Structure-property relationships from universal signatures of plasticity in disordered solids.

When deformed beyond their elastic limits, crystalline solids flow plastically via particle rearrangements localized around structural defects. Disordered solids also flow, but without obvious structural defects. We link structure to plasticity in disordered solids via a microscopic structural quantity, "softness," designed by machine learning to be maximally predictive of rearrangements. Experimental results and computations enabled us to measure the spatial correlations and strain response of softness, as well as two measures of plasticity: the size of rearrangements and the yield strain. All four quantities maintained remarkable commonality in their values for disordered packings of objects ranging from atoms to grains, spanning seven orders of magnitude in diameter and 13 orders of magnitude in elastic modulus. These commonalities link the spatial correlations and strain response of softness to rearrangement size and yield strain, respectively.

Copper as an antibacterial material in different facilities.

The present study was performed in real life settings in different facilities (hospital, kindergarten, retirement home, office building) with copper and copper alloy touch surface products (floor drain lids, toilet flush buttons, door handles, light switches, closet touch surfaces, corridor hand rails, front door handles and toilet support rails) in parallel to reference products. Pure copper surfaces supported lower total bacterial counts (16 ± 45 vs 105 ± 430 CFU cm-2 , n = 214, P < 0·001) and a lower occurrence of Staphylococcus aureus (2·6 vs 14%, n = 157, P < 0·01) and Gram-negatives (21 vs 34%, n = 214, P < 0·05) respectively than did reference surfaces, whereas the occurrence of enterococci (15%, n = 214, P > 0·05) was similar. The studied products could be assigned to three categories according to their bacterial loads as follows (P < 0·001): floor drain lids (300 ± 730 CFU cm-2 , n = 32), small area touch surfaces (8·0 ± 7·1 to 62 ± 160 CFU cm-2 , n = 90) and large area touch surfaces (1·1 ± 1·1 to 1·7 ± 2·4 CFU cm-2 , n = 92). In conclusion, copper touch surface products can function as antibacterial materials to reduce the bacterial load, especially on frequently touched small surfaces. SIGNIFICANCE AND IMPACT OF THE STUDY: The efficiency of copper as an antimicrobial material has been noted in laboratory studies and in the hospital environment. The present study further shows that copper exerted an antibacterial effect in different facilities, i.e. in a hospital, a kindergarten, an office building and in a retirement home for the elderly. The study suggests that copper has potential use as an antibacterial material and therefore might serve as a means to lower the incidence of transmission of infectious agents from inanimate surfaces in different facilities, with everyday functions.

Microstructural view of burrowing with a bioinspired digging robot.

RoboClam is a burrowing technology inspired by Ensis directus, the Atlantic razor clam. Atlantic razor clams should only be strong enough to dig a few centimeters into the soil, yet they burrow to over 70 cm. The animal uses a clever trick to achieve this: by contracting its body, it agitates and locally fluidizes the soil, reducing the drag and energetic cost of burrowing. RoboClam technology, which is based on the digging mechanics of razor clams, may be valuable for subsea applications that could benefit from efficient burrowing, such as anchoring, mine detonation, and cable laying. We directly visualize the movement of soil grains during the contraction of RoboClam, using a novel index-matching technique along with particle tracking. We show that the size of the failure zone around contracting RoboClam can be theoretically predicted from the substrate and pore fluid properties, provided that the timescale of contraction is sufficiently large. We also show that the nonaffine motions of the grains are a small fraction of the motion within the fluidized zone, affirming the relevance of a continuum model for this system, even though the grain size is comparable to the size of RoboClam.

Granular dynamics during impact.

We study the impact of a projectile onto a bed of 3 mm grains immersed in an index-matched fluid. We vary the amount of prestrain on the sample, strengthening the force chains within the system. We find this affects only the prefactor of the linear depth-dependent term in the stopping force. We propose a simple model to account for the strain dependence of this term, owing to increased pressure in the pile. Interestingly, we find that the presence of the fluid does not affect the impact dynamics, suggesting that dynamic friction is not a factor. Using a laser sheet scanning technique to visualize internal grain motion, we measure the trajectory of each grain throughout an impact. Microscopically, our results indicate that weaker initial force chains result in more irreversible, plastic rearrangements, suggesting static friction between grains does play a substantial role in the energy dissipation.

Rheology of soft colloids across the onset of rigidity: scaling behavior, thermal, and non-thermal responses.

We study the rheological behavior of colloidal suspensions composed of soft sub-micron-size hydrogel particles across the liquid-solid transition. The measured stress and strain-rate data, when normalized by thermal stress and time scales, suggest our systems reside in a regime wherein thermal effects are important. In a different vein, critical point scaling predictions for the jamming transition, typical in athermal systems, are tested. Near dynamic arrest, the suspensions exhibit scaling exponents similar to those reported in Nordstrom et al., Phys. Rev. Lett., 2010, 105, 175701. The observation suggests that our system exhibits a glass transition near the onset of rigidity, but it also exhibits a jamming-like scaling further from the transition point. These observations are thought-provoking in light of recent theoretical and simulation findings, which show that suspension rheology across the full range of microgel particle experiments can exhibit both thermal and athermal mechanisms.

Collection, processing and testing of bone, corneas, umbilical cord blood and haematopoietic stem cells by European Blood Alliance members.

BACKGROUND AND OBJECTIVES: A questionnaire study was carried out in collaboration with the European Blood Alliance (EBA) Tissues and Cells (T&C) working group. The aim was to assess the level of involvement and commonality of processes on the procurement, testing and storage of bone, corneas, umbilical cord blood (UCB) and haematopoietic stem cells (HSC) in order to identify different practices and to explore whether recommendations can be made for harmonization. MATERIALS AND METHODS: An online questionnaire was used for data collection in 2011, and 43 replies were received covering 71 product answers from 13 countries. RESULTS AND CONCLUSIONS: Estimated percentages of tissue and cell banking covered by EBA member blood banks as a proportion of all collections of each individual country varied markedly. There were also major differences in the amounts of products collected and discarded and in proportions tissues provided for grafting. However, discarding of certain collections also reflects the practice of increasing the likelihood of the very best units being used for transplantation. Harmonization of possible practices should focus on matching supply with demand and on identifying the most efficient operators. This could allow for the development of practices for minimizing unnecessary collections.

Granular convection in microgravity.

We investigate the role of gravity on convection in a dense granular shear flow. Using a microgravity-modified Taylor-Couette shear cell under the conditions of parabolic flight microgravity, we demonstrate experimentally that secondary, convective-like flows in a sheared granular material are close to zero in microgravity and enhanced under high-gravity conditions, though the primary flow fields are unaffected by gravity. We suggest that gravity tunes the frictional particle-particle and particle-wall interactions, which have been proposed to drive the secondary flow. In addition, the degree of plastic deformation increases with increasing gravitational forces, supporting the notion that friction is the ultimate cause.

Dynamical heterogeneity in soft-particle suspensions under shear.

We present experimental measurements of dynamical heterogeneities in a dense system of microgel spheres, sheared at different rates and at different packing fractions in a microfluidic channel, and visualized with high-speed digital video microscopy. A four-point dynamic susceptibility is deduced from video correlations, and is found to exhibit a peak that grows in height and shifts to longer times as the jamming transition is approached from two different directions. In particular, the time for particle-size root-mean square relative displacements is found to scale as τ*∼(γΔφ4)(-1), where γ is the strain rate and Δφ = |φ - φ(c)| is the distance from the random close-packing volume fraction. The typical number of particles in a dynamical heterogeneity is deduced from the susceptibility peak height and found to scale as n*∼(γΔφ4)(-0.3). Exponent uncertainties are less than ten percent. We emphasize that the same power-law behavior is found at packing fractions above and below φ(c). Thus our results considerably extend a previous observation of n*∼γ(-0.3) for granular heap flow at fixed packing below φ(c). Furthermore, the implied result n*∼(τ*)(0.3) compares well with the expectation from mode-coupling theory and with prior observations for driven granular systems.

Centrifugal compression of soft particle packings: theory and experiment.

An exact method is developed for computing the height of an elastic medium subjected to centrifugal compression, for arbitrary constitutive relation between stress and strain. Example solutions are obtained for power-law media and for cases where the stress diverges at a critical strain--for example as required by packings composed of deformable but incompressible particles. Experimental data are presented for the centrifugal compression of thermo-responsive N-isopropylacrylamide (NIPA) microgel beads in water. For small radial acceleration, the results are consistent with Hertzian elasticity, and are analyzed in terms of the Young elastic modulus of the bead material. For large radial acceleration, the sample compression asymptotes to a value corresponding to a space-filling particle volume fraction of unity. Therefore we conclude that the gel beads are incompressible, and deform without deswelling. In addition, we find that the Young elastic modulus of the particulate gel material scales with cross-link density raised to the power 3.3±0.8, somewhat larger than the Flory expectation.

Microfluidic rheology of soft colloids above and below jamming.

The rheology near jamming of a suspension of soft colloidal spheres is studied using a custom microfluidic rheometer that provides the stress versus strain rate over many decades. We find non-Newtonian behavior below the jamming concentration and yield-stress behavior above it. The data may be collapsed onto two branches with critical scaling exponents that agree with expectations based on Hertzian contacts and viscous drag. These results support the conclusion that jamming is similar to a critical phase transition, but with interaction-dependent exponents.

An experimental study on effects of increased ventilation flow on students' perception of indoor environment in computer classrooms.

UNLABELLED: The effects of ventilation in computer classrooms were studied with university students (n = 355) in a blinded study, 31% were women and 3.8% had asthma. Two classrooms had a higher air exchange (4.1-5.2 ac/h); two others had a lower air exchange (2.3-2.6 ac/h). After 1 week, ventilation conditions were shifted. The students reported environmental perceptions during the last hour. Room temperature, RH, CO2, PM10 and ultra-fine particles were measured simultaneously. Mean CO2 was 1185 ppm at lower and 922 ppm at higher air exchange. Mean temperature was 23.2 degrees C at lower and 22.1 degrees C at higher air exchange. After mutual adjustment (temperature, RH, CO2, air exchange), measured temperature was associated with a perception of higher temperature (P < 0.001), lower air movement (P < 0.001), and poorer air quality (P < 0.001). Higher air exchange was associated with a perception of lower temperature (P < 0.001), higher air movement (P = 0.001), and better air quality (P < 0.001). In the longitudinal analysis (n = 83), increased air exchange caused a perception of lower temperature (P = 0.002), higher air movement (P < 0.001), better air quality (P = 0.001), and less odor (P = 0.02). In conclusion, computer classrooms have CO2 levels above 1000 ppm and temperatures above 22 degrees C. Increased ventilation from 7 l/s per person to 10-13 l/s per person can improve thermal comfort and air quality. PRACTICAL IMPLICATIONS: Computer classrooms are crowded indoor environments with a high thermal load from both students and computer equipment. It is important to control room temperature either by air conditioning, sun shields, or sufficiently high ventilation flow. A high ventilation flow is also crucial to achieving good perceived air quality. Personal ventilation flow should be at least 10 l/s. Possible loss of learning ability due to poor indoor air quality in university buildings deserves more attention.

Mining the gene repertoire and ESTs for G protein-coupled receptors with evolutionary perspective.

The purpose of this article was to review recent progress in mining the gene repertoire and expressed sequence tags (ESTs) for the super-family of G protein-coupled receptors (GPCRs) in the form of a proceeding from the Nordic GPCR meeting held at the Nobel Forum, Karolinska Institute in August 2006. We update and give an overview of the expansion of the main families of GPCRs; Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin (GRAFS) in perspective of fully sequenced genomes. We look into the most recent findings including the work that has been carried out on the spotted green puffer fish (Tetraodon nigroviridis), mouse (Mus musculus), chicken (Gallus gallus), slime mold (Dictyostelium discoideum) and the plant pathogenic fungus Magnaporthe grisea. We use examples from our recent work on chicken GPCRs to highlight the importance of detailed assembly and curation of sequences and how that can affect percentage similarity and phylogeny. ESTs can give valuable information about expression patterns. GPCRs have comparatively low numbers of EST suggesting that GPCRs are in generally expressed in lower amount than other genes. We discuss similarities in the evolution of the trace amine associated receptors with other sensory receptors.

Suppression of the deafness and thyroid dysfunction in Thrb-null mice by an independent mutation in the Thra thyroid hormone receptor alpha gene.

Deletion of thyroid hormone receptor beta (TR beta), a ligand-dependent transcription factor encoded by the Thrb gene, causes deafness and thyroid hyperactivity in Thrb-null (Thrb(tm1/tm1)) mice and in a recessive form of the human syndrome of resistance to thyroid hormone. Here, we have determined that a targeted mutation (Thra(tm2)) in the related Thra gene, encoding thyroid hormone receptor alpha suppresses these phenotypes in mice. Thra encodes a TR alpha 1 receptor which is non-essential for hearing and a TR alpha 2 splice variant of unknown function that neither binds thyroid hormone nor transactivates. The Thra(tm2) mutation deletes TR alpha 2 and concomitantly causes overexpression of TR alpha 1 as a consequence of the exon structure of the gene. Thra(tm2/tm2) mice have normal auditory thresholds indicating that TR alpha 2 is dispensable for hearing, and have only marginally reduced thyroid activity. However, a potent function for the Thra(tm2) allele is revealed upon its introduction into Thrb(tm1/tm1) mice, where it suppresses the auditory and thyroid phenotypes caused by loss of TR beta. These findings reveal a novel modifying function for a Thra allele and suggest that increased expression of TR alpha 1 may substitute for the absence of TR beta. The TR isotypes generated by the distinct Thrb and Thra genes represent a small family of receptors that have diverged to mediate different physiological roles; however, the ability of changes in Thra expression to compensate for loss of Thrb indicates that many functions of these genes remain closely related.

Ablation of TRalpha2 and a concomitant overexpression of alpha1 yields a mixed hypo- and hyperthyroid phenotype in mice.

Thyroid hormone governs a diverse repertoire of physiological functions through receptors encoded in the receptor genes alpha and beta, which each generate variant proteins. In mammals, the alpha gene generates, in addition to the normal receptor TRalpha1, a non-hormone-binding variant TRalpha2 whose exact function is unclear. Here, we present the phenotype associated with the targeted ablation of TRalpha2 expression. Selective ablation of TRalpha2 resulted in an inevitable, concomitant overexpression of TRalpha1. Both TRalpha2 +/- and -/- mice show a complex phenotype with low levels of free T3 and free T4, and have inappropriately normal levels of TSH. The thyroid glands exhibit mild morphological signs of dysfunction and respond poorly to TSH, suggesting that the genetic changes affect the ability of the gland to release thyroid hormones. However, the phenotype of the mutant mice also has features of hyperthyroidism, including decreased body weight, elevated heart rate, and a raised body temperature. Furthermore, TRalpha2-/- and TRalpha2+/- mice are obese and exhibit skeletal alterations, associated with a late-onset growth retardation. The results thus suggest that the overexpression of TRalpha1 and the concomitant decrease in TRalpha2 expression lead to a mixed hyper- and hypothyroid phenotype, dependent on the tissue studied. The phenotypes suggest that the balance of TRalpha1:TRalpha2 expressed from the TRalpha gene provides an additional level of tuning the control of growth and homeostasis in mammalian species.

RecA-mediated rescue of Escherichia coli strains with replication forks arrested at the terminus.

The recombinational rescue of chromosome replication was investigated in Escherichia coli strains with the unidirectional origin oriR1, from the plasmid R1, integrated within oriC in clockwise (intR1(CW)) or counterclockwise (intR1(CC)) orientations. Only the intR1(CC) strain, with replication forks arrested at the terminus, required RecA for survival. Unlike the strains with RecA-dependent replication known so far, the intR1(CC) strain did not require RecBCD, RecF, RecG, RecJ, RuvAB, or SOS activation for viability. The overall levels of degradation of replicating chromosomes caused by inactivation of RecA were similar in oriC and intR1(CC) strains. In the intR1(CC) strain, RecA was also needed to maintain the integrity of the chromosome when the unidirectional replication forks were blocked at the terminus. This was consistent with suppression of the RecA dependence of the intR1(CC) strain by inactivating Tus, the protein needed to block replication forks at Ter sites. Thus, RecA is essential during asymmetric chromosome replication for the stable maintenance of the forks arrested at the terminus and for their eventual passage across the termination barrier(s) independently of the SOS and some of the major recombination pathways.

Fiber fractions from processing of barley in production and conservation of a biologic control agent.

Carriers are frequently used to overcome problems associated with microbial survival in soil after inoculation. Moreover, the use of carriers can prolong the shelf lives and lessen dusting of both biofungicides and biologic fertilizers. This study investigated the suitability of barley-based fiber fractions as growth media and immobilization matrices in the cultivation of a Streptomyces griseoviridis biologic control agent, as well as for the conservation of obtained biomass in dehydrated hydrogel capsules. The second main ingredient in all the examined carrier matrices was alginate. The aim was to find a hydrogel formulation suited for a production process in which all individual steps, including cultivation of the organism; downstream processing; and formulation, storage, and application of the product (i.e., biologic control agent), are carried out in the hydrogel matrix. Of the tested fractions, brewer's spent grain was the best choice, when considering the price vs the nutrient contents as well as the storage time and ease of processing of the crude and the finished products. It seems that cereal fibers can be replenished with cereal fractions less rich in fiber but having a higher content of utilizable nutrients and, hence, better suited for the production of biomass. A high content of water-insoluble fiber favorably influenced the appearance as well as the applicability of the products.

Partitioning of the Escherichia coli chromosome: superhelicity and condensation.

Segregation in Escherichia coli, the process of separating the replicated chromosomes into daughter progeny cells, seems to start long before the duplication of the genome reaches completion. Soon after initiation in mid-cell region, the daughter oriCs rapidly move apart to fixed positions inside the cell (quarter length positions from each pole) and are anchored there by yet unknown mechanism(s). As replication proceeds, the rest of the chromosome is sequentially unwound and then refolded. At termination, the two sister chromosomes are unlinked by decatenation and separated by supercoiling and/or condensation. Muk and Seq proteins are involved in different stages of this replication-cum-partition process and thus can be categorized as important partition proteins along with topoisomerases. E. coli strains, lacking mukB or seqA functions, are defective in segregation and cell division. The nucleoids in these mutant strains exhibit altered condensation and superhelicity as can be demonstrated by sedimentation analysis and by fluorescence microscopy. As the supercoiling of an extrachromosomal element (a plasmid DNA) was also influenced by the mukB and seqA mutations we concluded that the MukB and SeqA proteins are possibly involved in maintaining the general supercoiling activity in the cell. The segregation of E. coli chromosome might therefore be predominantly driven by factors that operate by affecting the superhelicity and condensation of the nucleoid (MukB, SeqA, topoisomerases and additional unknown proteins). A picture thus emerges in which replication and partition are no longer compartmentalized into separable stages with clear gaps (S and M phases in eukaryotes) but are parallel processes that proceed concomitantly through a cell cycle continuum.

Replication arrests during a single round of replication of the Escherichia coli chromosome in the absence of DnaC activity.

We used a flow cytometric assay to determine the frequency of replication fork arrests during a round of chromosome replication in Escherichia coli. After synchronized initiation from oriC in a dnaC(Ts) strain, non-permissive conditions were imposed, such that active DnaC was not available during elongation. Under these conditions, about 18% of the cells failed to complete chromosome replication. The sites of replication arrests were random and occurred on either arm of the bidirectionally replicating chromosome, as stalled forks accumulated at the terminus from both directions. The forks at the terminal Ter sites disappeared in the absence of Tus protein, as the active forks could then pass through the terminus to reach the arrest site, and the unfinished rounds of replication would be completed without DnaC. In a dnaC2(Ts)rep double mutant, almost all cells failed to complete chromosome replication in the absence of DnaC activity. As inactivation of Rep helicase (the rep gene product) has been shown to cause frequent replication arrests inducing double-strand breaks (DSBs) in a replicating chromosome, DnaC activity appears to be essential for replication restart from DSBs during elongation.

Asthma symptoms in relation to measured building dampness in upper concrete floor construction, and 2-ethyl-1-hexanol in indoor air.

SETTING: Asthma symptoms in adults in relation to the indoor environment. OBJECTIVES: To study the relationships between current asthma symptoms (wheeze or attacks of breathlessness) and the indoor environment and dampness in hospitals. DESIGN: A study among personnel (n = 87) in four geriatric hospitals in winter. Indoor air pollutants, dampness in the concrete floor, and allergens in settled dust were measured. Multiple logistic regression analysis was applied, adjusting for age, sex, atopy, and dampness in the participants' own dwellings. RESULTS: Current asthma symptoms were reported by 17%, and 8% had doctor's diagnosed asthma. Asthma symptoms were more common (adjusted odds ratio = 8.6; 95% confidence interval 1.3-56.7) in two buildings with signs of dampness-related degradation of di(ethylhexyl)-phthalate (DEHP) in polyvinyl chloride (PVC) floor material, detected as presence of 2-ethyl-1-hexanol (2-32 microg/m3) in indoor air (CAS nr 104-76-7). Asthma symptoms were related to higher relative humidity in the upper concrete floor construction, and ammonia in the floor. The newest hospital, built by an anthroposophic society, had low levels of dampness and few asthma symptoms (4%). Cat (Fel d1) and dog allergens (Can f1) were found in dust from all buildings (geometric mean 340 ng/g and 2490 ng/g, respectively). House dust mite allergens (Derp1, Derf1, or Derm1) were found in 75% of all samples (geometric mean 130 ng/g). There was no relationship between allergen levels and asthma symptoms. CONCLUSIONS: Asthma symptoms may be related to increased humidity in concrete floor constructions and emission of 2-ethyl-1-hexanol, an indicator of dampness-related alkaline degradation of plasticiser DEHP. Moreover, geriatric hospitals can be contaminated by significant amounts of cat, dog and mite allergens.

Role of the mukB gene in chromosome and plasmid partition in Escherichia coli.

The intracellular locations of oriC and oriR1, the replication origins of the chromosome and plasmid R1, respectively, were visualized by fluorescence in situ hybridization (FISH) in exponentially growing populations of Escherichia coli. The locations of oriC and oriR1 (from a Par+ R1 plasmid) were unique and different in the wild-type host. In a mukB mutant, the positions were perturbed for both origins. The position of oriR1 from a plasmid with active partition (Par+) in the mukB host was as randomized as that of oriR1 from the Par- plasmid in a wild-type host. However, this mukB-induced randomization did not result in unstable inheritance of the Par+ plasmid, as measured by the conventional segregation assay. This might result from the preferential association of the Par+ plasmid with the bigger, decondensed nucleoid-containing daughters during cell division of MukB- cells, whereas the Par- plasmids were distributed at random and were lost by frequently ending up in anucleate cells.