bluuebunny/crossref_metadata_2025 huggingface dataset:
Overview of OOI/RSN cabled ocean observatory
Authors: Denny Gerald , Harrington Michael , Manalang Dana , Kelley Deborah
Published: October 2018

The summer of 2014 saw the completion of installation and first data from the cabled portion of the Ocean Observatories Initiative (OOI) Regional Scaled Nodes (RSN). Data streams live from over 130 instruments to an OOI Data Portal via telecom cables that land in Pacific City, OR. The observatory encompasses a cross-section of the Juan de Fuca plate from the coastal shelf to an undersea volcano, with instruments from 80 m to 2900 m depth. Acoustic instrumentation includes 6 broadband hydrophones (capable of 120 kHz), 5 low frequency hydrophones (to 5 kHz), two 3-frequency upward looking fisheries sonars, and 6 upward looking ADCPs. Water-borne acoustic data have also been observed in the 5 broadband (3 mHz to 10 Hz) and 7 short-period (0.1 Hz to 100 Hz) seismometers. Two new acoustic experiments will be deployed in the 2018 O&M cruise. The raw and processed data are archived and are open access to all. An overview of the types of instruments and their locations, as well as discussion of data characteristics and how to access the data, will be given. Some examples of data will be shown as well as examples of specific event characterization and ongoing uses.
Two-dimensional high-resolution acoustic localization of distributed coherent sources for structural health monitoring
Authors: Flynn Tyler J. , Dowling David R.
Published: October 2018

Many high-resolution techniques exist for localizing acoustic sources; however, most of these methods suffer when applied to data containing spatially separated coherent signals. The Spectral Estimation Method with Additive Noise (SEMWAN) is an existing beamforming technique for high-resolution localization of incoherent monopole sources in low SNR environments. SEMWAN utilizes a reference measurement to subtract, and thereby suppress, background noise, but its performance suffers for cases involving mutually-coherent sources—such as a distributed radiating source. SEMWAN has previously been extended to one-dimensional coherent source scenarios by implementing the additional step of subarray averaging. This extra processing step reduces coherent background signatures and thereby permits localization of small acoustic changes (e.g., localized damage) provided a known baseline array recording is available. This presentation discusses the extension of this approach to two-dimensional problems using Cartesian planar arrays. Experimental results using multiple coherent sources and a remote receiver array (with varying numbers of elements and subarray geometry) at frequencies from 1.0 to 10 kHz are analyzed and compared to simulation results. Application of this technique for localization of mechanical changes in a 30-cm-square aluminum plate is also addressed. [Sponsored by NAVSEA through the NEEC and by the US DoD through an NDSEG Fellowship.]
Designing waveforms with desired ambiguity function mainlobe and sidelobe structure
Authors: Hague David A.
Published: October 2018

In active sonar, a transmit waveform’s ability to resolve closely spaced targets in range/Doppler and distinguish weak targets in the presence of a stronger one are determined by the mainlobe and sidelobe structure, respectively, of the waveform’s broadband ambiguity function (BAF). While it is often difficult to derive precise closed form expressions for the sidelobe structure, the mainlobe structure can be quite accurately modeled. The contour of the BAF’s mainlobe is well approximated by a coupled ellipse, or ellipse of ambiguity (EOA). The EOA parameters determine the mainlobe width in range and Doppler as well as the degree of range-Doppler coupling. If the waveform’s modulation function is known the EOA parameters may be calculated in closed form. The multi-tone sinusoidal frequency modulated (MTSFM) waveform possesses a modulation function that is represented using a Fourier series expansion. The coefficients are utilized as a set of tunable parameters that can be modified to synthesize waveforms with specific characteristics. This research presents closed form expressions for the MTSFM’s BAF EOA parameters. Simulations demonstrate that the EOA parameters facilitate the design of MTSFM waveforms with desirable mainlobe and sidelobe characteristics.
Ultrasonic endoscope in the form of a bundle of elastic rods for imaging in aggressive liquids
Authors: Tsysar Sergey , Petrosyan Suren , Svet Victor D. , Sapozhnikov Oleg A.
Published: October 2018

Modern ultrasonic imaging systems demonstrate high quality of the images obtained in non-aggressive media. Direct application of traditional systems under critical conditions, for example, at high temperature, in the presence of chemically active media or an increased level of radiation, is often impossible. We propose an approach based on the concept of an "ultrasound endoscope" to remotely display the area of interest through a long beam of solid rods. Each rod serves as a waveguide that carries an ultrasonic pulse from one end located in an aggressive medium to the other end located at a distance in favorable conditions. The diameter of the rods is less than half the wavelength to ensure that the ultrasonic pulses used to form the image propagate as the lowest-order longitudinal mode, which is non-dispersive and much faster than other possible modes (bending and torsional motions). The feasibility of the proposed concept is illustrated by numerical modeling and experiments. The results of studies of the 1024-channel waveguide system of megahertz range made of a bundle of stainless steel rods are presented. The obtained images of millimeter-sized scatterers in water demonstrate high resolution of the proposed system. [This work was supported by the RSF grant 17-72-10284.]
Observations of resonances and antiresonances in modal propagation over muddy sediment layer
Authors: Dall'Osto David R. , Dahl Peter H.
Published: October 2018

Measurements of signals generated over the New England mud patch, an area of ocean roughly 70 m deep characterized by a 10 m thick surficial mud-layer, by the Intensity Vector Autonomous Recorder (IVAR) are presented. IVAR is a bottom deployed system that measures both potential and kinetic energy roughly 1.2 m above the seafloor. Data originate from signals generated by a towed J15 source (transmission in the 50–500 Hz band), and signal underwater sound (SUS) MK-64 explosive sources, both part of the SCE17 signal set, and individual modes are identified by their unique Doppler shifts and/or through time-frequency analysis of dispersion. The density contrast between water and mud manifests a concentration kinetic energy in the water column, specifically when the water/mud interface intersects a node of the vertical mode functions. Following the work of Tolstoy (JASA 28(6), 1182–1192, 1956), data observations are fit to a representative sediment model through coupling two reduced waveguides, one representing the water column and the other the layered sediment, at their lattice points. The persistence of a resonance, which occurs at intersecting lattice points, is examined in terms of the range dependence in water depth and sediment structure.
Optimization of the acoustic treatments in order to achieve the Italian minimum environmental criteria (CAM) for classrooms
Authors: Berardi Umberto , Iannace Gino , Trematerra Amelia
Published: October 2018

A recent Italian legislation has established the "Minimum Environmental Criteria" (CAM) for working environments. With regard to schools, adequate acoustic comfort targets are required in terms of noise control and acoustic quality. Schools must comply with the UNI 11532 for their reverberation (T), clarity (C50) and speech intelligibility (STI). In classrooms, the following values are required: T<0.7s, C50>0dB and STI>0.6. In sports facilities such as gyms or swimming pools, the requirements are T<1.5 s, C50>-2 dB and STI>0.5. To achieve these objectives, the insertion of acoustic treatments is often unavoidable. Acousticians commonly use the perfectly diffused theory to calculate the amount of need sound-absorbing material to comply with current legislation. The purpose of this work is to evaluate the optimal position in which to place the minimum amount of sound-absorbing treatments to reach CAM. Some university classrooms are used. These classrooms have a marble floor and plastered walls and, at 1.0 kHz, have T values between 2.5s and 4.5s, C50 between 3 dB and -0.5 dB, and ST between 0.34 and 0.47. Using an acoustic software, it was possible to estimate the minimum quantity and the optimal placement of the sound-absorbing panels to insert to reach the CAM of these classrooms.
Cross-modal effects of noise and thermal conditions on indoor environmental perceptions
Authors: Yang Wonyoung , Moon Hyeun Jun , Kim Myung-Jun
Published: October 2018

Realistic thermal conditions with various humidity levels have been considered to examine cross-modal effects of noise and thermal conditions on indoor environmental perceptions. Subjective assessments of temperature, humidity and acoustics were conducted with 26 subjects under combined environments of seven thermal conditions (18°C: RH 30, 60%, 24°C: RH 27, 43, 65%, 30°C: RH 30, 60%), two noise types (fan and babble noises) and five noise levels (45, 50, 55, 60, and 65 dBA). Three-minute moderate noise exposure did not affect temperature or humidity sensations. However, temperature and humidity levels affected loudness, annoyance, and acoustic preferences. Men were more sensitive to hot sensations than women, and women were more sensitive to arid sensations than men. Women were more sensitive to noise levels than men. Gender differences were also found in terms of different types of noise. Men were found to be significantly less sensitive to fan noise than women. Even though psychoacoustic parameters were affected by indoor thermal conditions; thermal parameters were not affected by short-term moderate noise. The combined effect of various types of noise and temperature is still unclear, and this will be considered in a future larger cohort study.
Development of beluga calf calls (Delphinapterus leucas) in the first six months of life
Authors: Ames Audra , Wood Jason , Vergara Valeria
Published: October 2018

As part of an ongoing effort to understand beluga mother-calf communication and impacts of anthropogenic noise on neonate calls, we investigated a male beluga calf’s vocal development at Oceanogràfic, using a calibrated digital hydrophone with a sampling rate of 256 kHz. His initial vocalizations were broadband pulse-trains with upper frequency limits reaching ≥128 kHz on his first day of life, higher than reported by earlier studies limited by lower sampling rates. Over the calf’s first six months, pulsed trains were the predominant call type, increasing significantly in peak and first quartile frequencies and pulse repetition rate during this period. First and third quartile frequencies also increased significantly over the calf’s first month, indicating an early and continuous shift in pulse train energy distribution towards higher frequencies. While mixed and tonal calls appeared sporadically in the calf’s first month of life, they were not common until his third month, when they comprised 13% of his vocalizations. Additionally, estimated source levels of the calf’s calls increased throughout his first month, but were lower than those for adult belugas. This, coupled with the progressive shift in energy distribution, has important implications regarding a neonate’s ability to compensate for noise.
Sperm whale inter-pulse intervals and size: The anomaly called Yukusam
Authors: Turner Jesse C. , Wood Jason , Towers Jared
Published: October 2018

Yukusam is the name given to a male sperm whale who was first documented off northeastern Vancouver Island in February 2018. He spent several weeks in this area before traveling south to the inland waters of the Salish Sea in late March 2018. Sperm whale clicks have been used as a proxy to determine overall size by using the time difference of arrival between the initial noise pulse and its reflections within the spermaceti organ. Different equations have been derived in order to use this Inter-Pulse Interval (IPI) to estimate overall length. Here we use Yukusam’s usual clicks recorded from the Lime Kiln hydrophone on the west side of San Juan Island (WA State, USA) to compare IPI-based length estimates with visual observations. Photo and video documentation indicate that this whale is ~15 m in length. Our initial acoustic results indicate that equations in the literature underestimate his length by at least a few meters. The potential reasons behind these anomalies are explored in this presentation.
On an attenuation obeying a frequency power law
Authors: Buckingham Michael J.
Published: October 2018

An attenuation obeying a frequency power law scales as |ω|^β, where ω is angular frequency and β is a real constant. According to the strain-hardening shear-wave equation in the grain-shearing theory, the attenuation of the shear wave supported by a marine sediment follows a frequency power law. The associated dispersion formula, which is a causal transform, predicts that the phase speed is also a power law and that the product of the phase speed and the attenuation divided by ω is a constant, independent of frequency. From the dispersion formula, along with the conditions that the phase speed and attenuation must both be positive and the propagation factor must exhibit conjugate symmetry, it follows that the exponent β can take only certain values that fall in well-defined intervals extending indefinitely with no upper or lower limit. However, to satisfy the requirement that Green’s function be causal, β is further constrained to lie in the interval [0.5 1), under which condition the Green’s function is maximally flat at the time the source is activated. With other values of β the Green’s function is non-causal, exhibiting non-zero values at times preceding the onset of the source. [Research supported by ONR.]
Viscosity-based theory of phase velocity and attenuation of sound in mud consisting of water and flocculated clay particles
Authors: Brown Elisabeth M. , Pierce Allan D. , Siegmann William L.
Published: October 2018

Recent theory of authors ascribes attenuation in typical marine mud sediments to be caused by viscous interaction of sea water with embedded silt particles. Influence of underlying clay matrix is regarded as passive and of minor importance. Present paper considers silt-less mud where clay particles are flocculated to a card-house structure, with the flocculation hypothesis yielding a porosity of 90%. During the passage of a sound wave, Van-der-Waals forces between platelets cause the matrix to move to-and-fro as a unit; viscous forces are insufficient to cause the matrix to move perfectly with the water. The silt-less theory assumes that the local force on the matrix is the sum of the viscous forces on the platelets in the matrix. Forces on clay particles, which are thin platelets, are given by a low-Reynolds flow theory initiated by Stokes, and further developed by Oberbeck, Lamb, and Brenner. For each particle there is a characteristic frequency inversely proportional to the platelet thickness, which turns out to be extremely high for clay. Consequently, at acoustic frequencies, the clay matrix moves nearly in lock-step with the fluid motion associated with the sound wave. The inevitable very-small slip leads to an attenuation that is proportional to the square of the frequency, but which is very small compared with that of mud with embedded silt-particles. Current idealized theory results in prediction of attenuation inversely proportional to viscosity and of nearly constant phase velocity. [Work supported by ONR.]
Coherent processing of ocean ambient noise for sediment profiling and head-wave detection using a vertical line array in the Santa Barbara Channel
Authors: Muzi Lanfranco , Siderius Martin
Published: October 2018

In this study, sediment profiling using the passive fathometer and the head-wave phenomenon are investigated. Head waves are created by waves propagating in sediments parallel to the water-sediment interface (possibly at a speed higher than the water sound speed), and propagating back in the water at critical angles. Ocean ambient noise recorded by a vertical line array is processed using a generalization of the known “passive fathometer.” The technique can detect coherent time-separated arrivals at specific angles that are consistent with the propagation of head waves. The arrivals structure detected at endfire provides information on the sediment layering, while the head wave can be used to estimate the sediment sound speed, and may provide information about the attenuation. The technique is demonstrated using simulation and data from the Santa Barbara Channel Experiment of 2016, using both natural noise generated at the surface, and—for the first time—the noise generated by a ship. [Work supported by the Office of Naval Research, Ocean Acoustics Program.]
Acoustics on the roadmap for an Integrated Arctic Observing System
Authors: Sagen Hanne , Sandven Stein
Published: October 2018

The current status of the ocean in situ observing system in the Arctic are addressed in the EU funded Integrated Arctic Observation System (INTAROS). We describe how multipurpose acoustic systems can contribute to fill gaps and to establish an optimized Pan Arctic Ocean Observing System. A brief presentation of the steps from a series of experiments in the Eastern Arctic towards the upcoming pan-arctic Coordinated Arctic Acoustic Thermometry Experiment are given. How we can use this experience to ensure that multipurpose Arctic observation system will get on in roadmap for an Arctic Observing System? Any sustainable ocean observing systems in the Arctic depend on long-term funding, and that funding mechanisms other than research programs should be used for this. To achieve this, we need to engage with stakeholder groups outside the scientific community. How can this be done?
Guided shear waves and solitons in nonlinear viscoelastic materials
Authors: Dilly Emilien F. , Coulouvrat François , Tripathi Bharat , Pinton Gianmarco
Published: October 2018

The nonlinear propagation of elastic waves in soft solids, such as gelatin or brain, can easily give rise to shocks. Previous experimental and theoretical studies have described planar, focused, one dimensional, two dimensional polarized shear wave propagation in these media, as well as acoustic non linear propagation in wave guides. Here we present the behavior of guided shear waves in solid plates. A model based on a quasi-modal wave decomposition is described as well as a Fourier-based numerical solution that takes into account nonlinear, attenuating, dispersive, guided propagation. A mixed conventional time-space and Fourier domain numerical method is used to determine harmonic generation with propagation. These numerical solutions are validated by a comparison with experimental data for plane waves in gelatin and brain. It is then shown how the nonlinearity and dispersion due to the guiding geometry can act together to assist the formation of shocks. The model also predicts, similarly to fiber optics physics, that nonlinearity can give rise to a self phase modulation, which under specific conditions can be compensated by the dispersion resulting from the waveguide. It is shown that the model therefore predicts the existence of solitons -both theoretically and numerically.
Reflection of finite amplitude acoustic wave from a vapor-liquid interface
Authors: Yano Takeru
Published: October 2018

We numerically investigate the reflection of finite amplitude acoustic wave from a vapor-liquid interface and resulting evaporation or condensation flow induced by the reflected wave on the basis of the kinetic theory of gases. As an initial condition, we consider the finite amplitude plane acoustic wave propagating in a vapor bounded by the liquid layer of the same molecule as the vapor. The governing equation of wave motion in the vapor is the Boltzmann-Krook-Welander equation and the boundary condition at the interface is the complete condensation condition. The Boltzmann-Krook-Welander equation is numerically solved with a finite difference method. As a result, we clarify the reflection law of finite amplitude wave at the interface, which determines an evaporation or condensation flow established after the wave reflection.
Nonlinear viscoelasticity of a dilute suspension of Brownian spheroids in oscillatory shear flow
Authors: Bechtel Toni M. , Khair Aditya S.
Published: October 2018

The nonlinear viscoelasticity of a dilute suspension of Brownian spheroids subject to an oscillatory shear deformation is calculated numerically. This is achieved by determining the suspension microstructure, parameterized via the orientation distribution function. Specifically, the long-time periodic orientation distribution function is obtained via a numerical solution to the Fokker–Planck equation by combining a finite-difference approximation in space with a Fourier series in time. From an ensemble average of the particle stresslet, weighted by the orientation distribution function, the entire stress tensor and relevant birefringence parameters, namely, the average orientation angle and linear dichroism, are calculated; this is done over a range of the Weissenberg number (Wi) and the Deborah number (De), or dimensionless strain-rate amplitude and oscillation frequency, respectively. Detailed calculations are presented for prolate spheroids of aspect ratio r=20; however, our methodology is general and can be applied to spheroids of arbitrary aspect ratio. We provide results in four viscoelastic regimes: linear viscoelastic (Wi≪1), quasilinear viscoelastic (Wi>1 and Wi/De≪1), quasisteady viscoelastic (De→0), and finally, the nonlinear viscoelastic regime (Wi ≳ 1 and Wi/De ≳ 1), which is our main emphasis. In this last regime, where the nonlinear and unsteady viscoelasticity of the material is probed, multiple overshoots are observed in the shear stress and first normal stress difference. The mechanistic origin of these overshoots can be understood from the periodic orientation dynamics (i.e., Jeffery orbits) of a particle under steady shear in the absence of Brownian rotation (Wi→∞). This is achieved by simultaneously analyzing the microstructure, shear stress, first normal stress difference, and birefringence parameters specifically at Wi=20 and De=1. For these values of Wi,De, and r, the period of a Jeffery orbit is comparable to the period of an oscillation cycle, allowing sufficient time for a single Jeffery orbit (and subsequent overshoot) to occur during an oscillation cycle. We contrast this behavior to recent work by Khair [J. Fluid. Mech. 791, R5 (2016)] on nearly spherical particles, for which many more overshoots are observed during an oscillation cycle, due to the shorter period of the Jeffery orbit. We briefly provide results for oblate spheroids of aspect ratio r=0.05 and compare to the results for r=20. Finally, we comment on the relevance of the present micro-mechanical analysis to the nonlinear viscoelasticity of other complex fluid materials.
Planet hunter nears its end
Authors: Clery Daniel
Published: October 2018

Kepler space telescope found trove of exoplanets.
Quantum internet: A vision for the road ahead
Authors: Wehner Stephanie , Elkouss David , Hanson Ronald
Published: October 2018

The stages of a quantum internet

As indispensable as the internet has become in our daily lives, it still has many shortcomings, not least of which is that communication can be intercepted and information stolen. If, however, the internet attained the capability of transmitting quantum information—qubits—many of these security concerns would be addressed. Wehner
et al.
review what it will take to achieve this so-called quantum internet and propose stages of development that each correspond to increasingly powerful applications. Although a full-blown quantum internet, with functional quantum computers as nodes connected through quantum communication channels, is still some ways away, the first long-range quantum networks are already being planned.

Science
, this issue p.
eaam9288
Realizing private and practical pharmacological collaboration
Authors: Hie Brian , Cho Hyunghoon , Berger Bonnie
Published: October 2018

Sharing pharmaceutical research

Increased collaboration will enhance our ability to predict new therapeutic drug candidates. Such data sharing is currently limited by concerns about intellectual property and competing commercial interests. Hie
et al.
introduce an end-to-end pipeline, using modern cryptographic tools, for secure pharmacological collaboration. Multiple entities can thus securely combine their private datasets to collectively obtain more accurate predictions of new drug-target interactions. The computational pipeline is practical, producing results with improved accuracy in a few days over a wide area network on a real dataset with more than a million interactions.

Science
, this issue p.
347
Well-being in metrics and policy
Authors: Graham Carol , Laffan Kate , Pinto Sergio
Published: October 2018

Well-being metrics provide key insights for economic and environmental sustainability
Clinical microbiology of coryneform bacteria
Authors: Funke G , von Graevenitz A , Clarridge J E , Bernard K A
Published: October 2018

Coryneform bacteria are aerobically growing, asporogenous, non-partially-acid-fast, gram-positive rods of irregular morphology. Within the last few years, there has been a massive increase in the number of publications related to all aspects of their clinical microbiology. Clinical microbiologists are often confronted with making identifications within this heterogeneous group as well as with considerations of the clinical significance of such isolates. This review provides comprehensive information on the identification of coryneform bacteria and outlines recent changes in taxonomy. The following genera are covered: Corynebacterium, Turicella, Arthrobacter, Brevibacterium, Dermabacter. Propionibacterium, Rothia, Exiguobacterium, Oerskovia, Cellulomonas, Sanguibacter, Microbacterium, Aureobacterium, "Corynebacterium aquaticum," Arcanobacterium, and Actinomyces. Case reports claiming disease associations of coryneform bacteria are critically reviewed. Minimal microbiological requirements for publications on disease associations of coryneform bacteria are proposed.
Current methods of laboratory diagnosis of Chlamydia trachomatis infections
Authors: Black C M
Published: October 2018

Infections caused by Chlamydia trachomatis are probably the most common sexually transmitted diseases in the United States. Commonly unrecognized and often inadequately treated, chlamydial infections can ascend the reproductive tract and cause pelvic inflammatory disease, which often results in the devastating consequences of infertility, ectopic pregnancy, or chronic pelvic pain. C. trachomatis infections are also known to increase the risk for human immunodeficiency virus infection. The obligate intracellular life cycle of C. trachomatis has traditionally required laboratory diagnostic tests that are technically demanding, labor-intensive, expensive, and difficult to access. In spite of these historical challenges, however, laboratory diagnosis of C. trachomatis has been a rapidly advancing area in which there is presently a wide array of commercial diagnostic technologies, costs, manufacturers. This review describes and compares the diagnostic methods for C. trachomatis infection that are currently approved for use in the United States, including the newest DNA amplification technologies which are yet to be licensed for commercial use. Issues to consider in selecting a test for purposes of screening versus diagnosis based on prevalence, performance, legal, social, and cost issues are also discussed.
Infections in solid-organ transplant recipients
Authors: Patel R , Paya C V
Published: October 2018

Solid-organ transplantation is a therapeutic option for many human diseases. Infections are a major complication of solid-organ transplantation. All candidates should undergo a thorough infectious-disease screening prior to transplantation. There are three time frames, influenced by surgical factors, the level of immunosuppression, and environmental exposures, during which infections of specific types most frequently occur posttransplantation. Most infections during the first month are related to surgical complications. Opportunistic infections typically occur from the second to the sixth month. During the late posttransplant period (beyond 6 months), transplantation recipients suffer from the same infections seen in the general community. Opportunistic bacterial infections seen in transplant recipients include those caused by Legionella spp., Nocardia spp., Salmonella spp., and Listeria monocytogenes. Cytomegalovirus is the most common cause of viral infections. Herpes simplex virus, varicella-zoster virus, Epstein-Barr virus and others are also significant pathogens. Fungal infections, caused by both yeasts and mycelial fungi, are associated with the highest mortality rates. Mycobacterial, pneumocystis, and parasitic diseases may also occur.
Bartonella spp. as emerging human pathogens
Authors: Anderson B E , Neuman M A
Published: October 2018

Members of the genus Bartonella (formerly Rochalimaea) were virtually unknown to modern-day clinicians and microbiologists until they were associated with opportunistic infections in AIDS patients about 6 years ago. Since that time, Bartonella species have been associated with cat scratch disease, bacillary angiomatosis, and a variety of other disease syndromes. Clinical presentation of infection with Bartonella ranges from a relatively mild lymphadenopathy with few other symptoms, seen in cat scratch disease, to life-threatening systemic disease in the immunocompromised patient. In some individuals, infection manifests as lesions that exhibit proliferation of endothelial cells and neovascularization, a pathogenic process unique to this genus of bacteria. As the spectrum of disease attributed to Bartonella is further defined, the need for reliable laboratory methods to diagnose infections caused by these unique organisms also increases. A brief summary of the clinical presentations associated with Bartonella infections is presented, and the current status of laboratory diagnosis and identification of these organisms is reviewed.
Enterobacter spp.: pathogens poised to flourish at the turn of the century
Authors: Sanders W E , Sanders C C
Published: October 2018

Knowledge of the genus Enterobacter and its role in human disease has expanded exponentially in recent years. The incidence of infection in the hospital and the community has increased. New clinical syndromes have been recognized. Enterobacter spp. have also been implicated as causes of other syndromes that traditionally have been associated almost exclusively with more easily treatable pathogens, such as group A streptococci and staphylococci. Rapid emergence of multiple-drug resistance has been documented in individual patients during therapy and in populations and environments with strong selective pressure from antimicrobial agents, especially the cephalosporins. Therapeutic options for patients infected with multiply resistant strains have become severely limited. Carbapenems or, alternatively, fluoroquinolones are the most predictively active options, although resistance to both classes has been observed on rare occasions. Enterobacter spp. appear well adapted for survival and even proliferation as the turn of the century approaches.
Relevance of nucleic acid amplification techniques for diagnosis of respiratory tract infections in the clinical laboratory
Authors: Ieven M , Goossens H
Published: October 2018

Clinical laboratories are increasingly receiving requests to perform nucleic acid amplification tests for the detection of a wide variety of infectious agents. In this paper, the efficiency of nucleic acid amplification techniques for the diagnosis of respiratory tract infections is reviewed. In general, these techniques should be applied only for the detection of microorganisms for which available diagnostic techniques are markedly insensitive or nonexistent or when turnaround times for existing tests (e.g., viral culture) are much longer than those expected with amplification. This is the case for rhinoviruses, coronaviruses, and hantaviruses causing a pulmonary syndrome, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Coxiella burnetii. For Legionella spp. and fungi, contamination originating from the environment is a limiting factor in interpretation of results, as is the difficulty in differentiating colonization and infection. Detection of these agents in urine or blood by amplification techniques remains to be evaluated. In the clinical setting, there is no need for molecular diagnostic tests for the diagnosis of Pneumocystis carinii. At present, amplification methods for Mycobacterium tuberculosis cannot replace the classical diagnostic techniques, due to their lack of sensitivity and the absence of specific internal controls for the detection of inhibitors of the reaction. Also, the results of interlaboratory comparisons are unsatisfactory. Furthermore, isolates are needed for susceptibility studies. Additional work remains to be done on sample preparation methods, comparison between different amplification methods, and analysis of results. The techniques can be useful for the rapid identification of M. tuberculosis in particular circumstances, as well as the rapid detection of most rifampin-resistant isolates. The introduction of diagnostic amplification techniques into a clinical laboratory implies a level of proficiency for excluding false-positive and false-negative results.
Nasal carriage of Staphylococcus aureus: epidemiology, underlying mechanisms, and associated risks
Authors: Kluytmans J , van Belkum A , Verbrugh H
Published: October 2018

Staphylococcus aureus has long been recognized as an important pathogen in human disease. Due to an increasing number of infections caused by methicillin-resistant S. aureus (MRSA) strains, therapy has become problematic. Therefore, prevention of staphylococcal infections has become more important. Carriage of S. aureus appears to play a key role in the epidemiology and pathogenesis of infection. The ecological niches of S. aureus are the anterior nares. In healthy subjects, over time, three patterns of carriage can be distinguished: about 20% of people are persistent carriers, 60% are intermittent carriers, and approximately 20% almost never carry S. aureus. The molecular basis of the carrier state remains to be elucidated. In patients who repeatedly puncture the skin (e.g., hemodialysis or continuous ambulatory peritoneal dialysis [CAPD] patients and intravenous drug addicts) and patients with human immunodeficiency virus (HIV) infection, increased carriage rates are found. Carriage has been identified as an important risk factor for infection in patients undergoing surgery, those on hemodialysis or CAPD, those with HIV infection and AIDS, those with intravascular devices, and those colonized with MRSA. Elimination of carriage has been found to reduce the infection rates in surgical patients and those on hemodialysis and CAPD. Elimination of carriage appears to be an attractive preventive strategy in patients at risk. Further studies are needed to optimize this strategy and to define the groups at risk.
Prospects for the development of fungal vaccines
Authors: Deepe G S
Published: October 2018

In an era that emphasizes the term "cost-effective," vaccines are the ideal solution to preventing disease at a relatively low cost to society. Much of the previous emphasis has been on childhood scourges such as measles, mumps, rubella, poliomyelitis, and Haemophilus influenzae type b. The concept of vaccines for fungal diseases has had less impact because of the perceived limited problem. However, fungal diseases have become increasingly appreciated as serious medical problems that require recognition and aggressive management. The escalation in the incidence and prevalence of infection has prompted a renewed interest in vaccine development. Herein, I discuss the most recent developments in the search for vaccines to combat fungal infections. Investigators have discovered several inert substances from various fungi that can mediate protection in animal models. The next challenge will be to find the suitable mode of delivery for these immunogens.
Uses of inorganic hypochlorite (bleach) in health-care facilities
Authors: Rutala W A , Weber D J
Published: October 2018

Hypochlorite has been used as a disinfectant for more than 100 years. It has many of the properties of an ideal disinfectant, including a broad antimicrobial activity, rapid bactericidal action, reasonable persistence in treated potable water, ease of use, solubility in water, relative stability, relative nontoxicity at use concentrations, no poisonous residuals, no color, no staining, and low cost. The active species is undissociated hypochlorous acid (HOCl). Hypochlorites are lethal to most microbes, although viruses and vegetative bacteria are more susceptible than endospore-forming bacteria, fungi, and protozoa. Activity is reduced by the presence of heavy metal ions, a biofilm, organic material, low temperature, low pH, or UV radiation. Clinical uses in health-care facilities include hyperchlorination of potable water to prevent Legionella colonization, chlorination of water distribution systems used in hemodialysis centers, cleaning of environmental surfaces, disinfection of laundry, local use to decontaminate blood spills, disinfection of equipment, decontamination of medical waste prior to disposal, and dental therapy. Despite the increasing availability of other disinfectants, hypochlorites continue to find wide use in hospitals.
Clinical and Microbiological Aspects ofTrichomonas vaginalis
Authors: Petrin Dino , Delgaty Kiera , Bhatt Renuka , Garber Gary
Published: October 2018

Trichomonas vaginalis, a parasitic protozoan, is the etiologic agent of trichomoniasis, a sexually transmitted disease (STD) of worldwide importance. Trichomoniasis is the most common nonviral STD, and it is associated with many perinatal complications, male and female genitourinary tract infections, and an increased incidence of HIV transmission. Diagnosis is difficult, since the symptoms of trichomoniasis mimic those of other STDs and detection methods lack precision. Although current treatment protocols involving nitroimidazoles are curative, metronidazole resistance is on the rise, outlining the need for research into alternative antibiotics. Vaccine development has been limited by a lack of understanding of the role of the host immune response to T. vaginalis infection. The lack of a good animal model has made it difficult to conduct standardized studies in drug and vaccine development and pathogenesis. Current work on pathogenesis has focused on the host-parasite relationship, in particular the initial events required to establish infection. These studies have illustrated that the pathogenesis of T. vaginalis is indeed very complex and involves adhesion, hemolysis, and soluble factors such as cysteine proteinases and cell-detaching factor. T. vaginalis interaction with the members of the resident vaginal flora, an advanced immune evasion strategy, and certain stress responses enable the organism to survive in its changing environment. Clearly, further research and collaboration will help elucidate these pathogenic mechanisms, and with better knowledge will come improved disease control.
CampylobacterSpecies and Guillain-Barré Syndrome
Authors: Nachamkin Irving , Allos Ban Mishu , Ho Tony
Published: October 2018

Since the eradication of polio in most parts of the world, Guillain-Barré syndrome (GBS) has become the most common cause of acute flaccid paralysis. GBS is an autoimmune disorder of the peripheral nervous system characterized by weakness, usually symmetrical, evolving over a period of several days or more. Since laboratories began to isolate Campylobacter species from stool specimens some 20 years ago, there have been many reports of GBS following Campylobacter infection. Only during the past few years has strong evidence supporting this association developed. Campylobacter infection is now known as the single most identifiable antecedent infection associated with the development of GBS. Campylobacter is thought to cause this autoimmune disease through a mechanism called molecular mimicry, whereby Campylobacter contains ganglioside-like epitopes in the lipopolysaccharide moiety that elicit autoantibodies reacting with peripheral nerve targets. Campylobacter is associated with several pathologic forms of GBS, including the demyelinating (acute inflammatory demyelinating polyneuropathy) and axonal (acute motor axonal neuropathy) forms. Different strains of Campylobacter as well as host factors likely play an important role in determining who develops GBS as well as the nerve targets for the host immune attack of peripheral nerves. The purpose of this review is to summarize our current knowledge about the clinical, epidemiological, pathogenetic, and laboratory aspects of campylobacter-associated GBS.
Chagas’ Disease and the Autoimmunity Hypothesis
Authors: Kierszenbaum Felipe
Published: October 2018

The notion that the pathology of Chagas’ disease has an autoimmune component was initially based on the finding of circulating antibodies binding heart tissue antigens in patients and mice chronically infected with Trypanosoma cruzi. Later, T lymphocytes reactive with heart or nerve tissue antigens were found in chagasic mice and patients, extending the concept to include cell-mediated immunity. However, there is disagreement about whether the observed immunologic autoreactivities are triggered by T. cruzi epitopes and then affect host tissue antigens by virtue of molecular mimicry or are elicited by host antigens exposed to lymphocytes after tissue damage caused by the parasite. There is also disagreement about the relevance of immunologic autoreactivities to the pathogenesis of Chagas’ disease because of the lack of reproducibility of some key reports supporting the autoimmunity hypothesis, conflicting data from independent laboratories, conclusions invalidated by advances in our understanding of the immunologic mechanisms underlying cell lysis, and, last but not least, a lack of direct, incontrovertible evidence that cross-reacting antibodies or autoreactive cells mediate the typical pathologic changes associated with human Chagas’ disease. The data and views backing and questioning the autoimmunity hypothesis for Chagas’ disease are summarized in this review.
Resistance of Human Cytomegalovirus to Antiviral Drugs
Authors: Erice Alejo
Published: October 2018

Resistance of cytomegalovirus (CMV) to antiviral agents is a well-recognized phenomenon that has been observed in the laboratory and in the clinical setting. Infections caused by antiviral-resistant CMV have been found exclusively among immunocompromised individuals, including patients with AIDS, bone marrow and solid-organ transplant recipients, and patients with hematologic malignancies, and in individuals with primary immunodeficiencies. The majority of these infections have been described to occur in patients with AIDS receiving prolonged antiviral therapy for CMV end-organ disease. Antiviral agents currently licensed for the treatment of CMV infections include ganciclovir, foscarnet, and cidofovir. Resistance of CMV to ganciclovir is related to mutations in the UL97 region of the viral genome and/or mutations in the viral DNA polymerase. Resistance to foscarnet and cidofovir is associated with mutations in the viral DNA polymerase. Antiviral susceptibility of CMV strains containing DNA polymerase mutations is dependent on the region of the DNA polymerase where the mutations are located. Some DNA polymerase mutant viruses are cross-resistant to ganciclovir, foscarnet, and cidofovir. The recognition that specific UL97 and UL54 mutations are associated with resistance to antiviral agents has led to the development of molecular methods for detection of mutant viruses. This article reviews the mechanisms of resistance of CMV to antiviral agents, the laboratory methods for detection of resistant CMV, and the clinical aspects of infections caused by antiviral-resistant CMV.
Acquisition, Transport, and Storage of Iron by Pathogenic Fungi
Authors: Howard Dexter H.
Published: October 2018

Iron is required by most living systems. A great variety of means of acquisition, avenues of uptake, and methods of storage are used by pathogenic fungi to ensure a supply of the essential metal. Solubilization of insoluble iron polymers is the first step in iron assimilation. The two methods most commonly used by microorganisms for solubilization of iron are reduction and chelation. Reduction of ferric iron to ferrous iron by enzymatic or nonenzymatic means is a common mechanism among pathogenic yeasts. Under conditions of iron starvation, many fungi synthesize iron chelators known as siderophores. Two classes of compounds that function in iron gathering are commonly observed: hydroxamates and polycarboxylates. Two major responses to iron stress in fungi are a high-affinity ferric iron reductase and siderophore synthesis. Regulation of these two mechanisms at the molecular level has received attention. Uptake of siderophores is a diverse process, which varies among the different classes of compounds. Since free iron is toxic, it must be stored for further metabolic use. Polyphosphates, ferritins, and siderophores themselves have been described as storage molecules. The iron-gathering mechanisms used by a pathogen in an infected host are largely unknown and can only be posited on the basis of in vitro studies at present.
Plant Products as Antimicrobial Agents
Authors: Cowan Marjorie Murphy
Published: October 2018

The use of and search for drugs and dietary supplements derived from plants have accelerated in recent years. Ethnopharmacologists, botanists, microbiologists, and natural-products chemists are combing the Earth for phytochemicals and “leads” which could be developed for treatment of infectious diseases. While 25 to 50% of current pharmaceuticals are derived from plants, none are used as antimicrobials. Traditional healers have long used plants to prevent or cure infectious conditions; Western medicine is trying to duplicate their successes. Plants are rich in a wide variety of secondary metabolites, such as tannins, terpenoids, alkaloids, and flavonoids, which have been found in vitro to have antimicrobial properties. This review attempts to summarize the current status of botanical screening efforts, as well as in vivo studies of their effectiveness and toxicity. The structure and antimicrobial properties of phytochemicals are also addressed. Since many of these compounds are currently available as unregulated botanical preparations and their use by the public is increasing rapidly, clinicians need to consider the consequences of patients self-medicating with these preparations.