339 research outputs found
In vivo generation of DNA sequence diversity for cellular barcoding
Heterogeneity is a ubiquitous feature of biological systems. A complete understanding of such systems requires a method for uniquely identifying and tracking individual components and their interactions with each other. We have developed a novel method of uniquely tagging individual cells in vivo with a genetic 'barcode' that can be recovered by DNA sequencing. Our method is a two-component system comprised of a genetic barcode cassette whose fragments are shuffled by Rci, a site-specific DNA invertase. The system is highly scalable, with the potential to generate theoretical diversities in the billions. We demonstrate the feasibility of this technique in Escherichia coli. Currently, this method could be employed to track the dynamics of populations of microbes through various bottlenecks. Advances of this method should prove useful in tracking interactions of cells within a network, and/or heterogeneity within complex biological samples
Sequencing the Connectome
Connectivity determines the function of neural circuits. Historically, circuit mapping has usually been viewed as a problem of microscopy, but no current method can achieve high-throughput mapping of entire circuits with single neuron precision. Here we describe a novel approach to determining connectivity. We propose BOINC ("barcoding of individual neuronal connections"), a method for converting the problem of connectivity into a form that can be read out by high-throughput DNA sequencing. The appeal of using sequencing is that its scale--sequencing billions of nucleotides per day is now routine--is a natural match to the complexity of neural circuits. An inexpensive high-throughput technique for establishing circuit connectivity at single neuron resolution could transform neuroscience research
Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics
We propose a neural connectomics strategy called Fluorescent In-Situ
Sequencing of Barcoded Individual Neuronal Connections (FISSEQ-BOINC),
leveraging fluorescent in situ nucleic acid sequencing in fixed tissue
(FISSEQ). FISSEQ-BOINC exhibits different properties from BOINC, which relies
on bulk nucleic acid sequencing. FISSEQ-BOINC could become a scalable approach
for mapping whole-mammalian-brain connectomes with rich molecular annotations
Using high-throughput barcode sequencing to efficiently map connectomes
The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and joined into a form suitable for sequencing. Although our failure to develop an efficient barcode joining scheme precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost
Quadratic optimal functional quantization of stochastic processes and numerical applications
In this paper, we present an overview of the recent developments of
functional quantization of stochastic processes, with an emphasis on the
quadratic case. Functional quantization is a way to approximate a process,
viewed as a Hilbert-valued random variable, using a nearest neighbour
projection on a finite codebook. A special emphasis is made on the
computational aspects and the numerical applications, in particular the pricing
of some path-dependent European options.Comment: 41 page
Spatial representation of temporal information through spike timing dependent plasticity
We suggest a mechanism based on spike time dependent plasticity (STDP) of
synapses to store, retrieve and predict temporal sequences. The mechanism is
demonstrated in a model system of simplified integrate-and-fire type neurons
densely connected by STDP synapses. All synapses are modified according to the
so-called normal STDP rule observed in various real biological synapses. After
conditioning through repeated input of a limited number of of temporal
sequences the system is able to complete the temporal sequence upon receiving
the input of a fraction of them. This is an example of effective unsupervised
learning in an biologically realistic system. We investigate the dependence of
learning success on entrainment time, system size and presence of noise.
Possible applications include learning of motor sequences, recognition and
prediction of temporal sensory information in the visual as well as the
auditory system and late processing in the olfactory system of insects.Comment: 13 pages, 14 figures, completely revised and augmented versio
Buprenorphine versus dihydrocodeine for opiate detoxification in primary care: a randomised controlled trial
Background
Many drug users present to primary care requesting detoxification from illicit opiates. There are a number of detoxification agents but no recommended drug of choice. The purpose of this study is to compare buprenorphine with dihydrocodeine for detoxification from illicit opiates in primary care.
Methods
Open label randomised controlled trial in NHS Primary Care (General Practices), Leeds, UK. Sixty consenting adults using illicit opiates received either daily sublingual buprenorphine or daily oral dihydrocodeine. Reducing regimens for both interventions were at the discretion of prescribing doctor within a standard regimen of not more than 15 days. Primary outcome was abstinence from illicit opiates at final prescription as indicated by a urine sample. Secondary outcomes during detoxification period and at three and six months post detoxification were recorded.
Results
Only 23% completed the prescribed course of detoxification medication and gave a urine sample on collection of their final prescription. Risk of non-completion of detoxification was reduced if allocated buprenorphine (68% vs 88%, RR 0.58 CI 0.35–0.96, p = 0.065). A higher proportion of people allocated to buprenorphine provided a clean urine sample compared with those who received dihydrocodeine (21% vs 3%, RR 2.06 CI 1.33–3.21, p = 0.028). People allocated to buprenorphine had fewer visits to professional carers during detoxification and more were abstinent at three months (10 vs 4, RR 1.55 CI 0.96–2.52) and six months post detoxification (7 vs 3, RR 1.45 CI 0.84–2.49).
Conclusion
Informative randomised trials evaluating routine care within the primary care setting are possible amongst drug using populations. This small study generates unique data on commonly used treatment regimens
MUSIC CLASSROOMS AND THE FORCES THAT SHAPE THEM: INVESTIGATING CHINESE & U.S SECONDARY GENERAL MUSIC TEACHING
In recent years, the exchange of education policy reforms in China and the United States have had an impact on music teaching methodologies in both places. Where the U.S. system was traditionally decentralized so that authority was placed in the hands of local governments, today the system is becoming more nationalized and standardized causing the music education system to decrease in its relative importance within traditional school subjects. Meanwhile, China has been moving toward
decentralization. As its economic needs have shifted from manufacturing to tech-related entrepreneurial positions, the role of the creative arts and music education has grown in prominence. Research shows that as a result, a new interest has grown in investigating more and new teaching methodologies so that the more oral, tradition based rote and drilling methods are being exchanged for more step by step, prescriptive, and often Western-based methods. In the United States, the opposite has occurred as a result of testing movements causing teachers to have less time to cover more material which is often not
related to their subject. As a result, rote style teaching and learning as well as drilling has become more
common.
This study sought to determine whether the implications of policy change on music teaching methodologies are coming to fruition. To accomplish this, responses from six secondary general music teachers - three from China who completed questionnaires and three from the U.S. who were interviewed - were collected. Four areas of discussion/description were covered including the teacher’s educational background, relationships to sources of authority, instructional methodologies, and global perspectives. Qualitative data analysis was carried out using Dedoose to reach conclusions that can serve future research studies and inform policy makers about the current state of secondary general music
education. The study concluded that music teaching methods are embedded in culture and personal
practice. As a result, changes in teaching pedagogy and style are gradual, frequently met with resistance,
or undergone unknowingly. While to some degree mandates from the federal government have an impact on how music teachers carry out their day-to-day lesson plans in both countries, the stronger influences which determines pedagogical decisions are situational and draw from the teacher’s personal educational experiences, their prior role models, and knowledge of their individual classroom. The study examines the limits and values of cross-cultural research and concludes that while sharing best practices internationally is a worthwhile endeavor, perhaps the most successful path to changing practice occurs with full cultural immersion and understanding as a result of international teaching and learning experiences
Quantifying impacts of short-term plasticity on neuronal information transfer
Short-term changes in efficacy have been postulated to enhance the ability of
synapses to transmit information between neurons, and within neuronal networks.
Even at the level of connections between single neurons, direct confirmation of
this simple conjecture has proven elusive. By combining paired-cell recordings,
realistic synaptic modelling and information theory, we provide evidence that
short-term plasticity can not only improve, but also reduce information
transfer between neurons. We focus on a concrete example in rat neocortex, but
our results may generalise to other systems. When information is contained in
the timings of individual spikes, we find that facilitation, depression and
recovery affect information transmission in proportion to their impacts upon
the probability of neurotransmitter release. When information is instead
conveyed by mean spike rate only, the influences of short-term plasticity
critically depend on the range of spike frequencies that the target network can
distinguish (its effective dynamic range). Our results suggest that to
efficiently transmit information, the brain must match synaptic type, coding
strategy and network connectivity during development and behaviour.Comment: Accepted for publication in Phys Rev E. 42 pages in referee format, 9
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Identification of a brainstem locus that inhibits tumor necrosis factor
In the brain, compact clusters of neuron cell bodies, termed nuclei, are essential for maintaining parameters of host physiology within a narrow range optimal for health. Neurons residing in the brainstem dorsal motor nucleus (DMN) project in the vagus nerve to communicate with the lungs, liver, gastrointestinal tract, and other organs. Vagus nerve-mediated reflexes also control immune system responses to infection and injury by inhibiting the production of tumor necrosis factor (TNF) and other cytokines in the spleen, although the function of DMN neurons in regulating TNF release is not known. Here, optogenetics and functional mapping reveal cholinergic neurons in the DMN, which project to the celiacsuperior mesenteric ganglia, significantly increase splenic nerve activity and inhibit TNF production. Efferent vagus nerve fibers terminating in the celiac-superior mesenteric ganglia form varicose-like structures surrounding individual nerve cell bodies innervating the spleen. Selective optogenetic activation of DMN cholinergic neurons or electrical activation of the cervical vagus nerve evokes action potentials in the splenic nerve. Pharmacological blockade and surgical transection of the vagus nerve inhibit vagus nerve-evoked splenic nerve responses. These results indicate that cholinergic neurons residing in the brainstem DMN control TNF production, revealing a role for brainstem coordination of immunity
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