Unified master equation for molecules in phonon and radiation baths.

We have developed a unified quantum optical master equation that includes the dissipative mechanisms of an impurity molecule in crystals. Our theory applies generally to polyatomic molecules where several vibrational modes give rise to intramolecular vibrational redistributions. The usual assumption on identical shapes of the nuclear potentials in ground and excited electronic states and the rotating wave approximation have been relaxed, i.e. the vibrational coordinates are different in the ground and excited states, with counter-rotating terms included for generality. Linear vibrational coupling to the lattice phonons accounts for dissipations via non-radiative transitions. The interaction of a molecule with photons includes Herzberg-Teller coupling as the first order non-Condon interaction where the transition dipole matrix elements depend linearly on vibrational coordinates. We obtain new cross terms as the result of mixing the terms from the zeroth-order (Condon) and first-order (non-Condon) approximations. The corresponding Lamb shifts for all Liouvilleans are derived explicitly including the contributions of counter-rotating terms. The computed absorption and emission spectra for carbon monoxide is in good agreement with experimental data. We use our unified model to obtain the spectra for nitrogen dioxide, demonstrating the capability of our theory to incorporate all typical dissipative relaxation and decoherence mechanisms for polyatomic molecules. The molecular quantum master equation is a promising theory for studying molecular quantum memory.

Enhanced resonances by waveguide wrapping of a bulbed microring resonator.

A high Q-factor novel bulb design, to the best of our knowledge, inspired by the well-studied pulley microring resonator (MRR), is demonstrated and compared with circle and racetrack MRRs at wavelengths of 1.45-1.65 µm. A wrapping of 60% around the ring showed a three times Q-factor increment (Q=828) compared to a standard circle MRR (Q=206) at a telecom wavelength of 1.55 µm with a fixed ring radius of 2 µm, while further increasing the wrapping at 80% shows a decrease in its Q-factor (Q=454). A comparison of the wavelength dependence of the bulb design with other typical MRR designs suggests that bulb designs are highly sensitive to wavelength and have very high Q-factors at lower wavelengths.

Genetic diversity of secreted protein with an altered thrombospondin repeat (SPATR) of Plasmodium knowlesi clinical isolates from Malaysia.

The Plasmodium knowlesi secreted protein with an altered thrombospondin repeat (PkSPATR) is an important protein that helps in the parasite's invasion into the host cell. This protein has been regarded as one of the potential vaccine candidates against P. knowlesi infection. This study investigates the genetic diversity and natural selection of PkSPATR gene of P. knowlesi clinical isolates from Malaysia. PCR amplification of the full length PkSPATR gene was performed on 60 blood samples of infected P. knowlesi patients from Peninsular Malaysia and Malaysian Borneo. The amplified PCR products were cloned and sequenced. Sequence analysis of PkSPATR from Malaysia showed higher nucleotide diversity (CDS p: 0.01462) than previously reported Plasmodium vivax PvSPATR (p = 0.0003). PkSPATR from Peninsular Malaysia was observed to have slightly higher diversity (CDS p: 0.01307) than those from Malaysian Borneo (CDS p: 0.01212). Natural selection analysis on PkSPATR indicated significant purifying selection. Multiple amino acid sequence alignment revealed 69 polymorphic sites. The phylogenetic tree and haplotype network did not show any distinct clustering of PkSPATR. The low genetic diversity level, natural selection and absence of clustering implied functional constrains of the PkSPATR protein.

Genetic diversity of secreted protein with an altered thrombospondin repeat (SPATR) of Plasmodium knowlesi clinical isolates from Malaysia

@#The Plasmodium knowlesi secreted protein with an altered thrombospondin repeat (PkSPATR) is an important protein that helps in the parasite’s invasion into the host cell. This protein has been regarded as one of the potential vaccine candidates against P. knowlesi infection. This study investigates the genetic diversity and natural selection of PkSPATR gene of P. knowlesi clinical isolates from Malaysia. PCR amplification of the full length PkSPATR gene was performed on 60 blood samples of infected P. knowlesi patients from Peninsular Malaysia and Malaysian Borneo. The amplified PCR products were cloned and sequenced. Sequence analysis of PkSPATR from Malaysia showed higher nucleotide diversity (CDS p: 0.01462) than previously reported Plasmodium vivax PvSPATR (p = 0.0003). PkSPATR from Peninsular Malaysia was observed to have slightly higher diversity (CDS p: 0.01307) than those from Malaysian Borneo (CDS p: 0.01212). Natural selection analysis on PkSPATR indicated significant purifying selection. Multiple amino acid sequence alignment revealed 69 polymorphic sites. The phylogenetic tree and haplotype network did not show any distinct clustering of PkSPATR. The low genetic diversity level, natural selection and absence of clustering implied functional constrains of the PkSPATR protein.

High incidence of Plasmodium knowlesi malaria compared to other human malaria species in several hospitals in Malaysia.

Through the regional control programme, Malaysia has been successfully reducing the incidence of Plasmodium falciparum and Plasmodium vivax infections. However, the incidence of zoonotic malaria Plasmodium knowlesi infection is increasing and now has been the major cause of malaria in Malaysia especially Malaysian Borneo. The emergence of knowlesi infection has threatened the malaria elimination programme which the government aims to reduce the overall malaria infections by 2020. Unlike other benign human Plasmodium spp., P. knowlesi can cause fatal infections. The aim of this study was to determine the incidence and distribution of five human malaria parasites including P. knowlesi in Peninsular Malaysia and Malaysian Borneo. A total of 112 blood samples were collected from seven states and district hospitals in Peninsular Malaysia and Malaysian Borneo from year 2015 to 2016. The samples were examined by microscopy and further confirmed by nested PCR assay targeting 18S rRNA gene of Plasmodium spp. Following the nested PCR assays, a total of 54 (48.2%) samples were positive for P. knowlesi infections, 12 (10.7%) cases were positive for P. vivax infections, followed by 7 (6.3%) cases of P. falciparum and 4 (3.5%) cases of P. malariae. There were 3 cases (2.7%) of mixed infections (P. knowlesi/P. vivax). However, no cases were identified as P. ovale. A total of 32 (28.6%) cases were found as negative infections. LoopMediated Isothermal Amplification Assay (LAMP) was performed to confirm inconclusive results produced by microscopy and nested PCR. P. knowlesi showed the highest prevalence in Sarawak (n= 30), Sabah (n=13), Pulau Pinang (n=5) and Pahang (n=6). PCR and LAMP was not able to detect a large number of microscopy positive samples due to DNA degradation during storage and shipping. Among all the states involved in this study, the highest prevalence of P. knowlesi infection was found in Sabah and Sarawak.

Light absorption by interacting atomic gas in quantum optical regime.

Quantum optical theory of absorption properties of interacting atoms is developed. The concept of local absorptance is introduced as a derivative of the logarithm of intensity with respect to the distance in the vicinity of a given spatial point and a moment of time. The intensity is represented by the quantum and statistically averaged normal product of creation and annihilation operators of the electromagnetic field. The development of an analytical method of the estimation for the kinetic and optical parameters for the system is proposed here. The calculation method of the absorption coefficient includes thermal atomic motion, Doppler effect, and the short-range interaction between atoms. The absorption coefficient explicitly takes into account the quantum nature of the optical field. The ability of the system to absorb or emit quanta is quantitatively expressed through the special form of interaction integrals. The specific form of integrals results from the structure of the quantum brackets. The interplay between the collective (virtual photon exchange) and binary (optically induced inter-particle bonding) processes determines the system behavior. The spectral profile of the local absorption coefficient for different atomic densities and time intervals is simulated for realistic parameters.

The molecular mechanisms of probiotic strains in improving ageing bone and muscle of d-galactose-induced ageing rats.

AIM: The aim of this study was to evaluate the molecular mechanisms of Lactobacillus strains in improving ageing of the musculoskeletal system. METHODS AND RESULTS: The anti-ageing mechanism of three probiotics strains Lactobacillus fermentum DR9, Lactobacillus paracasei OFS 0291 and L. helveticus OFS 1515 were evaluated on gastrocnemius muscle and tibia of d-galactose-induced ageing rats. Upon senescence induction, aged rats demonstrated reduced antioxidative genes CAT and SOD expression in both bone and muscle compared to the young rats (P < 0·05). Strain L. fermentum DR9 demonstrated improved expression of SOD in bone and muscle compared to the aged rats (P < 0·05). In the evaluation of myogenesis-related genes, L. paracasei OFS 0291 and L. fermentum DR9 increased the mRNA expression of IGF-1; L. helveticus OFS 1515 and L. fermentum DR9 reduced the expression of MyoD, in contrast to the aged controls (P < 0·05). Protective effects of L. fermentum DR9 on ageing muscle were believed to be contributed by increased AMPK-α2 expression. Among the osteoclastogenesis genes studied, TNF-α expression was highly elevated in tibia of aged rats, while all three probiotics strains ameliorated the expression. Lactobacillus fermentum DR9 also reduced the expression of IL-6 and TRAP in tibia when compared to the aged rats (P < 0·05). All probiotics treatment resulted in declined proinflammatory cytokines IL-1ß in muscle and bone. CONCLUSIONS: Lactobacillus fermentum DR9 appeared to be the strongest strain in modulation of musculoskeletal health during ageing. SIGNIFICANCE AND IMPACT OF THE STUDY: The study demonstrated the protective effects of the bacteria on muscle and bone through antioxidative and anti-inflammatory actions. Therefore, L. fermentum DR9 may serve as a promising targeted anti-ageing therapy.

High incidence of Plasmodium knowlesi malaria compared to other human malaria species in several hospitals in Malaysia

@# Through the regional control programme, Malaysia has been successfully reducing the incidence of Plasmodium falciparum and Plasmodium vivax infections. However, the incidence of zoonotic malaria Plasmodium knowlesi infection is increasing and now has been the major cause of malaria in Malaysia especially Malaysian Borneo. The emergence of knowlesi infection has threatened the malaria elimination programme which the government aims to reduce the overall malaria infections by 2020. Unlike other benign human Plasmodium spp., P. knowlesi can cause fatal infections. The aim of this study was to determine the incidence and distribution of five human malaria parasites including P. knowlesi in Peninsular Malaysia and Malaysian Borneo. A total of 112 blood samples were collected from seven states and district hospitals in Peninsular Malaysia and Malaysian Borneo from year 2015 to 2016. The samples were examined by microscopy and further confirmed by nested PCR assay targeting 18S rRNA gene of Plasmodium spp. Following the nested PCR assays, a total of 54 (48.2%) samples were positive for P. knowlesi infections, 12 (10.7%) cases were positive for P. vivax infections, followed by 7 (6.3%) cases of P. falciparum and 4 (3.5%) cases of P. malariae. There were 3 cases (2.7%) of mixed infections (P. knowlesi/P. vivax). However, no cases were identified as P. ovale. A total of 32 (28.6%) cases were found as negative infections. LoopMediated Isothermal Amplification Assay (LAMP) was performed to confirm inconclusive results produced by microscopy and nested PCR. P. knowlesi showed the highest prevalence in Sarawak (n= 30), Sabah (n=13), Pulau Pinang (n=5) and Pahang (n=6). PCR and LAMP was not able to detect a large number of microscopy positive samples due to DNA degradation during storage and shipping. Among all the states involved in this study, the highest prevalence of P. knowlesi infection was found in Sabah and Sarawak.

Non-locality Correlation in Two Driven Qubits Inside an Open Coherent Cavity: Trace Norm Distance and Maximum Bell Function.

We analytically investigate two separated qubits inside an open cavity field. The cavity is initially prepared in a superposition coherent state. The non-locality correlations [including trace norm measurement induced non-locality, maximal Bell-correlation, and concurrence entanglement] of the two qubits are explored. It is shown that, the generated non-locality correlations crucially depend on the decay and the initial coherence intensity of the cavity field. The enhancement of the initial coherence intensity and its superposition leads to increasing the generated non-locality correlations. The phenomena of sudden birth and death entanglement are found.

Phase I study of emactuzumab single agent or in combination with paclitaxel in patients with advanced/metastatic solid tumors reveals depletion of immunosuppressive M2-like macrophages.

BACKGROUND: Emactuzumab is a monoclonal antibody against the colony-stimulating factor-1 receptor and targets tumor-associated macrophages (TAMs). This study assessed the safety, clinical activity, pharmacokinetics (PK) and pharmacodynamics (PD) of emactuzumab, as monotherapy and in combination with paclitaxel, in patients with advanced solid tumors. PATIENTS AND METHODS: This open-label, phase Ia/b study comprised two parts (dose escalation and dose expansion), each containing two arms (emactuzumab, every 2 or 3 weeks, as monotherapy or in combination with paclitaxel 80 mg/m2 weekly). The dose-escalation part explored the maximum tolerated dose and optimal biological dose (OBD). The dose-expansion part extended the safety assessment and investigated the objective response rate. A PK/PD analysis of serial blood, skin and tumor biopsies was used to explore proof of mechanism and confirm the OBD. RESULTS: No maximum tolerated dose was reached in either study arm, and the safety profile of emactuzumab alone and in combination does not appear to preclude its use. No patients receiving emactuzumab monotherapy showed an objective response; the objective response rate for emactuzumab in combination with paclitaxel was 7% across all doses. Skin macrophages rather than peripheral blood monocytes or circulating colony-stimulating factor-1 were identified as an optimal surrogate PD marker to select the OBD. Emactuzumab treatment alone and in combination with paclitaxel resulted in a plateau of immunosuppressive TAM reduction at the OBD of 1000 mg administered every 2 weeks. CONCLUSIONS: Emactuzumab showed specific reduction of immunosuppressive TAMs at the OBD in both treatment arms but did not result in clinically relevant antitumor activity alone or in combination with paclitaxel. (ClinicalTrials.gov Identifier: NCT01494688).

Large-scale structure formation in ionic solution and its role in electrolysis and conductivity.

That water may not be an inert medium was indicated by the presence at water's interfaces a negatively charged solute free zone of several hundred microns in thickness called the exclusion zone (EZ). Further evidence was demonstrated by Ovchinnikova's experiments (2009) showing that water can store and release substantial amount of charge. We demonstrate that the charge storage capacity of water arises from highly stable large-scale ionic structures with measurable charge imbalances and discrete levels of charge density. We also show evidence that the charge zones formation requires ionic solutes, and their formation correlate to large change in conductivity, by as much as 250%. Our experiments indicate that large-scale structuring plays a pivotal role in electrolysis and conductivity in ionic solution. We propose that water is an electrochemically active medium and present a new model of electrolysis and conductivity in ionic solution.

Investigation of possible rickettsial infection in patients with malaria.

Rickettsioses are a common health problem in many geographical areas, including rural areas in Southeast Asia. Co-infection of rickettsioses and malaria has been reported in Africa, where common reservoir and vectors are available. In this study, blood samples of Malaysian patients microscopically positive (n=148) and negative (n=88) for malaria parasites (Plasmodium knowlesi, Plasmodium malariae, Plasmodium falciparum, and Plasmodium vivax) were screened for the presence of rickettsial DNA, using PCR assays targeting specific genes. A partial fragment of rickettsial ompB gene was successfully amplified and sequenced from a patient microscopically positive for Plasmodium spp. and PCR-positive for P. vivax. BLAST analysis of the ompB sequence demonstrated the highest sequence similarity (99.7% similarity, 408/409nt) with Rickettsia sp. RF2125 (Genbank accession no. JX183538) and 91.4% (374/409 nt) similarity with Rickettsia felis URRWXCal2 (Genbank accession no. CP000053). This study reports rickettsial infection in a malaria patient for the first time in the Southeast Asia region.

Investigation of possible rickettsial infection in patients with malaria

@#Rickettsioses are a common health problem in many geographical areas, including rural areas in Southeast Asia. Co-infection of rickettsioses and malaria has been reported in Africa, where common reservoir and vectors are available. In this study, blood samples of Malaysian patients microscopically positive (n=148) and negative (n=88) for malaria parasites (Plasmodium knowlesi, Plasmodium malariae, Plasmodium falciparum, and Plasmodium vivax) were screened for the presence of rickettsial DNA, using PCR assays targeting specific genes. A partial fragment of rickettsial ompB gene was successfully amplified and sequenced from a patient microscopically positive for Plasmodium spp. and PCR-positive for P. vivax. BLAST analysis of the ompB sequence demonstrated the highest sequence similarity (99.7% similarity, 408/409nt) with Rickettsia sp. RF2125 (Genbank accession no. JX183538) and 91.4% (374/409 nt) similarity with Rickettsia felis URRWXCal2 (Genbank accession no. CP000053). This study reports rickettsial infection in a malaria patient for the first time in the Southeast Asia region.

Effects of ultrashort laser pulses on angular distributions of photoionization spectra.

We study the photoelectron spectra by intense laser pulses with arbitrary time dependence and phase within the Keldysh framework. An efficient semianalytical approach using analytical transition matrix elements for hydrogenic atoms in any initial state enables efficient and accurate computation of the photoionization probability at any observation point without saddle point approximation, providing comprehensive three dimensional photoelectron angular distribution for linear and elliptical polarizations, that reveal the intricate features and provide insights on the photoionization characteristics such as angular dispersions, shift and splitting of photoelectron peaks from the tunneling or above threshold ionization(ATI) regime to non-adiabatic(intermediate) and multiphoton ionization(MPI) regimes. This facilitates the study of the effects of various laser pulse parameters on the photoelectron spectra and their angular distributions. The photoelectron peaks occur at multiples of 2hω for linear polarization while  odd-ordered peaks are suppressed in the direction perpendicular to the electric field. Short pulses create splitting and angular dispersion where the peaks are strongly correlated to the angles. For MPI and elliptical polarization with shorter pulses the peaks split into doublets and the first peak vanishes. The carrier envelope phase(CEP) significantly affects the ATI spectra while the Stark effect shifts the spectra of intermediate regime to higher energies due to interference.

Real-time path-integral approach for dissipative quantum dot-cavity quantum electrodynamics: impure dephasing-induced effects.

A dissipative quantum dot (QD)-cavity system, where the QD is initially prepared in the excited state with no photon in the cavity, coupled to a longitudinal acoustic (LA) phonon reservoir is studied using a numerically exact real-time path-integral approach. Three distinct dynamical regimes of weak (WC), strong (SC), and coherent coupling (CC) are discussed and more accurate conditions identifying them are presented. Our results show that to have the CC regime, which is characterized by clear vacuum Rabi oscillation (VRO), vacuum Rabi splitting (VRS) should be larger than the sum of the widths of the corresponding peaks. In order to distinguish between contributions of population decay and impure dephasing, induced by LA phonon bath and the dissipations, we propose a two-part phenomenological expression, corresponding to the population decay and impure dephasing, which fits the QD-cavity decay curves perfectly and is used to calculate the corresponding spectra. We demonstrate that the effective population decay rate (the emission rate) increases from the carrier recombination rate to a maximum value, which is the mean of the QD and cavity dissipation rates, with QD-cavity coupling strength. To study the role of the effective impure dephasing rate on the width of the central peak of the spectra we introduce a quantity that can also be applied in determining the distinct coupling regimes. This quantity enables us to identify the onset of the SC regime as the point where the impure dephasing term begins to contribute to the central band of the spectrum significantly, as a result of the existence of VRO with a very small frequency (unclear VRO) at the corresponding decay curve. Its contribution to the width of the central peak increases with the coupling strength up to the onset of the CC regime, then reduces as a result of the appearance of sidebands in the spectra, which originates from clear VRO. The effective population decay and impure dephasing rate contribute solely to the width-of the central and sideband peaks of the triplet spectra respectively-only beyond a very large coupling strength which is the same across the considered temperature range. For higher temperatures, the maximum achievable emission rate can be obtained at larger coupling strengths.

Intricate Plasma-Scattered Images and Spectra of Focused Femtosecond Laser Pulses.

We report on some interesting phenomena in the focusing and scattering of femtosecond laser pulses in free space that provide insights on intense laser plasma interactions. The scattered image in the far field is analyzed and the connection with the observed structure of the plasma at the focus is discussed. We explain the physical mechanisms behind the changes in the colorful and intricate image formed by scattering from the plasma for different compressions, as well as orientations of plano-convex lens. The laser power does not show significant effect on the images. The pulse repetition rate above 500 Hz can affect the image through slow dynamics The spectrum of each color in the image shows oscillatory peaks due to interference of delayed pulse that correlate with the plasma length. Spectral lines of atomic species are identified and new peaks are observed through the white light emitted by the plasma spot. We find that an Ar gas jet can brighten the white light of the plasma spot and produce high resolution spectral peaks. The intricate image is found to be extremely sensitive and this is useful for applications in sensing microscale objects.

Probing infinity in bounded two-dimensional electrostatic systems.

The total electrostatic energy of systems of identical particles of equal charge is studied in configurations bounded in space, but divergent in the number of charges. This approach shall guide us to unveil a non-linear, functional form specifying the divergent nature of system energy. We consider fractals to be physical entities, with charges located in their vertices or nodes. This description is interesting since features, such as the corresponding fractal dimension, can characterize the total energy EN. Finally, at local length scales, we describe how energy diverges at charge accumulation points in the fractal, that is, almost everywhere by definition.

Corrosion and bioactivity performance of graphene oxide coating on TiNb shape memory alloys in simulated body fluid.

In the present work, the microstructure, corrosion, and bioactivity of graphene oxide (GO) coating on the laser-modified and -unmodified surfaces of TiNb shape memory alloys (SMAs) were investigated. The surface morphology and chemical composition was examined using field emission scanning electron microscopy (FE-SEM) and X-ray diffraction (XRD). The surface modification was carried out via a femtosecond laser with the aim to increase the surface roughness, and thus increase the adhesion property. FE-SEM analysis of the laser-treated Ti-30at.% Nb revealed the increase in surface roughness and oxygen/nitrogen containing groups on the Ti-30at.% Nb surface after being surface modified via a femtosecond laser. Furthermore, the thickness of GO was increased from 35µm to 45µm after the surface was modified. Potentiodynamic polarisation and electrochemical impedance spectroscopy studies revealed that both the GO and laser/GO-coated samples exhibited higher corrosion resistance than that of the uncoated TiNb SMA sample. However, the laser/GO-coated sample presented the highest corrosion resistance in SBF at 37°C. In addition, during soaking in the simulated body fluid (SBF), both the GO and laser/GO coating improved the formation of apatite layer. Based on the bioactivity results, the GO coating exhibited a remarkable antibacterial activity against gram-negative bacteria compared with the uncoated. In conclusion, the present results indicate that Ti-30at.% Nb SMAs may be promising alternatives to NiTi for certain biomedical applications.

Coherently Tunable Triangular Trefoil Phaseonium Metamaterial.

Phaseonium is a three-level Λ quantum system, in which a coherent microwave and an optical control (pump) beams can be used to actively modulate the dielectric response. Here we propose a new metamaterial structure comprising of a periodic array of triangular phaseonium metamolecules arranged as a trefoil. We present a computational study of the spatial distribution of magnetic and electric fields of the probe light and the corresponding transmission and reflection, for various parameters of the optical and microwave beams. For specific values of the probing frequencies and control fields, the phaseonium can display either metallic or dielectric optical response. We find that, in the metallic regime, the phaseonium metamaterial structure supports extremely large transmission, with optical amplification at large enough intensity of the microwave thanks to strong surface plasmon coupling; while, in the dielectric regime without microwave excitation, the transmission bandwidth can be tuned by varying the control beam intensity. Implementation of such phaseonium metamaterial structure in solid-state systems, such as patterned crystals doped with rare-earth elements or dielectric matrices embedded with quantum dots, could enable a new class of actively tunable quantum metamaterials.

High-performance dye-sensitized solar cells based on morphology-controllable synthesis of ZnO-ZnS heterostructure nanocone photoanodes.

High-density and well-aligned ZnO-ZnS core-shell nanocone arrays were synthesized on fluorine-doped tin oxide glass substrate using a facile and cost-effective two-step approach. In this synthetic process, the ZnO nanocones act as the template and provide Zn2+ ions for the ZnS shell formation. The photoluminescence spectrum indicates remarkably enhanced luminescence intensity and a small redshift in the UV region, which can be associated with the strain caused by the lattice mismatch between ZnO and ZnS. The obtained diffuse reflectance spectra show that the nanocone-based heterostructure reduces the light reflection in a broad spectral range and is much more effective than the bare ZnO nanocone and nanorod structures. Dye-sensitized solar cells based on the heterostructure ZnO-ZnS nanocones are assembled, and high conversion efficiency (η) of approximately 4.07% is obtained. The η improvement can be attributed primarily to the morphology effect of ZnO nanocones on light-trapping and effectively passivating the interface surface recombination sites of ZnO nanocones by coating with a ZnS shell layer.