bluuebunny/crossref_metadata_2025 huggingface dataset:
Elastic Properties of Lithium Disilicate Versus Feldspathic Inlays: Effect on the Bonding by 3D Finite Element Analysis
Authors: Trindade Flávia Zardo , Valandro Luiz Felipe , de Jager Niek , Bottino Marco Antônio , Kleverlaan Cornelis Johannes
Published: October 2016

Purpose

To determine the elastic properties of five ceramic systems with different compositions (lithium disilicate vs. feldspathic ceramics) and processing methods and compare the stress distribution in premolars in the interface with inlays made with these systems loaded with the maximum normal bite force (665 N) using 3D finite element analysis (FEA).

Materials and Methods

The elastic properties of five ceramic restoration materials (IPS e.max Press, IPS e.max CAD, Vita PM9, Vita Mark II, Vita VM7) were obtained using the ultrasonic pulse‐echo method. Three‐dimensional FEA simplified models of maxillary premolars restored with these ceramic materials were created. The models were loaded with a load at the two nodes on the occlusal surface in the middle of the tooth, 2 mm from the outside of the tooth, simulating a loading ball with a radius of 6 mm.

Results

The means values of density (g/cm³), Young's modulus (GPa), and Poison's ratio was 2.6 ± 0.3, 82.3 ± 18.3, and 0.22 ± 0.01 for IPS e.max Press; 2.3 ± 0.1, 83.5 ± 15.0, and 0.21 ± 0.01 for IPS e.max CAD; 2.5 ± 0.1, 44.4 ± 11.5, and 0.26 ± 0.08 for PM9; 2.4 ± 0.1, 70.6 ± 4.9, and 0.22 ± 0.01 for Vitamark II; 2.4 ± 0.1, 63.3 ± 3.9, and 0.23 ± 0.01 for VM7, respectively. The 3D FEA showed the tensile stress at the interface between the tooth and the inlay was dependent on the elastic properties of the materials, since the Vita PM9 and IPS e.max CAD ceramics presented the lowest and the highest stress concentration in the interface, respectively.

Conclusions

The elastic properties of ceramic materials were influenced by composition and processing methods, and these differences influenced the stress concentration at the bonding interface between tooth and restoration. The lower the elastic modulus of inlays, the lower is the stress concentration at the bonding interfaces.
Does the visibility of a congenital anomaly affect maternal–infant attachment levels?
Authors: Boztepe Handan , Ay Ayşe , Kerimoğlu Yıldız Gizem , Çınar Sevil
Published: October 2016

Purpose

To determine whether congenital anomaly visibility affects maternal–infant attachment levels.

Design and Methods

The study population consisted of mothers who had infants with cleft lip/palate or congenital heart anomalies who were receiving treatment in a university hospital. The data were collected using the Structured Questionnaire Form and the Maternal Attachment Inventory.

Results

Statistically significant differences in maternal–infant attachment levels were observed between infants with cleft lips/palates and healthy infants and between infants with congenital heart anomalies and healthy infants.

Practice implications

It is important to apply appropriate nursing interventions for these mothers during the postpartum period.
Gene flow in, and mating system of, Rhododendron simsii in a nature reserve in subtropical China
Authors: Hahn Christoph Z. , Michalski Stefan G. , Durka Walter
Published: October 2016

Mating system and gene dispersal distances are two important characteristics that govern the distribution of genetic variation within species. Genetic variation is an important resource for adaptation, but also allows insight into a species reproductive biology. As the reproductive biology is species specific, general inferences across species may be inaccurate and for many species not much is known about the details of gene flow and mating, especially in species‐rich ecosystems such as the subtropics.

We characterised the mating system and determined historical and current gene flow distances in Rhododendron simsii using microsatellite markers. Adult individuals and seeds were sampled in a near‐natural nature reserve in southeast China. We examined the fine‐scale spatial genetic structure (SGS), kinship coefficients, outcrossing rates and biparental inbreeding coefficients. Furthermore, we estimated pollen dispersal distances using paternity analysis.

We found high outcrossing rates and significant biparental inbreeding. Population differentiation was low while observed heterozygosity and allelic richness were high. Estimates of historical and current gene flow were similar, indicating that genes are on average dispersed over distances of between 10 and 20 m. Paternity analyses suggest frequent mating among neighbouring individuals.

We conclude that R. simsii is predominantly, but not obligately outcrossing. Moderate amounts of biparental inbreeding and overall low fine‐scale SGS indicate that mating among related individuals is common, but does neither lead to pronounced population differentiation nor to strong aggregation of related individuals. Most likely, gene flow distances in this species are affected by its flowering phenology. Mass‐flowering, pollen/pollinator limitation and gravity/wind dispersal of seeds in concert cause short gene dispersal distances. Lastly, population genetic descriptors suggest that R. simsii in the study area represents a large, well connected population in which large amounts of genetic variability are maintained.
Influence of sleep duration on cortical oxygenation in elderly individuals
Authors: Kato Kazuko , Miyata Seiko , Ando Motoo , Matsuoka Hiroki , Yasuma Fumihiko , Iwamoto Kunihiro , Kawano Naoko , Banno Masahiro , Ozaki Norio , Noda Akiko
Published: October 2016

Aim

Short sleep duration is a risk factor for cardiovascular diseases. Cerebral blood flow and its regulation are affected by pathological conditions commonly observed in the elderly population, such as dementia, atherosclerosis, diabetes mellitus (DM), stroke, and hypertension. The purpose of this study was to examine the influence of sleep duration on cortical oxygenated hemoglobin (OxyHb) using near‐infrared spectroscopy (NIRS).

Methods

Seventy‐three individuals (age, 70.1 ± 3.9 years, 51 men and 22 women) participated in this study. Cortical OxyHb levels were measured with NIRS. We evaluated age, body mass index (BMI), smoking status, alcohol intake, sleep duration, hypertension, DM, and hyperlipidemia using a questionnaire. Blood pressure was measured using plethysmography.

Results

Peak OxyHb and area under the NIRS curve significantly decreased in participants with sleep duration <7 h compared with those with sleep duration ≥7 h (0.136 ± 0.212 mM·mm vs 0.378 ± 0.342 mM·mm, P = 0.001; 112.0 ± 243.6 vs 331.7 ± 428.7,
P
 = 0.012, respectively). Sleep duration was significantly correlated with peak OxyHb level and area under the NIRS curve (r = 0.378,
P
 = 0.001; r = 0.285,
P
 = 0.015, respectively). Multiple regression analysis, including age, BMI, sex, smoking status, alcohol intake, sleep duration, hypertension, DM, and hyperlipidemia revealed that sleep duration was the only significant independent factor associated with peak OxyHb and area under the NIRS curve (β = 0.343,
P
 = 0.004; β = 0.244,
P
 = 0.049, respectively), and smoking status was independently correlated with time to the peak OxyHb (β = −0.319,
P
 = 0.009).

Conclusion

Sleep duration may be an important factor that influences cortical oxygenation in the elderly population.
Aid for Trade and Global Growth
Authors: Naito Takumi
Published: October 2016

Aid for trade increases a recipient's public services, which lower its import and export transport costs. Formulating a two‐country endogenous growth model, we obtain two main results. First, a permanent increase in the donor's aid/gross domestic product (GDP) ratio raises the steady‐state growth rate as well as both countries' long‐run fractions and cost shares of imported varieties if and only if it lowers the product of transport costs. Second, under a plausible condition, there exists a unique interior growth‐maximizing aid/GDP ratio. These results are robust to alternative specifications for congestion and stock‐flow nature of public goods.
Transfusion of 35‐day stored red blood cells does not result in increase of plasma non‐transferrin bound iron in human endotoxemia
Authors: Peters Anna L. , Kunanayagam Renoja K. , van Bruggen Robin , de Korte Dirk , Juffermans Nicole P. , Vlaar Alexander P.J.
Published: October 2016

BACKGROUND

Transfusion of a single unit of stored red blood cells (RBCs) has been hypothesized to induce supra‐physiological levels of non‐transferrin bound iron (NTBI), which may enhance inflammation and act as a nutrient for bacteria. We investigated the relation between RBC storage time and iron levels in a clinically relevant “two‐hit” human transfusion model.

STUDY DESIGN AND METHODS

Eighteen healthy male volunteers (ages 18‐35 years) were infused with 2 ng lipopolysaccharide (LPS)/kg to induce systemic inflammatory response syndrome. Two hours later, each participant received either 1 unit of 2‐day stored (2D) autologous RBCs, 35‐day stored (35D) autologous RBCs, or an equal volume of saline. Every 2 hours up to 8 hours after LPS infusion, hemoglobin, hemolysis parameters, and iron parameters, including NTBI, were measured.

RESULTS

Transfusion of both 2D and 35D RBCs caused increases in hemoglobin, plasma iron, and transferrin saturation; whereas levels remained stable in the saline group. Transfusion of 35D RBCs did not result in hemolysis nor did it lead to increased levels of NTBI compared with 2D RBCs or saline. LPS induced increases in ferritin, haptoglobin, bilirubin, and lactate dehydrogenase that were similar in all three groups.

CONCLUSION

We conclude that 35D autologous RBCs do not cause hemolysis or increased levels of NTBI during human endotoxemia.
A stochastic location and allocation model for critical items to response large-scale emergencies: A case of Turkey
Authors: Celik Erkan , Aydin Nezir , Taskin Gumus Alev
Published: October 2016

This paper aims to decide on the number of facilities and their locations, procurement for pre and post-disaster, and allocation to mitigate the effects of large-scale emergencies. A two-stage stochastic mixed integer programming model is proposed that combines facility location- prepositioning, decisions on pre-stocking levels for emergency supplies, and allocation of located distribution centers (DCs) to affected locations and distribution of those supplies to several demand locations after large-scale emergencies with uncertainty in demand. Also, the use of the model is demonstrated through a case study for prepositioning of supplies in probable large-scale emergencies in the eastern and southeastern Anatolian sides of Turkey. The results provide a framework for relief organizations to determine the location and number of DCs in different settings, by using the proposed model considering the main parameters, as; capacity of facilities, probability of being affected for each demand points, severity of events, maximum distance between a demand point and distribution center.
Energy Exchange and Localization in Essentially Nonlinear Oscillatory Systems: Canonical Formalism
Authors: Gendelman O. V. , Sapsis T. P.
Published: October 2016

Over recent years, a lot of progress has been achieved in understanding of the relationship between localization and transport of energy in essentially nonlinear oscillatory systems. In this paper, we are going to demonstrate that the structure of the resonance manifold can be conveniently described in terms of canonical action–angle (AA) variables. Such formalism has important theoretical advantages: all resonance manifolds may be described at the same level of complexity, appearance of additional conservation laws on these manifolds is easily proven both in autonomous and nonautonomous settings. The harmonic balance-based complexification approach, used in many previous studies on the subject, is shown to be a particular case of the canonical formalism. Moreover, application of the canonic averaging allows treatment of much broader variety of dynamical models. As an example, energy exchanges in systems of coupled trigonometrical and vibro-impact oscillators are considered.
Rapid short-pulse sequences enhance the spatiotemporal uniformity of acoustically driven microbubble activity during flow conditions
Authors: Pouliopoulos Antonios N. , Li Caiqin , Tinguely Marc , Garbin Valeria , Tang Meng-Xing , Choi James J.
Published: October 2016

Despite the promise of microbubble-mediated focused ultrasound therapies, in vivo findings have revealed over-treated and under-treated regions distributed throughout the focal volume. This poor distribution cannot be improved by conventional pulse shapes and sequences, due to their limited ability to control acoustic cavitation dynamics within the ultrasonic focus. This paper describes the design of a rapid short-pulse (RaSP) sequence which is comprised of short pulses separated by μs off-time intervals. Improved acoustic cavitation distribution was based on the hypothesis that microbubbles can freely move during the pulse off-times. Flowing SonoVue® microbubbles (flow velocity: 10 mm/s) were sonicated with a 0.5 MHz focused ultrasound transducer using RaSP sequences (peak-rarefactional pressures: 146–900 kPa, pulse repetition frequency: 1.25 kHz, and pulse lengths: 5–50 cycles). The distribution of cavitation activity was evaluated using passive acoustic mapping. RaSP sequences generated uniform distributions within the focus in contrast to long pulses (50 000 cycles) that produced non-uniform distributions. Fast microbubble destruction occurred for long pulses, whereas microbubble activity was sustained for longer durations for shorter pulses. High-speed microscopy revealed increased mobility in the direction of flow during RaSP sonication. In conclusion, RaSP sequences produced spatiotemporally uniform cavitation distributions and could result in efficient therapies by spreading cavitation throughout the treatment area.
Effect of High
N
-Acetylcysteine Concentrations on Antibiotic Activity against a Large Collection of Respiratory Pathogens
Authors: Landini Giulia , Di Maggio Tiziana , Sergio Francesco , Docquier Jean-Denis , Rossolini Gian Maria , Pallecchi Lucia
Published: October 2016

The effect of high
N
-acetylcysteine (NAC) concentrations (10 and 50 mM) on antibiotic activity against 40 strains of respiratory pathogens was investigated. NAC compromised the activity of carbapenems (of mostly imipenem and, to lesser extents, meropenem and ertapenem) in a dose-dependent fashion. We demonstrated chemical instability of carbapenems in the presence of NAC. With other antibiotics, 10 mM NAC had no major effects, while 50 mM NAC sporadically decreased (ceftriaxone and aminoglycosides) or increased (penicillins) antibiotic activity.
eis
Promoter C14G and C15G Mutations Do Not Confer Kanamycin Resistance in Mycobacterium tuberculosis
Authors: Pholwat Suporn , Stroup Suzanne , Heysell Scott , Ogarkov Oleg , Zhdanova Svetlana , Ramakrishnan Girija , Houpt Eric
Published: October 2016

We studied the significance of particular
eis
mutations on
Mycobacterium tuberculosis
drug resistance using a specialized transduction strategy. Recombinant strains harboring
eis
promoter mutations C14T, C12T, and G10A exhibited kanamycin resistance with MICs of 40, 10, and 20 μg/ml, respectively, while recombinant strains harboring C14G and C15G mutations were kanamycin susceptible (MIC, 2.5 to 5 μg/ml). Each of the
eis
mutants tested remained amikacin susceptible (MIC, 0.5 to 4 μg/ml). The identification of specific
eis
mutations is needed for accurate genotypic susceptibility testing for kanamycin.
Antibiofilm Activities of a Novel Chimeolysin against Streptococcus mutans under Physiological and Cariogenic Conditions
Authors: Yang Hang , Bi Yongli , Shang Xiaoran , Wang Mengyue , Linden Sara B. , Li Yunpeng , Li Yuhong , Nelson Daniel C. , Wei Hongping
Published: October 2016

Streptococcus mutansoften survives as a biofilm on the tooth surface and contributes to the development of dental caries. We investigated the efficacy of ClyR, an engineered chimeolysin, againstS. mutansbiofilms under physiological and cariogenic conditions. Susceptibility tests showed that ClyR was active against all clinicalS. mutansisolates tested as well asS. mutansbiofilms that displayed resistance to penicillin. TheS. mutansbiofilms that formed on hydroxyapatite discs under physiological sugar conditions and cariogenic conditions were reduced ∼2 logs and 3 logs after treatment with 100 μg/ml ClyR, respectively. In comparison, only a 1-log reduction was observed in the chlorhexidine gluconate (ChX)-treated group, and no killing effect was observed in the NaF-treated group. A mouse dental colonization model showed that repeated use of ClyR for 3 weeks (5 μg/day) reduced the number of colonizedS. mutanscells in the dental plaques significantly (P< 0.05) and had no harmful effects on the mice. Furthermore, toxicity was not noted at concentrations exceeding those used for thein vitroandin vivostudies, and ClyR-specific antibodies could not be detected in mouse saliva after repeated use of ClyR in the oral cavity. Our data collectively demonstrate that ClyR is active againstS. mutansbiofilms bothin vitroandin vivo, thus representing a preventative or therapeutic agent for use against dental caries.
Chromosome 5 of Human Pathogen Candida albicans Carries Multiple Genes for Negative Control of Caspofungin and Anidulafungin Susceptibility
Authors: Suwunnakorn Sumanun , Wakabayashi Hironao , Rustchenko Elena
Published: October 2016

Candida albicansis an important fungal pathogen with a diploid genome that can adapt to caspofungin, a major drug from the echinocandin class, by a reversible loss of one copy of chromosome 5 (Ch5). Here, we explore a hypothesis that more than one gene for negative regulation of echinocandin tolerance is carried on Ch5. We constructedC. albicansstrains that each lacked one of the following Ch5 genes:CHT2for chitinase,PGA4for glucanosyltransferase, andCSU51, a putative transcription factor. We demonstrate that independent deletion of each of these genes increased tolerance for caspofungin and anidulafungin, another echinocandin. Our data indicate that Ch5 carries multiple genes for negative control of echinocandin tolerance, although the final number has yet to be established.
Triclosan: an Instructive Tale
Authors: McNamara Patrick J. , Levy Stuart B.
Published: October 2016

The Food and Drug Administration (FDA) recently released a final rule to ban triclosan and 18 other antimicrobial chemicals from soaps. We applaud this rule specifically because of the associated risks that triclosan poses to the spread of antibiotic resistance throughout the environment. This persistent chemical constantly stresses bacteria to adapt, and behavior that promotes antibiotic resistance needs to be stopped immediately when the benefits are null.
Genome-Wide Association Study of Cell-Mediated Response in Dogs Naturally Infected by Leishmania infantum
Authors: Batista Luís F. S. , Utsunomiya Yuri T. , Silva Thaís B. F. , Dias Raíssa A. , Tomokane Thaise Y. , Pacheco Acácio D. , da Matta Vânia L. R. , Silveira Fernando T. , Marcondes Mary , Nunes Cáris M. , Laurenti Márcia D.
Published: October 2016

A genome-wide association study (GWAS) could unravel the complexity of the cell-mediated immunity (CMI) to canine leishmaniasis (CanL). Therefore, we scanned 110,165 single-nucleotide polymorphisms (SNPs), aiming to identify chromosomal regions associated with the leishmanin skin test (LST), lymphocyte proliferation assay (LPA), and cytokine responses to further understand the role played by CMI in the outcome of naturalLeishmania infantuminfection in 189 dogs. Based on LST and LPA, four CMI profiles were identified (LST−/LPA−, LST+/LPA−, LST−/LPA+, and LST+/LPA+), which were not associated with subclinically infected or diseased dogs. LST+/LPA+dogs showed increased interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α) levels and mild parasitism in the lymph nodes, whereas LST−/LPA+dogs, in spite of increased IFN-γ, also showed increased interleukin-10 (IL-10) and transforming growth factor β (TGF-β) levels and the highest parasite load in lymph nodes. Low T cell proliferation under low parasite load suggested thatL. infantumwas not able to induce effective CMI in the early stage of infection. Altogether, genetic markers explained 87%, 16%, 15%, 11%, 0%, and 0% of phenotypic variance in TNF-α, TGF-β, LST, IL-10, IFN-γ, and LPA, respectively. GWAS showed that regions associated with TNF-α include the following genes:IL12RB1,JAK3,CCRL2,CCR2,CCR3, andCXCR6, involved in cytokine and chemokine signaling; regions associated with LST, includingCOMMD5andSHARPIN, involved in regulation of NF-κB signaling; and regions associated with IL-10, includingLTBP1andRASGRP3, involved in T regulatory lymphocytes differentiation. These findings pinpoint chromosomic regions related to the cell-mediated response that potentially affect the clinical complexity and the parasite replication in canineL. infantuminfection.
Skin and Soft Tissue Infections
Authors: Moffarah Anne Spichler , Al Mohajer Mayar , Hurwitz Bonnie L. , Armstrong David G.
Published: October 2016

The skin is colonized by a diverse collection of microorganisms which, for the most part, peacefully coexist with their hosts. Skin and soft tissue infections (SSTIs) encompass a variety of conditions; in immunocompromised hosts, SSTIs can be caused by diverse microorganisms—most commonly bacteria, but also fungi, viruses, mycobacteria, and protozoa. The diagnosis of SSTIs is difficult because they may commonly masquerade as other clinical syndromes or can be a manifestation of systemic disease. In immunocompromised hosts, SSTI poses a major diagnostic challenge, and clinical dermatological assessment should be initially performed; to better identify the pathogen and to lead to appropriate treatment, etiology should include cultures of lesions and blood, biopsy with histology, specific microbiological analysis with special stains, molecular techniques, and antigen-detection methodologies. Here, we reviewed the epidemiology, pathophysiology, clinical presentation, and diagnostic techniques, including molecular biological techniques, used for SSTIs, with a focus on the immunocompromised host, such as patients with cellular immunodeficiency, HIV, and diabetic foot infection.
Adenovirus
Authors: Ison Michael G. , Hayden Randall T.
Published: October 2016

Adenoviruses are a highly prevalent infection that can cause a range of clinical syndromes in immunocompromised patients, ranging from localized disease of the respiratory tract, gastrointestinal tract, or urinary tract to disseminated disease. Adenovirus infections may develop in this unique population as the result of primary infection or reactivation of latent virus. Disease can be potentially progressive with high rates of mortality in patients with pneumonia and disseminated disease. Fortunately, cidofovir and its lipid ester, brincidofovir, appear to be effective for the treatment of adenovirus, although neither is specifically approved for this indication. Adenovirus should always be considered when immunocompromised patients present with any clinical syndrome that could be compatible with adenoviral infection. Once disease is suspected, cultures or molecular testing of appropriate specimens should be obtained and blood should be sent for adenovirus polymerase chain reaction (PCR) whenever adenovirus is suspected. Monitoring of quantitative viral loads in blood is helpful in predicting response to therapy with a significant drop (>1 log) associated with a higher probability of clinical response.
Cytomegalovirus
Authors: Dioverti M. Veronica , Razonable Raymund R.
Published: October 2016

Cytomegalovirus (CMV), the largest of the herpesviruses, causes a wide range of clinical syndromes, from asymptomatic infection to severe disease in immunocompromised hosts. Laboratory methods for diagnosis include molecular testing, antigenemia, culture, serology, and histopathology. Treatment of CMV infection and disease is indicated in selected immunocompromised hosts, and preventive approaches are indicated in high-risk groups. This chapter reviews the epidemiology, clinical aspects, and the laboratory diagnosis and management of CMV in immunocompromised hosts.
Overview of Infections in the Immunocompromised Host
Authors: Dropulic Lesia K. , Lederman Howard M.
Published: October 2016

Understanding the components of the immune system that contribute to host defense against infection is key to recognizing infections that are more likely to occur in an immunocompromised patient. In this review, we discuss the integrated system of physical barriers and of innate and adaptive immunity that contributes to host defense. Specific defects in the components of this system that predispose to particular infections are presented. This is followed by a review of primary immunodeficiency diseases and secondary immunodeficiencies, the latter of which develop because of a specific illness or condition or are treatment-related. The effects of treatment for neoplasia, autoimmune diseases, solid organ and stem cell transplants on host defenses are reviewed and associated with susceptibility to particular infections. In conclusion, an approach to laboratory screening for a suspected immunodeficiency is presented. Knowledge of which host defects predispose to specific infections allows clinicians to prevent, diagnose, and manage infections in their immunocompromised patients most effectively.
Lower Respiratory Tract Infections
Authors: Carroll Karen C. , Adams La’tonzia L.
Published: October 2016

This review will focus on the infectious etiologies and more common noninfectious causes of lower respiratory tract syndromes among major immunosuppressed populations. The changing epidemiology of infections in the era of highly active antiretroviral therapy (HAART) in the case of HIV-positive patients and the impacts of both newer immune-suppressant therapies and anti-infective prophylaxis for other immunocompromised hosts will be discussed, with emphasis on diagnostic approaches and practice algorithms.
Bloodstream Infections
Authors: Martinez Raquel M. , Wolk Donna M.
Published: October 2016

Bacteremia and sepsis are conditions associated with high mortality and are of great impact to health care operations. Among the top causes of mortality in the United States, these conditions cause over 600 fatalities each day. Empiric, broad-spectrum treatment is a common but often a costly approach that may fail to effectively target the correct microbe, may inadvertently harm patients via antimicrobial toxicity or downstream antimicrobial resistance. To meet the diagnostic challenges of bacteremia and sepsis, laboratories must understand the complexity of diagnosing and treating septic patients, in order to focus on creating algorithms that can help direct a more targeted approach to antimicrobial therapy and synergize with existing clinical practices defined in new Surviving Sepsis Guidelines. Significant advances have been made in improving blood culture media; as yet no molecular or antigen-based method has proven superior for the detection of bacteremia in terms of limit of detection. Several methods for rapid molecular identification of pathogens from blood cultures bottles are available and many more are on the diagnostic horizon. Ultimately, early intervention by molecular detection of bacteria and fungi directly from whole blood could provide the most patient benefit and contribute to tailored antibiotic coverage of the patient early on in the course of the disease. Although blood cultures remain as the best means of diagnosing bacteremia and candidemia, complementary testing with antigen tests, microbiologic investigations from other body sites, and histopathology can often aid in the diagnosis of disseminated disease, and application of emerging nucleic acid test methods and other new technology may greatly impact our ability to bacteremic and septic patients, particularly those who are immunocompromised.
Microbial Forensics in Food Safety
Authors: Yeung Marie
Published: October 2016

Foodborne diseases represent a significant public health burden to the United States, considering that they cause illness in 1 in 6 people annually, which amounts to ∼48 million people (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, M. A. Widdowson, S. L. Roy, J. L. Jones, and P. M. Griffin,
Emerg Infect Dis
17:7–15, 2011). The average national cost of illness associated with 30 foodborne pathogens is estimated to be $55.5 to $93.2 billion based on two cost-of-illness models (R.L. Scharff,
J Food Prot
78:1064–1071, 2015). Predominately, foodborne illnesses are the result of accidental contamination or unintentional mishandling of food materials during the farm-to-table continuum. Nevertheless, principles and methodologies derived from microbial forensics are applied in foodborne outbreaks investigation to determine the source of the pathogen. Drawing from multiple real-life examples and case studies, this review discusses how the current food industry practice, demography, and consumer preference are shaping the landscape of food safety. The approaches to source tracking, or traceback, are described, with a focus on bacterial pathogens associated with food-producing animals. Current challenges and opportunities in microbial forensics in food safety are also addressed.
Statistical Considerations in Environmental Microbial Forensics
Authors: McBride Graham , Gilpin Brent
Published: October 2016

In environmental microbial forensics, as in other pursuits, statistical calculations are sometimes inappropriately applied, giving rise to the appearance of support for a particular conclusion or failing to support an innately obvious conclusion. This is a reflection of issues related to dealing with sample sizes, the methodologies involved, and the difficulty of communicating uncertainties. In this brief review, we attempt to illustrate ways to minimize such problems. In doing so, we consider one of the most common applications of environmental microbial forensics—the use of genotyping in food and water and disease investigations. We explore three important questions. (i) Do hypothesis tests’
P
values serve as adequate metrics of evidence? (ii) How can we quantify the value of the evidence? (iii) Can we turn a value-of-evidence metric into attribution probabilities? Our general conclusions are as follows. (i)
P
values have the unfortunate property of regularly detecting trivial effects when sample sizes are large. (ii) Likelihood ratios, rather than any kind of probability, are the better strength-of-evidence metric, addressing the question “what do these data say?” (iii) Attribution probabilities, addressing the question “what should I believe?,” can be calculated using Bayesian methods, relying in part on likelihood ratios but also invoking prior beliefs which therefore can be quite subjective. In legal settings a Bayesian analysis may be required, but the choice and sensitivity of prior assumptions should be made clear.
Growth and Differentiation Factors
Authors: Metcalf† Donald
Published: October 2016

This review is restricted to neutrophilic granulocytes (granulocytes), monocytes (macrophages), and eosinophils, with only passing reference to cells that are also usually included in the “myeloid” category—megakaryocytes, mast cells, and erythroid cells. Although some dendritic cells are of myeloid origin, they are discussed elsewhere. The validity of the information to be described depends on two assumptions: (a) thatin vitrodata are applicable to eventsin vivoand (b) that mouse data reflect events in man. Both assumptions are likely to be broadly correct.
Multifaceted Functions of NOD-Like Receptor Proteins in Myeloid Cells at the Intersection of Innate and Adaptive Immunity
Authors: Kufer Thomas A. , Nigro Giulia , Sansonetti Philippe J.
Published: October 2016

NOD-like receptor (NLR) proteins, as much as Toll-like receptor proteins, play a major role in modulating myeloid cells in their immune functions. There is still, however, limited knowledge on the expression and function of several of the mammalian NLR proteins in myeloid lineages. Still, the function of pyrin domain-containing NLR proteins and NLRC4/NAIP as inflammasome components that drive interleukin-1β (IL-1β) and IL-18 maturation and secretion upon pathogen stimulation is well established. NOD1, NOD2, NLRP3, and NLRC4/NAIP act as bona fide pattern recognition receptors (PRRs) that sense microbe-associated molecular patterns (MAMPs) but also react to endogenous danger-associated molecular patterns (DAMPs). Ultimately, activation of these receptors achieves macrophage activation and maturation of dendritic cells to drive antigen-specific adaptive immune responses. Upon infection, sensing of invading pathogens and likely of DAMPs that are released in response to tissue injury is a process that involves multiple PRRs in both myeloid and epithelial cells, and these act in concert to design tailored, pathogen-adapted immune responses by induction of different cytokine profiles, giving rise to appropriate lymphocyte polarization.
Mechanisms of Myeloid Cell Modulation of Atherosclerosis
Authors: Swirski Filip K. , Nahrendorf Matthias , Libby Peter
Published: October 2016

Inflammation furnishes a series of pathogenic pathways that couple the risk factors for atherosclerosis with altered behavior of the intrinsic cells of the arterial wall, endothelium, and smooth muscle and promote the disease and its complications. Myeloid cells participate critically in all phases of atherosclerosis from initiation through progression, and ultimately the thrombotic consequences of this disease. Foam cells, lipid-laden macrophages, constitute the hallmark of atheromata. Much of the recent expansion in knowledge of the roles of myeloid cells in atherosclerosis revolves around the functional contributions of subsets of monocytes, precursors of macrophages, the most abundant myeloid cells in the atheroma. Proinflammatory monocytes preferentially accumulate in nascent atherosclerotic plaques. The most dramatic manifestations of atherosclerosis result from blood clot formation. Myocardial infarction, ischemic stroke, and abrupt limb ischemia all arise primarily from thrombi that complicate atherosclerotic plaques. Myeloid cells contribute pivotally to triggering thrombosis, for example, by elaborating enzymes that degrade the plaque’s protective extracellular matrix, rendering it fragile, and by producing the potent procoagulant tissue factor. While most attention has focused on mononuclear phagocytes, the participation of polymorphonuclear leukocytes may aggravate local thrombus formation. Existing therapies such as statins may exert some of their protective effects by altering the functions of myeloid cells. The pathways of innate immunity that involve myeloid cells provide a myriad of potential targets for modifying atherosclerosis and its complications, and provide a fertile field for future attempts to address the residual burden of this disease, whose global prevalence is on the rise.
Role of the Cytoskeleton in Myeloid Cell Function
Authors: Fine Noah , Khaliq Samira , Hassanpour Siavash , Glogauer Michael
Published: October 2016

During an innate immune response, myeloid cells undergo complex morphological adaptations in response to inflammatory cues, which allow them to exit the vasculature, enter the tissues, and destroy invading pathogens. The actin and microtubule cytoskeletons are central to many of the most essential cellular functions including cell division, cell morphology, migration, intracellular trafficking, and signaling. Cytoskeletal structure and regulation are crucial for many myeloid cell functions, which require rapid and dynamic responses to extracellular signals. In this chapter, we review the roles of the actin and microtubule cytoskeletons in myeloid cells, focusing primarily on their roles in chemotaxis and phagocytosis. The role of myeloid cell cytoskeletal defects in hematological disorders is highlighted throughout.
Egg Safety in the Realm of Preharvest Food Safety
Authors: Singh Manpreet , Brar Jagpinder
Published: October 2016

Eggs are nutritious, yet they are a highly perishable commodity like other protein sources such as meat. Even though steps are taken all along the production process of shell eggs, from farm to table, the potential for contamination of the shells and egg contents poses a high risk to consumers. The main sources of contamination can be categorized as vertical transmission, in which the layers can be carriers of pathogens and can pass them on during egg formation, and horizontal transmission, in which environmental factors such as water, feed, layer houses, and personnel are the main source of contamination. Ongoing preharvest practices might not be enough to completely eliminate pathogens from shell eggs; however, consistently following good practices along with proper handling during transportation and retail sale and by consumers can be significant in reducing the risk. This article discusses the various aspects of production practices, their potential for cross-contamination, and decontamination technologies for shell eggs.
Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities
Authors: Berry Elaine D. , Wells James E.
Published: October 2016

Preharvest strategies to reduce zoonotic pathogens in food animals are important components of the farm-to-table food safety continuum. The problem is complex; there are multiple pathogens of concern, multiple animal species under different production and management systems, and a variety of sources of pathogens, including other livestock and domestic animals, wild animals and birds, insects, water, and feed. Preharvest food safety research has identified a number of intervention strategies, including probiotics, direct-fed microbials, competitive exclusion cultures, vaccines, and bacteriophages, in addition to factors that can impact pathogens on-farm, such as seasonality, production systems, diet, and dietary additives. Moreover, this work has revealed both challenges and opportunities for reducing pathogens in food animals. Animals that shed high levels of pathogens and predominant pathogen strains that exhibit long-term persistence appear to play significant roles in maintaining the prevalence of pathogens in animals and their production environment. Continued investigation and advancements in sequencing and other technologies are expected to reveal the mechanisms that result in super-shedding and persistence, in addition to increasing the prospects for selection of pathogen-resistant food animals and understanding of the microbial ecology of the gastrointestinal tract with regard to zoonotic pathogen colonization. It is likely that this continued research will reveal other challenges, which may further indicate potential targets or critical control points for pathogen reduction in livestock. Additional benefits of the preharvest reduction of pathogens in food animals are the reduction of produce, water, and environmental contamination, and thereby lower risk for human illnesses linked to these sources.
Emerging Foodborne and Agriculture-Related Viruses
Authors: Kingsley David H.
Published: October 2016

Viruses rapidly evolve and can emerge in unpredictable ways. Transmission pathways by which foodborne viruses may enter human populations and evolutionary mechanisms by which viruses can become virulent are discussed in this chapter. A majority of viruses emerge from zoonotic animal reservoirs, often by adapting and infecting intermediate hosts, such as domestic animals and livestock. Viruses that are known foodborne threats include hepatitis E virus, tick-borne encephalitis virus, enteroviruses, adenovirus, and astroviruses, among others. Viruses may potentially evolve and emerge as a result of modern agricultural practices which can concentrate livestock and bring them into contact with wild animals. Examples of viruses that have emerged in this manner are influenza, coronaviruses such as severe acute respiratory syndrome and Middle East respiratory syndrome, and the Nipah virus. The role of bats, bush meat, rodents, pigs, cattle, and poultry as reservoirs from which infectious pathogenic viruses emerge are discussed.
Animal Models of Tuberculosis: An Overview
Authors: Williams Ann , Orme Ian M.
Published: October 2016

This article provides an overview of the animal models currently used in tuberculosis research, both for understanding the basic science of the disease process and also for practical issues such as testing new vaccine candidates and evaluating the activity of potential new drugs. Animals range in size, from zebrafish to cattle, and in degrees of similarity to the human disease from both an immunological and pathologic perspective. These models have provided a great wealth of information (impossible to obtain simply from observing infected humans), but we emphasize here that one must use care in interpreting or applying this information, and indeed the true art of animal modeling is in deciding what is pertinent information and what might not be. These ideas are discussed in the context of current approaches in vaccine and drug development, including a discussion of certain limitations the field is currently facing in such studies.
The Evolutionary History, Demography, and Spread of the
Mycobacterium tuberculosis
Complex
Authors: Barbier Maxime , Wirth Thierry
Published: October 2016

With the advent of next-generation sequencing technology, the genotyping of clinical
Mycobacterium tuberculosis
strains went through a major breakup that dramatically improved the field of molecular epidemiology but also revolutionized our deep understanding of the
M. tuberculosis
complex evolutionary history. The intricate paths of the pathogen and its human host are reflected by a common geographical origin in Africa and strong biogeographical associations that largely reflect the past migration waves out of Africa. This long coevolutionary history is cardinal for our understanding of the host-pathogen dynamic, including past and ongoing demographic components, strains’ genetic background, as well as the immune system genetic architecture of the host. Coalescent- and Bayesian-based analyses allowed us to reconstruct population size changes of
M. tuberculosis
through time, to date the most recent common ancestor and the several phylogenetic lineages. This information will ultimately help us to understand the spread of the Beijing lineage, the rise of multidrug-resistant sublineages, or the fall of others in the light of socioeconomic events, antibiotic programs, or host population densities. If we leave the present and go through the looking glass, thanks to our ability to handle small degraded molecules combined with targeted capture, paleomicrobiology covering the Pleistocene era will possibly unravel lineage replacements, dig out extinct ones, and eventually ask for major revisions of the current model.
A novel method for determining the small-strain shear modulus of soil using the bender elements technique
Authors: Wang Yejiao , Benahmed Nadia , Cui Yu-Jun , Tang Anh Minh
Published: October 2016

Bender elements technique has become a popular tool for determining shear wave velocity, Vs, hence the small-strain shear modulus of soils, Gmax, thanks to its simplicity and nondestructive character among other advantages. Several methods were proposed to determine the first arrival of Vs. However, none of them can be widely adopted as a standard and there is still an uncertainty on the detection of the first arrival. In this study, bender elements tests were performed on lime-treated soil and both shear wave and compression wave velocities at various frequencies were measured. In-depth analysis showed that the S-wave received signal presents an identical travel time and opposite polarity compared with that of the S-wave components in P-wave received signal, especially at high frequency. From this observation, a novel interpretation method based on the comparison between the S-wave and P-wave received signals at high frequency is proposed. This method enables the determination of the arrival time of the S-wave objectively, avoiding a less reliable first arrival pick-up point. Furthermore, the “π-point” method and cross-correlation method were also employed and the obtained results agree well with those from the proposed method, indicating the accuracy and reliability of the latter. The effects of frequency on the shear wave velocity are also discussed.
Uncertainty analysis of a spatially-distributed hydrological model with rainfall multipliers
Authors: Datta Arpana Rani , Bolisetti Tirupati
Published: October 2016

This paper has developed an input error model to account for input uncertainty, and applied the rainfall multiplier approaches to the calibration and uncertainty analysis of Soil and Water Assessment Tool (SWAT), a spatially-distributed hydrological model. The developed input error model has introduced the season-dependent rainfall multipliers to the Bayesian framework and reduced the dimension of the posterior probability density function. The method is applied to a watershed located in Southwestern Ontario, Canada. The results of the developed method are compared with two other methods. The SWAT model parameters and the input error model parameters are jointly inferred by a Markov chain Monte Carlo sampler. The results show the measured precipitation data overestimates the true precipitation values for the study area. The uncertainty in model prediction is underestimated for high flows and overestimated for low flows. There is no significant change in the estimation of parameter uncertainty and streamflow prediction uncertainty in the developed method from those in the other methods. The study emphasizes that the rainfall multiplier approaches are applicable to spatially-distributed hydrological modelling for accounting of input uncertainty.
DAMA/LIBRA–phase1 model independent results
Authors: Bernabei R. , Belli P. , d’Angelo S. , Di Marco A. , Montecchia F. , d’Angelo A. , Incicchitti A. , Prosperi D. , Cappella F. , Caracciolo V. , Cerulli R. , Dai C. J. , He H. L. , Kuang H. H. , Ma X. H. , Sheng X. D. , Wang R. G. , Ye Z. P.
Published: October 2016

Experimental observations and theoretical arguments at Galaxy and larger scales have suggested that a large fraction of the Universe is composed by Dark Matter (DM) particles. This has motivated the DAMA experimental efforts to investigate the presence of such particles in the galactic halo by exploiting a model independent signature with highly radiopure setups deep underground. In this paper, a review of the results obtained with the total exposure of 1.04 ton × yr collected by DAMA/LIBRA–phase1 deep underground at the Gran Sasso National Laboratory (LNGS) of the INFN during seven annual cycles is given. The DAMA/LIBRA–phase1 data give evidence for the presence of DM particles in the galactic halo, on the basis of the exploited model independent DM annual modulation signature by using highly radiopure NaI(Tl) target, at 7.5[Formula: see text] C.L. Including also the data of the first generation DAMA/NaI experiment (cumulative exposure 1.33 ton × yr, corresponding to 14 annual cycles), the C.L. is 9.3[Formula: see text] and the modulation amplitude of the single-hit scintillation events in the (2–6) keV energy interval is: (0.0112 ± 0.0012) cpd/kg/keV; the measured phase is (144 ± 7) days and the measured period is (0.998 ± 0.002) yr, values well in agreement with those expected for DM particles. No systematic or side reaction able to mimic the exploited DM signature has been found or suggested by anyone over more than a decade.