1,309 research outputs found

    Statistical inference of the generation probability of T-cell receptors from sequence repertoires

    Full text link
    Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Since any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on non-productive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our distribution predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.Comment: 20 pages, including Appendi

    An analytical model for granular jamming beams with applications in morphing aerostructures

    Get PDF

    Participatory management for conservation of seahorses in the Gulf of Mannar, South-east coast of India

    Get PDF
    The Inception Workshop of the research project “Participatory management for conservation of seahorses in the Gulf of Mannar, south-east coast of India” was organized on 27 December 2014 at the Mandapam Regional Centre of the Central Marine Fisheries Research Institute (ICAR), Mandapam Camp, Tamil Nadu. The workshop was aimed to mark the beginning of the project activities in the Gulf of Mannar and also to bring to one place all the concerned stakeholders who are directly or indirectly associated with sustainable management of seahorse fishery and conservation, and to inform them about the project, its objectives and the expectations. The workshop was also aimed to discuss and get feedback on the methodology and approach for implementation of the project activities such as field surveys and interviews with the stakeholders. The workshop also focused to gather valuable inputs from various stakeholders, which are vital for the on-going project

    Ultrasonic technology applied against mosquito larvae

    Get PDF
    The effective management of mosquito vectors is a timely challenge for medical and veterinary entomology. In this study, we evaluated the acoustic Larvasonic device to control young instars of the mosquito Aedes aegypti in diverse freshwater environments. Under laboratory conditions, we investigated the effect of exposure time and distance from the transducer on the mortality of larvae and pupae of Ae. aegypti. Furthermore, we evaluated the effectiveness of the ultrasound window of the electromagnetic spectrum under different field conditions. Results showed that first and second instar larvae were more sensitive to the frequency range of 18-30 kHz of the Larvasonic device. Ultrasonic waves applied for 180 s at a frequency from 18 to 30 kHz caused 100% larval mortality at a distance of 60 cm from the transducer. No mortality was observed in the non-target copepod Megacyclops formosanus. The exposure to the soundwaves produced by the acoustic larvicidal device over different distances effectively damaged Ae. aegypti through destruction of the larval dorsal tracheal trunk, thorax and abdomen. Overall, results indicated that the Larvasonic device tested can provide an alternative tool to reduce young instar populations of Ae. aegypti, without any effects on non-target aquatic invertebrates like copepods. It turned out to be a useful device for mosquito biocontrol. This technology has a relevant potential to fight the spread of mosquito-borne diseases

    On the Trace-Free Einstein Equations as a Viable Alternative to General Relativity

    Full text link
    The quantum field theoretic prediction for the vacuum energy density leads to a value for the effective cosmological constant that is incorrect by between 60 to 120 orders of magnitude. We review an old proposal of replacing Einstein's Field Equations by their trace-free part (the Trace-Free Einstein Equations), together with an independent assumption of energy--momentum conservation by matter fields. While this does not solve the fundamental issue of why the cosmological constant has the value that is observed cosmologically, it is indeed a viable theory that resolves the problem of the discrepancy between the vacuum energy density and the observed value of the cosmological constant. However, one has to check that, as well as preserving the standard cosmological equations, this does not destroy other predictions, such as the junction conditions that underlie the use of standard stellar models. We confirm that no problems arise here: hence, the Trace-Free Einstein Equations are indeed viable for cosmological and astrophysical applications.Comment: Substantial changes from v1 including added author, change of title and emphasis of the paper although all original results of v1. remai

    Efficiency of universal barcode gene (Cox1) on morphologically cryptic Mugilidae fishes delineation.

    Get PDF
    An effort was made to assess the utility of 650 bp partial Cytochrome C oxidase subunit I (DNA barcode) gene in delineating the members of taxonomically ambiguous marine fin fishes (Family: Mugilidae). To address the issue we used all the 95 barcode sequences of Mugilidae family available at NCBI (National Centre for Biotechnological Information) along with the barcode data generated from Mugilidae fishes of Parangipettai coastal waters. The average GC content of Mugilidae was found to be 46.46%. Crenimugil crenilabis showed less GC content (44.55%) whereas Liza macrolepis showed high GC content (48.53%) among the mullet species studied. The phylogenetic and genetic distance data showed that Mugil platanus and M. liza represent the continuum of same species. Among the members of family Mugilidae, the genus Mugil might possibly contains more haplotype diversity as revealed by intra-species genetic distance data. Species within genera of Mugilidae family invariably clustered in single clade with high bootstrap value. We conclude that partial COI sequencing (barcoding) in identifying the members of the family and that way has resolved the taxonomic ambiguity among the members of the family Mugilidae

    Fabrication of green nanoinsecticides from agri-waste of corn silk and its larvicidal and antibiofilm properties

    Get PDF
    he corn silk (CS) is composed of the thread- like stigmas of female inflorescences of Zea mays L. and represents an important waste material from maize crop production that can be recycled in further applications. In this research, the CS was used for the bio-fabrication of Ag nanoparticles (AgNPs) that were evaluated against (I–V) larval instars and pupae of the mosquito vector Aedes aegypti. CS-AgNPs were characterized by UV-Vis spectroscopy, TEM, EDAX, XRD, FTIR, DLS, and zeta potential analysis. Z. mays extract analyzed by gas chro- matography mass spectrometry reveals 14 compounds. The larvicidal effectiveness of CS-fabricated AgNPs was 2.35 μg·mL−1 (I Instar) to 6.24 μg·mL−1 (pupae). The field application in water storage reservoirs of both CS extracts and CS-AgNPs (10 × LC50) led to a 68–69% reduction in larval density after 72 h post-treatment. Ecotoxicological impact of CS-fabricated AgNPs was evaluated on the pre- datory efficacy of Poecilia reticulata on all the larval instars and pupae of Ae. aegypti. Finally, CS-AgNPs were tested to elucidate its anti-biofilm attributes. The CS-AgNPs at 125 μg·mL−1 showed a biofilm inhibition of 90% on S. aureus and 79% on S. epidermidis. These results support the use of CS-AgNPs for futuristic green alternative to mosquito vector management

    Holonomy in the Schwarzschild-Droste Geometry

    Get PDF
    Parallel transport of vectors in curved spacetimes generally results in a deficit angle between the directions of the initial and final vectors. We examine such holonomy in the Schwarzschild-Droste geometry and find a number of interesting features that are not widely known. For example, parallel transport around circular orbits results in a quantized band structure of holonomy invariance. We also examine radial holonomy and extend the analysis to spinors and to the Reissner-Nordstr\"om metric, where we find qualitatively different behavior for the extremal (Q=MQ = M) case. Our calculations provide a toolbox that will hopefully be useful in the investigation of quantum parallel transport in Hilbert-fibered spacetimes.Comment: 18 Latex pages, 3 figures. Second replacement. This version as published in CQG with some misprints correcte

    Non-Abelian BIonic Brane Intersections

    Full text link
    We study "fuzzy funnel" solutions to the non-Abelian equations of motion of the D-string. Our funnel describes n^6/360 coincident D-strings ending on n^3/6 D7-branes, in terms of a fuzzy six-sphere which expands along the string. We also provide a dual description of this configuration in terms of the world volume theory of the D7-branes. Our work makes use of an interesting non-linear higher dimensional generalization of the instanton equations.Comment: 17 pages uses harvmac; v2: small typos corrected, refs adde
    corecore