Simrank: Rapid and sensitive general-purpose k-mer search tool

Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project (http://nihroadmap.nih.gov/hmp). Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity

Current measurement by real-time counting of single electrons

The fact that electrical current is carried by individual charges has been known for over 100 years, yet this discreteness has not been directly observed so far. Almost all current measurements involve measuring the voltage drop across a resistor, using Ohm's law, in which the discrete nature of charge does not come into play. However, by sending a direct current through a microelectronic circuit with a chain of islands connected by small tunnel junctions, the individual electrons can be observed one by one. The quantum mechanical tunnelling of single charges in this one-dimensional array is time correlated, and consequently the detected signal has the average frequency f=I/e, where I is the current and e is the electron charge. Here we report a direct observation of these time-correlated single-electron tunnelling oscillations, and show electron counting in the range 5 fA-1 pA. This represents a fundamentally new way to measure extremely small currents, without offset or drift. Moreover, our current measurement, which is based on electron counting, is self-calibrated, as the measured frequency is related to the current only by a natural constant.Comment: 9 pages, 4 figures; v2: minor revisions, 2 refs added, words added to title, typos correcte

Self-Organization, Layered Structure, and Aggregation Enhance Persistence of a Synthetic Biofilm Consortium

Microbial consortia constitute a majority of the earth’s biomass, but little is known about how these cooperating communities persist despite competition among community members. Theory suggests that non-random spatial structures contribute to the persistence of mixed communities; when particular structures form, they may provide associated community members with a growth advantage over unassociated members. If true, this has implications for the rise and persistence of multi-cellular organisms. However, this theory is difficult to study because we rarely observe initial instances of non-random physical structure in natural populations. Using two engineered strains of Escherichia coli that constitute a synthetic symbiotic microbial consortium, we fortuitously observed such spatial self-organization. This consortium forms a biofilm and, after several days, adopts a defined layered structure that is associated with two unexpected, measurable growth advantages. First, the consortium cannot successfully colonize a new, downstream environment until it selforganizes in the initial environment; in other words, the structure enhances the ability of the consortium to survive environmental disruptions. Second, when the layered structure forms in downstream environments the consortium accumulates significantly more biomass than it did in the initial environment; in other words, the structure enhances the global productivity of the consortium. We also observed that the layered structure only assembles in downstream environments that are colonized by aggregates from a previous, structured community. These results demonstrate roles for self-organization and aggregation in persistence of multi-cellular communities, and also illustrate a role for the techniques of synthetic biology in elucidating fundamental biological principles

Vortex counting from field theory

The vortex partition function in 2d N = (2,2) U(N) gauge theory is derived from the field theoretical point of view by using the moduli matrix approach. The character for the tangent space at each moduli space fixed point is written in terms of the moduli matrix, and then the vortex partition function is obtained by applying the localization formula. We find that dealing with the fermionic zero modes is crucial to obtain the vortex partition function with the anti-fundamental and adjoint matters in addition to the fundamental chiral multiplets. The orbifold vortex partition function is also investigated from the field theoretical point of view.Comment: 21 pages, no figure

Filial obligations to elderly parents: a duty to care?

A continuing need for care for elderly, combined with looser family structures prompt the question what filial obligations are. Do adult children of elderly have a duty to care? Several theories of filial obligation are reviewed. The reciprocity argument is not sensitive to the parent–child relationship after childhood. A theory of friendship does not offer a correct parallel for the relationship between adult child and elderly parent. Arguments based on need or vulnerability run the risk of being unjust to those on whom a needs-based claim is laid. To compare filial obligations with promises makes too much of parents’ expectations, however reasonable they may be. The good of being in an unchosen relationship seems the best basis for filial obligations, with an according duty to maintain the relationship when possible. We suggest this relationship should be maintained even if one of the parties is no longer capable of consciously contributing to it. We argue that this entails a duty to care about one’s parents, not for one’s parents. This implies that care for the elderly is not in the first place a task for adult children

Identification of Five Developmental Processes during Chondrogenic Differentiation of Embryonic Stem Cells

Chondrogenesis is the complex process that leads to the establishment of cartilage and bone formation. Due to their ability to differentiate in vitro and mimic development, embryonic stem cells (ESCs) show great potential for investigating developmental processes. In this study, we used chondrogenic differentiation of ESCs as a model to analyze morphogenetic events during chondrogenesis.ESCs were differentiated into the chondrocyte lineage, forming small cartilaginous aggregates in suspension. Differentiated ESCs showed that chondrogenesis was typically characterized by five overlapping stages. During the first stage, cell condensation and aggregate formation was observed. The second stage was characterized by differentiation into chondrocytes and fibril scaffold formation within spherical aggregates. Deposition of cartilaginous extracellular matrix and cartilage formation were hallmarks of the third stage. Apoptosis of chondrocytes, hypertrophy and/or degradation of cartilage occurred during the fourth stage. Finally, during the fifth stage, bone replacement with membranous calcified tissues took place.We demonstrate that ESCs show the chondrogenic differentiation pathway from the pluripotent stem cell to terminal skeletogenesis through these five stages in vitro. During each stage, morphological changes acquired in preceding stages played an important role in further development as a scaffold or template in subsequent stages. The study of chondrogenesis via ESC differentiation may be informative to our further understanding of skeletal growth and regeneration

Distress, anxiety, and depression in cancer patients undergoing chemotherapy

BACKGROUND: Chemotherapy for cancer is an intense and cyclic treatment associated with number of side-effects. The present study evaluated the effect of chemotherapy on distress, anxiety and depression. PATIENTS AND METHODS: A total of 117 patients were evaluated by using distress inventory for cancer (DIC2) and hospital anxiety and depression scale (HADS). Majority of the patients were taking chemotherapy for solid tumors (52; 44.4%). RESULTS: The mean distress score was 24, 18 (15.38%) were found to have anxiety while 19 (16.23%) had depression. High social status was the only factor found to influence distress while female gender was the only factor found to influence depression in the present study. CONCLUSION: The study highlights high psychological morbidity of cancer patients and influence of gender on depression. Construct of distress as evaluated by DIC 2 may have a possible overlap with anxiety

Ground-Based Measurements of the 2014–2015 Holuhraun Volcanic Cloud (Iceland)

The 2014–2015 Bárðarbunga fissure eruption at Holuhraun in central Iceland was distinguished by the high emission of gases, in total 9.6 Mt SO2, with almost no tephra. This work collates all ground-based measurements of this extraordinary eruption cloud made under particularly challenging conditions: remote location, optically dense cloud with high SO2 column amounts, low UV intensity, frequent clouds and precipitation, an extensive and hot lava field, developing ramparts, and high-latitude winter conditions. Semi-continuous measurements of SO2 flux with three scanning DOAS instruments were augmented by car traverses along the ring-road and along the lava. The ratios of other gases/SO2 were measured by OP-FTIR, MultiGAS, and filter packs. Ratios SO2/HCl = 30–110 and SO2/HF = 30–130 show a halogen-poor eruption cloud. Scientists on-site reported extremely minor tephra production during the eruption. OPC and filter packs showed low particle concentrations similar to non-eruption cloud conditions. Three weather radars detected a droplet-rich eruption cloud. Top of eruption cloud heights of 0.3–5.5 km agl were measured with ground- and aircraft-based visual observations, web camera and NicAIR II infrared images, triangulation of scanning DOAS instruments, and the location of SO2 peaks measured by DOAS traverses. Cloud height and emission rate measurements were critical for initializing gas dispersal simulations for hazard forecasting

Multimodal Management of Atrophic Acne Scarring in the Aging Face

Atrophic facial acne scarring is a widely prevalent condition that can have a negative impact on a patient’s quality of life. The appearance of these scars is often worsened by the normal effects of aging. A number of options are available for the treatment of acne scarring, including chemical peeling, dermabrasion, ablative or nonablative laser resurfacing, dermal fillers, and surgical techniques such as subcision or punch excision. Depending on the type and extent of scarring, a multimodal approach is generally necessary to provide satisfactory results. Resurfacing techniques correct surface irregularities, long-lasting dermal fillers address the volume loss resulting from acne, and sub-superficial musculoaponeurotic system (SMAS) face-lift procedures counter the soft tissue laxity and ptosis associated with aging. This article briefly reviews the evolution of individual approaches to treating atrophic acne scarring, followed by case examples illustrating results that can be achieved using a multimodal approach. Representative cases from patients in their 30s, 40s, and 50s are presented. In the author’s clinical practice, multimodal approaches incorporating fractionated laser, injectable poly-l-lactic acid, and sub-SMAS face-lift procedures have achieved optimal aesthetic outcomes, high patient satisfaction, and durability of aesthetic effect over time