The Histidine Phosphocarrier Kinase/Phosphorylase from Bacillus Subtilis Is an Oligomer in Solution with a High Thermal Stability

The histidine phosphocarrier protein (HPr) kinase/phosphorylase (HPrK/P) modulates the phosphorylation state of the HPr protein, and it is involved in the use of carbon sources by Gram-positive bacteria. Its X-ray structure, as concluded from crystals of proteins from several species, is a hexamer; however, there are no studies about its conformational stability, and how its structure is modified by the pH. We have embarked on the conformational characterization of HPrK/P of Bacillus subtilis (bsHPrK/P) in solution by using several spectroscopic (namely, fluorescence and circular dichroism (CD)) and biophysical techniques (namely, small-angle X-ray-scattering (SAXS) and dynamic light-scattering (DLS)). bsHPrK/P was mainly a hexamer in solution at pH 7.0, in the presence of phosphate. The protein had a high conformational stability, with an apparent thermal denaturation midpoint of ~70 °C, at pH 7.0, as monitored by fluorescence and CD. The protein was very pH-sensitive, precipitated between pH 3.5 and 6.5; below pH 3.5, it had a molten-globule-like conformation; and it acquired a native-like structure in a narrow pH range (between pH 7.0 and 8.0). Guanidinium hydrochloride (GdmCl) denaturation occurred through an oligomeric intermediate. On the other hand, urea denaturation occurred as a single transition, in the range of concentrations between 1.8 and 18 µM, as detected by far-UV CD and fluorescence.     

Nelder-Mead Simplex Optimization Routine for Large-Scale Problems: A Distributed Memory Implementation

The Nelder-Mead simplex method is an optimization routine that works well with irregular objective functions. For a function of $n$ parameters, it compares the objective function at the $n+1$ vertices of a simplex and updates the worst vertex through simplex search steps. However, a standard serial implementation can be prohibitively expensive for optimizations over a large number of parameters. We describe an implementation of the Nelder-Mead method in parallel using a distributed memory. For $p$ processors, each processor is assigned $(n+1)/p$ vertices at each iteration. Each processor then updates its worst local vertices, communicates the results, and a new simplex is formed with the vertices from all processors. We also describe how the algorithm can be implemented with only two MPI commands. In simulations, our implementation exhibits large speedups and is scalable to large problem sizes.     

An efficient method for a numerical description of virgin olive oil color with only two absorbance measurements

Four polynomial expressions are obtained that provide a good approximation and an easy, rapid calculation of the chromatic coordinates and the chroma—L ^*, a ^*, b ^*, and C—for the illuminant C and the standard observer, for a virgin or extra virgin olive oil; absorbance is measured at only 480 and 670 nm. These are as follows: L ^*=0.556458(A₄₈₀)²−2.51145A₄₈₀+0.55504(A₆₇₀)²−8.53016A₆₇₀+98.4089; a ^*=0.177372(A₄₈₀)²+2.1363A₄₈₀+1.43254(A₆₇₀)²−0.789231A₆₇₀−13.9246; b ^*=−16.0277(A₄₈₀)²+79.8932A₄₈₀−5.06558(A₆₇₀)²+3.36169A₆₇₀+31.9405; C=−15.8439(A₄₈₀)²+78.9312A₄₈₀−5.26784(A₆₇₀)²+3.56917A₆₇₀+33.3927. These give acceptable results, making the method a practical alternative to the extremely laborious Commission Internationale d’Eclairage (CIE) L ^* a ^* b ^* system, by which 391 absorbance values must be measured individually, nanometer by nanometer, before applying more complex equations. The validity of the proposed method has been confirmed by comparison, using a set of 20 sample oils different from the set of 25 oils used to generate the order of the equations. The variations between the values provided by the proposed and standard methods, respectively, had a mean of 0.00 for each of the chromatic variables—L ^* , a ^* , b ^* , and C; SD were moderate (0.71, 0.52, 1.22, and 1.22, respectively); the root mean square and the R ²-terms also confirmed the validity of the method.     

Microfluidic Tumor-on-a-Chip Model to Study Tumor Metabolic Vulnerability

Tumor-specific metabolic adaptations offer an interesting therapeutic opportunity to selectively destroy cancer cells. However, solid tumors also present gradients of nutrients and waste products across the tumor mass, forcing tumor cells to adapt their metabolism depending on nutrient availability in the surrounding microenvironment. Thus, solid tumors display a heterogenous metabolic phenotype across the tumor mass, which complicates the design of effective therapies that target all the tumor populations present. In this work, we used a microfluidic device to study tumor metabolic vulnerability to several metabolic inhibitors. The microdevice included a central chamber to culture tumor cells in a three-dimensional (3D) matrix, and a lumen in one of the chamber flanks. This design created an asymmetric nutrient distribution across the central chamber, generating gradients of cell viability. The results revealed that tumor cells located in a nutrient-enriched environment showed low to no sensitivity to metabolic inhibitors targeting glycolysis, fatty acid oxidation, or oxidative phosphorylation. Conversely, when cell density inside of the model was increased, compromising nutrient supply, the addition of these metabolic inhibitors disrupted cellular redox balance and led to tumor cell death.     

A comparison of loop closing techniques in monocular SLAM

Loop closure detection systems for monocular SLAM come in three broad categories: (i) map-to-map, (ii) image-to-image and (iii) image-to-map. In this paper, we have chosen an implementation of each and performed experiments allowing the three approaches to be compared. The sequences used include both indoor and outdoor environments and single and multiple loop trajectories.     

Late Bronze Age hoard studied by PIXE

The hoards of metallic objects belonging to the Late European Bronze Age can be interpreted differently depending on the type, number and composition of the artefacts. PIXE analysis has been performed in nine items from the Hoard of Freixanda in Portugal comprising four socket axes, a palstave axe, a ring, a chisel, a dagger, and a casting debris. Besides the composition of the main matrix elements, that is Cu and Sn, the amount of trace elements of interest like, As, Pb, Ni, and Ag has been determined using this ion beam technique. The high tin content alloy and the high purity of the metals from the Freixanda hoard are characteristic of the Portuguese and Spanish Late Bronze Age metallurgy, supporting the idea of a regional production.     

Surface modification of carbon nanofibers via deposition of an ultrathin coating of plasma‐polymerized poly(acrylic acid) and its effect on the properties of polyamide 6/CNF nanocomposites

Carbon nanofibers (CNFs) were coated with an ultrathin layer of poly(acrylic acid) (PAA) via plasma polymerization. The effect of the plasma reactor parameters on the extent of the CNF modification was studied. SEM micrographs showed that surface roughness increased with the plasma treatment. The thickness of the ultrathin PAA layer deposited on the CNF was determined by STEM to be ca. 8 nm. Untreated and treated CNF were melt‐mixed with polyamide 6 (PA6) in a Brabender mixing chamber to obtain PA6/CNF nanocomposites. The effect of the plasma treatment on the dispersion and compatibility was examined and found to improve markedly. Fractured tensile specimens showed that the CNF seemed to be completely embedded in the polymer matrix, indicating high compatibility between the PA6 and the PAA‐coated CNF. Tensile stress and tensile modulus of PA6 nanocomposites with treated CNF were found to increase by 30 and 48%, respectively, when compared with those with untreated CNF. However, the increase in tensile stress and modulus with respect to pure PA6 was 52 and 88%, respectively. Finally, XRD showed that the CNF induce the formation of the α (alpha)‐crystalline phase in PA6. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009     

The necessity of sample quality assessment in 14C AMS dating: The case of Cova des Pas (Menorca – Spain)

The Cova des Pas cave is a karstic cave in the cliffs of the Barranc (canyon) de Trebalúger. It is a small cave only 6.5 m deep, 4.5 m wide and 1.7 m high. Yet more than 70 burials, in foetal position, from the Early Iron Age were found in this small cave. The conservation of the archaeological remains was very unusual. Not only wood, ropes and other plant material was found, but also remains of body tissue, hair and leather. In spite of the remarkable preservation of the bodies and artefacts, the state of conservation of the bone material was very bad. The bones contained little and heavily deteriorated collagen and the organic plant material was very fragile. The special environmental conditions of the cave are the cause of these unusual preservation conditions. Although the cave is situated in a limestone cliff, the soil of the cave is very acid. Unexpectedly bad sample quality seemed to be the major drawback for AMS radiocarbon dating on hair, wood, ropes and bone collagen, as well as on bio-apatite.     

Opportunistic Grassmannian Beamforming for Multiuser and Multiantenna Downlink Communications

Scheduling in a broadcast channel based on partial channel-state-information at the transmitter is carried out in an opportunistic way. In this paper, the number of generated beams is larger than the number of available base station antennas, where the beams are obtained through Grassmannian line packing to guarantee the largest orthogonality among them. Approximate expressions and bounds are derived for the sum capacity of the proposed approach together with its scaling law. For practical systems, we show that this scheme can increase the number of serviced users under a minimum-rate-per-user requirement.