1. The specific capacity of a suspension is that capacity which) combined in parallel with a certain resistance, electrically balances 1 cm. cube of the suspension. 2. The following formula holds for the specific capacity of a suspension of spheroids, each of which is composed of a well conducting interior surrounded by a thin membrane of a comparatively high resistance: See PDF for Equation C, specific capacity of suspension; C(o), static capacity of one sq. cm. of membrane; r, r(1) specific resistances respectively of suspension and of suspending liquid; 2 q major axis of spheroid, alpha constant tabulated in Table I. 3. The following formula holds practically for any suspension whatever the form of the suspended particle. See PDF for Equation C = C(100) being the specific capacity of a suspension with a concentration of 100 per cent. Formulae (1a) and (1b) hold only for the case, when the frequency is so low, that the impedance of the static capacity of the membrane around a single particle is high as compared with the resistance of the interior of the particle. The formulae hold also for a suspension of homogeneous particles, when polarization takes place at the surface of each particle, provided the polarization resistance is low as compared with the impedance of the polarization capacity. 4. A description is given of a method for measuring the capacity of a suspension at frequencies between 800 and 4(1/2) million cycles. By means of a specially designed bridge, a substitution method is employed, by which in the last analysis the suspension is compared with the suspending liquid which is so diluted as to have the same specific resistance as the suspension, consecutive measurements being made in the same electrolytic cell. 5. Formula (1b) is verified by measurements of the capacity of suspensions of varying volume concentrations of the red corpuscles of a dog. 6. By means of the above measurements, the value of C(o) is calculated by equation (1a). 7. It is found that C(o) is independent of the frequency up to 4(1/2) million cycles and that it is also independent of the suspending liquid. These results furnish considerable evidence of the validity of the theory, that C(o) represents the static capacity of a corpuscle membrane. 8. On this assumption and using a probable value for the dielectric constant of the membrane, the thickness of the membrane is calculated to be 3.3.10(-7)cm.

OBJECTIVE

To determine independent prognostic factors in a group of 1875 patients with invasive carcinoma of the intact uterine cervix treated with radiotherapy alone in a French cooperative study from 1970 to 1993.

METHODS

Patients were staged according to the UICC-FIGO and MDAH substaging. The distribution per FIGO stage was Ia-Ib: 25.5%; IIa: 12%; IIb: 29%; IIIa: 5%; IIIb: 25%, and IV: 3.5%. Ninety-two percent had squamous cell carcinoma. The maximum diameter of the clinically detectable cervical disease was less than 3 cm in 24.5% of Stages I-II and in 10% of Stages III-IV, more than 5 cm in 13.5% of Stages I-II, and in 16% of Stages III-IV. Nodal involvement was shown on lymphangiogram in 16% of Stages I-II and in 32.5% of Stages III-IV.

RESULTS

1) Univariate analysis of Stages I and II: stage, cervical disease diameter, and nodal involvement are significant prognostic factors. Five-year specific survival rate (5ySS) is 83.5% in Stage Ib, 81% in IIa and 71% in IIb. Five-year disease-free survival rate (5yDFS) is 86% in tumors less of 3 cm, 76% in tumors of 3 to 5 cm, and 61.5% in tumor larger than 5 cm. Lymphangiogram strongly influences the 5-year pelvic disease-free survival rate (5yPDFS): respectively, 90% in nonpositive lymphangiogram vs. 65% when positive. A significant drop in specific and disease-free survival is observed (10 and 14%, respectively (p = 0.04) when comparing adenocarcinoma and squamous cell carcinoma. Age is a significant prognostic factor for specific survival because patients aged less than 30 years old have 91% vs. about 75% for patients over 30 years (p = 0.03). 2) Univariate analysis of Stages III-IV: Stage and positive lymphangiogram are predictive factors for relapse and death. The MDAH substaging is more reliable to predict the probability of pelvic disease-free survival in Stage III. At 5 years, the FIGO Stages IIIa and IIIb have a rather similar PDFS (65% vs. 59%). Conversely, the difference of survival rates between MDAH Stage IIIA and Stage IIIB is more demonstrative (69% vs. 47.5%). 3) Multivariate analysis (Cox P. H. R. model). Nodal involvement and stage remain significant for all three models in all stages (p < 0.0001). Age above 70 years influences specific survival for Stage I-II (p = 0.01). Tumors larger than 5 cm and adenocarcinoma also appear to be independent prognostic factors for specific and disease-free survival in Stage I-II (p = 0.05 and p = 0.005, respectively).

CONCLUSIONS

The relevance of tumor size (less or greater than 4 cm) is now recognized in the 1995 revised FIGO staging in Stage Ib but unfortunately not in other stages. Tumor size per stage and nodal status should be systematically recorded to allow a better prediction of failure rates and to compare literature reports.

As a part of the study to identify genes associated with hormone-refractory stage of human prostate cancer, we have recently identified several genetic and epigenetic changes that seem to be associated with the progression of androgen-sensitive to androgen-independent prostate tumor cells. In the present study, we report a novel gene, macrophage inhibitory cytokine-1 (MIC-1) also known as prostate derived factor (PDF), that was highly expressed in androgen-independent LNCaP-C81 cells and its metastatic variant LNCaP-Ln3 compared to androgen-sensitive LNCaP-C33 cells. The MIC-1/PDF expression was dysregulated (very low to non-detectable) in the androgen-independent PC3 and DU145 cells. Interestingly, serum factors demonstrated a differential regulation of MIC-1/PDF in the androgen-sensitive and the androgen-independent cells of LNCaP cells. Immunohistochemical analysis on 15 prostatic adenocarcinomas showed a weak staining in the benign prostatic glandular area (intensity score 2.38+/-0.25; n=13), while the immunoreactivity was significantly stronger (p<0.05) in areas of adenocarcinoma (score 7.33+/-0.88; n=15). Altogether, these data suggest that the serum factors (including androgens and cytokines) might contribute to the regulation of the MIC-1/PDF gene that seems to be associated with the progression of prostate cancer.

Formulae are derived for the time-intensity relations for stimulation by direct currents using the following hypotheses: first, the current produces an excitatory effect whose rate of growth is proportional to the voltage; and second, the tissue reacts toward the normal state at a rate proportional to the amount of excitation. If p represents the local excitatory process numerically, the hypotheses are represented by the differential equation See PDF for Structure. where K and k are constants and V the applied voltage. For the stimulus to be adequate it is assumed that p must be built up to a certain liminal value. It appears as a deduction from the data that this liminal value is a function of the voltage of the form h +/- alphaV where h and alpha are constants. alpha is zero or negligible for certain electrodes. alphaV is a measure of electrotonus or a similar phenomenon. Experimental data are discussed and are shown to agree satisfactorily with the derived formulae for stimulation both at the anode and cathode.

A primary function of males for many species involves mating with females for reproduction. Drosophila melanogaster males respond to the presence of other males by prolonging mating duration to increase the chance of passing on their genes. To understand the basis of such complex behaviors, we examine the genetic network and neural circuits that regulate rival-induced Longer-Mating-Duration (LMD). Here, we identify a small subset of clock neurons in the male brain that regulate LMD via neuropeptide signaling. LMD requires the function of pigment-dispersing factor (PDF) in four s-LNv neurons and its receptor PDFR in two LNd neurons per hemisphere, as well as the function of neuropeptide F (NPF) in two neurons within the sexually dimorphic LNd region and its receptor NPFR1 in four s-LNv neurons per hemisphere. Moreover, rival exposure modifies the neuronal activities of a subset of clock neurons involved in neuropeptide signaling for LMD.

This report presents new recommendations adopted in June 2009 by CDC's Advisory Committee on Immunization Practices (ACIP) regarding use of the combination measles, mumps, rubella, and varicella vaccine (MMRV, ProQuad, Merck & Co., Inc.). MMRV vaccine was licensed in the United States in September 2005 and may be used instead of measles, mumps, rubella vaccine (MMR, M-M-RII, Merck & Co., Inc.) and varicella vaccine (VARIVAX, Merck & Co., Inc.) to implement the recommended 2-dose vaccine schedule for prevention of measles, mumps, rubella, and varicella among children aged 12 months-12 years. At the time of its licensure, use of MMRV vaccine was preferred for both the first and second doses over separate injections of equivalent component vaccines (MMR vaccine and varicella vaccine), which was consistent with ACIP's 2006 general recommendations on use of combination vaccines (CDC. General recommendations on immunization: recommendations of the Advisory Committee on Immunization Practices [ACIP]. MMWR 2006;55;[No. RR-15]). Since July 2007, supplies of MMRV vaccine have been temporarily unavailable as a result of manufacturing constraints unrelated to efficacy or safety. MMRV vaccine is expected to be available again in the United States in May 2010. In February 2008, on the basis of preliminary data from two studies conducted postlicensure that suggested an increased risk for febrile seizures 5-12 days after vaccination among children aged 12-23 months who had received the first dose of MMRV vaccine compared with children the same age who had received the first dose of MMR vaccine and varicella vaccine administered as separate injections at the same visit, ACIP issued updated recommendations regarding MMRV vaccine use (CDC. Update: recommendations from the Advisory Committee on Immunization Practices [ACIP] regarding administration of combination MMRV vaccine. MMWR 2008;57:258-60). These updated recommendations expressed no preference for use of MMRV vaccine over separate injections of equivalent component vaccines for both the first and second doses. The final results of the two postlicensure studies indicated that among children aged 12--23 months, one additional febrile seizure occurred 5-12 days after vaccination per 2,300-2,600 children who had received the first dose of MMRV vaccine compared with children who had received the first dose of MMR vaccine and varicella vaccine administered as separate injections at the same visit. Data from postlicensure studies do not suggest that children aged 4--6 years who received the second dose of MMRV vaccine had an increased risk for febrile seizures after vaccination compared with children the same age who received MMR vaccine and varicella vaccine administered as separate injections at the same visit. In June 2009, after consideration of the postlicensure data and other evidence, ACIP adopted new recommendations regarding use of MMRV vaccine for the first and second doses and identified a personal or family (i.e., sibling or parent) history of seizure as a precaution for use of MMRV vaccine. For the first dose of measles, mumps, rubella, and varicella vaccines at age 12--47 months, either MMR vaccine and varicella vaccine or MMRV vaccine may be used. Providers who are considering administering MMRV vaccine should discuss the benefits and risks of both vaccination options with the parents or caregivers. Unless the parent or caregiver expresses a preference for MMRV vaccine, CDC recommends that MMR vaccine and varicella vaccine should be administered for the first dose in this age group. For the second dose of measles, mumps, rubella, and varicella vaccines at any age (15 months-12 years) and for the first dose at age>>or=48 months, use of MMRV vaccine generally is preferred over separate injections of its equivalent component vaccines (i.e., MMR vaccine and varicella vaccine). This recommendation is consistent with ACIP's 2009 provisional general recommendations regarding use of combination vaccines (available at http://www.cdc.gov/vaccines/recs/provisional/downloads/combo-vax-Aug2009-508.pdf), which state that use of a combination vaccine generally is preferred over its equivalent component vaccines.

Peptide deformylases (PDFs) have been investigated as potential specific targets for antibiotics, but the possible existence of a functional human PDF (HsPDF) presents a potential hurdle to the design of specific drugs. We have expression cloned a HsPDF that has deformylase activity, although it is a slower and catalytically less active enzyme than bacterial or plant PDFs. A cobalt-substituted form of HsPDF (but not nickel or zinc) is active, and the enzyme appears to be active at a pH between 6.0 and 7.2, a temperature range of 25-50 degrees C, and in a low KCl ionic strength buffer. Actinonin inhibits HsPDF activity with an IC50 of 43 nM and kills Daudi and HL60 human cancer cell lines with an LC50 of 5.3 and 8.8 microM, respectively. The inhibition of HsPDF may provide an explanation for the mechanism by which actinonin is cytotoxic against various human tumor cell lines.

Computational techniques within the population density function (PDF) framework have provided time-saving alternatives to classical Monte Carlo simulations of neural network activity. Efficiency of the PDF method is lost as the underlying neuron model is made more realistic and the number of state variables increases. In a detailed theoretical and computational study, we elucidate strengths and weaknesses of dimension reduction by a particular moment closure method (Cai, Tao, Shelley, & McLaughlin, 2004; Cai, Tao, Rangan, & McLaughlin, 2006) as applied to integrate-and-fire neurons that receive excitatory synaptic input only. When the unitary postsynaptic conductance event has a single-exponential time course, the evolution equation for the PDF is a partial differential integral equation in two state variables, voltage and excitatory conductance. In the moment closure method, one approximates the conditional kth centered moment of excitatory conductance given voltage by the corresponding unconditioned moment. The result is a system of k coupled partial differential equations with one state variable, voltage, and k coupled ordinary differential equations. Moment closure at k = 2 works well, and at k = 3 works even better, in the regime of high dynamically varying synaptic input rates. Both closures break down at lower synaptic input rates. Phase-plane analysis of the k = 2 problem with typical parameters proves, and reveals why, no steady-state solutions exist below a synaptic input rate that gives a firing rate of 59 s(1) in the full 2D problem. Closure at k = 3 fails for similar reasons. Low firing-rate solutions can be obtained only with parameters for the amplitude or kinetics (or both) of the unitary postsynaptic conductance event that are on the edge of the physiological range. We conclude that this dimension-reduction method gives ill-posed problems for a wide range of physiological parameters, and we suggest future directions.

We explored the neural basis of age- and task-related plasticity in circadian patterns of activity in the honeybee. To identify putative circadian pacemakers in the bee brain, we used antibodies against Drosophila melanogaster and Antheraea pernyi PERIOD and an antiserum to crustacean pigment-dispersing hormone (PDH) known to cross-react with insect pigment-dispersing factors (PDFs). In contrast to previous results from Drosophila, PDH and PER immunoreactivity (-ir) were not colocalized in bee neurons. The most intense PER-ir was cytoplasmic, in two groups of large neurons in the protocerebrum. The number of protocerebral PER-ir neurons and PER-ir intensity within individual cells were highest in brains collected during subjective night and higher in old bees than in young bees. These results are consistent with previous analyses of brain per mRNA in honeybees. Nuclear PER-ir was found throughout the brain, including the optic and antennal lobes. A single group of PDH-ir neurons (approximately 20/optic lobe) was consistently and intensely labeled at the medial margin of the medulla, independent of age or time of day. The processes of these neurons extended to specific neuropils in the protocerebrum and the optic lobes but not to the deutocerebrum. The patterns displayed by PER- and PDH-ir do not completely match any patterns previously described. This suggests that, although clock proteins are conserved across insect groups, there is no universal pattern of coexpression that allows ready identification of pacemaker neurons within the insect brain.

Recent studies in Drosophila melanogaster indicate that the neuropeptide pigment-dispersing factor (PDF) is an important output signal from a set of major clock neurons, s-LN(v)s (small ventral lateral neurons), which transmit the circadian phase to subsets of other clock neurons, DNs (dorsal neurons). Both s-LN(v)s and DNs have fiber projections to the dorsal protocerebrum of the brain, so that this area is a conspicuous locus for coupling between different subsets of clock neurons. To unravel the neural circuits underlying the fly's circadian rhythms, we examined the detailed subcellular morphology of the PDF-positive fibers of the s-LN(v)s in the dorsal protocerebrum, focusing on their synaptic connections, using preembedding immunoelectron microscopy. To examine the distribution of synapses, we also reconstructed the three-dimensional morphology of PDF-positive varicosities from fiber profiles in the dorsal protocerebrum. The varicosities contained large dense-core vesicles (DCVs), and also numerous small clear vesicles, forming divergent output synapses onto unlabeled neurites. The DCVs apparently dock at nonsynaptic sites, suggesting their nonsynaptic release. In addition, a 3D reconstruction revealed the presence of input synapses onto the PDF-positive fibers. These were detected less frequently than output sites. These observations suggest that the PDF-positive clock neurons receive neural inputs directly through synaptic connections in the dorsal protocerebrum, in addition to supplying dual outputs, either synaptic or via paracrine release of the DCV contents, to unidentified target neurons.

Thionins are a group of antimicrobial polypeptides that form part of the plant's defense mechanism against pathogens. The Thi 2.1 thionin gene of Arabidopsis thaliana has been shown to be inducible by jasmonic acid (JA), an oxylipin-like hormone derived from oxygenated linolenic acid and synthesized via the octadecanoid pathway. The JA-dependent regulation of the Thi 2.1 gene has been exploited for setting up a genetic screen for the isolation of signal transduction mutants that constitutively express the Thi 2.1 gene. Ten cet-mutants have been isolated which showed a constitutive expression of the thionin gene. Allelism tests revealed that they represent at least five different loci. Some mutants are dominant, others recessive, but all cet mutations behaved as monogenic traits when backcrossed with Thi 2.1-GUS plants. Some of the mutants overproduce JA and its bioactive precursor 12-oxophytodienoic acid (OPDA) up to 40-fold while others have the same low levels as the control wildtype plants. Two of the mutants showed a strong induction of both the salicylic acid (SA)- and the JA-dependent signaling pathways, while the majority seems to be affected only in the octadecanoid pathway. The Thi 2.1 thionin gene and the Pdf 1.2 defensin gene are activated independently, though both are regulated by JA. The cet-mutants, except for one, also show a spontaneous leaf cell necrosis, a reaction often associated with the systemic acquired resistance (SAR) pathway.

The microenvironment of a tumour, in particular its hypoxic status, is a crucial factor in its response to radiotherapy. Conventional techniques for measuring hypoxia are either invasive or follow surgical intervention, and thus not ideal. Positron emission tomography allows the non-invasive pre-surgical assessment of oxygen status by measuring the spatiotemporal distribution of hypoxia-specific tracers. However, the relationship between levels of uptake and the underlying oxygen tension are yet to be elucidated. Furthermore, it is not fully understood how changes in the underlying physiology affect the appearance of uptake. This paper presents a modular simulation of the tumour microenvironment, underpinned by a probability density function (PDF) to model the vasculature. The model is solved numerically, to simulate both the steady-state oxygenation of a tumour and the spatiotemporal distribution of the hypoxia-specific tracer, [18F]-fluoromisonidazole (Fmiso), in a 2D environment. The results show that using a PDF to represent the vasculature effectively captures the 'hypoxic island' appearance of oxygen-deficient tissues seen ex vivo. Simulated tissue activity curves (TACs) demonstrate the general two-stage trend of empirical data, with an initial perfusion-dominated uptake, followed by hypoxia-specific binding. In well-perfused tissue, activity follows plasma levels in early stages, with binding of Fmiso only becoming apparent at a later stage. In structurally hypoxic tissue, a more gradual initial increase in activity is observed, followed by the same accumulation slope. We demonstrate the utility of theoretical modelling of tracer uptake, by quantifying the changes in TAC structure that arise as a result of altering key physiological characteristics. For example, by decreasing either the proximity of tissue to the vasculature, or the effective diffusion coefficient of Fmiso, we can observe a shift of TAC structure from corresponding to well-perfused to avascular regions, despite wholly different underlying causes.

BACKGROUND

The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis--something that is extremely important given the speed with which the platform is evolving.

RESULTS

NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others.

METHODS

NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK. A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/. A Docker image is also available from Docker Hub--see program documentation https://documentation.tgac.ac.uk/display/NANOOK.

BACKGROUND

richard.leggett@tgac.ac.uk

BACKGROUND

Supplementary data are available at Bioinformatics online.

TGF-β/Smad3 signaling plays a pivotal role in the pathogenesis of peritoneal fibrosis associated with peritoneal dialysis (PD). MicroRNA-29 (miR-29) is known as a potent downstream inhibitor of TGF-β/Smad3 in renal fibrosis. In this study, we examined the therapeutic potential for miR-29b on PD-related peritoneal fibrosis in a mouse model of PD induced by daily infusion of 4.25% dextrose-containing PD fluid (PDF). MiR-29b-expressing plasmid was delivered into the peritoneum via an ultrasound-microbubble-mediated system before and at day 14 after PDF. We found that mice on PD developed peritoneal fibrosis with impaired peritoneal function, which was associated with a loss of miR-29b. In contrast, overexpression of miR-29b before the PDF infusion showed a protective effect on peritoneal fibrosis including EMT and prevented peritoneal dysfunction. Moreover, delayed miR-29b treatment until peritoneal fibrosis was established at day 14 also halted the progression of peritoneal fibrosis at day 28. Further studies identified that blockade of the Sp1-TGF-β/Smad3 pathway may be a mechanism by which miR-29b inhibited peritoneal fibrosis. In conclusion, treatment with miR-29b may represent a novel and effective therapy for PD-associated peritoneal fibrosis.

A common in vitro response for many chemopreventive and antitumor agents, including some cyclooxygenase inhibitors, is the increased expression of nonsteroidal anti-inflammatory drug-activated gene (NAG)-1/macrophage inhibitory cytokine (MIC)-1/prostate-derived factor (PDF). The experimental anticancer drug 2-(4-amino-3-methylphenyl)-5-fluorobenzothiazole (5F203) was a potent inducer of NAG-1 expression, and in MCF-7 cells, it inhibited cell growth and induced apoptosis. NAG-1 small interfering RNA blocked NAG-1 expression and 5F203-induced apoptosis in MCF-7 cells, indicating that NAG-1 may mediate the apoptosis and anticancer activity. One mechanism by which 5F203 increases NAG-1 expression is by increasing the stability of NAG-1 mRNA, dependent of de novo protein synthesis. Extracellular signal-regulated kinase (ERK) 1/2 phosphorylation was increased by 5F203, and inhibition of ERK1/2 phosphorylation abolished the induction of NAG-1 protein expression and increased the stability of NAG-1 mRNA. Thus, 5F203 regulates NAG-1 expression by a unique mechanism compared with other drugs. A mouse orthotopic mammary tumor model was used to determine whether 5F203 increased NAG-1 expression in vivo and suppressed tumor growth. Treatment of the mice with Phortress, the prodrug of 5F203, increased the in vivo expression of NAG-1 as measured by real-time reverse transcription-polymerase chain reaction from RNA obtained by needle biopsy, and the expression correlated with a reduction of tumor volume. These results confirm that NAG-1 suppresses tumor growth, and its in vivo expression can be controlled by treating mice with anticancer drugs, such as Phortress. Drugs that target NAG-1 could lead to a unique strategy for the development of chemotherapeutic and chemopreventive agents.

OBJECTIVE

We examined the effects of a cognitive behavioral self-help program (Refresh) to improve sleep, on sleep quality and symptoms of depression among first-year college students.

METHODS

Students in one residence hall (n = 48) participated in Refresh and students in another residence hall (n = 53) participated in a program of equal length (Breathe) designed to improve mood and increase resilience to stress. Both programs were delivered by e-mail in 8 weekly PDF files. Of these, 19 Refresh program participants and 15 Breathe program participants reported poor sleep quality at baseline (scores ≥ 5 on the Pittsburgh Sleep Quality Index [PSQI]). Participants completed the PSQI and the Center for Epidemiological Studies-Depression Scale (CES-D) at baseline and post-intervention.

RESULTS

Among students with poor sleep (PSQI>> 5) at baseline, participation in Refresh was associated with greater improvements in sleep quality and greater reduction in depressive symptoms than participation in Breathe. Among students with high sleep quality at baseline there was no difference in baseline to post-intervention changes in sleep (PSQI) or depressive symptom severity (CES-D).

CONCLUSIONS

A cognitive behavioral sleep improvement program delivered by e-mail may be a cost effective way for students with poor sleep quality to improve their sleep and reduce depressive symptoms. An important remaining question is whether improving sleep will also reduce risk for future depression.

The clock network of Drosophila melanogaster expresses various neuropeptides, but a function in clock-mediated behavioral control was so far only found for the neuropeptide pigment dispersing factor (PDF). Here, we propose a role in the control of behavioral rhythms for the ion transport peptide (ITP), which is expressed in the fifth small ventral lateral neuron, one dorsal lateral neuron, and in only a few nonclock cells in the brain. Immunocytochemical analyses revealed that ITP, like PDF, is most probably released in a rhythmic manner at projection terminals in the dorsal protocerebrum. This rhythm continues under constant dark conditions, indicating that ITP release is clock controlled. ITP expression is reduced in the hypomorph mutant Clk(AR), suggesting that ITP expression is regulated by CLOCK. Using a genetically encoded RNAi construct, we knocked down ITP in the two clock cells and found that these flies show reduced evening activity and increased nocturnal activity. Overexpression of ITP with two independent timeless-GAL4 lines completely disrupted behavioral rhythms, but only slightly dampened PER cycling in important pacemaker neurons, suggesting a role for ITP in clock output pathways rather than in the communication within the clock network. Simultaneous knockdown (KD) of ITP and PDF made the flies hyperactive and almost completely arrhythmic under constant conditions. Under light-dark conditions, the double-KD combined the behavioral characteristics of the single-KD flies. In addition, it reduced the flies' sleep. We conclude that ITP and PDF are the clock's main output signals that cooperate in controlling the flies' activity rhythms.

Newly synthesized polypeptides undergo various cotranslational maturation steps, including N-terminal enzymatic processing, chaperone-assisted folding and membrane targeting, but the spatial and temporal coordination of these steps is unclear. We show that Escherichia coli methionine aminopeptidase (MAP) associates with ribosomes through a charged loop that is crucial for nascent-chain processing and cell viability. MAP competes with peptide deformylase (PDF), the first enzyme to act on nascent chains, for binding sites at the ribosomal tunnel exit. PDF has extremely fast association and dissociation kinetics, which allows it to frequently sample ribosomes and ensure the processing of nascent chains after their emergence. Premature recruitment of the chaperone trigger factor, or polypeptide folding, negatively affect processing efficiency. Thus, the fast ribosome association kinetics of PDF and MAP are crucial for the temporal separation of nascent-chain processing from later maturation events, including chaperone recruitment and folding.

Modern imaging and dissemination methods enable morphologists to share complex, three-dimensional (3D) data in ways not previously possible. Here we present a 3D interactive model of the jaw musculature of the American Alligator (Alligator mississippiensis). Alligator and crocodylian jaw musculature is notoriously challenging to inspect and interpret because of the derived nature of the feeding apparatus. Using Iodine-contrast enhanced microCT imaging, a segmented model of jaw muscles, trigeminal nerve, brain and skull are presented as a cross-sectional atlas and 3D, interactive pdf of the rendered model. Modern 3D dissemination methods like this 3D Alligator hold great potential for morphologists to share anatomical information to scientists, educators, and the public in an easily downloadable format.

The intrinsic resistance of P. aeruginosa PAO1 to the peptide deformylase inhibitor (PDF-I) LBM415 was mediated by the MexAB-OprM and MexXY-OprM efflux pumps, the latter of which was strongly induced by LBM415. Single-step exposure of PAO1 deleted for mexAB-oprM (therefore lacking both MexAB-OprM and MexXY-OprM functions) to PDF-Is selected for nfxB mutants, which express the MexCD-OprJ efflux pump, indicating that these compounds are also substrates for this pump. Selection of resistant mutants by use of levels of LBM415 greater than that accommodated by efflux yielded two additional groups of mutations, in the methionyl-tRNA(fmet) formyltransferase (fmt) and folD genes. Both mechanisms are known to impose an in vitro growth deficit (also observed here), presumably due to impairment of protein synthesis. We surmised that this inherent impairment of protein synthesis would upregulate expression of mexXY in a fashion similar to upregulation by LBM415 or by ribosome inhibitory compounds. Transcriptional profiling and/or mexX::lux promoter fusion analysis revealed that fmt and folD mutants were strongly upregulated for mexXY and another gene known to be required for upregulation of the pump, PA5471. Complementation of the fmt mutation in trans reversed this constitutive expression. This supports the notion that MexXY has a natural physiological function responding to impairment of ribosome function or protein synthesis and that fmt mutation (Fmt bypass) and folD mutation generate the intracellular mexXY-inducing signal.

Restriction factors are cellular proteins that inhibit viruses at different steps of their replication cycle and represent an important first line of defense against viral pathogens. This SnapShot provides an overview of cell-intrinsic antiviral factors, describes their properties, and illustrates the striking variety of antiviral mechanisms as well the sophisticated viral countermeasures. To view this SnapShot, open or download the PDF.

Circadian clocks synchronize to the solar day by sensing the diurnal changes in light and temperature. In adult Drosophila, the brain clock that controls rest-activity rhythms relies on neurons showing Period oscillations. Nine of these neurons are present in each larval brain hemisphere. They can receive light inputs through Cryptochrome (CRY) and the visual system, but temperature input pathways are unknown. Here, we investigate how the larval clock network responds to light and temperature. We focused on the CRY-negative dorsal neurons (DN2s), in which light-dark (LD) cycles set molecular oscillations almost in antiphase to all other clock neurons. We first showed that the phasing of the DN2s in LD depends on the pigment-dispersing factor (PDF) neuropeptide in four lateral neurons (LNs), and on the PDF receptor in the DN2s. In the absence of PDF signaling, these cells appear blind, but still synchronize to temperature cycles. Period oscillations in the DN2s were stronger in thermocycles than in LD, but with a very similar phase. Conversely, the oscillations of LNs were weaker in thermocycles than in LD, and were phase-shifted in synchrony with the DN2s, whereas the phase of the three other clock neurons was advanced by a few hours. In the absence of any other functional clock neurons, the PDF-positive LNs were entrained by LD cycles but not by temperature cycles. Our results show that the larval clock neurons respond very differently to light and temperature, and strongly suggest that the CRY-negative DN2s play a prominent role in the temperature entrainment of the network.

A previously developed method for efficiently simulating complex networks of integrate-and-fire neurons was specialized to the case in which the neurons have fast unitary postsynaptic conductances. However, inhibitory synaptic conductances are often slower than excitatory ones for cortical neurons, and this difference can have a profound effect on network dynamics that cannot be captured with neurons that have only fast synapses. We thus extend the model to include slow inhibitory synapses. In this model, neurons are grouped into large populations of similar neurons. For each population, we calculate the evolution of a probability density function (PDF), which describes the distribution of neurons over state-space. The population firing rate is given by the flux of probability across the threshold voltage for firing an action potential. In the case of fast synaptic conductances, the PDF was one-dimensional, as the state of a neuron was completely determined by its transmembrane voltage. An exact extension to slow inhibitory synapses increases the dimension of the PDF to two or three, as the state of a neuron now includes the state of its inhibitory synaptic conductance. However, by assuming that the expected value of a neuron's inhibitory conductance is independent of its voltage, we derive a reduction to a one-dimensional PDF and avoid increasing the computational complexity of the problem. We demonstrate that although this assumption is not strictly valid, the results of the reduced model are surprisingly accurate.

In imaging tasks where the observer is uncertain whether lesions are present, and where they could be present, the image is searched for lesions. In the free-response paradigm, which closely reflects this task, the observer provides data in the form of a variable number of mark-rating pairs per image. In a companion paper a statistical model of visual search has been proposed that has parameters characterizing the perceived lesion signal-to-noise ratio, the ability of the observer to avoid marking non-lesion locations, and the ability of the observer to find lesions. The aim of this work is to relate the search model parameters to receiver operating characteristic (ROC) curves that would result if the observer reported the rating of the most suspicious finding on an image as the overall rating. Also presented are the probability density functions (pdfs) of the underlying latent decision variables corresponding to the highest rating for normal and abnormal images. The search-model-predicted ROC curves are 'proper' in the sense of never crossing the chance diagonal and the slope is monotonically changing. They also have the interesting property of not allowing the observer to move the operating point continuously from the origin to (1, 1). For certain choices of parameters the operating points are predicted to be clustered near the initial steep region of the curve, as has been observed by other investigators. The pdfs are non-Gaussians, markedly so for the abnormal images and for certain choices of parameter values, and provide an explanation for the well-known observation that experimental ROC data generally imply a wider pdf for abnormal images than for normal images. Some features of search-model-predicted ROC curves and pdfs resemble those predicted by the contaminated binormal model, but there are significant differences. The search model appears to provide physical explanations for several aspects of experimental ROC curves.