bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stable isotopic and elemental characteristics of recent tufa from a karstic Krka River (south‐east Slovenia): useful environmental proxies?
Authors: Zavadlav Saša , Rožič Boštjan , Dolenec Matej , Lojen Sonja 
Published: October 2016

AbstractTufa samples from 16 consecutive barrages along a 13 km section of the groundwater‐fed Krka River (Slovenia) were analysed for their petrographical, mineralogical, elemental and stable carbon (δ13C) and oxygen (δ18O) isotope composition, to establish their relation to current climatic and hydrological conditions. Waters constantly oversaturated with calcite and the steep morphology of the Krka riverbed stimulate rapid CO2 degassing and subsequent tufa precipitation. The carbon isotope fractionation (Δ13C) between dissolved inorganic carbon and tufa in the Krka River evolves towards isotopic equilibrium being controlled by continuous CO2 degassing and tufa precipitation rate downstream. The Δ13C increased from 1·9 to 2·5‰ (VPDB); however, since tufa precipitation rates remain similar downstream, the major controlling factor of carbon isotope exchange is most probably related to the continuous 12CO2 degassing downstream leaving the carbon pool enriched in 13C. In the case of oxygen, the isotope fractionation (Δ18O) was found to be from 1·0 to 2·3‰ (VSMOW) smaller than reported in the literature. The observed discrepancies are due to different precipitation rates of calcite deposits because Krka tufas on cascades grow relatively faster compared to slowly precipitated calcite deposits in cave or stream pools. Due to non‐equilibrium oxygen isotope exchange between Krka tufa and water, the δ18O proxy showed from 1·2 to 8·2°C higher calculated water temperatures compared to measured water temperatures, demonstrating that δ18O proxy‐based temperature equations are not reliable for water temperature calculations of fast‐growing tufa on cascades. Because Mg is bound to the terrigenous dolomite fraction in the Krka tufa samples, the Mg/Ca was also found to be an unreliable temperature proxy yielding over up to 20°C higher calculated water temperatures.
Asymptomatic cryptococcal antigen prevalence detected by lateral flow assay in hospitalised HIV‐infected patients in São Paulo, Brazil
Authors: Vidal José E. , Toniolo Carolina , Paulino Adriana , Colombo Arnaldo , dos Anjos Martins Marilena , da Silva Meira Cristina , Pereira‐Chioccola Vera Lucia , Figueiredo‐Mello Claudia , Barros Tiago , Duarte Jequelie , Fonseca Fernanda , Alves Cunha Mirella , Mendes Clara , Ribero Taiana , dos Santos Lazera Marcia , Rajasingham Radha , Boulware David R. 
Published: October 2016

AbstractObjectiveTo determine the prevalence of asymptomatic cryptococcal antigen (CRAG) using lateral flow assay (LFA) in hospitalised HIV‐infected patients with CD4 counts <200 cells/μl.MethodsHospitalised HIV‐infected patients were prospectively recruited at Instituto de Infectologia Emilio Ribas, a tertiary referral hospital to HIV‐infected patients serving the São Paulo State, Brazil. All patients were >18 years old without prior cryptococcal meningitis, without clinical suspicion of cryptococcal meningitis, regardless of antiretroviral (ART) status, and with CD4 counts <200 cells/μl. Serum CRAG was tested by LFA in all patients, and whole blood CRAG was tested by LFA in positive cases.ResultsWe enrolled 163 participants of whom 61% were men. The duration of HIV diagnosis was a median of 8 (range, 1–29) years. 26% were antiretroviral (ART)‐naïve, and 74% were ART‐experienced. The median CD4 cell count was 25 (range, 1–192) cells/μl. Five patients (3.1%; 95%CI, 1.0–7.0%) were asymptomatic CRAG‐positive. Positive results cases were cross‐verified by performing LFA in whole blood.Conclusions3.1% of HIV‐infected inpatients with CD4 <200 cells/μl without symptomatic meningitis had cryptococcal antigenemia in São Paulo, suggesting that routine CRAG screening may be beneficial in similar settings in South America. Our study reveals another targeted population for CRAG screening: hospitalised HIV‐infected patients with CD4 <200 cells/μl, regardless of ART status. Whole blood CRAG LFA screening seems to be a simple strategy to prevention of symptomatic meningitis.
Functional characterization of UDP‐rhamnose‐dependent rhamnosyltransferase involved in anthocyanin modification, a key enzyme determining blue coloration in Lobelia erinus
Authors: Hsu Yang‐Hsin , Tagami Takayoshi , Matsunaga Kana , Okuyama Masayuki , Suzuki Takashi , Noda Naonobu , Suzuki Masahiko , Shimura Hanako 
Published: October 2016

SummaryBecause structural modifications of flavonoids are closely related to their properties, such as stability, solubility, flavor and coloration, characterizing the enzymes that catalyze the modification reactions can be useful for engineering agriculturally beneficial traits of flavonoids. In this work, we examined the enzymes involved in the modification pathway of highly glycosylated and acylated anthocyanins that accumulate in Lobelia erinus. Cultivar Aqua Blue (AB) of L. erinus is blue‐flowered and accumulates delphinidin 3‐O‐p‐coumaroylrutinoside‐5‐O‐malonylglucoside‐3′5′‐O‐dihydroxycinnamoylglucoside (lobelinins) in its petals. Cultivar Aqua Lavender (AL) is mauve‐flowered, and LC‐MS analyses showed that AL accumulated delphinidin 3‐O‐glucoside (Dp3G), which was not further modified toward lobelinins. A crude protein assay showed that modification processes of lobelinin were carried out in a specific order, and there was no difference between AB and AL in modification reactions after rhamnosylation of Dp3G, indicating that the lack of highly modified anthocyanins in AL resulted from a single mutation of rhamnosyltransferase catalyzing the rhamnosylation of Dp3G. We cloned rhamnosyltransferase genes (RTs) from AB and confirmed their UDP‐rhamnose‐dependent rhamnosyltransferase activities on Dp3G using recombinant proteins. In contrast, the RT gene in AL had a 5‐bp nucleotide deletion, resulting in a truncated polypeptide without the plant secondary product glycosyltransferase box. In a complementation test, AL that was transformed with the RT gene from AB produced blue flowers. These results suggest that rhamnosylation is an essential process for lobelinin synthesis, and thus the expression of RT has a great impact on the flower color and is necessary for the blue color of Lobelia flowers.
Accuracy of dose calculations on kV cone beam CT images of lung cancer patients
Authors: de Smet Mariska , Schuring Danny , Nijsten Sebastiaan , Verhaegen Frank 
Published: October 2016

PurposeTo develop a clinically feasible method for dose calculations on cone beam CT (CBCT) images of two different vendors, and to determine the accuracy of these dose calculations for lung cancer patients.MethodsLung cancer patients with CBCT imaging (n = 10 for Elekta, n = 6 for Varian) and a repeated planning CT scan on the same day were selected. For CBCT dose calculations, an adapted Hounsfield units‐to‐mass density table (HU table) was used which was obtained by comparing CT values of corresponding points on the CBCT and the repeated planning CT scan. Dose calculations with three different HU tables were compared: a patient‐specific, a general thorax‐CBCT, and the standard CT HU table. Planning CT data were used to compensate for the limited field of view (FOV) (Elekta) or scan length (Varian) of the CBCT. For evaluation, clinically relevant dose metrics were compared between the repeated CT and CBCT to assess the accuracy of dose calculations on CBCT for both vendors.ResultsFor both vendors, isodose lines and dose volume histograms were very similar between dose calculation on CBCT and CT. For Varian, average differences between CT and CBCT dose calculations were 2%–3% for most dose metrics when the standard CT HU table was used. A better agreement was observed when a thorax‐CBCT HU table was used, with differences of 1%–2%. No added value was found by using a patient‐specific HU table, showing similar results as the general thorax‐CBCT HU table. For Elekta, the dose metrics showed large deviations when the CT HU table was used, but using a patient‐specific HU table resulted in similar accuracy as for Varian CBCT dose calculations, with average differences between repeated CT and CBCT dose metrics below 3%, and for most dose metrics even below 2%.ConclusionsDifferences between Elekta and Varian CBCT, including hardware, reconstruction software, HU calibration, FOV, and scan length, resulted in different challenges for CBCT dose calculations for the different vendors. For Elekta CBCT scans, the procedure with a patient‐specific HU table resulted in similar accuracy as for Varian CBCT dose calculations with a general HU correction for all thorax patients. The vendor‐specific corrective methods used in this study resulted in dose calculations feasible for treatment re‐evaluation for both Elekta and Varian CBCT scans.
Sorting Out Antibiotics' Mechanisms of Action: a Double Fluorescent Protein Reporter for High-Throughput Screening of Ribosome and DNA Biosynthesis Inhibitors
Authors: Osterman Ilya A. , Komarova Ekaterina S. , Shiryaev Dmitry I. , Korniltsev Ilya A. , Khven Irina M. , Lukyanov Dmitry A. , Tashlitsky Vadim N. , Serebryakova Marina V. , Efremenkova Olga V. , Ivanenkov Yan A. , Bogdanov Alexey A. , Sergiev Petr V. , Dontsova Olga A. 
Published: October 2016

ABSTRACT

In order to accelerate drug discovery, a simple, reliable, and cost-effective system for high-throughput identification of a potential antibiotic mechanism of action is required. To facilitate such screening of new antibiotics, we created a double-reporter system for not only antimicrobial activity detection but also simultaneous sorting of potential antimicrobials into those that cause ribosome stalling and those that induce the SOS response due to DNA damage. In this reporter system, the red fluorescent protein gene
rfp
was placed under the control of the SOS-inducible
sulA
promoter. The gene of the far-red fluorescent protein,
katushka2S
, was inserted downstream of the tryptophan attenuator in which two tryptophan codons were replaced by alanine codons, with simultaneous replacement of the complementary part of the attenuator to preserve the ability to form secondary structures that influence transcription termination. This genetically modified attenuator makes possible Katushka2S expression only upon exposure to ribosome-stalling compounds. The application of red and far-red fluorescent proteins provides a high signal-to-background ratio without any need of enzymatic substrates for detection of the reporter activity. This reporter was shown to be efficient in high-throughput screening of both synthetic and natural chemicals.
Polyomaviruses
Authors: Cook Linda 
Published: October 2016

ABSTRACT
Over the last 10 years, the number of identified polyomaviruses has grown to more than 35 subtypes, including 13 in humans. The polyomaviruses have similar genetic makeup, including genes that encode viral capsid proteins VP1, 2, and 3 and large and small T region proteins. The T proteins play a role in viral replication and have been implicated in viral chromosomal integration and possible dysregulation of growth factor genes. In humans, the Merkel cell polyomavirus has been shown to be highly associated with integration and the development of Merkel cell cancers. The first two human polyomaviruses discovered, BKPyV and JCPyV, are the causative agents for transplant-related kidney disease, BK commonly and JC rarely. JC has also been strongly associated with the development of progressive multifocal leukoencephalopathy (PML), a rare but serious infection in untreated HIV-1-infected individuals and in other immunosuppressed patients including those treated with monoclonal antibody therapies for autoimmune diseases systemic lupus erythematosus, rheumatoid arthritis, or multiple sclerosis. The trichodysplasia spinulosa-associated polyomavirus (TSAPyV) may be the causative agent of the rare skin disease trichodysplasia spinulosa. The remaining nine polyomaviruses have not been strongly associated with clinical disease to date. Antiviral therapies for these infections are under development. Antibodies specific for each of the 13 human polyomaviruses have been identified in a high percentage of normal individuals, indicating a high rate of exposure to each of the polyomaviruses in the human population. PCR methods are now available for detection of these viruses in a variety of clinical samples.
Aerobic Actinomycetes of Clinical Significance
Authors: Mochon A. Brian , Sussland Den , Saubolle Michael A. 
Published: October 2016

ABSTRACTThe group of Gram-positive bacillary organisms broadly known as “aerobic actinomycetes” consists of heterogeneous and taxonomically divergent genera. They are found in a wide variety of natural and man-made environments but are rarely considered a part of the normal human flora, with infections normally originating from exogenous sources. An extensive number of genera have been described, but only a minority of these has been associated with human or veterinary health. The association with human disease is usually of an opportunistic nature, either through accidental means of inoculation or through involvement with immunocompromising conditions in the host. They cause a wide spectrum of diseases in humans, which may differ greatly between the genera and even between species, but which also may have a great amount of overlap. The occurrence of such infections is probably greater than appreciated, since many may go unrecognized. Etiologic prevalence of specific genera and species varies geographically within the United States and worldwide. Traditional phenotypic identification methods for separation of the many genera and species of aerobic actinomycetes have found great difficulties. Recent use of chemotaxonomic analyses and emerging technologies such as molecular analysis of nucleic acids, and more recently proteomics for identification to the genus/species level, has provided a far more robust technique to understand the organisms’ relatedness, distribution, epidemiology, and pathogenicity in humans.
Human Immunodeficiency Virus
Authors: Armstrong Wendy S. , Guarner Jeannette , Kraft Colleen S. , Caliendo Angela M. 
Published: October 2016

ABSTRACT
In this chapter we will discuss the diagnosis and monitoring of individuals with HIV infection. The application and interpretation of these tests does not change dramatically when used in the immunocompromised host. The principal approach to the diagnosis of HIV infection involves serologic testing, although nucleic acid amplification tests play an important role in the diagnosis of acute HIV infection. The algorithm for diagnosis of HIV continues to evolve with newer assays that are able to detect infection within an earlier timeframe after HIV transmission. Viral load testing for HIV-1 is the cornerstone for monitoring patients on antiretroviral therapy. Genotypic and phenotypic resistance tests are employed when antiretroviral resistance is suspected and results help guide therapy. The tropism assay must be performed to determine the efficacy of CCR5 chemokine receptor antagonists. Next-generation sequencing methods are an innovative approach to assessing archived antiretroviral resistance in patients with virologic suppression. The success of antiretroviral therapy with improved long-term outcomes has made transplantation in HIV-infected patients a reality.
Selected Topics in Aerobic Bacteriology
Authors: Hall† Geraldine , Carroll Karen C. 
Published: October 2016

ABSTRACTAerobic Gram-positive and Gram-negative bacteria can be important pathogens in the immunocompromised host. These bacteria can be found in many environments, as part of the normal microbiota of the human host and animals, in soil and water, on plants, on fomites in the hospital, and on hospital equipment. This review provides information from relevant studies about what are the most common aerobic bacteria associated with patients who have cancer and/or are being treated for it, or who have other diseases which lead to immunodeficiencies, such as HIV, multiple myeloma, aplastic anemia, chronic diseases, and aging. A discussion of the appropriate laboratory tests needed for diagnosis of aerobic infections and information about antibiotics and susceptibility testing are also included.
Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology
Authors: Rivera-Perez Jessica I. , Santiago-Rodriguez Tasha M. , Toranzos Gary A. 
Published: October 2016

ABSTRACT
Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.
The NADPH Oxidase and Microbial Killing by Neutrophils, With a Particular Emphasis on the Proposed Antimicrobial Role of Myeloperoxidase within the Phagocytic Vacuole
Authors: Levine Adam P. , Segal Anthony W. 
Published: October 2016

ABSTRACTThis review is devoted to a consideration of the way in which the NADPH oxidase of neutrophils, NOX2, functions to enable the efficient killing of bacteria and fungi. It includes a critical examination of the current dogma that its primary purpose is the generation of hydrogen peroxide as substrate for myeloperoxidase-catalyzed generation of hypochlorite. Instead, it is demonstrated that NADPH oxidase functions to optimize the ionic and pH conditions within the vacuole for the solubilization and optimal activity of the proteins released into this compartment from the cytoplasmic granules, which kill and digest the microbes. The general role of other NOX systems as electrochemical generators to alter the pH and ionic composition in compartments on either side of a membrane in plants and animals will also be examined.
G Protein-Coupled Receptors in Macrophages
Authors: Lin Hsi-Hsien , Stacey Martin 
Published: October 2016

ABSTRACTAs the largest receptor gene family in the human genome, with >800 members, the signal-transducing G protein-coupled receptors (GPCRs) play critical roles in nearly all conceivable physiological processes, ranging from the sensing of photons and odorants to metabolic homeostasis and migration of leukocytes. Unfortunately, an exhaustive review of the several hundred GPCRs expressed by myeloid cells/macrophages (P.J. Groot-Kormelink, L .Fawcett, P.D. Wright, M. Gosling, and T.C. Kent,BMC Immunol12:57, 2012,doi:10.1186/1471-2172-13-57) is beyond the scope of this chapter; however, we will endeavor to cover the GPCRs that contribute to the major facets of macrophage biology, i.e., those whose expression is restricted to macrophages and the GPCRs involved in macrophage differentiation/polarization, microbial elimination, inflammation and resolution, and macrophage-mediated pathology. The chemokine receptors, a major group of myeloid GPCRs, will not be extensively covered as they are comprehensively reviewed elsewhere.
Paul Ehrlich and the Early History of Granulocytes
Authors: Kay A. Barry 
Published: October 2016

ABSTRACT
Paul Ehrlich’s techniques, published between 1879 and 1880, for staining blood films using coal tar dyes, and his method of differential blood cell counting, ended years of speculation regarding the classification of white cells. Acidic and basic dyes had allowed him to recognize eosinophil and basophil granules, respectively, work that was a direct continuation of his discovery of the tissue mast cell described in his doctoral thesis. Ehrlich went on to develop neutral dyes that identified epsilon granules in neutrophils (“cells with polymorphous nuclei”). He also speculated, for the most part correctly, on the formation, function, and fate of blood neutrophils and eosinophils. Before Ehrlich, a number of important observations had been made on white cells and their role in health and disease. Among the most notable were William Hewson’s studies of blood and lymph; the early descriptions of leukemia by Alfred Donné, John Hughes Bennett, Rudolf Virchow, and others; as well as seminal observations on inflammation by William Addison, Friedrich von Recklinghausen, and Julius Cohnheim. Eosinophils were almost certainly recognized previously by others. In 1846, Thomas Wharton Jones (1808-1891) described “granule blood-cells” in several species including humans. The term “granule cell” had also been used by Julius Vogel (1814-1880), who had previously observed similar cells in inflammatory exudates. Vogel, in turn, was aware of the work of Gottlieb Gluge (1812-1898), who had observed “compound inflammatory globules” in pus and serum that resembled eosinophils. Almost 20 years before Ehrlich developed his staining methods, Max Johann Schultze (1825-1874) performed functional experiments on fine and coarse granular cells using a warm stage microscopic technique and showed they had amoeboid movement and phagocytic abilities. Despite these earlier observations, it was Ehrlich’s use of stains that heralded the modern era of studies of leukocyte biology and pathology.
Mathematical Modeling Tools to Study Preharvest Food Safety
Authors: Lanzas Cristina , Chen Shi 
Published: October 2016

ABSTRACTThis article provides an overview of the emerging field of mathematical modeling in preharvest food safety. We describe the steps involved in developing mathematical models, different types of models, and their multiple applications. The introduction to modeling is followed by several sections that introduce the most common modeling approaches used in preharvest systems. We finish the chapter by outlining potential future directions for the field.
Preharvest Food Safety in Broiler Chicken Production
Authors: Alali Walid Q. , Hofacre Charles L. 
Published: October 2016

ABSTRACT

Preharvest food safety in broiler production is a systematic approach to control the introduction, propagation, and dissemination of
Salmonella
and
Campylobacter
from breeder flocks to the end of their progeny (broilers) life cycle. New and revised more stringent performance standards for these pathogens at the processing plant level require continuous evaluation of the preharvest management practices and intervention strategies used by the poultry industry. The implementation of stricter biosecurity plans, vaccination of breeder flocks for
Salmonella
, and usage of feed that is free of animal by-products are some of the measures recommended to control the pathogens. Interventions shown to be effective in experimental settings need to be assessed for their cost-effectiveness and efficiency when applied at the farm level.