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Clostridioides difficile infection (CDI) causes significant morbidity and mortality; however, the diagnosis of CDI remains controversial. The primary aim of our study was to evaluate the association of polymerase chain reaction (PCR) cycle threshold (Ct) values with CDI disease severity, recurrence, and mortality among adult patients with CDI.
Retrospective cohort study.
Single tertiary-care hospital.
Adult patients diagnosed with hospital-onset, healthcare facility–associated CDI from June 2014 to September 2015.
We performed a retrospective chart review of included patients. Univariate and multivariable logistic regression methods were used to evaluate the association between Ct values and CDI severity, 8-week recurrence, and 30-day mortality.
Among 318 included patients, 51% were male and the mean age was 62 years; ~32% of the patients developed severe CDI and 11% developed severe–complicated CDI. The 30-day all-cause mortality rate was 11% and the 8-week recurrence rate was 9.5%. The overall mean Ct value was 32.9 (range, 23–40). Multivariable analyses showed that lower values of PCR Ct were associated with increased odds of 30-day morality (odds ratio [OR] 0.83; 95% confidence interval [CI], 0.72–0.96) but were not independently associated with CDI severity (OR, 0.99; 95% CI, 0.90–1.09) or recurrence (OR, 0.88; 95% CI, 0.77–1.00).
Our findings suggest that PCR Ct values at the time of diagnosis may have a limited predictive value and utility in clinical decision making for inpatients with CDI. Larger, prospective studies across different patient populations are needed to confirm our findings.
The first demonstration of laser action in ruby was made in 1960 by T. H. Maiman of Hughes Research Laboratories, USA. Many laboratories worldwide began the search for lasers using different materials, operating at different wavelengths. In the UK, academia, industry and the central laboratories took up the challenge from the earliest days to develop these systems for a broad range of applications. This historical review looks at the contribution the UK has made to the advancement of the technology, the development of systems and components and their exploitation over the last 60 years.
This is the first report on the association between trauma exposure and depression from the Advancing Understanding of RecOvery afteR traumA(AURORA) multisite longitudinal study of adverse post-traumatic neuropsychiatric sequelae (APNS) among participants seeking emergency department (ED) treatment in the aftermath of a traumatic life experience.
We focus on participants presenting at EDs after a motor vehicle collision (MVC), which characterizes most AURORA participants, and examine associations of participant socio-demographics and MVC characteristics with 8-week depression as mediated through peritraumatic symptoms and 2-week depression.
Eight-week depression prevalence was relatively high (27.8%) and associated with several MVC characteristics (being passenger v. driver; injuries to other people). Peritraumatic distress was associated with 2-week but not 8-week depression. Most of these associations held when controlling for peritraumatic symptoms and, to a lesser degree, depressive symptoms at 2-weeks post-trauma.
These observations, coupled with substantial variation in the relative strength of the mediating pathways across predictors, raises the possibility of diverse and potentially complex underlying biological and psychological processes that remain to be elucidated in more in-depth analyses of the rich and evolving AURORA database to find new targets for intervention and new tools for risk-based stratification following trauma exposure.
Fast pixelated detectors incorporating direct electron detection (DED) technology are increasingly being regarded as universal detectors for scanning transmission electron microscopy (STEM), capable of imaging under multiple modes of operation. However, several issues remain around the post-acquisition processing and visualization of the often very large multidimensional STEM datasets produced by them. We discuss these issues and present open source software libraries to enable efficient processing and visualization of such datasets. Throughout, we provide examples of the analysis methodologies presented, utilizing data from a 256 × 256 pixel Medipix3 hybrid DED detector, with a particular focus on the STEM characterization of the structural properties of materials. These include the techniques of virtual detector imaging; higher-order Laue zone analysis; nanobeam electron diffraction; and scanning precession electron diffraction. In the latter, we demonstrate a nanoscale lattice parameter mapping with a fractional precision ≤6 × 10−4 (0.06%).
We report on the successful demonstration of a 150 J nanosecond pulsed cryogenic gas cooled, diode-pumped multi-slab Yb:YAG laser operating at 1 Hz. To the best of our knowledge, this is the highest energy ever recorded for a diode-pumped laser system.
Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84–88) presented a critique of our recently published paper in Cell Reports entitled ‘Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets’ (Lam et al., Cell Reports, Vol. 21, 2017, 2597–2613). Specifically, Hill offered several interrelated comments suggesting potential problems with our use of a new analytic method called Multi-Trait Analysis of GWAS (MTAG) (Turley et al., Nature Genetics, Vol. 50, 2018, 229–237). In this brief article, we respond to each of these concerns. Using empirical data, we conclude that our MTAG results do not suffer from ‘inflation in the FDR [false discovery rate]’, as suggested by Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84–88), and are not ‘more relevant to the genetic contributions to education than they are to the genetic contributions to intelligence’.
OBJECTIVES/SPECIFIC AIMS: The purpose of the present secondary data analysis was to examine the effect of moderate-severe disturbed sleep before the start of radiation therapy (RT) on subsequent RT-induced pain. METHODS/STUDY POPULATION: Analyses were performed on 676 RT-naïve breast cancer patients (mean age 58, 100% female) scheduled to receive RT from a previously completed nationwide, multicenter, phase II randomized controlled trial examining the efficacy of oral curcumin on radiation dermatitis severity. The trial was conducted at 21 community oncology practices throughout the US affiliated with the University of Rochester Cancer Center NCI’s Community Oncology Research Program (URCC NCORP) Research Base. Sleep disturbance was assessed using a single item question from the modified MD Anderson Symptom Inventory (SI) on a 0–10 scale, with higher scores indicating greater sleep disturbance. Total subjective pain as well as the subdomains of pain (sensory, affective, and perceived) were assessed by the short-form McGill Pain Questionnaire. Pain at treatment site (pain-Tx) was also assessed using a single item question from the SI. These assessments were included for pre-RT (baseline) and post-RT. For the present analyses, patients were dichotomized into 2 groups: those who had moderate-severe disturbed sleep at baseline (score≥4 on the SI; n=101) Versus those who had mild or no disturbed sleep (control group; score=0–3 on the SI; n=575). RESULTS/ANTICIPATED RESULTS: Prior to the start of RT, breast cancer patients with moderate-severe disturbed sleep at baseline were younger, less likely to have had lumpectomy or partial mastectomy while more likely to have had total mastectomy and chemotherapy, more likely to be on sleep, anti-anxiety/depression, and prescription pain medications, and more likely to suffer from depression or anxiety disorder than the control group (all p’s≤0.02). Spearman rank correlations showed that changes in sleep disturbance from baseline to post-RT were significantly correlated with concurrent changes in total pain (r=0.38; p<0.001), sensory pain (r=0.35; p<0.001), affective pain (r=0.21; p<0.001), perceived pain intensity (r=0.37; p<0.001), and pain-Tx (r=0.35; p<0.001). In total, 92% of patients with moderate-severe disturbed sleep at baseline reported post-RT total pain compared with 79% of patients in the control group (p=0.006). Generalized linear estimating equations, after controlling for baseline pain and other covariates (baseline fatigue and distress, age, sleep medications, anti-anxiety/depression medications, prescription pain medications, and depression or anxiety disorder), showed that patients with moderate-severe disturbed sleep at baseline had significantly higher mean values of post-RT total pain (by 39%; p=0.033), post-RT sensory pain (by 41%; p=0.046), and post-RT affective pain (by 55%; p=0.035) than the control group. Perceived pain intensity (p=0.066) and pain-Tx (p=0.086) at post-RT were not significantly different between the 2 groups. DISCUSSION/SIGNIFICANCE OF IMPACT: These findings suggest that moderate-severe disturbed sleep prior to RT is an important predictor for worsening of pain at post-RT in breast cancer patients. There could be several plausible reasons for this. Sleep disturbance, such as sleep loss and sleep continuity disturbance, could result in impaired sleep related recovery and repair of tissue damage associated with cancer and its treatment; thus, resulting in the amplification of pain. Sleep disturbance may also reduce pain tolerance threshold through increased sensitization of the central nervous system. In addition, pain and sleep disturbance may share common neuroimmunological pathways. Sleep disturbance may modulate inflammation, which in turn may contribute to increased pain. Further research is needed to confirm these findings and whether interventions targeting sleep disturbance in early phase could be potential alternate approaches to reduce pain after RT.
This chapter presents a brief overview of the spectra of the shortwave solar and longwave terrestrial radiation fields and the basic structure of atmospheres and oceans. Some general properties of the emission spectra of the Sun and the Earth are described. Their broad features are shown to be understandable from a few basic radiative transfer principles. We introduce the four basic types of matter which interact with radiation: gaseous, aqueous, particles, and surfaces. The stratified vertical structure of the bulk properties of an atmosphere or ocean are shown to be a consequence of hydrostatic balance. The vertical temperature structure of the Earth's atmosphere is shown to result mainly from radiative processes. Optical paths in stratified media are described for a general line-of-sight direction. Radiative equilibrium, the greenhouse effect, feedbacks and radiative forcing are introduced as examples of concepts to be dealt with in greater detail in Chapter 8.
The ocean's vertical temperature structure, and its variations with season are discussed as resulting from solar heating, radiative cooling, latent heat exchange, and vertical mixing of water masses of different temperature and salinity. Its optical properties are briefly described, along with ocean color. The last section prepares the reader for the notation and units used consistently throughout the book. Finally in the last section, we describe the conventions used for the various symbols which may depart from standard usage.
Parts of the Spectrum
In Table 1.1, we summarize the nomenclature attached to the various parts of the visible and infrared spectrum. The spectral variable is the wavelength. Here where c is the speed of light and ν is the frequency [s−1] or [Hz]. In the infrared (IR), is usually expressed in micrometers (where 1). In the ultraviolet (UV) and visible spectral ranges, is expressed in nanometers (1 nm = 10−9 m). A wavelength unit widely used in astrophysics and laboratory spectroscopy is the Ångström. For completeness we list both X-rays and the shorter-wavelength UV regions, even though they are not discussed in this book. A column lists the known solar variability, defined as the maximum minus minimum divided by the minimum in percentages.
We now describe several approximate methods of solution of the radiative transfer equation. Approximate methods play an important role in the subject, since they usually provide more insight than the more accurate methods: indeed, their simple mathematical forms help clarify physical aspects that are not easily discerned from the numerical output of a computer code. Another redeeming feature of approximate methods is that they are often sufficiently accurate that no further effort is necessary. Unlike some of the more sophisticated numerical techniques, these methods also yield approximations for the internal radiation field, including the source function. Of central importance is the two-stream approximation. This class of solutions has been given various names in the past (Schuster–Schwarzschild, Eddington, two-stream, diffusion approximation, two-flow analysis, etc.). In all variations of the method, the intractable integro-differential equation of radiative transfer is replaced with representations of the angular dependence of the radiation field in terms of just two functions of optical depth. These two functions obey two linear, coupled, ordinary differential equations.When the medium is homogeneous, the coefficients of these equations are constants, and analytic closed-form solutions are possible. The mathematical forms of these solutions are exponentials in optical depth, depending on the total optical depth of the medium, the single-scattering albedo, one or two moments of the scattering phase function, and the boundary radiances. Some disadvantages are that two-stream solutions maintain acceptable accuracy over a rather restricted range of the parameters; there is no useful a priori method to estimate the accuracy; and one generally needs an accurate solution to obtain a useful estimate of the accuracy.
Two-stream methods have been applied to multi-layer problems, and to the computation of photolysis and heating rates in the presence of scattering. Although computationally intensive radiative transfer schemes are capable of accuracy better than 1%, it is unlikely that the inputs to the models are nearly this accurate.
In the present era of fast computers, there is still a need for fast computational radiation algorithms (such as the two-stream method), particularly in threedimensional photochemical/dynamical models. For example, the Community Climate System Model CCSM4 uses an algorithm for shortwave radiative transfer computations based on a two-stream (Eddington) method (Gent et al., 2011).
In comparison with shortwave radiative transfer, where nonlocal effects of multiple scattering are important, longwave radiative transfer is simple because the local thermodynamic equilibrium (LTE) source function (the Planck function) is determined strictly by the local temperature and is a smooth, analytic function of wavenumber. On the other hand, it is more complicated, due to the strong dependence of the absorption coefficient on wavenumber, and its dependence on the pressure and temperature along the optical path. In §8.2–8.3 of this chapter, we concentrate on the more practical aspects of computation of atmospheric irradiances and heating rates which are important for the energy flow. IR remote sensing is not considered, as other fine references are available.
In §8.2.1, we consider the basic equations describing monochromatic transfer of radiation in a slab medium, consisting of purely absorbing (nonscattering) molecules. The necessary averaging of the irradiances over wavenumber and angle to yield quantities relevant for the energy flow poses significant computational problems. These problems are of a “mechanical” nature and have not yet been fully overcome, despite the current availability of super fast computers. Various schemes to solve this problem are discussed, including the brute-force line-by-line methods and the narrowband and widebandmodels. The IR warming (cooling) rate is derived in a wideband context, providing a convenient framework for introducing the important cooling-to-space concept. Modern correlated-k techniques are discussed briefly, and some examples of accurate cooling rates are shown.
Atmospheric particles (cloud droplets, ice particles, and aerosols) add richness and complications to the radiative transfer problem. Here, the uncertainties become greater because of the wide ranges of particle types, shapes, distributions, and optical properties. Ultimately, the problem is so complicated that statistical techniques are needed, since clouds and aerosol distributions are generally not available in the detail needed for conventional radiative transfer computations. Furthermore, even if we were capable of measuring the entire microphysical structure of a particle ensemble, it would change with time, and furthermore would strain even today's computational resources. Nevertheless, classical descriptions of clouds in terms of plane-parallel entities embrace a significant portion of the effects of clouds on climate. Thus we confine our attention to these abstractions of nonexistent (but useful) scenarios. Weighting the clear-sky and cloudy scenarios by the cloud “fractional coverage” is a useful device in constructing 1D models of climate that are still useful today, despite its apparently crude nature.
Two problems in atmospheric and environmental science have received much attention: the occurrence of widespread ozone depletion and global warming. Ozone depletion has been related directly to the release of man-made trace gases, notably chlorofluorocarbons used in the refrigeration industry and as “propellants” in spray cans. Since ozone provides an effective shield against damaging ultraviolet radiation from the Sun, there is indeed good reason to be concerned, because a thinning of the ozone layer has serious biological ramifications. The most harmful ultraviolet (UV) radiation reaching the Earth's surface, commonly referred as UV-B radiation, lies in the wavelength range between 280 and 320 nm (see Table 1.1). UV-B radiation, which has enough energy to damage the DNA molecule, is strongly absorbed by ozone. Radiation with wavelengths between 320 and 400 nm, referred to as UVA radiation, is relatively little affected by ozone. UV-A radiation can mitigate some of the damage inflicted by UV-B radiation (a phenomenon known as photo-repair), but it causes sunburn and is therefore believed to be a partial cause of skin cancer. In addition to the harmful effects on humans, too much UV radiation has deleterious effects on terrestrial animals and plants, as well as aquatic life forms.
Ozone is a trace gas, whose bulk content resides in the stratosphere. Its abundance is determined by a balance between production and loss processes. Chemical reactions as well as photolysis are responsible for the destruction of atmospheric ozone. Its formation in the stratosphere relies on the availability of atomic oxygen, which is produced by photodissociation of molecular oxygen. Ozone is then formed when an oxygen atom (O) and an oxygen molecule (O2) combine to yield O3. It is produced mainly high in the atmosphere at low latitudes where light is abundant, and subsequently transported to higher latitudes by the equator-to-pole circulation (Brasseur and Solomon, 2006). Thus, the distribution of ozone in the atmosphere, vertically and globally, is a result of a subtle interplay between radiation, chemistry, and dynamics.
Ozone absorbs ultraviolet/visible radiation as well as thermal infrared (terrestrial) radiation in the 9.6 μm band. A thinning of the ozone layer renders the stratosphere more transparent in the 9.6 μm region, thereby allowing more transmission, and less surface backwarming.
In this chapter, we further refine the mathematical description of the radiative transfer process. We will find that it is as important to be able to set up a problem correctly as it is to solve it. Experience has shown that an investment of attention at the “front-end” is well rewarded when it comes time to submit the problem to analytic or numerical solutions. To quote Einstein and Infeld (1966, page 92):
The formulation of a problem is often more essential than its solution, which may be merely a matter of mathematical or experimental skill.
For example, some applications aremore amenable to an integral-equation approach. In other cases, a transformation can convert a problem which might involve hundreds of terms in the expansion of the scattering phase function, to one involving just a few terms. Also, in scattering problems it is usually advisable to separate the direct solar component from the diffuse component. Finally, we will introduce several prototype problems, which are invaluable as tools for learning various solution techniques. Since accurate solutions to these problems are readily available, they provide a practical means of testing numerical techniques which can then be applied to more realistic problems.
Separation into Diffuse and Direct (Solar) Components
There are two distinctly different components of the shortwave radiation field. The first one is the direct or solar component Iνs, which is that part of the solar radiation field which has survived extinction, that is,
This part is sometimes called the “uncollided” component. The second part of the radiation is the diffuse component Iνd, which consists of light that has been scattered at least once. This part is also called the multiple-scattering component, which may be thought of as the medium's “self-illumination.” A particular volume element of the medium can be said to be illuminated by two sources: by the Sun and by the rest of the medium (including the planetary surface or the bottom of the ocean).
In the next two chapters, we will study the physical basis for the three types of light-matter interactions which are important in planetary media – scattering, absorption, and emission. In this chapter, we concentrate on scattering, which may be thought of as the “first step” in both the emission and absorption processes. The classical concept of the Lorentz atom is first used to visualize the process of scattering, which encompasses both coherent processes, such as refraction and reflection, as well as the many incoherent processes which are the main topic of this chapter.
Consideration of the classical interaction of a plane wave with an isolated, damped, simple harmonic oscillator helps to introduce the concept of the cross section. The scattering cross section is expressed in terms of the frequency of the incident light, the natural frequency of the oscillator, and the damping rate. A simple extension of the concept is then made to scattering involving excited quantum states. This approach also helps to understand three different scattering processes (Rayleigh, resonance, and Thomson scattering) using one unified description. It also gives the Lorentz profile for absorption in terms of the classical damping rate, which apart from a numerical constant agrees with the quantum mechanical result. This approach also allows for a description of the two principal mechanisms responsible for broadening of absorption lines in realistic molecular media: pressure broadening and Doppler broadening.
Radiation interacts with matter in three different ways: emission, absorption, and scattering. We first contrast these three interactions in terms of their energy conversions between internal energy states of matter, EI (which includes kinetic energy of motion), and radiative energy, ER. It is convenient to consider monochromatic radiation. Emission converts internal energy to radiative energy. Absorption converts radiative energy to internal energy. Scattering is a “double-conversion”, where the radiative energy is first absorbed by matter and then radiated. Thus, the radiated field is generally modified in frequency, direction of propagation, and polarization relative to the absorbed field.
Some general relationships between these interactions follow from the energy-conversion viewpoint. For example, emission and absorption appear to be inverse processes.
In this book, we are mostly concerned with the flow of radiative energy through atmospheres and oceans. We will ignore polarization effects, which means that we disregard the Q, U, and V components of the Stokes vector, and consider only the first, radiance, component denoted by I. This approach is known as the scalar approximation, in contrast to the more accurate vector description. In general, this approximation is valid for longwave radiation where thermal emission and absorption dominate scattering processes. However, at short wavelengths where scattering is important, the radiation is generally partially polarized. For example, polarization is a basic part of a description of scattering of sunlight in a clear atmosphere or in pure water (so-called Rayleigh scattering). Generally, a coupling occurs between the various Stokes components, and an accurate description requires the full Stokes vector representation.
In the scalar approximation the radiance plays as central a role in radiative transfer theory as the wave function does in quantum theory. Its full specification as a function of position, direction, and frequency variables conveys all of the desired information about the radiation field (except for polarization).
In this chapter, we define the basic state variable of the theory, the radiance. We first review the most basic concepts of geometrical optics, those of pencils and beams of light. We then define the various state variables in a transparent medium, involving flow of radiative energy in beams traveling in specific directions and over a hemisphere. Several theorems governing the propagation of the radiance are described. The Extinction Law is stated in both differential and integral forms. The radiative transfer equation is shown to be a consequence of extinction and the existence of radiation sources.
A brief description of our notation is in order. Radiation state variables are described in terms of both spectral (or monochromatic) quantities and frequency-integrated quantities. Frequency is measured in cycles per second or Hertz, abbreviated as [Hz]. For spectral quantities, we may visualize a small frequency interval over which all properties of the radiation and its interaction with matter are constant. A general quantity, is identified with a frequency subscript if it is defined on a per-frequency basis. If f is a function of frequency, it is written.