p aggravated vascular endothelial injury by inhibiting autophagy and promoting the apoptosis of HUVECs via downregulation of the AMPK/ULK1 signaling pathway.

Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) Checklist. (DOC 135 kb)

Background Diabetic kidney disease (DKD) is a major microvascular complication of diabetes mellitus and the primary cause of end-stage renal disease. Existing therapies for DKD are not sufficiently effective. We report the protocol of a pragmatic randomized controlled trial of the use of traditional Chinese herbal medicine to treat patients with DKD. Methods/design This will be a multicenter randomized controlled trial. A total of 266 patients with DKD (106 with early stage, 80 with middle-stage, and 80 with advanced-stage disease) with an estimated glomerular filtration rate (eGFR) ≥ 30 mL/min/1.73m2will be included. Participants with DKD of each stage will be randomly allocated at a 1:1 ratio to either the experimental group, which will receive Xiaozhen formula and basic treatment, or the control group, which will receive basic treatment only. The study duration will be 24 weeks. The primary outcome will be urinary microalbumin excretion rate for early stage DKD, 24-h urinary protein for middle-stage DKD, and eGFR for advanced-stage DKD. Adverse events will also be evaluated. Data for all outcome indicators will be collected at baseline and weeks 4, 12, and 24. Discussion This study will provide evidence of the effectiveness and safety of traditional Chinese herbal medicine in treating patients with DKD. Trial registration Chinese Clinical Trials Registry: ChiCTR-IOR-16010072. Registered on 2 December 2016. Electronic supplementary material The online version of this article (10.1186/s13063-018-2749-6) contains supplementary material, which is available to authorized users.

Bromodomains (BRDs) are protein modules that selectively recognize histones as a "reader" by binding to an acetylated lysine substrate. The human BRD4 has emerged as a promising drug target for a number of disease pathways, and several potent BRD inhibitors have been discovered experimentally recently. However, the detailed inhibition mechanism especially for the inhibitor binding kinetics is not clear. Herein, by employing classical molecular dynamics (MD) and state-of-the-art density functional QM/MM MD simulations, the dynamic characteristics of ZA-loop in BRD4 are revealed. And then the correlation between binding pocket size and ZA-loop motion is elucidated. Moreover, our simulations found that the compound (-)-JQ1 could be accommodated reasonably in thermodynamics whereas it is infeasible in binding kinetics against BRD4. Its racemate (+)-JQ1 proved to be both thermodynamically reasonable and kinetically achievable against BRD4, which could explain the previous experimental results that (+)-JQ1 shows a high inhibitory effect toward BRD4 (IC50 is 77 nM) while (-)-JQ1 is inactive (>10 μM). Furthermore, the L92/L94/Y97 in the ZA-loop and Asn140 in the BC-loop are identified to be critical residues in (+)-JQ1 binding/releasing kinetics. All these findings shed light on further selective inhibitor design toward BRD family, by exploiting the non-negligible ligand binding kinetics features and flexible ZA-loop motions of BRD, instead of only the static ligand-protein binding affinity.

A series of experiments are conducted in which specially designed periodic air jets are applied to a heated surface for the purpose of enhancing heat transfer relative to the corresponding steady air jet. The periodic jets are produced by a mass flow rate controller. The experiments are performed for steady jets and for specially designed periodic jets, including a combination of sinusoidal, triangular and rectangular jets at frequencies from 1.25 to 20 Hz, the triangular signal having a different symmetry (representing the ratio of time to increasing velocity in one cycle to total cycle time) and the rectangular jets having a variable duty cycle (representing the ratio of the pulse cycle on-time to off-time) at frequencies of 10 Hz and 20 Hz. Various unsteady jets show distinguishing frequency dependences and the step change, i.e. the sudden increase or decrease of signal, shows some advantageous influence on heat transfer improvement, especially negative step change. Therefore, the enhancement of combined signals lies between the performances of the individual signals. The enhancement for triangular (or sinusoidal) plus rectangular signals shows some improved performance compared with that of rectangular plus triangular (or sinusoidal) signals. The heat transfers are enhanced as Strouhal number increases from 0.004 to 0.068 on the whole for impinging jet with such combined signals. The signals of triangular jet with symmetry parameter of 0 and 1 have improved heat transfer, and the latter has a slightly better result than the former. The instantaneous changing rate of velocity also has an influence on heat transfer improvements. Thus the duty cycle of 1:2 has the best performance in terms of heat transfer enhancement in this study.

Geranyl pyrophosphate synthase (GPPS) is responsible for the formation of geranyl pyrophosphate (GPP), a key intermediate which has the potential to derive numerous functionally and structurally diverse groups of terpenoid natural products via the head-to-tail assembly of two isoprenoid building blocks (dimethylallyl diphosphate, DMAPP; isopentenyl diphosphate, IPP) in the initial step of carbon-chain elongation during isoprenoid biosynthesis. Elucidating the detailed catalytic mechanism in GPPS is of significant interests as it will stimulate the development of new technology in generating novel natural productlike scaffolds. It has been known that the catalytic reaction involves three sequential steps, namely “ionization–condensation–elimination”, but the exact catalytic mechanism has remained controversial since the 1970s. By employing Born–Oppenheimer density functional quantum mechanics (B3LYP/6-31(+)G*)/molecular mechanics dynamics simulations, here we suggest that GPPS adopts a protonation-induced ...

The conversion of 1-deoxy-D-xylulose 5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP) catalyzed by DXP reductoisomerase (DXR) is the committing step in the biosynthesis of terpenoids. This MEP pathway is essential for most pathogenic bacteria but absent in human, and thus, it is an attractive target for the development of novel antibiotics. To this end, it is critical to elucidate the conversion mechanism and identify the transition state, as many drugs are transition-state analogues. Here we performed extensive combined quantum mechanical (density functional theory B3LYP/6-31G*) and molecular mechanical molecular dynamics simulations to elucidate the catalytic mechanism. Computations confirmed the transient existence of two metastable fragments of DXP by the heterolytic C3–C4 bond cleavage, namely, 1-propene-1,2-diol and glycoaldehyde phosphate, in accord with the most recent kinetic isotope effect (KIE) experiments. Significantly, the heterolytic C3–C4 bond cleavage and C2–C4 bond formatio...

Single-gene mutants tolerant or sensitive to salt stress are ideal materials for identifying and cloning genes related to salt tolerance in rice (Oryza sativa L.). In the present study, a salt-sensitive mutant was obtained from the ethyl methanesulfonate (EMS)-induced Nipponbare bank. The mutant, designated rice salt sensitive 4 (rss4), showed a significant increase in salt sensitivity at the seedling stage and accumulated high levels of Na⁺ in shoots, particularly in the blades of old leaves, under conditions of NaCl stress. Genetic analysis indicated that the mutation was controlled by a single recessive gene. Quantitative trait locus (QTL) analysis for shoot Na⁺ content was performed using an F₂ population derived from a cross between the rss4 mutant and the indica cultivar Zhaiyeqing 8 (ZYQ8). Three QTLs were identified and one located on the long arm of chromosome 6 was determined to be the candidate locus of the rss4 gene based on comparison and analysis, which explained 40.5% of the phenotypic variance in the shoot Na⁺ content of the F₂ population. Further analysis of recombination events in 165 mutant individuals of an enlarged mapping population of rss4/ZYQ8 defined the rss4 locus to an interval of 230.5 kb bracketed by markers RM20566 and IM28706 on chromosome 6.

Development of isoform-selective histone deacetylase (HDAC) inhibitors is of great biological and medical interest. Among 11 zinc-dependent HDAC isoforms, it is particularly challenging to achieve isoform inhibition selectivity between HDAC1 and HDAC2 due to their very high structural similarities. In this work, by developing and applying a novel de novo reaction-mechanism-based inhibitor design strategy to exploit the reactivity difference, we have discovered the first HDAC2-selective inhibitor, β-hydroxymethyl chalcone. Our bioassay experiments show that this new compound has a unique time-dependent selective inhibition on HDAC2, leading to about 20-fold isoform-selectivity against HDAC1. Furthermore, our ab initio QM/MM molecular dynamics simulations, a state-of-the-art approach to study reactions in biological systems, have elucidated how the β-hydroxymethyl chalcone can achieve the distinct time-dependent inhibition toward HDAC2.

Autotaxin (ATX) is a key enzyme that converts lysophosphatidylcholine to lysophosphatidic acid (LPA). ATX is a crucial factor that facilitates cancer progression; however, the effect of ATX on endometrial cancer has not been explored. The aim of the present study was to investigate the role of ATX in the progression of endometrial cancer. The immunohistochemical results revealed higher protein expression levels of ATX and LPA receptors (LPA 1, 2 and 3) in human endometrial cancer tissue than in non‑carcinoma tissue. In addition, reverse transcription‑quantitative polymerase chain reaction and western blotting analysis demonstrated that ATX and LPA receptor mRNA and protein expression was greater in Ishikawa cells, which are positive for estrogen receptor (ER), than in Hec‑1A cells that exhibit low ER expression. Short interfering RNA knockdown of ATX in Ishikawa cells led to decreased cell proliferation and cell colony number, as determined by Cell Counting kit‑8 and colony formation assays. Estrogen stimulated ATX mRNA expression. Inhibition of ATX decreased estrogen and LPA‑induced cell proliferation. High LPA levels markedly elevated the phosphorylation levels of extracellular signal‑regulated kinase (ERK). ATX downregulation moderately decreased estrogen‑ and LPA‑induced phosphorylation of ERK. In addition, the ERK inhibitor, PD98059, reduced cell proliferation with estrogen, ATX and LPA treatment. The present study suggested that the ATX‑LPA axis may facilitate estrogen‑induced cell proliferation in endometrial cancer via the mitogen‑activated protein kinase/ERK signaling pathway. The present study may provide ideas and an experimental basis for clinicians to identify new molecular targeted drugs for the treatment of endometrial cancer.

Background Xian-Fang-Huo-Ming-Yin (XFHM), a traditional herbal formula, has been used to treat sores and carbuncles for hundreds of years in Asia. Nowadays, its clinical effects in treatment of rheumatoid arthritis (RA) have been validated. In this study, we want to study its possible molecular mechanisms of regulating the differentiation of lymphocytes and production of pro-inflammatory cytokines in collagen-induced arthritis (CIA) mice for RA treatment. Methods A high performance liquid chromatography-electrospray ionization/mass spectrometer (HPLC-ESI/MSn) system was used to analyze the constituents of XFHM granules. An arthritics mouse model was induced by collagen and leflunomide (LEF) was used as a positive control medicine. Pathological changes at the metatarsophalangeal joint were studied through Safranin O and immunohistochemical staining. The differentiation of T, B and NK cells was examined by flow cytometry and pro-inflammatory cytokines were assayed using an Inflammation Antibody Array assay. The expression of key molecules of the nuclear factor κB (NF-κB) and Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathways in spleen were studied by western-blot analysis. Results In our study. 21 different dominant chemical constituents were identified in XFHM. Treatment with XFHM suppressed the pathological changes in arthrosis of CIA. Additionally, XFHM down-regulated the proliferation and differentiation of CD3+ T cells and CD3−CD19+ B cells significantly. However, XFHM had no significant effect on CD3−NK1.1+ NK cells. Further study showed that the production of pro-inflammatory cytokines had been suppressed by inhibiting the activation of NF-κB and JAK/STAT signaling. Conclusions XFHM can regulate and maintain the immunologic balance of lymphocytic immunity and inhibit the production of pro-inflammatory cytokines, thus suppressing the pathological changes of RA. Therefore, XFHM may be used as an application of traditional medicine against RA in modern complementary and alternative therapeutics. Electronic supplementary material The online version of this article (doi:10.1186/s12906-016-1526-x) contains supplementary material, which is available to authorized users.

Network virtualization has been proposed as a promising method to mitigate the ossification of the Internet by allowing multiple heterogeneous virtual networks (VNs) to coexist on a shared substrate network. One of the major challenges in this method is the VN embedding (VNE) problem of how to map efficiently the virtual nodes and links onto the substrate network considering constraints associated with different substrate networks. This paper aims to solve the VNE problem with geographical constraints in the context of flexi-grid optical networks where modulation modes can be selected optimally. We provide an integer linear programming (ILP) formulation for the problem with the objective function of minimizing the embedding cost of an arriving VN. To achieve scalability, we also propose three polynomial-time heuristic algorithms where virtual links are embedded sequentially by three different sequences, respectively. We find that the sequence considering the bandwidth requirements of the virtual links outperforms the others. Such a sequence leads to a cost-effective VNE solution in terms of spectrum resource usage, which aims to optimize modulation modes and transmission distances of the virtual links that have high bandwidth requirements. Numerical results show that the heuristic algorithm with the sequence considering the bandwidth requirements performs closely to the ILP for a small size network, and we also demonstrate its applicability to larger networks.

Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease, and satisfactory therapeutic strategies have not yet been established. The Shen-Yan-Fang-Shuai Formula (SYFSF) is a traditional Chinese formula composed of Astragali radix, Radixangelicae sinensis, Rheum officinale Baill, and four other herbs. It has been widely used as an effective treatment for DKD patients in China. However, little is known about the molecular mechanisms underlying SYFSF’s renoprotection. In this study, we compared the protective effect of SYFSF to irbesartan on the histology and renal cells in type 2 DKD rat model and high-glucose (HG) cultured mesangial cells, respectively. We found that SYFSF could significantly decrease urinary albumin, cholesterol, and triglyceride. And a decrease in serum creatinine was also found in SYFSF-treated group compared with irbesartan-treated rats. In addition, SYFSF inhibited the interstitial expansion and glomerulosclerosis in diabetic rats. Notably, SYFSF markedly downregulated the expression of MCP-1, TGF-β1, collagen IV, and fibronectin in diabetic rat models and HG-induced mesangial cell models. The renoprotection was closely associated with a reduced expression of TNF-α and phosphorylated NF-κBp65. Our study suggests that SYFSF may ameliorate diabetic kidney injury. The observed renoprotection is probably attributable to an inhibition of inflammatory response and extracellular matrix (ECM) accumulation mediated by TNF-α/NF-κBp65 signaling pathway.

The hypoalbuminuric effect of sulodexide (SDX) on diabetic kidney disease (DKD) was suggested by some clinical trials but was denied by the Collaborative Study Group. In this study, the diabetic rats were treated with SDX either from week 0 to 24 or from week 13 to 24. We found that 24-week treatment significantly decreased the urinary protein and HAVCR1 excretion, inhibited the interstitial expansion, and downregulated the renal cell apoptosis and interstitial fibrosis. Renoprotection was also associated with a reduction in renocortical/urinary oxidative activity and the normalization of renal klotho expression. However, all of these actions were not observed when SDX was administered only at the late stage of diabetic nephropathy (from week 13 to 24). In vitro, advanced glycation end products (AGEs) dose-dependently enhanced the oxidative activity but lowered the klotho expression in cultured proximal tubule epithelial cells (PTECs). Also, H2O2 could downregulate the expression of klotho in a dose-dependent manner. However, overexpression of klotho reduced the HAVCR1 production and the cellular apoptosis level induced by AGEs or H2O2. Our study suggests that SDX may prevent the progression of DKD at the early stage by upregulating renal klotho expression, which inhibits the tubulointerstitial injury induced by oxidative stress.

The infrared spectrum fingerprint (IRFP) of YQHXJD compound. The x-axis indicated wavelength of absorption, and y-axis indicated absorption intensity. (PDF 128Â kb)

Aims Upregulation of heme oxygenase (HO)-1 plays an important role in vascular protection. Valsartan attenuates neointimal hyperplasia in animal studies. The objective of this study was to examine the role of HO-1 and angiotensin II type 1 (AT 1 ) receptor in the action of valsartan on neointimal hyperplasia in balloon-injured rat aortic arteries. Main methods Thirty-six male Wistar rats were randomly divided into the following three groups with twelve rats in each group: control group, surgery (model) group, and valsartan group. Aortic balloon injury was performed to elicit endothelial denudation with a 2F balloon catheter. On days 14 and 28 after injury, blood was harvested to measure bilirubin levels. Aortic arteries were harvested for morphometry analysis, to determine angiotensin II (Ang II) level, and to analyze mRNA or protein expression. Key findings Compared with the control group, proliferation and intimal thickening of vascular smooth muscle cells (VSMCs) were obvious in the surgery group rats on days 14 and 28 after injury. Valsartan significantly reduced the proliferation and intimal thickening. Additionally, pretreatment with valsartan significantly reduced Ang II levels, AT 1 receptor, and p38 mitogen-activated protein kinase (MAPK) expression. Valsartan increased HO-1 protein and mRNA expression, as well as increased serum bilirubin levels compared with the surgery group. Significance Valsartan treatment decreased neointimal hyperplasia in balloon-injured rats. The mechanism of action might be linked to the upregulation of HO-1, downregulation of AT 1 receptor and inhibition of p38MAPK signal pathway.

The Nitrogen-Vacancy (NV) center is becoming a promising qubit for quantum information processing. The defect has a long coherence time at room temperature and it allows spin state initialized and read out by laser and manipulated by microwave pulses. It has been utilized as a ultra sensitive probe for magnetic fields and remote spins as well. Here, we review the recent progresses in experimental demonstrations based on NV centers. We first introduce our work on implementation of the Deutsch-Jozsa algorithm with a single electronic spin in diamond. Then the quantum nature of the bath around the center spin is revealed and continuous wave dynamical decoupling has been demonstrated. By applying dynamical decoupling, a multi-pass quantum metrology protocol is realized to enhance phase estimation. In the final, we demonstrated NV center can be regarded as a ultra-sensitive sensor spin to implement nuclear magnetic resonance (NMR) imaging at nanoscale.

In order to investigate the effect and mechanism of action of rosuvastatin on atherosclerotic lesion in a Wistar rat model, 16 Wistar rats were fed a cholesterol-rich, vitamin D 3 overload diet and underwent balloon injury of the aorta. One day prior to injury, half of the rats began rosuvastatin treatment (5 mg/kg/d) via oral gavage. Eight control rats received a basal diet and sham operation. After 14 weeks of treatment, the animals were sacrificed. Blood was collected to measure lipid and angiotensin II (Ang II) levels and morphologic analysis was performed on the aorta. Scavenger receptor-class B type I (SR-BI), Ang II type-1 (AT 1 ) receptor and phosphorylated extracellular signal regulated kinase 1/2 (p-ERK1/2) protein and mRNA levels were measured via Western blot and real time reverse transcriptase polymerase chain reaction, respectively. Spearman's rank correlation was utilized to examine the relationships between SR-BI and Ang II or AT 1 receptor expression. The atherosclerosis model group demonstrated an increase in plasma lipid levels and aortic plaque formation. After 14 weeks of treatment with rosuvastatin, there was a significant decrease in plasma lipid and Ang II levels accompanied by an improvement in aortic lesions. Rosuvastatin increased the expression of SR-BI but significantly inhibited the expression of AT 1 receptor and p-ERK1/2. SR-BI protein expression was inversely correlated with both the level of Ang II and expression of the AT 1 receptor. In conclusion, rosuvastatin attenuates atherosclerosis in the Wistar rat model, and its anti-atherosclerotic activity may be through upregulation of SR-BI expression and inhibition of p-ERK1/2 levels and AT 1 receptor expression.

A salt-sensitive mutant designated rice salt sensitive 2 (rss2) was isolated from the M2 generation of the rice cultivar Nipponbare mutagenized with ethyl methanesulfonate (EMS). This mutant exhibited a greater decrease in salt tolerance with a significant increase in Na(+) content in its shoots. Genetic analysis indicated that the increase in Na(+) in rss2 was controlled by a single recessive gene. Further genome-wide analysis of the linkage map constructed from the F2 population of rss2/Zhaiyeqing 8 (ZYQ8) showed that two quantitative trait loci (QTLs) on chromosomes 1 and 6 were responsible for the Na(+) concentration in shoots, which explained 14.5% and 53.3%, respectively, of the phenotypic variance. The locus on chromosome 1, but not that on chromosome 6, was also detected in the F2 population of Nipponbare/ZYQ8, suggesting that the QTL on chromosome 6 was responsible for the salt sensitivity in rss2. By analyzing the recombination events in 220 mutant individuals of an enlarged mapping population of rss2/ZYQ8, the rss2 locus was precisely mapped to an interval of 605.3 kb between insertion/deletion (InDel) markers IM21962 and IM22567. This finding will facilitate the cloning of the rss2 locus and provide insight into the physiological mechanisms of salt sensitivity in rice.

Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease, and satisfactory therapeutic strategies have not yet been established. The Shen-Yan-Fang-Shuai Formula (SYFSF) is a traditional Chinese formula composed of Astragali radix, Radixangelicae sinensis, Rheum officinale Baill, and four other herbs. It has been widely used as an effective treatment for DKD patients in China. However, little is known about the molecular mechanisms underlying SYFSF's renoprotection. In this study, we compared the protective effect of SYFSF to irbesartan on the histology and renal cells in type 2 DKD rat model and high-glucose (HG) cultured mesangial cells, respectively. We found that SYFSF could significantly decrease urinary albumin, cholesterol, and triglyceride. And a decrease in serum creatinine was also found in SYFSF-treated group compared with irbesartan-treated rats. In addition, SYFSF inhibited the interstitial expansion and glomerulosclerosis in diabetic rats. Notably, SYFSF markedly downregulated the expression of MCP-1, TGF-β1, collagen IV, and fibronectin in diabetic rat models and HG-induced mesangial cell models. The renoprotection was closely associated with a reduced expression of TNF-α and phosphorylated NF-κBp65. Our study suggests that SYFSF may ameliorate diabetic kidney injury. The observed renoprotection is probably attributable to an inhibition of inflammatory response and extracellular matrix (ECM) accumulation mediated by TNF-α/NF-κBp65 signaling pathway.

Sustainability research faces many challenges as respective environmental, urban and regional contexts are experiencing rapid changes at an unprecedented spatial granularity level, which involves growing massive data and the need for spatial relationship detection at a faster pace. Spatial join is a fundamental method for making data more informative with respect to spatial relations. The dramatic growth of data volumes has led to increased focus on high-performance large-scale spatial join. In this paper, we present Spatial Join with Spark (SJS), a proposed high-performance algorithm, that uses a simple, but efficient, uniform spatial grid to partition datasets and joins the partitions with the built-in join transformation of Spark. SJS utilizes the distributed in-memory iterative computation of Spark, then introduces a calculation-evaluating model and in-memory spatial repartition technology, which optimize the initial partition by evaluating the calculation amount of local join algorithms without any disk access. We compare four in-memory spatial join algorithms in SJS for further performance improvement. Based on extensive experiments with real-world data, we conclude that SJS outperforms the Spark and MapReduce implementations of earlier spatial join approaches. This study demonstrates that it is promising to leverage high-performance computing for large-scale spatial join analysis. The availability of large-sized geo-referenced datasets along with the high-performance computing technology can raise great opportunities for sustainability research on whether and how these new trends in data and technology can be utilized to help detect the associated trends and patterns in the human-environment dynamics.

In traditional Chinese medicine (TCM), xianfanghuomingyin (XFHM) is used to treat autoimmune diseases, including rheumatoid arthritis (RA). Here, we studied the mechanisms underlying its treatment effects, especially its anti-inflammatory effects in a collagen-induced arthritis (CIA) mouse model. We found that cartilage destruction and pannus formation were alleviated by treatment with XFHM. The abnormal differentiation of Th1 and Th17 cells was downregulated significantly by XFHM, and Th2 and Treg cells were upregulated. Moreover, the expression levels of specific cytokines and transcription factors related to Th1 cells (interferonγ[IFNγ], T-bet) and Th17 cells (interleukin- [IL-] 17) and the nuclear receptor retinoic acid receptor-related orphan receptor-gamma (RORγ) were downregulated. Serum IL-4 and GATA-3, which contribute to Th2 cells differentiation, increased significantly after XFHM administration. These results indicate that XFHM can restore the balance of T lymphocytes and reestablish the immunological tolerance to inhibit autoinflammatory disorder of RA. Taken together, XFHM can be used as a complementary or alternative traditional medicine to treat RA.

The use of graphene oxide (GO) nanosheets for functional enzyme support has attracted intensive interest owing to their unique planar structure and intriguing physical and chemical properties. However, the detailed effects of the interface properties of GO and its functionalized derivatives on active biomolecules are not well understood. We immobilize nuclease P1, a common industrial nucleic acid production enzyme, on pristine and amino poly(ethylene glycol) (PEG-NH2) modified GO nanosheets with interface property heterogeneity using two approaches, physical adsorption and chemical crosslinking. It is demonstrated that nuclease P1 could be stable immobilized on the surface of pristine GO by physical adsorption and on the edge of modified GO nanosheets by chemical crosslinking. The resultant loading capacity of nuclease P1 on pristine GO is as high as 6.45mg/mg as a consequence of strong electrostatic and hydrophobic interactions between the enzyme and carrier. However, it is determined that the acid resistance, thermal stability, reusability and degradation efficiency of the immobilized enzyme on PEG-NH2-modified GO are obviously improved compared to those of the enzyme immobilized on pristine GO. The enhanced catalytic behavior demonstrates that GO and its derivatives have great potential in efficient biocatalytic systems.

Generating non-reciprocal radio frequency transduction plays important roles in a wide range of research and applications, and an aspiration is to integrate this functionality into micro-circuit without introducing magnetic field, which, however, remains challenging. By designing a 1D artificial lattice structure with neighbor-interaction engineered parametrically, we predicted a non-reciprocity transduction with giant unidirectionality. We then experimentally demonstrated the phenomenon on a nano-electromechanical chip fabricated by conventional complementary metal-silicon processing. A unidirectionality with isolation as high as 24dB is achieved and several different transduction schemes are realized by programming the control voltages topology. Apart from being used as a radio frequency isolator, the system provides a way to build practical on-chip programmable device for many researches and applications in radio frequency domain., 12 pages, 4 figures

Nonlinearity in macroscopic mechanical systems may lead to abundant phenomena for fundamental studies and potential applications. However, it is difficult to generate nonlinearity due to the fact that macroscopic mechanical systems follow Hooke's law and respond linearly to external force, unless strong drive is used. Here we propose and experimentally realize high cubic nonlinear response in a macroscopic mechanical system by exploring the anharmonicity in chemical bonding interactions. We demonstrate the high tunability of nonlinear response by precisely controlling the chemical bonding interaction, and realize, at the single-bond limit, a cubic elastic constant of 1 × 1020 N m−3. This enables us to observe the resonator's vibrational bi-states transitions driven by the weak Brownian thermal noise at 6 K. This method can be flexibly applied to a variety of mechanical systems to improve nonlinear responses, and can be used, with further improvements, to explore macroscopic quantum mechanics., Macroscopic mechanical systems typically respond linearly to external force, and generating nonlinearity is challenging. Here, the authors generate nonlinearity in a macroscopic mechanical resonator by linking it to a gold contact and exploiting the anharmonicity in the chemical bonding interactions.

Three soil bacterial strains were identified as Chryseobacterium sp. TFB on the basis of their 16S rRNA gene sequences. Conidia of Arthrobotrys oligospora produced a few mycelial traps (MT) and conidial traps (CT) when cultured with bacterial cells that they did not produce when cultured with a bacterial cell-free culture filtrate. However, co-culture of A. oligospora with bacterial cells and bacteria-free filtrate simultaneously induced MT and CT in large amounts. With the increased concentration of bacteria-free filtrate, the number of typical CT increased, but conidial germination was progressively inhibited. Scanning electron microscopy of A. oligospora co-cultured with bacteria revealed that bacterial attachment to hyphae was a prerequisite to trap formation and that bacteria-free filtrate facilitated bacterial attachments to hyphae. The results that the addition of nutrients in co-culture medium decreased the number of traps suggest that this type of trap formation may be favoured at a low nutrient status. Eight fungi tested were able to form MT and CT when co-cultured with bacterial cells and bacteria-free culture filtrate, but the abilities varied among species. This study provides novel evidence that under laboratory conditions, soil bacteria attaching to hyphae could induce traps in nematode-trapping fungi.

Network virtualization provides means for efficient management of network resources by embedding multiple virtual networks (VNs) to share efficiently the same substrate network. Such virtual network embedding (VNE) gives rise to a challenging problem of how to optimize resource allocation to VNs and to guarantee their performance requirements. In this paper, we provide VNE algorithms for efficient management of flexi-grid optical networks. We provide an exact algorithm aiming to minimize the total embedding cost in terms of spectrum cost and computation cost for a single VN request. Then, to achieve scalability, we also develop a heuristic algorithm for the same problem. We apply these two algorithms for a dynamic traffic scenario where many VN requests arrive one-by-one. We first demonstrate by simulations for the case of a six-node network that the heuristic algorithm obtains very close blocking probabilities to exact algorithm (about 0.2% higher). Then, for a network of realistic size (namely, USnet) we demonstrate that the blocking probability of our new heuristic algorithm is about one magnitude lower than a simpler heuristic algorithm, which was a component of an earlier published algorithm. Published version

Rationale: Behcet's disease (BD) is a rare systemic vasculitis disorder that can involve vessels of any size. Patient Concerns: A 60-year-old female had recurrent painful mouth ulcers about 30 years ago and recently presented with abdominal distension, conjunctival congestion, and chest pain in sequence. Diagnoses: The patient was diagnosed with BD according to the International Criteria for Behcet's Disease (ICBD). Interventions: A therapy of glucocorticoids and cyclophosphamide was administered. Outcomes: After a 3-month treatment, follow-up examination showed a depression of the inflammation and a slight decrease of the arterial aneurysms. Lessons: BD patients may get a delayed diagnosis because of the long duration between the first and subsequent manifestations. Suspect patients should be followed-up and the diagnosis of BD should be considered when multiple tissues or organs are involved.

SAHA (vorinostat, Merck) is a famous clinical drug for zinc-containing histone deacetylase (HDAC) targets against cancer and several other human disorders, whose inhibition mechanism (namely the protonation mechanism) upon binding to HDAC has been debated for more than ten years. It is very challenging to verify experimentally and is still controversial theoretically. The popular "Class-dependent" (namely "Tyr-dependent") hypothesis is that the deprotonation of SAHA is mostly regulated by the conserved Tyr308 in class I HDAC while it is replaced by the His843 in class IIa HDAC. Herein, by elaborate QM(DFT)/MM MD simulations, we exclude the prevalent "Class-dependent" mechanism and advance a novel "Metal-dependent" mechanism, where the remote second metal site (K(+) in most HDAC and Ca(2+) in HDAC2) determines the protonation of SAHA. This proof-of-principle "Metal-dependent" mechanism opens up a new avenue to utilize the second metal site for isoform-selective inhibitor design.