Visual organs perceive environmental stimuli required for rapid initiation of behaviors and can also entrain the circadian clock. The larval eye of Drosophila is capable of both functions. Each eye contains only 12 photoreceptors (PRs), which can be subdivided into two subtypes. Four PRs express blue-sensitive rhodopsin5 (rh5) and eight express green-sensitive rhodopsin6 (rh6). We found that either PR-subtype is sufficient to entrain the molecular clock by light, while only the Rh5-PR subtype is essential for light avoidance. Acetylcholine (ACh) released from PRs confers both functions. Both subtypes of larval PRs innervate the main circadian pacemaker neurons of the larva, the PDF-expressing lateral neurons (LNs), providing sensory input to control circadian rhythms. However, we show that PDF-expressing LNs are dispensable for light avoidance, and a distinct set of three clock neurons is required. Thus we have identified distinct sensory and central circuitry regulating light avoidance behavior and clock entrainment. Our findings provide insights into the coding of sensory information for distinct behavioral functions and the underlying molecular and neuronal circuitry.

Extensive mats of Fe oxyhydroxides and associated Fe-oxidizing microbial organisms form in diverse geochemical settings – freshwater seeps to deep-sea vents – where ever opposing Fe(II)-oxygen gradients prevail. The mineralogy, reactivity, and structural transformations of Fe oxyhydroxides precipitated from submarine hydrothermal fluids within microbial mats remains elusive in active and fossil systems. In response, a study of Fe microbial mat formation at the Loihi Seamount was conducted to describe the physical and chemical characteristics of Fe-phases using extended X-ray absorption fine structure spectroscopy, powder X-ray diffraction, synchrotron radiation X-ray total scattering, low-temperature magnetic measurements, and Mössbauer spectroscopy. Particle sizes of 3.5–4.6 nm were estimated from magnetism data, and coherent scattering domain (CSD) sizes as small as 1.6 nm are indicated by pair distribution function (PDF) analysis. Disorder in the nanostructured Fe-bearing phases results in limited intermediate-range structural order: less than that of standard two-line ferrihydrite (Fh), except for the Pohaku site. The short-range ordered natural Fh (FhSRO) phases were stable at 4°C in the presence of oxygen for at least 1 year and during 400°C treatment. The observed stability of the FhSRO is consistent with magnetic observations that point to non-interacting nanoparticles. PDF analyses of total scattering data provide further evidence for FhSRO particles with a poorly ordered silica coating. The presence of coated particles explains the small CSD for the mat minerals...

Chlamydia trachomatis, an obligate intracellular bacterium, is a highly prevalent human pathogen. Hydroxamic-acid-based matrix metalloprotease inhibitors can effectively inhibit the pathogen both in vitro and in vivo, and have exhibited therapeutic potential. Here, we provide genome sequencing data indicating that peptide deformylase (PDF) is the sole target of the inhibitors in this organism. We further report molecular mechanisms that control chlamydial PDF (cPDF) expression and inhibition efficiency. In particular, we identify the σ66-dependent promoter that controls cPDF gene expression and demonstrate that point mutations in this promoter lead to resistance by increasing cPDF transcription. Furthermore, we show that substitution of two amino acids near the active site of the enzyme alters enzyme kinetics and protein stability.

To achieve optimal PET image reconstruction through better system modeling, we developed a system matrix that is based on the probability density function for each line of response (LOR-PDF). The LOR-PDFs are grouped by LOR-to-detector incident angles to form a highly compact system matrix. The system matrix was implemented in the MOLAR list mode reconstruction algorithm for a small animal PET scanner. The impact of LOR-PDF on reconstructed image quality was assessed qualitatively as well as quantitatively in terms of contrast recovery coefficient (CRC) and coefficient of variance (COV), and its performance was compared with a fixed Gaussian (iso-Gaussian) line spread function. The LOR-PDFs of 3 coincidence signal emitting sources, 1) ideal positron emitter that emits perfect back-to-back γ rays (γγ) in air; 2) fluorine-18 (18F) nuclide in water; and 3) oxygen-15 (15O) nuclide in water, were derived, and assessed with simulated and experimental phantom data.

In this response, we discuss the major differences that clearly distinguish our results from those mentioned by Faust et al. In particular, the experiments have been conducted on nanoparticles of different nature, what mainly explains the observed discrepancies. This is a reply to http://www.particleandfibretoxicology.com/content/pdf/1743-8977-9-39.pdf.

Modeling of cancer hazards at age t deals with a dichotomous population, a small part of which (the fraction at risk) will get cancer, while the other part will not. Therefore, we conditioned the hazard function, h(t), the probability density function (pdf), f(t), and the survival function, S(t), on frailty α in individuals. Assuming α has the Bernoulli distribution, we obtained equations relating the unconditional (population level) hazard function, hU(t), cumulative hazard function, HU(t), and overall cumulative hazard, H0, with the h(t), f(t), and S(t) for individuals from the fraction at risk. Computing procedures for estimating h(t), f(t), and S(t) were developed and used to fit the pancreatic cancer data collected by SEER9 registries from 1975 through 2004 with the Weibull pdf suggested by the Armitage-Doll model. The parameters of the obtained excellent fit suggest that age of pancreatic cancer presentation has a time shift about 17 years and five mutations are needed for pancreatic cells to become malignant.

We present an information theoretic approach to define the problem of structure from motion (SfM) as a blind source separation one. Given that for almost all practical joint densities of shape points, the marginal densities are non-Gaussian, we show how higher-order statistics can be used to provide improvements in shape estimates over the methods of factorization via Singular Value Decomposition (SVD), bundle adjustment and Bayesian approaches. Previous techniques have either explicitly or implicitly used only second-order statistics in models of shape or noise. A further advantage of viewing SfM as a blind source problem is that it easily allows for the inclusion of noise and shape models, resulting in Maximum Likelihood (ML) or Maximum a Posteriori (MAP) shape and motion estimates. A key result is that the blind source separation approach has the ability to recover the motion and shape matrices without the need to explicitly know the motion or shape pdf. We demonstrate that it suffices to know whether the pdf is sub-or super-Gaussian (i.e., semi-parametric estimation) and derive a simple formulation to determine this from the data. We provide extensive experimental results on synthetic and real tracked points in order to quantify the improvement obtained from this technique.

Animals undergo periods of behavioral quiescence and arousal in response to environmental, circadian, or developmental cues. During larval molts, C. elegans undergoes a period of profound behavioral quiescence termed lethargus. Locomotion quiescence during lethargus was abolished in mutants lacking a neuropeptide receptor (NPR-1), and was reduced in mutants lacking NPR-1 ligands (FLP-18 and -21). Wild type strains are polymorphic for the npr-1 gene, and their lethargus behavior varies correspondingly. Locomotion quiescence and arousal were mediated by decreased and increased secretion of an arousal neuropeptide (PDF-1) from central neurons. PDF receptors (PDFR-1) expressed in peripheral mechanosensory neurons enhanced touch-evoked calcium transients. Thus, a central circuit stimulates arousal from lethargus by enhancing the sensitivity of peripheral mechanosensory neurons in the body. These results define a circuit mechanism controlling a developmentally programmed form of quiescence.

Inhibitors of peptide deformylase (PDF) represent a new class of antibacterial agents with a novel mechanism of action. Mutations that inactivate formyl methionyl transferase (FMT), the enzyme that formylates initiator methionyl-tRNA, lead to an alternative initiation of protein synthesis that does not require deformylation and are the predominant cause of resistance to PDF inhibitors in Staphylococcus aureus. Here, we report that loss-of-function mutations in FMT impart pleiotropic effects that include a reduced growth rate, a nonhemolytic phenotype, and a drastic reduction in production of multiple extracellular proteins, including key virulence factors, such as α-hemolysin and Panton-Valentine leukocidin (PVL), that have been associated with S. aureus pathogenicity. Consequently, S. aureus FMT mutants are greatly attenuated in neutropenic and nonneutropenic murine pyelonephritis infection models and show very high survival rates compared with wild-type S. aureus. These newly discovered effects on extracellular virulence factor production demonstrate that FMT-null mutants have a more severe fitness cost than previously anticipated, leading to a substantial loss of pathogenicity and a restricted ability to produce an invasive infection.

A barrier to dissemination of research is that it depends on the end-user searching for or ‘pulling’ relevant knowledge from the literature base. Social media instead ‘pushes’ relevant knowledge straight to the end-user, via blogs and sites such as Facebook and Twitter. That social media is very effective at improving dissemination seems well accepted, but, remarkably, there is no evidence to support this claim. We aimed to quantify the impact of social media release on views and downloads of articles in the clinical pain sciences. Sixteen PLOS ONE articles were blogged and released via Facebook, Twitter, LinkedIn and ResearchBlogging.org on one of two randomly selected dates. The other date served as a control. The primary outcomes were the rate of HTML views and PDF downloads of the article, over a seven-day period. The critical result was an increase in both outcome variables in the week after the blog post and social media release. The mean ± SD rate of HTML views in the week after the social media release was 18±18 per day, whereas the rate during the other three weeks was no more than 6±3 per day. The mean ± SD rate of PDF downloads in the week after the social media release was 4±4 per day, whereas the rate during the other three weeks was less than 1±1 per day (p<0.05 for all comparisons). However...

The behavior of seismicity in the area candidate to suffer a main shock is investigated after the observation of the Seismic Electric Signal activity until the impending main shock. This is based on the view that the occurrence of earthquakes is a critical phenomenon to which statistical dynamics may be applied. In the present work, analysing the time series of small earthquakes, the concept of natural time χ was used and the results revealed that the approach to criticality itself can be manifested by the probability density function (PDF) of κ1 calculated over an appropriate statistical ensemble. Here, κ1 is the variance κ1(= 〈χ2〉 − 〈χ〉2) resulting from the power spectrum of a function defined as Φ(ω)=∑k=1Npkexp(iωχk), where pk is the normalized energy of the k-th small earthquake and ω the natural frequency. This PDF exhibits a maximum at κ1 ≈ 0.070 a few days before the main shock. Examples are presented, referring to the magnitude 6∼7 class earthquakes that occurred in Greece.

This work builds on a suite of studies related to the ‘interplay’, or lack thereof, for respiratory motion with helical tomotherapy (HT). It helps explain why HT treatments without active motion management had clinical outcomes that matched positive expectations. An analytical calculation is performed to illuminate the frequency range for which interplay-type dose errors could occur. Then, an experiment is performed which completes a suite of tests. The experiment shows the potential for a stable motion probability distribution function (PDF) with HT and respiratory motion. This PDF enables one to use a motion-robust or probabilistic optimization to intrinsically include respiratory motion into the treatment planning. The reason why HT is robust to respiratory motion is related to the beam modulation sampling of the tumor motion. Because active tracking-based motion management is more complicated for a variety of reasons, HT optimization that is robust to motion is a useful alternative for those many patients that cannot benefit from active motion management.

Current guidelines for air sampling for bacteria and fungi in compounding pharmacies require the use of a medium for each type of organism. U.S. Pharmacopeia (USP) chapter <797> (http://www.pbm.va.gov/linksotherresources/docs/USP797PharmaceuticalCompoundingSterileCompounding.pdf) calls for tryptic soy agar with polysorbate and lecithin (TSApl) for bacteria and malt extract agar (MEA) for fungi. In contrast, the Controlled Environment Testing Association (CETA), the professional organization for individuals who certify hoods and clean rooms, states in its 2012 certification application guide (http://www.cetainternational.org/reference/CAG-009v3.pdf?sid=1267) that a single-plate method is acceptable, implying that it is not always necessary to use an additional medium specifically for fungi. In this study, we reviewed 5.5 years of data from our laboratory to determine the utility of TSApl versus yeast malt extract agar (YMEA) for the isolation of fungi. Our findings, from 2,073 air samples obtained from compounding pharmacies, demonstrated that the YMEA yielded >2.5 times more fungal isolates than TSApl.

Amlodipine besilate, a calcium channel antagonist, exists in several solid forms. Processing of anhydrate and dihydrate forms of this drug may lead to solid state changes, and is therefore the focus of this study. Milling was performed for the anhydrate form, whereas the dihydrate form was subjected to quench cooling thereby creating an amorphous form of the drug from both starting materials. The milled and quench cooled samples were, together with the crystalline starting materials, analyzed with X-ray powder diffraction (XRPD), Raman spectroscopy and atomic pair-wise distribution function (PDF) analysis of the XRPD pattern. When compared to XRPD and Raman spectroscopy, the PDF analysis was superior in displaying the difference between the amorphous samples prepared by milling and quench cooling approaches of the two starting materials.

A 74-yr-old woman presented with fever and abdominal discomfort. She was in a septic condition caused by urinary tract infection. Her computed tomogram of the abdomen revealed features of hydronephrosis with ureteral stones in both kidneys. During percutaneous nephrostomies, right pyeloduodenal fistula (PDF) was diagnosed. Elective surgery was originally planned but the patient was in a poor condition to undergo surgery. Instead, 2 times endoscopic clipping and ligation by endoloop were applied with parenteral antibiotics for the fistula lesion. On admission day 30, she was discharged from the hospital after confirmation of no more contrast leakage on fistulography. We reviewed the literature and discuss the etiologies, clinical presentations, diagnosis, and treatment of PDF.

Most organisms use 24-hr circadian clocks to keep temporal order and anticipate daily environmental changes. In Drosophila melanogaster CLOCK (CLK) and CYCLE (CYC) initiates the circadian system by promoting rhythmic transcription of hundreds of genes. However, it is still not clear whether high amplitude transcriptional oscillations are essential for circadian timekeeping. In order to address this issue, we generated flies in which the amplitude of CLK-driven transcription can be reduced partially (approx. 60%) or strongly (90%) without affecting the average levels of CLK-target genes. The impaired transcriptional oscillations lead to low amplitude protein oscillations that were not sufficient to drive outputs of peripheral oscillators. However, circadian rhythms in locomotor activity were resistant to partial reduction in transcriptional and protein oscillations. We found that the resilience of the brain oscillator is depending on the neuronal communication among circadian neurons in the brain. Indeed, the capacity of the brain oscillator to overcome low amplitude transcriptional oscillations depends on the action of the neuropeptide PDF and on the pdf-expressing cells having equal or higher amplitude of molecular rhythms than the rest of the circadian neuronal groups in the fly brain. Therefore...

Through the wind velocity and direction monitoring system installed on Jiubao Bridge of Qiantang River, Hangzhou city, Zhejiang province, China, a full range of wind velocity and direction data was collected during typhoon HAIKUI in 2012. Based on these data, it was found that, at higher observed elevation, turbulence intensity is lower, and the variation tendency of longitudinal and lateral turbulence intensities with mean wind speeds is basically the same. Gust factor goes higher with increasing mean wind speed, and the change rate obviously decreases as wind speed goes down and an inconspicuous increase occurs when wind speed is high. The change of peak factor is inconspicuous with increasing time and mean wind speed. The probability density function (PDF) of fluctuating wind speed follows Gaussian distribution. Turbulence integral scale increases with mean wind speed, and its PDF does not follow Gaussian distribution. The power spectrum of observation fluctuating velocity is in accordance with Von Karman spectrum.

Fibrosis is a significant health problem associated with a chronic inflammatory reaction. The precise mechanisms involved in the fibrotic process are still poorly understood. However, given that inflammation is a major causative factor, immunomodulation is a possible therapeutic approach to reduce fibrosis. The vitamin D receptor (VDR) that is present in all hematopoietic cells has been associated with immunomodulation. We investigated whether the intraperitoneal administration of paricalcitol, a specific activator of the VDR, modulates peritoneal dialysis fluid (PDF)-induced peritoneal fibrosis. We characterized the inflammatory process in the peritoneal cavity of mice treated or not treated with paricalcitol and analyzed the ensuing fibrosis. The treatment reduced peritoneal IL-17 levels, which strongly correlated with a significantly lower peritoneal fibrotic response. In vitro studies demonstrate that both CD4+ and CD8+ regulatory T cells appear to impact the regulation of IL-17. Paricalcitol treatment resulted in a significantly increased frequency of CD8+ T cells showing a regulatory phenotype. The frequency of CD4+ Tregs tends to be increased, but it did not achieve statistical significance. However, paricalcitol treatment increased the number of CD4+ and CD8+ Treg cells in vivo. In conclusion...

We present LO, NLO and NNLO sets of parton distribution functions (PDFs) of the proton determined from global analyses of the available hard scattering data. These MMHT2014 PDFs supersede the ‘MSTW2008’ parton sets, but they are obtained within the same basic framework. We include a variety of new data sets, from the LHC, updated Tevatron data and the HERA combined H1 and ZEUS data on the total and charm structure functions. We also improve the theoretical framework of the previous analysis. These new PDFs are compared to the ‘MSTW2008’ parton sets. In most cases the PDFs, and the predictions, are within one standard deviation of those of MSTW2008. The major changes are the documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} egin{document}$$u-d$$end{document}u-d valence quark difference at small documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} egin{document}$$x$$end{document}x due to an improved parameterisation and...

Despite an established link between epilepsy and sleep behavior, it remains unclear how specific epileptogenic mutations affect sleep and subsequently influence seizure susceptibility. Recently, Sun et al. (2012) created a fly knock-in model of human generalized epilepsy with febrile seizures plus (GEFS+), a wide-spectrum disorder characterized by fever-associated seizing in childhood and lifelong affliction. GEFS+ flies carry a disease-causing mutation in their voltage-gated sodium channel (VGSC) gene and display semidominant heat-induced seizing, likely due to reduced GABAergic inhibitory activity at high temperature. Here, we show that at room temperature the GEFS+ mutation dominantly modifies sleep, with mutants exhibiting rapid sleep onset at dusk and increased nighttime sleep as compared to controls. These characteristics of GEFS+ sleep were observed regardless of sex, mating status, and genetic background. GEFS+ mutant sleep phenotypes were more resistant to pharmacologic reduction of GABA transmission by carbamazepine (CBZ) than controls, and were mitigated by reducing GABAA receptor expression specifically in wake-promoting pigment dispersing factor (PDF) neurons. These findings are consistent with increased GABAergic transmission to PDF neurons being mainly responsible for the enhanced nighttime sleep of GEFS+ mutants. Additionally...