The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions

Background

A composite biological structure, such as an insect head or abdomen, contains many internal structures with distinct functions. Composite structures are often used in RNA-seq studies, though it is unclear how expression of the same gene in different tissues and structures within the same structure affects the measurement (or even utility) of the resulting patterns of gene expression. Here we determine how complex composite tissue structure affects measures of gene expression using RNA-seq.

Results

We focus on two structures in the honey bee (the sting gland and digestive tract) both contained within one larger structure, the whole abdomen. For each of the three structures, we used RNA-seq to identify differentially expressed genes between two developmental stages, nurse bees and foragers. Based on RNA-seq for each structure-specific extraction, we found that RNA-seq with composite structures leads to many false negatives (genes strongly differentially expressed in particular structures which are not found to be differentially expressed within the composite structure). We also found a significant number of genes with one pattern of differential expression in the tissue-specific extraction, and the opposite in the composite extraction, suggesting multiple signals from such genes within the composite structure. We found these patterns for different classes of genes including transcription factors.

Conclusions

Many RNA-seq studies currently use composite extractions, and even whole insect extractions, when tissue and structure specific extractions are possible. This is due to the logistical difficultly of micro-dissection and unawareness of the potential errors associated with composite extractions. The present study suggests that RNA-seq studies of composite structures are prone to false negatives and difficult to interpret positive signals for genes with variable patterns of local expression. In general, our results suggest that RNA-seq on large composite structures should be avoided unless it is possible to demonstrate that the effects shown here do not exist for the genes of interest.

Hospitalisation rates in patients switched from oral anti-psychotics to aripiprazole once-monthly for the management of schizophrenia

OBJECTIVE

To report the design and preliminary results of a mirror-image study comparing total psychiatric hospitalisation rates pre- and post-switch to aripiprazole once-monthly, an extended release injectable solution.

METHODS

A multi-center, open-label mirror-image study of patients (18-65 years) with schizophrenia to compare total psychiatric hospitalisation rates between retrospective treatment with oral standard-of-care (SOC) anti-psychotics and prospective treatment with aripiprazole once-monthly in a naturalistic community setting in North America. Total psychiatric hospitalisation rates were assessed between retrospective (Months -4 to -1) and prospective treatment periods (Months 4-6) for patients who completed ≥3 months aripiprazole once-monthly.

RESULTS

One hundred and eighty-three patients entered the prospective phase. After switching to aripiprazole once-monthly, total psychiatric hospitalisation rates for the 3-month prospective period were significantly lower (p < 0.0001, Exact McNemar's test) compared with the retrospective 3-month period when the same patients received SOC anti-psychotics (6.6% [n = 8/121] vs 28.1% [n = 34/121], respectively; rate ratio = 0.24). Similarly, total psychiatric hospitalisation rates for all patients who entered the prospective treatment phase were significantly lower (p < 0.0001, Exact McNemar's test) for the prospective 6 months following switch to aripiprazole once-monthly, compared with the retrospective 6-month SOC period (14.2% [n = 26/183] vs 41.5% [n = 76/183], respectively; rate ratio = 0.34). Common treatment-emergent adverse events (occurring in ≥5% of patients) were psychotic disorder (7.7%), akathisia (7.2%), and insomnia (7.2%). Discontinuation (all causes) during the prospective phase was 44.8% (n = 82/183).

LIMITATIONS

Mirror-image studies do not include a parallel active control; as each patient serves as their own control, it cannot be determined whether other treatments may have similar effects. Treatment and trial effects may be difficult to separate. Independent factors such as admission patterns, insurance coverage, availability of hospital beds, and community support may influence rates of hospitalisation.

CONCLUSIONS

Switching to aripiprazole once-monthly substantially reduced total psychiatric hospitalisation rates compared with retrospective rates in the same patients taking oral SOC.

Prospective multicentre study of the effect of voluntary plasmapheresis on plasma cholesterol levels in donors

Background and Objectives LDL apheresis is used to treat patients with familial hypercholesterolaemia, and low-volume plasmapheresis for plasma donation may similarly lower cholesterol levels in some donors. This study was designed to assess the effect of plasmapheresis on total, LDL and HDL cholesterol levels in a plasma donor population.

Materials and Methods This was a prospective, unblinded longitudinal cohort study in which a blood sample was obtained for analysis before each donation. Data from 663 donors were analysed using a multivariable repeated measures regression model with a general estimating equations approach with changes in cholesterol as the primary outcome measure.

Results The model predicted a significant decrease in total and LDL cholesterol for both genders and all baseline cholesterol levels (P < 0·01). The greatest total cholesterol decreases (women, −46·8 mg/dL; men, −32·2 mg/dL) were associated with high baseline levels and 2–4 days between donations. Small but statistically significant increases (P ≤ 0·01) in HDL cholesterol were predicted for donors with low baseline levels.

Conclusions These results suggest that, in donors with elevated baseline cholesterol levels, total and LDL cholesterol levels may decrease during routine voluntary plasmapheresis.

The golden goose in the crosshairs: the transition to defined contribution pension plans in the public sector: unintended consequences

State, county, and local governments are currently facing a myriad of economic issues, based on shrinking tax revenues combined with increased expenditures. Of these, the costs related to defined benefit pension plans are one of the most serious issues facing many public employers. Through a comprehensive review of the existing literature, this article examines how the shift from the defined benefit (DB) to defined contribution (DC) pension plan has the potential to enhance levels of labor unrest due to changes in union militancy, bargaining skills deficits, intra-organizational conflict, and issues related to economic trade-offs. Besides the capacity for immediate and deleterious ramifications in the collective bargaining process, the transition to the DC pension also presents some potentially negative consequences related to human resource management, including changes in the psychological contract, recruitment strategies, employee turnover, and changes in retirement patterns. Recommendations to improve labor relations and human resource management practices in the DC pension environment are also explored.

Characterization of addressability by simultaneous randomized benchmarking

The control and handling of errors arising from cross talk and unwanted interactions in multiqubit systems is an important issue in quantum information processing architectures. We introduce a benchmarking protocol that provides information about the amount of addressability present in the system and implement it on coupled superconducting qubits. The protocol consists of randomized benchmarking experiments run both individually and simultaneously on pairs of qubits. A relevant figure of merit for the addressability is then related to the differences in the measured average gate fidelities in the two experiments. We present results from two similar samples with differing cross talk and unwanted qubit-qubit interactions. The results agree with predictions based on simple models of the classical cross talk and Stark shifts.

Efficient measurement of quantum gate error by interleaved randomized benchmarking

We describe a scalable experimental protocol for estimating the average error of individual quantum computational gates. This protocol consists of interleaving random Clifford gates between the gate of interest and provides an estimate as well as theoretical bounds for the average error of the gate under test, so long as the average noise variation over all Clifford gates is small. This technique takes into account both state preparation and measurement errors and is scalable in the number of qubits. We apply this protocol to a superconducting qubit system and find a bounded average error of 0.003 [0,0.016] for the single-qubit gates X(π/2) and Y(π/2). These bounded values provide better estimates of the average error than those extracted via quantum process tomography.

Frequency multiplexed superconducting quantum interference device readout of large bolometer arrays for cosmic microwave background measurements

A technological milestone for experiments employing transition edge sensor bolometers operating at sub-Kelvin temperature is the deployment of detector arrays with 100s-1000s of bolometers. One key technology for such arrays is readout multiplexing: the ability to read out many sensors simultaneously on the same set of wires. This paper describes a frequency-domain multiplexed readout system which has been developed for and deployed on the APEX-SZ and South Pole Telescope millimeter wavelength receivers. In this system, the detector array is divided into modules of seven detectors, and each bolometer within the module is biased with a unique ∼MHz sinusoidal carrier such that the individual bolometer signals are well separated in frequency space. The currents from all bolometers in a module are summed together and pre-amplified with superconducting quantum interference devices operating at 4 K. Room temperature electronics demodulate the carriers to recover the bolometer signals, which are digitized separately and stored to disk. This readout system contributes little noise relative to the detectors themselves, is remarkably insensitive to unwanted microphonic excitations, and provides a technology pathway to multiplexing larger numbers of sensors.

Measurements of quasiparticle tunneling dynamics in a band-gap-engineered transmon qubit

We have engineered the band gap profile of transmon qubits by combining oxygen-doped Al for tunnel junction electrodes and clean Al as quasiparticle traps to investigate energy relaxation due to quasiparticle tunneling. The relaxation time T1 of the qubits is shown to be insensitive to this band gap engineering. Operating at relatively low-E(J)/E(C) makes the transmon transition frequency distinctly dependent on the charge parity, allowing us to detect the quasiparticles tunneling across the qubit junction. Quasiparticle kinetics have been studied by monitoring the frequency switching due to even-odd parity change in real time. It shows the switching time is faster than 10  μs, indicating quasiparticle-induced relaxation has to be reduced to achieve T1 much longer than 100  μs.

Aripiprazole intramuscular depot as maintenance treatment in patients with schizophrenia: a 52-week, multicenter, randomized, double-blind, placebo-controlled study

OBJECTIVE

To evaluate the efficacy and tolerability of a once-monthly intramuscular (IM) depot formulation of the dopamine partial agonist aripiprazole as maintenance treatment in adults meeting DSM-IV-TR schizophrenia criteria.

METHOD

The study was conducted from July 2008 until February 2011. Subjects requiring chronic treatment with an antipsychotic entered a 4- to 12-week oral stabilization phase and received oral aripiprazole (10-30 mg/d). Subjects meeting stability criteria for 4 weeks entered an IM-depot stabilization phase in which they received 400-mg aripiprazole-IM-depot injections every 4 weeks (single decrease to 300 mg permitted) with coadministration of oral aripiprazole tablets in the first 2 weeks. Subjects meeting stability criteria for 12 consecutive weeks were randomly assigned (2:1) to aripiprazole-IM-depot or placebo during a 52-week, double-blind maintenance phase. The primary outcome measure was time to exacerbation of psychotic symptoms/impending relapse (event). Safety and tolerability were also assessed.

RESULTS

710 patients entered oral stabilization, 576 progressed to IM-depot stabilization, and 403 were randomly assigned to double-blind treatment. The study was terminated early because efficacy was demonstrated by the preplanned interim analysis (conducted after 64 events). Time to impending relapse was significantly delayed with aripiprazole-IM-depot treatment compared with placebo in both the interim analysis and the final analysis (P < .0001, log-rank test). The hazard ratio (placebo/aripiprazole-IM-depot) at final analysis was 5.03 (95% CI, 3.15-8.02). The rate of impending relapse was significantly lower with aripiprazole-IM-depot than placebo at endpoint (final analysis, 10.0% [n = 27/269] vs 39.6% [n = 53/134]). Improvements in Clinical Global Impressions-Severity of Illness scale and Positive and Negative Syndrome Scale total scores were maintained with aripiprazole-IM-depot treatment but showed significant worsening with placebo (change from double-blind baseline, P < .0001 for aripiprazole-IM-depot vs placebo). The most common treatment-emergent adverse events (occurring in ≥ 5% of aripiprazole-IM-depot subjects and greater than placebo) were insomnia, tremor, and headache.

CONCLUSIONS

Aripiprazole-IM-depot significantly delayed time to impending relapse compared with placebo and appears to be a well-tolerated maintenance treatment option for schizophrenia.

TRIAL REGISTRATION

ClinicalTrials.gov identifier: NCT00705783.

Observation of high coherence in Josephson junction qubits measured in a three-dimensional circuit QED architecture

Superconducting quantum circuits based on Josephson junctions have made rapid progress in demonstrating quantum behavior and scalability. However, the future prospects ultimately depend upon the intrinsic coherence of Josephson junctions, and whether superconducting qubits can be adequately isolated from their environment. We introduce a new architecture for superconducting quantum circuits employing a three-dimensional resonator that suppresses qubit decoherence while maintaining sufficient coupling to the control signal. With the new architecture, we demonstrate that Josephson junction qubits are highly coherent, with T2 ∼ 10 to 20  μs without the use of spin echo, and highly stable, showing no evidence for 1/f critical current noise. These results suggest that the overall quality of Josephson junctions in these qubits will allow error rates of a few 10(-4), approaching the error correction threshold.

Invited article: millimeter-wave bolometer array receiver for the Atacama pathfinder experiment Sunyaev-Zel'dovich (APEX-SZ) instrument

The Atacama pathfinder experiment Sunyaev-Zel'dovich (APEX-SZ) instrument is a millimeter-wave cryogenic receiver designed to observe galaxy clusters via the Sunyaev-Zel'dovich effect from the 12 m APEX telescope on the Atacama plateau in Chile. The receiver contains a focal plane of 280 superconducting transition-edge sensor (TES) bolometers instrumented with a frequency-domain multiplexed readout system. The bolometers are cooled to 280 mK via a three-stage helium sorption refrigerator and a mechanical pulse-tube cooler. Three warm mirrors, two 4 K lenses, and a horn array couple the TES bolometers to the telescope. APEX-SZ observes in a single frequency band at 150 GHz with 1' angular resolution and a 22' field-of-view, all well suited for cluster mapping. The APEX-SZ receiver has played a key role in the introduction of several new technologies including TES bolometers, the frequency-domain multiplexed readout, and the use of a pulse-tube cooler with bolometers. As a result of these new technologies, the instrument has a higher instantaneous sensitivity and covers a larger field-of-view than earlier generations of Sunyaev-Zel'dovich instruments. The TES bolometers have a median sensitivity of 890 μK(CMB)√s (NEy of 3.5 × 10(-4) √s). We have also demonstrated upgraded detectors with improved sensitivity of 530 μK(CMB)√s (NEy of 2.2 × 10(-4) √s). Since its commissioning in April 2007, APEX-SZ has been used to map 48 clusters. We describe the design of the receiver and its performance when installed on the APEX telescope.

Simple all-microwave entangling gate for fixed-frequency superconducting qubits

We demonstrate an all-microwave two-qubit gate on superconducting qubits which are fixed in frequency at optimal bias points. The gate requires no additional subcircuitry and is tunable via the amplitude of microwave irradiation on one qubit at the transition frequency of the other. We use the gate to generate entangled states with a maximal extracted concurrence of 0.88, and quantum process tomography reveals a gate fidelity of 81%.

Taxonomically restricted genes are associated with the evolution of sociality in the honey bee

Background

Studies have shown that taxonomically restricted genes are significant in number and important for the evolution of lineage specific traits. Social insects have gained many novel morphological and behavioral traits relative to their solitary ancestors. The task repertoire of an advanced social insect, for example, can be 40-50 tasks, about twice that of a solitary wasp or bee. The genetic basis of this expansion in behavioral repertoire is still poorly understood, and a role for taxonomically restricted genes has not been explored at the whole genome level.

Results

Here we present comparative genomics results suggesting that taxonomically restricted genes may have played an important role in generating the expansion of behavioral repertoire associated with the evolution of eusociality. First, we show that the current honey bee official gene set contains about 700 taxonomically restricted genes. These are split between orphans, genes found only in the Hymenoptera, and genes found only in insects. Few of the orphans or genes restricted to the Hymenoptera have been the focus of experimental work, but several of those that have are associated with novel eusocial traits or traits thought to have changed radically as a consequence of eusociality. Second, we predicted that if taxonomically restricted genes are important for generating novel eusocial traits, then they should be expressed with greater frequency in workers relative to the queen, as the workers exhibit most of the novel behavior of the honey bee relative to their solitary ancestors. We found support for this prediction. Twice as many taxonomically restricted genes were found amongst the genes with higher expression in workers compared to those with higher expression in queens. Finally, we compiled an extensive list of candidate taxonomically restricted genes involved in eusocial evolution by analyzing several caste specific gene expression data sets.

Conclusions

This work identifies a large number of candidate taxonomically restricted genes that may have played a role in eusocial evolution. This work thus lays the foundation for future functional genomics work on the evolution of novelty in the context of social behavior. We also present preliminary evidence, based on biased patterns of gene expression, that taxonomically restricted genes may have played a role in the evolution of caste systems, a characteristic lineage specific social trait.

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses.

Preparation and measurement of three-qubit entanglement in a superconducting circuit

Traditionally, quantum entanglement has been central to foundational discussions of quantum mechanics. The measurement of correlations between entangled particles can have results at odds with classical behaviour. These discrepancies grow exponentially with the number of entangled particles. With the ample experimental confirmation of quantum mechanical predictions, entanglement has evolved from a philosophical conundrum into a key resource for technologies such as quantum communication and computation. Although entanglement in superconducting circuits has been limited so far to two qubits, the extension of entanglement to three, eight and ten qubits has been achieved among spins, ions and photons, respectively. A key question for solid-state quantum information processing is whether an engineered system could display the multi-qubit entanglement necessary for quantum error correction, which starts with tripartite entanglement. Here, using a circuit quantum electrodynamics architecture, we demonstrate deterministic production of three-qubit Greenberger-Horne-Zeilinger (GHZ) states with fidelity of 88 per cent, measured with quantum state tomography. Several entanglement witnesses detect genuine three-qubit entanglement by violating biseparable bounds by 830 ± 80 per cent. We demonstrate the first step of basic quantum error correction, namely the encoding of a logical qubit into a manifold of GHZ-like states using a repetition code. The integration of this encoding with decoding and error-correcting steps in a feedback loop will be the next step for quantum computing with integrated circuits.

Modeling the Adaptive Role of Negative Signaling in Honey Bee Intraspecific Competition

Collective decision making in the social insects often proceeds via feedback cycles based on positive signaling. Negative signals have, however, been found in a few contexts in which costs exist for paying attention to no longer useful information. Here we incorporate new research on the specificity and context of the negative stop signal into an agent based model of honey bee foraging to explore the adaptive basis of negative signaling in the dance language. Our work suggests that the stop signal, by acting as a counterbalance to the waggle dance, allows colonies to rapidly shut down attacks on other colonies. This could be a key adaptation, as the costs of attacking a colony strong enough to defend itself are significant. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10905-010-9229-5) contains supplementary material, which is available to authorized users.

Eliminating the mystery from the concept of emergence

While some branches of complexity theory are advancing rapidly, the same cannot be said for our understanding of emergence. Despite a complete knowledge of the rules underlying the interactions between the parts of many systems, we are often baffled by their sudden transitions from simple to complex. Here I propose a solution to this conceptual problem. Given that emergence is often the result of many interactions occurring simultaneously in time and space, an ability to intuitively grasp it would require the ability to consciously think in parallel. A simple exercise is used to demonstrate that we do not possess this ability. Our surprise at the behaviour of cellular automata models, and the natural cases of pattern formation they mimic, is then explained from this perspective. This work suggests that the cognitive limitations of the mind can be as significant a barrier to scientific progress as the limitations of our senses.

High-fidelity readout in circuit quantum electrodynamics using the Jaynes-Cummings nonlinearity

We demonstrate a qubit readout scheme that exploits the Jaynes-Cummings nonlinearity of a superconducting cavity coupled to transmon qubits. We find that, in the strongly driven dispersive regime of this system, there is the unexpected onset of a high-transmission "bright" state at a critical power which depends sensitively on the initial qubit state. A simple and robust measurement protocol exploiting this effect achieves a single-shot fidelity of 87% using a conventional sample design and experimental setup, and at least 61% fidelity to joint correlations of three qubits.

Deconstructing the superorganism: social physiology, groundplans, and sociogenomics

Our understanding of insect societies is rapidly expanding due to an emphasis on integrative approaches. Emerging tools enabling the molecular dissection of social behavior, together with novel hypotheses for the evolution of eusociality, are emblematic of this progress. However, an obstacle to a truly integrative approach remains, as social physiology--the basis of group-level coordination--has generally been neglected by geneticists. In this paper, we begin a synthesis of these fields by first reviewing three classes of social insect organization that mark major transitions in increasing social complexity. We then develop an expansion of the superorganism concept in order to place eusociality into a broad evolutionary context, and we also interpret current molecular and genetic work on the evolution of eusociality. The ground plan hypothesis proposes that eusociality arose via simple changes in the regulation of ancestral gene sets affecting reproductive physiology and behavior, and we argue that this hypothesis is explanatory for the evolution of division of labor (social anatomy) but not for the regulatory systems that ensure group-level coordination of action (social physiology), which we propose is dependent on previously unrelated traits that are brought together into novel genetic networks. We conclude with a review of recent work in sociogenomics that supports our hypotheses.

A self-organizing model for task allocation via frequent task quitting and random walks in the honeybee

Social insect colonies are able to quickly redistribute their thousands of workers between tasks that vary strongly in space and time. How individuals collectively track spatial variability is particularly puzzling because bees have access only to local information. This work presents and tests a model showing how honeybees solve their fundamental within-nest spatial task-allocation problem. The algorithm, which is self-organizing and derived from empirical studies, couples two processes with opposing effects. Frequent task quitting, followed by patrols, during which bees are insensitive to task stimuli, serves to randomize individual location throughout the nest without reference to variation in task demand, while a foraging-for-work-like mechanism provides the opposing force of localizing individuals to areas of high task demand. This simple model is shown to generate sophisticated patterns of task allocation. It allocates bees to tasks in proportion to their demand, independent of their spatial distribution in the nest, and also reallocates labor in response to temporal changes in task demand. Finally, the model shows that task-allocation patterns at the colony level do not reflect colonies allocating particular individuals to tasks. In contrast, they reflect a dynamic equilibrium of workers switching between tasks and locations in the nest.

Division of labor in honeybees: form, function, and proximate mechanisms

Honeybees exhibit two patterns of organization of work. In the spring and summer, division of labor is used to maximize growth rate and resource accumulation, while during the winter, worker survivorship through the poor season is paramount, and bees become generalists. This work proposes new organismal and proximate level conceptual models for these phenomena. The first half of the paper presents a push–pull model for temporal polyethism. Members of the nursing caste are proposed to be pushed from their caste by the development of workers behind them in the temporal caste sequence, while middle-aged bees are pulled from their caste via interactions with the caste ahead of them. The model is, hence, an amalgamation of previous models, in particular, the social inhibition and foraging for work models. The second half of the paper presents a model for the proximate basis of temporal polyethism. Temporal castes exhibit specialized physiology and switch caste when it is adaptive at the colony level. The model proposes that caste-specific physiology is dependent on mutually reinforcing positive feedback mechanisms that lock a bee into a particular behavioral phase. Releasing mechanisms that relate colony level information are then hypothesized to disrupt particular components of the priming mechanisms to trigger endocrinological cascades that lead to the next temporal caste. Priming and releasing mechanisms for the nursing caste are mapped out that are consistent with current experimental results. Less information-rich, but plausible, mechanisms for the middle-aged and foraging castes are also presented.