[Textual research on wei sheng (hygiene) and gong gong wei sheng (public health)]

Wei sheng, a verb-object word group existed since the ancient time, referring to"protection of life", and it was evolved as a single word which can be translated as"hygiene"in modern times with multiple implications like"cleanliness","sterilization", and"prevention of disease", etc. Gong gong wei sheng was isolated from"hygiene", which has become a new term. In the Republic of China, scholars had made preliminary studies on the translation of"hygiene"during which gong gong wei sheng, and"guo min wei sheng"(national hygiene) and"gong zhong wei sheng"(people's hygiene) appeared also. Though the term"public health"was defined by the WHO and gong gong wei sheng was defined by Chinese scholars with gradual improvement, yet, the implications of both terms are still imperfect.

Dynamics and Diffusion Mechanism of Low-Density Liquid Silicon

A first-order phase transition from a high-density liquid to a low-density liquid has been proposed to explain the various thermodynamic anomies of water. It also has been proposed that such liquid-liquid phase transition would exist in supercooled silicon. Computer simulation studies show that, across the transition, the diffusivity drops roughly 2 orders of magnitude, and the structures exhibit considerable tetrahedral ordering. The resulting phase is a highly viscous, low-density liquid silicon. Investigations on the atomic diffusion of such a novel form of liquid silicon are of high interest. Here we report such diffusion results from molecular dynamics simulations using the classical Stillinger-Weber (SW) potential of silicon. We show that the atomic diffusion of the low-density liquid is highly correlated with local tetrahedral geometries. We also show that atoms diffuse through hopping processes within short ranges, which gradually accumulate to an overall random motion for long ranges as in normal liquids. There is a close relationship between dynamical heterogeneity and hopping process. We point out that the above diffusion mechanism is closely related to the strong directional bonding nature of the distorted tetrahedral network. Our work offers new insights into the complex behavior of the highly viscous low density liquid silicon, suggesting similar diffusion behaviors in other tetrahedral coordinated liquids that exhibit liquid-liquid phase transition such as carbon and germanium.

Is vertebroplasty a risk factor for subsequent vertebral fracture, meta-analysis of published evidence?

In our paper, we systemically retrieved the eligible study evaluating whether increased incidence of subsequent vertebral fracture is associated with vertebroplasty. Main effect sizes were vertebral fracture rates reported in terms of hazard ratio (HR) for time-to-event data or relative risk (RR) for dichotomous outcome. Our results do not support the hypothesis that vertebroplasty contributes to increased risk of subsequent vertebral fracture, neither adjacent nor total vertebral fracture.

INTRODUCTION

Vertebroplasty has been implicated in significant changes in vertebral strength, vertebral shape, and consequently increased risk for subsequent vertebral fracture, especially the adjacent level. Here, we further tested the hypothesis whether new-onset vertebral fracture is a natural result of osteoporosis or consequence of cement augmentation.

METHODS

Relevant literatures were retrieved using PubMed, Web of Knowledge, and Cochrane Central Register of Controlled Trials (CENTRAL), supplemented by a hand-search of the reference lists of selected articles. Eligible studies assessed whether increased morbidity of subsequent vertebral fracture is associated with vertebroplasty. Main effect sizes were vertebral fracture rates reported in terms of hazard ratio (HR) for time-to-event data or relative risk (RR) for dichotomous outcome. Random-effects model was used to account for clinical or methodological heterogeneity across studies.

RESULTS

Thirteen studies with a number of 2,551 individuals (1,631 in vertebroplasty group and 920 in control group) were suitable for this meta-analysis. In trials that reported adjacent vertebral fracture as time-to-event data (two trials, n = 328), we found a similar incidence of vertebral fracture in percutaneous vertebroplasty (PVP) group compared to conservative therapy (HR 0.60, 95% confidence interval 0.29 to 1.26; P = 0.18). In trials that reported overall vertebral fracture as time-to-event data (three trials, n = 704), vertebroplasty was associated with a slightly increased but non-significant risk for vertebral fracture (HR 1.14, 95% confidence interval 0.65 to 2.00; P = 0.65). The outcome was further confirmed in the secondary meta-analysis of studies that reported vertebral fracture as dichotomous data. Subgroup analysis according to study design revealed no difference either.

CONCLUSIONS

Our results do not support the hypothesis that vertebroplasty contributes to increased risk of subsequent vertebral fracture, neither adjacent nor total vertebral fracture. However, adequately designed randomized controlled trials are warranted to confirm the present findings.

Impact of hard vs. soft wheat and monensin level on rumen acidosis in feedlot heifers

Many feedlot finishing diets include wheat when the relative wheat prices are low. This study was conducted to examine the responses in ruminal pH and fermentation as well as site and extent of digestion from substituting soft or hard wheat for barley grain and to determine whether an elevated monensin concentration might decrease indicators of ruminal acidosis in feedlot heifers. Five ruminally cannulated beef heifers were used in a 5 × 5 Latin square with 2 × 2 + 1 factorial arrangement. Treatments included barley (10% barley silage, 86% barley, 4% supplement, with 28 mg monensin/kg DM) and diets where barley was substituted by either soft or hard wheat with either 28 or 44 mg monensin/kg diet DM. Intake of DM was not affected by grain source, whereas increasing monensin with wheat diets reduced (P < 0.02) DMI. Mean ruminal pH was lower (P < 0.04) and durations of pH < 5.8 and pH < 5.5 greater (P < 0.03) for wheat than for barley diets. However, ruminal pH was not affected by wheat type or monensin level. Total VFA concentrations were greater (P < 0.03) for wheat than barley diets with no effect of wheat type. The molar proportion of propionate was greater (P < 0.04), whereas butyrate (P < 0.01) and ratio of acetate to propionate tended to be lower (P < 0.09), with the high as compared to low level of monensin. Replacing barley with wheat in finishing diets did not affect the duodenal flow or the digestibility of OM, likely as a result of greater (P < 0.01) NDF digestion from barley offsetting the increased (P < 0.03) supply of digested starch from wheat. Feeding soft vs. hard wheat delivered a greater (P < 0.03) duodenal supply of OM and nonammonia N with no differences in total tract nutrient digestion. The increased monensin concentration decreased the flow of OM (P < 0.01), total N (P < 0.05), and microbial protein (P < 0.05) to the small intestine due to decreased DMI. These results indicated that hard and soft wheat exhibited digestive characteristics similar to barley, but ruminal pH measurements indicate that compared with barley, wheat increased the risk of ruminal acidosis. Although an increased level of monensin had limited impact on ruminal indicators of acidosis, an increase in propionate would be expected to improve efficiency of feed use by heifers fed wheat-based finishing diets.

A portable microfluidic device for the rapid diagnosis of cancer metastatic potential which is programmable for temperature and CO2

If metastasis of lung cancer can be found and treated early, a victim might have an improved chance to prevail over it, but routine examinations such as chest radiography, computed tomography and biopsy cannot characterize the metastatic potential of lung cancer cells; critical diagnoses to define optimal therapeutic strategies are thus lost. We designed a portable microfluidic device for the rapid diagnosis of cancer metastatic potential. Featuring a micro system to control temperature and a bicarbonate buffered environment, our device discriminates a rate of surface detachment as an index of the migratory ability of cells cultured on pH-responsive chitosan. We labeled metastatic subpopulations of lung cancer cell lines, and verified that our device is capable of separating cells according to their metastatic ability. As only few cells are needed, a patient's specimen from biopsies, e.g. from fine-needle aspiration, can be processed on site to offer immediate information to physicians. We expect that our design will provide valuable information in pre-operative evaluations to assist the definition of therapeutic plans for lung cancer, as well as for metastatic tumors of other types.

Proliferative effects of melatonin on Schwann cells: implication for nerve regeneration following peripheral nerve injury

Activation of proliferation of Schwann cells is crucial for axonal guidance and successful nerve regeneration following peripheral nerve injury (PNI). Considering melatonin plays an important role in proliferative regulation of central glial cells, the present study determined whether melatonin can effectively promote Schwann cell proliferation and improve nerve regeneration after PNI. The spontaneous immortalized rat Schwann cell line (RSC 96 cells) was first analyzed by quantitative polymerase chain reaction (QPCR) to detect the potential existence of melatonin receptors. The melatonin receptor-mediated signaling responsible for proliferation was examined by measuring the phosphorylation of extracellular signal-regulated kinases (ERK1/2) pathway. The in vivo model of PNI was performed by the end-to-side neurorrhaphy. The quantity of Schwann cells as well as the number of re-innervated motor end plates (MEP) on target muscles was examined to represent the functional recovery of injured nerves. QPCR results indicated that MT1 is the dominant receptor in Schwann cells. Immunoblotting and proliferation assay revealed an enhanced phosphorylation of ERK1/2 and increased number of RSC 96 cells following melatonin administration. Nonselective melatonin receptor antagonist (luzindole) treatment significantly suppressed all the above findings, suggesting that the proliferative effects of melatonin were mediated by a receptor-dependent pathway. In vivo results corresponded well with in vitro findings in which melatonin effectively increased the amount of proliferated Schwann cells and re-innervated MEP on target muscles following PNI. As melatonin successfully improves nerve regeneration by promoting Schwann cell proliferation, therapeutic use of melatonin may thus serve as a promising strategy to counteract the PNI-induced neuronal disability.

Optical and magneto-optical anisotropies in large-area two-dimensional Co antidots film

In this work, we investigate the plasmon-induced optical and magneto-optical anisotropies in the large-area square-ordered Co antidots film. It shows that both the outline of reflectivity spectrum and Kerr spectrum are significantly modified by surface plasmon polarition (SPP) resonances. Moreover, the magnitude of Kerr angle reaches to about 10 minutes at the azimuthal angle 45°, which is over 3 times of that of pure Co film. These phenomena are attributed to the SPP resonances with different diffraction orders of reciprocal lattice vectors.

Development of frequency modulated continuous wave reflectometer for electron density profile measurement on the HL-2A tokamak

The frequency modulated continuous wave reflectometer was developed for the first time on the HL-2A tokamak. The system utilizes a voltage controlled oscillator and an active multiplier for broadband coverage and detects as heterodyne mode. Three reflectometers have been installed and operated in extraordinary mode polarization on HL-2A to measure density profiles at low field side, covering the Q-band (33-50 GHz), V-band (50-75 GHz), and W-band (75-110 GHz). For density profile reconstruction from the phase shift of the probing wave, a corrected phase unwrapping method is introduced in this article. The effectiveness of the method is demonstrated. The density profile behavior of a fast plasma event is presented and it demonstrates the capability of the reflectometer. These diagnostics will be contributed to the routine density profile measurements and the plasma physics study on HL-2A.

Effects of strontium impurity on the structure and dynamics of Al88Si12 liquid

The effects of strontium modification on the structure and dynamics of Al88Si12 liquid are studied by means of ab initio molecular dynamics simulations. By replacing 0.5% and 4.0% of Al with Sr, we show that the addition of Sr lowers the self-diffusion of Al and Si of the liquid and reduces the nearest-neighbor correlation between Si atoms. The simulation provides an explanation for the change in morphology of the eutectic phases observed in rapidly solidified Al-Si alloys modified with Sr.

Common genetic variation near the connexin-43 gene is associated with resting heart rate in African Americans: a genome-wide association study of 13,372 participants

BACKGROUND

Genome-wide association studies have identified several genetic loci associated with variation in resting heart rate in European and Asian populations. No study has evaluated genetic variants associated with heart rate in African Americans.

OBJECTIVE

To identify novel genetic variants associated with resting heart rate in African Americans.

METHODS

Ten cohort studies participating in the Candidate-gene Association Resource and Continental Origins and Genetic Epidemiology Network consortia performed genome-wide genotyping of single nucleotide polymorphisms (SNPs) and imputed 2,954,965 SNPs using HapMap YRI and CEU panels in 13,372 participants of African ancestry. Each study measured the RR interval (ms) from 10-second resting 12-lead electrocardiograms and estimated RR-SNP associations using covariate-adjusted linear regression. Random-effects meta-analysis was used to combine cohort-specific measures of association and identify genome-wide significant loci (P≤2.5×10(-8)).

RESULTS

Fourteen SNPs on chromosome 6q22 exceeded the genome-wide significance threshold. The most significant association was for rs9320841 (+13 ms per minor allele; P = 4.98×10(-15)). This SNP was approximately 350 kb downstream of GJA1, a locus previously identified as harboring SNPs associated with heart rate in Europeans. Adjustment for rs9320841 also attenuated the association between the remaining 13 SNPs in this region and heart rate. In addition, SNPs in MYH6, which have been identified in European genome-wide association study, were associated with similar changes in the resting heart rate as this population of African Americans.

CONCLUSIONS

An intergenic region downstream of GJA1 (the gene encoding connexin 43, the major protein of the human myocardial gap junction) and an intragenic region within MYH6 are associated with variation in resting heart rate in African Americans as well as in populations of European and Asian origin.

In silico study of Aquaporin V: Effects and affinity of the central pore-occluding lipid

Because of its roles in human physiology, Aquaporin V (AQP5), a major intrinsic protein, has been a subject of many in vitro studies. In particular, a 2008 experiment produced its crystal structure at 2.0Å resolution, which is in a tetrameric conformation consisting of four protomers. Each protomer forms an amphipathic pore that is fit for water permeation. The tetramer has a pore along its quasi-symmetry axis formed by quadruplets of hydrophobic residues (every protomer contributes equally to the quadruplets). A lipid, phosphatidylserine (PS6), is bound to AQP5 in the central pore, totally occluding it. A 2009 experiment showed that AQP5 facilitates not only permeation of water but also permeation of hydrophobic gas molecules across the cell membrane. In this article, we present an in silico study of AQP5 to elucidate the effects of PS6's binding to and dissociating from AQP5's central pore. Computing the lipid's chemical-potential along its dissociation path, we find that PS6 inhibits the function of the central pore with an IC(50) in the micromolar range. Examining the central pore and the interstices between two adjacent protomers, we propose that nonpolar gas molecules (O(2)) permeate through AQP5's hydrophobic central pore when un-occluded.

Atomic-scale mechanisms of the glass-forming ability in metallic glasses

The issue, composition dependence of glass-forming ability (GFA) in metallic glasses (MG), has been investigated by systematic experimental measurements coupled with theoretical calculations in Cu-Zr and Ni-Nb alloy systems. It is found that the atomic-level packing efficiency strongly relates to their GFA. The best GFA is located at the largest difference in the packing efficiency of the solute-centered clusters between the glassy and crystal alloys in both MG systems. This work provides an understanding of GFA from atomic level and will shed light on the development of new MGs with larger critical sizes.

Theoretical study and pathways for nanoparticle capture during solidification of metal melt

Nanocomposites can provide exciting physical, chemical, and mechanical properties for numerous applications. The solidification processing method has great potential for economical fabrication of bulk nanocomposites, especially for those with crystalline materials as the matrix, such as metal matrix nanocomposites (MMNCs). However, it is extremely difficult to effectively capture nanoparticles (less than 100 nm) into the solidification fronts during solidification. It is thus very important to initiate a theoretical study to examine the physics that governs the interactions between nanoparticles and the solidification front, and to provide enabling pathways for effective nanoparticle capture during solidification. The aim of this paper is to establish a theoretical framework for the fundamental understanding of nanoparticle capture during solidification of metal melt in order to obtain bulk MMNCs. A thermodynamically favorable condition is set as the starting point for further theoretical analysis of the three-party model system, namely a nanoparticle-metal-melt-solidification front. Three key interaction potentials, the interfacial energy at short range (0.2-0.4 nm), the van der Waals potential (especially at a longer range beyond 0.4 nm and up to ∼10 nm) and the Brownian potential, were studied. Three possible pathways for nanoparticle capture were thus devised: viscous capture, Brownian capture and spontaneous capture. Spontaneous capture is proposed as the most favorable for nanoparticle capture during solidification of metal melt. The theoretical model of nanoparticle capture from this study will serve as a powerful tool for future experimental studies to realize exciting functionalities offered by bulk MMNCs.

Novel brain targeting prodrugs of naproxen based on dimethylamino group with various linkages

As a preventive and treatment drug for Alzheimer's disease (AD), naproxen's clinical application is hampered by its limited distribution in the brain. To increase the delivery of naproxen across the blood-brain barrier (BBB), 3 prodrugs (P1, P2 and P3) of naproxen were synthesized through either ester bond or amido bond using the dimethylamino moiety as a brain-targeting ligand. The in vitro release of naproxen from the 3 prodrugs was studied in PBS, rat plasma and brain homogenate. P3 with an amido bond appeared to be highly stable in all incubation media, whereas P1 and P2 with ester bonds were partially hydrolyzed in alkaline environment and brain homogenate to yield the parent drug. After i. v. administration to rats, the brain concentration of total naproxen (summation of released and bound naproxen, TN) of P1, P2 and P3 groups were 28.81, 24.51 and 15.54 times greater than that of the control naproxen group at 5 min, respectively, and the brain AUC0-t were 6.94, 10.06 and 6.70 times greater than that of the control naproxen group. In addition, the Cmax of TN in the brain after the administration of prodrugs with ester bonds (P1 and P2) was higher than that of the amide prodrug (P3). The results highlighted the possibility of brain delivery of naproxen using prodrug strategies based on the brain-targeting ligand with dimethylamino moiety, in which the linkage between drug and targeting group might play an important role in modulating the in vivo behaviors of these prodrugs.

Cooperative and redundant signaling of leukotriene B4 and leukotriene D4 in human monocytes

BACKGROUND

Leukotriene B(4) (LTB(4)) and cysteinyl leukotrienes (cysLTs) are important immune mediators, often found concomitantly at sites of inflammation. Although some of the leukotriene-mediated actions are distinctive (e.g., bronchial constriction for cysLTs), many activities such as leukocyte recruitment to tissues and amplification of inflammatory responses are shared by both classes of leukotrienes.

OBJECTIVE

We used human monocytes to characterize leukotriene-specific signaling, gene expression signatures, and functions and to identify interactions between LTB(4)- and cysLTs-induced pathways.

METHODS

Responsiveness to leukotrienes was assessed using oligonucleotide microarrays, real-time PCR, calcium mobilization, kinase activation, and chemotaxis assays.

RESULTS

Human monocytes were found to express mRNA for high- and low-affinity LTB(4) receptors, BLT(1) and BLT(2), but signal predominantly through BLT(1) in response to LTB(4) stimulation as shown using selective agonists, inhibitors, and gene knock down experiments. LTB(4) acting through BLT(1) coupled to G-protein α inhibitory subunit activated calcium signaling, p44/42 mitogen-activated protein kinase, gene expression, and chemotaxis. Twenty-seven genes, including immediate early genes (IEG), transcription factors, cytokines, and membrane receptors were significantly up-regulated by LTB(4). LTB(4) and LTD(4) had similar effects on signaling, gene expression, and chemotaxis indicating redundant cell activation pathways but costimulation with both lipid mediators was additive for many monocyte functions.

CONCLUSION

Leukotriene B(4) and LTD(4) display both redundant and cooperative effects on intracellular signaling, gene expression, and chemotaxis in human monocytes. These findings suggest that therapies targeting either leukotriene alone may be less effective than approaches directed at both.

Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation

Molecular dynamics simulations and free energy calculation have been performed to study how the single-chain variable fragment (scFv) binds methamphetamine (METH) and amphetamine (AMP). The structures of the scFv:METH and the scFv:AMP complexes are analyzed by examining the time-dependence of their RMSDs, by analyzing the distance between some key atoms of the selected residues, and by comparing the averaged structures with their corresponding crystallographic structures. It is observed that binding an AMP to the scFv does not cause significant changes to the binding pocket of the scFv:ligand complex. The binding free energy of scFv:AMP without introducing an extra water into the binding pocket is much stronger than scFv:METH. This is against the first of the two scenarios postulated in the experimental work of Celikel et al. (Protein Science 18, 2336 (2009)). However, adding a water to the AMP (at the position of the methyl group of METH), the binding free energy of the scFv:AMP-H2O complex, is found to be significantly weaker than scFv:METH. This is consistent with the second of the two scenarios given by Celikel et al. Decomposition of the binding energy into ligand-residue pair interactions shows that two residues (Tyr175 and Tyr177) have nearly-zero interactions with AMP in the scFv:AMP-H2O complex, whereas their interactions with METH in the scFv:METH complex are as large as -0.8 and -0.74 kcal mol(-1). The insights gained from this study may be helpful in designing more potent antibodies in treating METH abuse.

Diffusion in periodic potentials with path integral hyperdynamics

We consider the diffusion of brownian particles in one-dimensional periodic potentials as a test bench for the recently proposed stochastic path integral hyperdynamics (PIHD) scheme [Chen and Horing, J. Chem. Phys. 126, 224103 (2007)]. First, we consider the case where PIHD is used to enhance the transition rate of activated rare events. To this end, we study the diffusion of a single brownian particle moving in a spatially periodic potential in the high-friction limit at low temperature. We demonstrate that the boost factor as compared to straight molecular dynamics (MD) has nontrivial behavior as a function of the bias force. Instead of growing monotonically with the bias, the boost attains an optimal maximum value due to increased error in the finite path sampling induced by the bias. We also observe that the PIHD method can be sensitive to the choice of numerical integration algorithm. As the second case, we consider parallel resampling of multiple bias force values in the case of a brownian particle in a periodic potential subject to an external ac driving force. We confirm that there is no stochastic resonance in this system. However, while the PIHD method allows one to obtain data for multiple values of the ac bias, the boost with respect to MD remains modest due to the simplicity of the equation of motion in this case.

Exploring the free-energy landscapes of biological systems with steered molecular dynamics

We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period of time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreement with the experimental data and/or other computational studies available in the literature.

Melatonin inhibits microglial activation, reduces pro-inflammatory cytokine levels, and rescues hippocampal neurons of adult rats with acute Klebsiella pneumoniae meningitis

Acute bacterial meningitis caused by Klebsiella pneumoniae (K. pneumoniae) is a major health threat with a high mortality rate and severe neuro-cognitive sequelae. The intense pro-inflammatory cytokine released from calcium-mediated microglial activation plays an important role in eliciting neuronal damage in the hippocampal region. Considering melatonin possesses anti-inflammatory and immuno-modulatory properties, the present study determined whether melatonin can effectively decrease inflammatory responses and prevent hippocampal damage in animals subjected to K. pneumoniae. Adult rats inoculated with K. pneumoniae received a melatonin injection immediately thereafter at doses of 5, 25, 50, or 100 mg/kg. Following 24 h of survival, all experimental animals were processed for time-of-flight secondary ion mass spectrometry (for detecting glial calcium intensity), isolectin-B4 histochemistry (reliable marker for microglial activation), pro-inflammatory cytokine measurement as well as cytochrome oxidase and in situ dUTP end-labeling (representing neuronal bio-energetic status and apoptotic changes, respectively). Results indicate that in K. pneumoniae-infected rats, numerous calcium-enriched microglia, enhanced pro-inflammatory cytokine, and various apoptotic neurons with low bio-energetic activity were detected in hippocampus. Following melatonin administration, however, all parameters including glial calcium intensity, microglial activation, pro-inflammatory cytokine levels, and number of apoptotic neurons were successfully decreased with maximal change observed at a melatonin dose of 100 mg/kg. Enzymatic data corresponded well with above findings in which all surviving neurons displayed high bio-energetic activity. As effectively reducing glia-mediated inflammatory response is neuro-protective to hippocampal neurons, the present study supports the clinical use of melatonin as a potential therapeutic agent to counteract K. pneumoniae meningitis-induced neuro-cognitive damage.

In silico experiments of single-chain antibody fragment against drugs of abuse

Three sets of in silico experiments have been conducted to elucidate the binding mechanics of two drugs, (+)-methamphetamine (METH) and amphetamine (AMP) to the single-chain variable fragment (scFv) recently engineered from anti-METH monoclonal antibody mAb6H4 (IgG, κlight chain, K(d)=11nM). The first set of in silico experiments are long time equilibration runs of scFv:drug complexes and of drug-free scFv both in the solution. They demonstrate how the solution structures of scFv deviate from its crystallographic form with or without drug molecules bound to it. They lead to the prediction that the Arrhenius activation barrier is nearly zero for transitions from the dissociated state to the bound state. The second set of in silico experiments are nonequilibrium dynamics of pulling the drug molecules out of the binding pocket of scFv and the equilibration runs for drugs to fall back into the binding pocket. They demonstrate that extra water molecules (in addition to the two crystallographic waters) exist inside the binding pocket, underneath the drug molecules. These extra waters must have been evaporated from the binding pockets during the crystallization process of the in vitro experiments of structural determination. The third set of in silico experiments are nonequilibrium steered molecular dynamics simulations to determine the absolute binding free energies of METH and AMP to scFv. The center of mass of a drug molecule (METH or AMP) is steered (pulled) towards (forward) and away from (reverse) the binding site, sampling forward and reverse pulling paths. Mechanic work is measured along the pulling paths. The work measurements are averaged through the Brownian dynamics fluctuation dissipation theorem to produce the free-energy profiles of the scFv:drug complexes as a function of the drug-scFv separation. These experiments lead to the theoretical prediction of absolute binding energies of METH and AMP that are in agreement with the in vitro experimental results.

Determination of equilibrium free energy from nonequilibrium work measurements

The fluctuation-dissipation theorem (FDT) of Brownian dynamics (BD) is applied to extract the equilibrium free-energy profile from the nonequilibrium, irreversible work measured in single-molecule pulling experiments. Two sets of in silico experiments are performed to explore the free-energy landscape of deca-alanine peptide as a function of its end-to-end distance and to determine the free-energy profile of water permeation through the channels of aquaglyceroporin GlpF. With a small number of pulling paths sampled, the BD-FDT is shown to produce accurate estimates of the free-energy profiles for both systems.

On the Crooks fluctuation theorem and the Jarzynski equality

The Jarzynski equality (JE) and the undergirding Crooks fluctuation theorem (CFT) have generated intense interest recently among researchers in physical and biological sciences. It has been held that the CFT has wider applicability than the JE. This note shows that the two are equally applicable and that their applicability is possibly limited to near-equilibrium processes, where the linear fluctuation-dissipation theorem holds.

Ampakines cause sustained increases in brain-derived neurotrophic factor signaling at excitatory synapses without changes in AMPA receptor subunit expression

Recent demonstrations that positive modulators of AMPA-type glutamate receptors (ampakines) increase neuronal brain-derived neurotrophic factor (BDNF) expression have suggested a novel strategy for treating neurodegenerative diseases. However, reports that AMPA and BDNF receptors are down-regulated by prolonged activation raise concerns about the extent to which activity-induced increases in BDNF levels can be sustained without compromising glutamate receptor function. The present study constitutes an initial test of whether ampakines can cause enduring increases in BDNF content and signaling without affecting AMPA receptor (AMPAR) expression. Prolonged (12-24 h) treatment with the ampakine CX614 reduced AMPAR subunit (glutamate receptor subunit (GluR) 1-3) mRNA and protein levels in cultured rat hippocampal slices whereas treatment with AMPAR antagonists had the opposite effects. The cholinergic agonist carbachol also depressed GluR1-3 mRNA levels, suggesting that AMPAR down-regulation is a global response to extended periods of elevated neuronal activity. Analyses of time courses and thresholds indicated that BDNF expression is influenced by lower doses of, and shorter treatments with, the ampakine than is AMPAR expression. Accordingly, daily 3 h infusions of CX614 chronically elevated BDNF content with no effect on GluR1-3 concentrations. Restorative deconvolution microscopy provided the first evidence that chronic up-regulation of BDNF is accompanied by increased activation of the neurotrophin's TrkB-Fc receptor at spine synapses. These results show that changes in BDNF and AMPAR expression are dissociable and that up-regulation of the former leads to enhanced trophic signaling at excitatory synapses. These findings are encouraging with regard to the feasibility of using ampakines to tonically enhance BDNF-dependent functions in adult brain.

Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics

Studying the Brownian motion of a system driven by an external control from one macroscopic state to another macroscopic state, this paper presents the derivation of a nonlinear fluctuation-dissipation theorem (FDT). The new FDT relates the nonequilibrium work to the equilibrium free-energy difference in a very simple manner. It is valid wherever the Brownian dynamics is applicable. It recovers the well-known Crooks fluctuation theorem (CFT) within the quasiequilibrium regime where the dissipative work is nearly zero. It will also be shown that the CFT's fundamental assumption of microscopic reversibility is not obeyed in experiments such as mechanically unfolding biological molecules, in which the external driving forces depend on the system's coordinates.