bluuebunny/crossref_metadata_2025 huggingface dataset:
Organic photolysis reactions in tropospheric aerosols: effect on secondary organic aerosol formation and lifetime
Authors: Hodzic A. , Madronich S. , Kasibhatla P. S. , Tyndall G. , Aumont B. , Jimenez J. L. , Lee-Taylor J. , Orlando J.
Published: August 2015

Abstract. This study presents the first modeling estimates of the potential effect of gas- and particle-phase organic photolysis reactions on the formation and lifetime of secondary organic aerosols (SOAs). Typically only photolysis of smaller organic molecules (e.g., formaldehyde) for which explicit data exist is included in chemistry–climate models. Here, we specifically examine the photolysis of larger molecules that actively partition between the gas and particle phases. The chemical mechanism generator GECKO-A is used to explicitly model SOA formation from α-pinene, toluene, and C12 and C16 n-alkane reactions with OH at low and high NOx. Simulations are conducted for typical mid-latitude conditions and a solar zenith angle of 45° (permanent daylight). The results show that after 4 days of chemical aging under those conditions (equivalent to 8 days in the summer mid-latitudes), gas-phase photolysis leads to a moderate decrease in SOA yields, i.e., ~15 % (low NOx) to ~45 % (high NOx) for α-pinene, ~15 % for toluene, ~25 % for C12 n-alkane, and ~10 % for C16 n-alkane. The small effect of gas-phase photolysis on low-volatility n-alkanes such as C16 n-alkane is due to the rapid partitioning of early-generation products to the particle phase, where they are protected from gas-phase photolysis. Minor changes are found in the volatility distribution of organic products and in oxygen to carbon ratios. The decrease in SOA mass is increasingly more important after a day of chemical processing, suggesting that most laboratory experiments are likely too short to quantify the effect of gas-phase photolysis on SOA yields. Our results also suggest that many molecules containing chromophores are preferentially partitioned into the particle phase before they can be photolyzed in the gas phase. Given the growing experimental evidence that these molecules can undergo in-particle photolysis, we performed sensitivity simulations using an empirically estimated SOA photolysis rate of JSOA = 4 × 10−4 JNO2. Modeling results indicate that this photolytic loss rate would decrease SOA mass by 40–60 % for most species after 10 days of equivalent atmospheric aging at mid-latitudes in the summer. It should be noted that in our simulations we do not consider in-particle or aqueous-phase reactions which could modify the chemical composition of the particle and thus the quantity of photolabile species. The atmospheric implications of our results are significant for both the SOA global distribution and lifetime. GEOS-Chem global model results suggest that particle-phase photolytic reactions could be an important loss process for SOA in the atmosphere, removing aerosols from the troposphere on timescales of less than 7 days that are comparable to wet deposition.
The potential effects of fresh water content on the primary production in the Chukchi Sea
Authors: Yun M. S. , Whitledge T. E. , Stockwell D. , Lee J. H. , Park J. W. , Lee D. B. , Park J. , Lee S. H.
Published: August 2015

Abstract. The in situ primary production rates and various environmental variables were investigated in the Chukchi Sea during the 3rd RUSALCA expedition, which was conducted in 2012, to identify the current status of primary production. A 13C-15N dual tracer technique was used to measure the daily primary production rates, which ranged from 0.02 to 1.61 g C m−2 d−1 (mean ± SD = 0.42 ± 0.52 g C m−2 d−1). The primary production rates showed large regional differences, with the southern region (0.66 ± 0.62 g C m−2 d−1) producing approximately five times as much as the northern region (0.14 ± 0.10 g C m−2 d−1), which was primarily due to the differences in phytoplankton biomasses induced by regional nutrient conditions. The primary production rates in the Chukchi Sea were averaged using data acquired during the three different RUSALCA expeditions (2004, 2009, and 2012) as 0.33 g C m−2 d−1 (SD = 0.40 g C m−2 d−1), which was significantly lower than previously reported rates. In addition to strong seasonal and interannual variations in primary production, recent decreases in the concentrations of major inorganic nutrients and chlorophyll a could be among the reasons for the recent low primary production in the Chukchi Sea because the primary production is mainly affected by nutrient concentration and phytoplankton biomass. The nutrient inventory and primary production appear to be largely influenced by the freshwater content (FWC) variability in the region due to the significant relationships between FWC, nitrate concentrations (r = 0.54, p < 0.05) and primary production rates (r = 0.56, p < 0.05). Moreover, we found highly significant relationships between the nutrient levels and the primary production rates (r = 0.75, p < 0.001). In conclusion, the primary production in the Chukchi Sea is primarily controlled by nutrient availability which is strongly related to the FWC variability. Our results imply that the predicted increase in freshwater accumulation might cause a decrease in primary production by lowering the nutrient inventory in the euphotic zone of the Chukchi Sea.
Data assimilation in integrated hydrological modelling in the presence of observation bias
Authors: Rasmussen J. , Madsen H. , Jensen K. H. , Refsgaard J. C.
Published: August 2015

Abstract. The use of bias-aware Kalman filters for estimating and correcting observation bias in groundwater head observations is evaluated using both synthetic and real observations. In the synthetic test, groundwater head observations with a constant bias and unbiased stream discharge observations are assimilated in a catchment scale integrated hydrological model with the aim of updating stream discharge and groundwater head, as well as several model parameters relating to both stream flow and groundwater modeling. The Colored Noise Kalman filter (ColKF) and the Separate bias Kalman filter (SepKF) are tested and evaluated for correcting the observation biases. The study found that both methods were able to estimate most of the biases and that using any of the two bias estimation methods resulted in significant improvements over using a bias-unaware Kalman Filter. While the convergence of the ColKF was significantly faster than the convergence of the SepKF, a much larger ensemble size was required as the estimation of biases would otherwise fail. Real observations of groundwater head and stream discharge were also assimilated, resulting in improved stream flow modeling in terms of an increased Nash-Sutcliffe coefficient while no clear improvement in groundwater head modeling was observed. Both the ColKF and the SepKF tended to underestimate the biases, which resulted in drifting model behavior and sub-optimal parameter estimation, but both methods provided better state updating and parameter estimation than using a bias-unaware filter.
Three-dimensional finite element model of the drilling process used for fixation of Salter–Harris type-3 fractures by using a K-wire
Authors: Gok A. , Gok K. , Bilgin M. B.
Published: August 2015

Abstract. In this study, the drilling process was performed with Kirschner wire (K-wire) for stabilization after reduction of Salter–Harris (SH) type-3 epiphyseal fractures of distal femur. The study was investigated both experimentally and numerically. The numerical analyses were performed with finite element method (FEM), using DEFORM-3D software. Some conditions such as friction, material model and load and boundary must be identified exactly while using FEM. At the same time, an analytic model and software were developed, which calculate the process parameters such as drilling power and thrust power, heat transfer coefficients and friction coefficient between tool–chip interface in order to identify the temperature distributions occurring in the K-wire and bone model (Keklikoǧlu Plastik San.) material during the drilling process. Experimental results and analysis results have been found as consistent with each other. The main cutting force, thrust force, bone model temperature and K-wire temperature were measured as 80° N, 120° N, 69 °C and 61 °C for 400 rpm in experimental studies. The main cutting force, thrust force, bone model temperature and K-wire temperature were measured as 65° N, 87° N, 91 °C and 82 °C for 800 rpm in experimental studies. The main cutting force, thrust force, bone model temperature and K-wire temperature were measured as 85° N, 127° N, 72 °C and 67 °C for 400 rpm in analysis studies. The main cutting force, thrust force, bone model temperature and K-wire temperature were measured as 69° N, 98° N, 83 °C and 76 °C for 800 rpm in analysis studies. A good consistency was obtained between experimental results and finite element analysis (FEA) results. This proved the validity of the software and finite element model. Thus, this model can be used reliably in such drilling processes.
Lightning fatalities and injuries in Turkey
Authors: Tilev-Tanriover Ş. , Kahraman A. , Kadioğlu M. , Schultz D. M.
Published: August 2015

Abstract. A database of lightning-related fatalities and injuries in Turkey was constructed by collecting data from the Turkish State Meteorological Service, newspaper archives, European Severe Weather Database, and the internet. The database covers January 1930 to June 2014. In total, 742 lightning incidents causing human fatalities and injuries were found. Within these 742 incidents, there were 895 fatalities, 149 serious injuries, and 535 other injuries. Most of the incidents (89 %) occurred during April through September, with a peak in May and June (26 and 28 %) followed by July (14 %). Lightning-related fatalities and injuries were most frequent in the afternoon. Most of the incidents (86 %) occurred in rural areas, with only 14 % in the urban areas. Approximately, two thirds of the victims with known gender were male. Because of the unrepresentativeness of the historical data, determining an average mortality rate over a long period is not possible. Nevertheless, there were 31 fatalities (0.42 per million) in 2012, 26 fatalities (0.35 per million) in 2013, and 25 fatalities (0.34 per million) in 2014 (as of June). There were 36 injuries (0.49 per million) in each of 2012 and 2013, and 62 injuries (0.84 per million) in 2014 (as of June).
Effect of NAA and IAA on Stem Cuttings of Dalbergia Sissoo (Roxb)
Authors: Omar Taha Jalal , Khudhur Sargul Ahmed
Published: August 2015

The plant cuttings is one of the most common methods of vegetative reproduction which is, today, used extensively due to low cost. In order to study the effect of various concentrations of Naphthalene acetic acid (NAA) and Indole acetic acid (IAA) on the rooting of semi- hardwood cuttings of Dalbergia sissoo , an experiment was carried out in a private field in Koya city in 2014. In this research, the treatments were prepared to include hormone of Naphthalene acetic acid in four levels of: (0, 100, 300 and 500 ppm) and Indole acetic acid in four levels of: (0, 100, 300 and 500 ppm), and the bottom part of the cutting was dipped into above solutions for 30 seconds. The results showed that the maximum percentage of the shooted cuttings, shoot length, number of main branch, diameter of main branch, leaf area, number & length of root, dry weight & biomass &dry matter of shoot, fresh &dry weight of root, biomass &dry matter of root and chlorophyll a belonged to IAA treatment with concentration of 500 ppm, NAA treatment with concentration of 500 ppm. Nitrogen and protein increased with concentration 300 ppm for IAA amd NAA auxins. The highest length of root belonged to IAA treatment with concentration of 500 ppm. All growth parameters were increased up to the highest concentrations of IAA 500 ppm. IAA was the most effective in promoting growth of Dalbergia sissoo cuttings.
Study of Relationship Between Depression and Quality of Life in Patients With Chronic Schizophrenia
Authors: Abedi Shargh Najme , Rostami Bahareh , Kosari Bahareh , Toosi Zakiye , Majelan Ghazaleh Ashrafzadeh
Published: August 2015

Depression is among the personality traits of schizophrenic patients, which results from psychotic features or is a consequence of a period of psychosis. Depression in schizophrenic patients is one of the important factors affecting their quality of life. The study population of this descriptive and analytic study consists of patients with chronic schizophrenia in Zahedan in 2014. The sample included 60 patients who simultaneously suffered from depression and were selected using random sampling (30 males and 30 females). The research instruments included the Schizophrenia Quality of Life Scale (SQLS) and the Beck Depression Inventory (the inventory was filled out by the tester). In order to form a statistics analysis, we used Pearson correlation and regression multivariate. Investigating the study hypotheses showed that there was a negative correlation between the high level of depression and low quality of life. the relationship between depression and the quality of life subscales showed that in women, the variable of symptoms and complications was a significant predictor; however, the other two variables (energy and motivation and psychosocial) were not significant predictors. In case of men, psychosocial variable was a significant predictor; however, the other two variables (energy and motivation and symptoms and complications) were not significant predictors. In general, depression on these patients makes discontent of life on them; therefore, elimination of their depression on their treatment is necessary.
Controlled Blood Pressure in Iranian Patients: A Multi-Center Report
Authors: Sadeghi Ezzatollah , Behnood-Rod Azin , Aerab-Sheibani Hossein , Shobeiri Elham , Pourzargar Pirouz , Ormoz Ehsan , Sadigh Nader , Moharamzad Yashar
Published: August 2015

We decided to determine the percentage of hypertensive patients whose blood pressure (BP) measurements were within recommended controlled range and to identify predictive factors for controlled BP. In this study carried out in 2014, 280 patients were included consecutively through sampling from both university and private medical centers/pharmacies in four Iranian cities. Demographic data as well as information about duration of HTN and prescribed medications, admission to emergency department (ED) because of HTN crisis, comorbidities, and control of HTN during the last 6 months by a healthcare provider were gathered. Adherence to anti-hypertensives was also determined using the validated Persian version of the 8-item Morisky Medication Adherence Scale (MMAS-8). Controlled BP was defined as systolic BP< 140 and diastolic BP< 90 mmHg in non-diabetics and < 130/80 mmHg in diabetics. Of 280 patients, 122 subjects (43.6%) had controlled BP. Among 55 diabetics, only two patients (3.6%) had controlled BP. Multiple logistic regression revealed the following variables as significant predictors of controlled BP: higher MMAS-8 score (adjusted odds ratio (OR)= 1.19, P= 0.03), fewer number of comorbid conditions (adjusted OR= 0.71, P = 0.03), having occupation as clerk/military personnel (adjusted OR= 1.03, P= 0.04), and not having history of ED admission during the last 6 months because of HTN crisis (adjusted OR= 2.11, P= 0.01). Considerable number of the studied patients had uncontrolled BP. Regarding the dramatic consequences of uncontrolled high BP in long term, it is advisable that careful attention by health care providers to the aforementioned factors could raise the likelihood of achieving controlled BP.
Selective Synthesis of Ortho-substituted 3-Cyclohexyl-2-phenyl-1,3-thiazolidin-4-one Sulfoxides and Sulfones by S-Oxidation with Oxone
Authors: Cannon Kevin , Gandla Deepa , Lauro Samantha , Silverberg Lee , Tierney John , Lagalante Anthony
Published: August 2015

1,3-thiazolidin-4-ones, also known as thiazolidin-4-ones, are known to have a very wide range of biological activity. The corresponding S-oxides may show enhanced activity, and therefore viable synthetic routes to these S-oxides are required. S-oxidation of 3-cyclohexyl-2-phenyl-1,3-thiazolidin-4-ones with Oxone® was investigated. For all compounds evaluated, selective oxidation to the sulfoxide was realized using 3 equivalents of Oxone® at room temperature. Alternatively, the sulfone was prepared selectively at high temperature by increasing the equivalents of Oxone® used; the extent of this selectivity was affected by the substituent of the aromatic ring. In those cases in which the reaction produced a mixture of the sulfoxide and sulfone, the ratio of the products was quantified by 1H NMR.
The Full‐Scale Implementation of an Innovative Biological Ammonia Treatment Process
Authors: Lytle Darren A. , Williams Dan , Muhlen Christy , Pham Maily , Kelty Keith , Wildman Matthew , Lang Glenn , Wilcox Mitch , Kohne Melissa
Published: August 2015

Across the United States, high levels of ammonia in drinking water sources can be found. Although ammonia in water does not pose a direct health concern, ammonia nitrification can cause a number of issues and reduce the effectiveness of some treatment processes. An innovative biological ammonia‐removal drinking water treatment process was developed and, after the success of a pilot study, a full‐scale treatment system using the process was built in a small Iowa community. The treatment plant included a unique aeration contactor design that is able to consistently reduce ammonia from 3.3 mg of nitrogen/L to nearly nondetectable after a biofilm acclimation period. Close system monitoring was performed to avoid excess nitrite release during acclimation, and phosphate was added to enhance biological activity on the basis of pilot study findings. The treatment system is robust, reliable, and relatively simple to operate. The operations and effectiveness of the treatment plant were documented in the study.
MIB and 2,4‐D Removal by Biofilters During Episodic Loading
Authors: Zearley Thomas L. , Summers R. Scott
Published: August 2015

Episodic occurrences of trace organic contaminants may affect their removal by biofilters. Removal of the naturally occurring algal metabolite 2‐methylisoborneol (MIB) and the herbicide 2,4‐dichlorphenoxyacetic acid (2,4‐D) by seven biofilters with an average empty bed contact time (EBCT) of 8.7 min is presented under a range of intermittent exposure conditions with continuous presence of dissolved organic matter. An average 70% removal of both MIB and 2,4‐D was found under constant exposure conditions over seven months. With the use of a pseudo‐first‐order model, much of the variability in removal during this time could be explained by EBCT changes. Microorganisms in the biofilters retained the capacity to biodegrade MIB and 2,4‐D after non‐exposure periods of up to five months. However, after nine months of non‐exposure, the MIB and 2,4‐D removals were lower than with the control biofilter, although the biofilter began to quickly reacclimate to these contaminants.
Fast-food: um estudo sobre a globalização alimentar
Authors: Ângelo Wenceslau Goés José
Published: August 2015

A industrialização trouxe mudanças de hábitos alimentares com o consumo de alimentos enlatados, pré-cozidos, fast-food. A chamada “comida caseira” foi ficando cada vez mais rara. Este livro busca compreender as representações sociais e os significados desse tipo de alimentação, descrevendo e interpretando as mudanças de hábitos alimentares dos consumidores de duas lanchonetes de uma grande franquia, com o surgimento dessa alimentação em Salvador. Através de relatos, foi possível buscar nas relações socioculturais e simbólicas dos indivíduos um novo “olhar” do ato alimentar e sua influência na saúde.
First observations, trends, and emissions of HCFC‐31 (CH2ClF) in the global atmosphere
Authors: Schoenenberger Fabian , Vollmer Martin K. , Rigby Matt , Hill Matthias , Fraser Paul J. , Krummel Paul B. , Langenfelds Ray L. , Rhee Tae Siek , Peter Thomas , Reimann Stefan
Published: August 2015

We report the first multiyear atmospheric record of HCFC‐31 (CH2ClF), based on flask samples and in situ analyses of air from both hemispheres. Although HCFC‐31 has never been produced in large amounts, observed mole fractions in the Northern Hemisphere increased from 2000 onward, reaching 170 ppq (parts per quadrillion, 10−15) in 2011–2012 before decreasing rapidly. By combining our observations with a two‐dimensional atmospheric chemistry‐transport model, we infer an increase in global emissions from 240 t yr−1 in 2000 to 840 t yr−1 in 2011–2012, followed by a relatively fast decline to 570 t yr−1 in 2014. Emissions of HCFC‐31 originate most probably from intermediate product release during the manufacturing process of HFC‐32 (CH2F2). The rapid decline in recent years could be due to changes in production methods rather than declines in diffusive sources such as landfills or HCFC‐31 contaminations in merchandised HFC‐32.
Dynamic SEP event probability forecasts
Authors: Kahler S. W. , Ling A.
Published: August 2015

The forecasting of solar energetic particle (SEP) event probabilities at Earth has been based primarily on the estimates of magnetic free energy in active regions and on the observations of peak fluxes and fluences of large (≥ M2) solar X‐ray flares. These forecasts are typically issued for the next 24 h or with no definite expiration time, which can be deficient for time‐critical operations when no SEP event appears following a large X‐ray flare. It is therefore important to decrease the event probability forecast with time as a SEP event fails to appear. We use the NOAA listing of major (≥10 pfu) SEP events from 1976 to 2014 to plot the delay times from X‐ray peaks to SEP threshold onsets as a function of solar source longitude. An algorithm is derived to decrease the SEP event probabilities with time when no event is observed to reach the 10 pfu threshold. In addition, we use known SEP event size distributions to modify probability forecasts when SEP intensity increases occur below the 10 pfu event threshold. An algorithm to provide a dynamic SEP event forecast, Pd, for both situations of SEP intensities following a large flare is derived.
Identification of Procaryotes
Authors: Krieg Noel R.
Published: August 2015

An identification scheme for a group of organisms can be devised only
after
that group has first been classified (i.e., recognized as being different from other organisms). Identification of that group is based on one or more characteristics, or on a pattern of characteristics, which all the members of the group have and which other groups do not have. The particular pattern of characteristics used for identifying a bacterial group should not be found in any other bacterial group. The identifying characteristics may be phenotypic, such as cell shape and Gram reaction or the ability to ferment certain sugars, or they may be genotypic, such as a particular nucleotide sequence. There should be universal systems for identifying a pure culture. Phenotypic characteristics chosen for an identification scheme should be easily determinable by most microbiology laboratories. Identification should rely on relatively few characteristics compared to classification schemes. Determination of the characteristics chosen for an identification scheme should be relatively inexpensive. The identification scheme should give results rapidly.
The Lithoautotrophic Nitrite‐Oxidizing Bacteria
Authors: Spieck Eva , Bock Eberhard
Published: August 2015

The lithotrophic nitrite oxidizers are Gram‐negative eubacteria that are able to use nitrite as a sole source of energy and CO
2
as the main source of carbon. Some strains are able to grow mixotrophically. These organisms are obligate lithoautotrophs with the exception of
Nitrobacter
, which can grow heterotrophically.
Nitrobacter
has been shown to grow anaerobically by dissimilatory nitrate reduction
Nucleic Acid Probes and Their Application in Environmental Microbiology
Authors: Amann Rudolf , Schleifer Karl‐Heinz
Published: August 2015

Microbiology has entered the molecular age. It is now routine to start the classification of a newly isolated microorganism with the determination and comparative analysis of at least one nucleic acid sequence. Clearly, the most commonly used molecule for this purpose is the ribonucleic acid of the small subunit of the ribosome, the 16S rRNA ofBacteriaandArchaea. Nucleic acid hybridization techniques, such as DNA–DNA reassociation or DNA–rRNA hybridization, have been used by bacterial taxonomists at times when nucleic acid sequencing was still difficult and available only to specialists. The increasing availability of nucleic acid sequences in databases, the ease of synthesizing oligonucleotide probes, and numerous other methodological advances in molecular biology, such as the polymerase chain reaction (PCR), have made nucleic acid probes a routinely used tool in microbiological laboratories.
Overview: A Phylogenetic Backbone and Taxonomic Framework for Procaryotic Systematics
Authors: Ludwig Wolfgang , Klenk Hans‐Peter
Published: August 2015

Microbial systematics has never been static but rather constantly subject to change. The evidence of this change is provided by many reclassifications in which bacterial taxa have been created, emended, or dissected, and organisms renamed or transferred. The development of a procaryotic systematics that reflects the natural relationships between microorganisms has always been a fundamental goal of taxonomists. However, the task of elucidating these relationships could not be addressed until the development of molecular methods (the analysis of macromolecules) that could be applied to bacterial identification and classification. Determination of genomic DNA G + C content and chemotaxonomic methods, such as analysis of cell wall and lipid composition, in many cases proved superior to classical methods based upon morphological and physiological traits. These tools provide information that can be used to differentiate taxa, but do not allow a comprehensive insight into the genetic and phylogenetic relationships of the organisms. DNA–DNA reassociation techniques provide data on genomic similarity and hence indirect phylogenetic information, but the resolution of this approach is limited to closely related strains. DNA–DNA hybridization is the method of choice for delimiting procaryotic species and estimating phylogeny at and below the species level.
Polyphasic Taxonomy
Authors: Gillis Monique , Vandamme Peter , Vos Paul De , Swings Jean , Kersters Karel
Published: August 2015

Bacterial taxonomy comprises the interrelated areas of classification, nomenclature, and identification and is supposed to reflect phylogeny and evolution. Polyphasic taxonomy refers to a consensus type of taxonomy and aims to utilize all the available data in delineating consensus groups, decisive for the final conclusions.

The minimal requirements for obtaining useful polyphasic data are (i) a preliminary screening for groups of similar strains; (ii) determination of the phylogenetic placement of these groups; (iii) measurement of the relationships between the groups and their closest neighbors, and (iv) collection of various descriptive data, preferentially on different aspects of the cell. Different theoretical possibilities for studying the relationships among the consensus groups and providing an emended or a new description of taxa exist. Many examples of polyphasic taxonomic studies of diverse bacterial groups are available, and a general evaluation of the results shows that the various conclusions of these studies depend on the bacterial group(s) studied, on the techniques applied, and on the researcher involved. The major sources of conflict in practicing consensus taxonomy are (i) DNA–DNA hybridizations, (ii) rRNA gene sequencing, (iii) phenotypic analysis, and (iv) genus delineation. Replacing minimal number of characteristics by large numbers of features should be taken care. In practice, a choice of complementary methods has to be made to tackle any taxonomic problem. Comparison with a standardized, accessible, universal database is a
condilio sine qua non
. One of the most interesting perspectives in bacterial systematics is the technological progress to be expected in the near future and its enormous impact on polyphasic methodology. The design of an accessible, cumulative, dynamic system allows continuous recalculation of all existing information into “new synthetic taxonomies of the moment”.
Road map of the phyla
Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae
, and
Planctomycetes
Authors: Ludwig Wolfgang , Euzéby Jean , Whitman William B.
Published: August 2015

The taxonomic road map proposed was derived from phylogenetic and principal‐component analyses of comprehensive datasets of small‐subunit rRNA gene sequences. Since the introduction of comparative rRNA sequencing there has been a continuous debate concerning the justification and power of a single marker molecule for elucidating phylogeny and establishing taxonomy of organisms. Although generally well established in taxonomy, the polyphasic approach cannot currently be applied for sequence‐based analyses due to the lack of adequate comprehensive datasets for alternative marker molecules. Even in the age of genomics, the datasets for non‐rRNA markers are poor in comparison to more than 400,000 rRNA primary structures available in general and special databases. Nevertheless, the data provided by the full genome‐sequencing projects allow the definiton of a small set of genes representing the conserved core of prokaryotic genomes. Furthermore, comparative analyses of the core gene sequences globally support the small subunit rRNA derived view of prokaryotic evolution. Although the tree topologies reconstructed from alternative markers differ in detail, the major groups (and taxa) are verified or at least not disproved. Consequently, the structuring of this volume is based on updated and curated databases of processed small‐subunit rRNA primary structures.
Road map of the phylum
Actinobacteria
Authors: Ludwig Wolfgang , Euzéby Jean , Schumann Peter , Busse Hans‐Jürgen , Trujillo Martha E. , Kämpfer Peter , Whitman William B.
Published: August 2015

The arrangement of content follows a phylogenetic framework or road map based largely on analyses of nucleotide sequences of the ribosomal small subunit RNA rather than on phenotypic data. Implicit in the use of the road map are the convictions that prokaryotes have a phylogeny and that phylogeny matters. However, phylogenies, like other experimentally derived hypotheses, are not static but may change whenever new data and/or improved methods of analysis become available. Thus, the large increases in data have led to a re‐evaluation of the road map. Not surprisingly, the taxonomic hierarchy has been modified or newly interpreted for a number of taxonomic units.
General Characteristics of the Cyanobacteria
Authors: Castenholz Richard W.
Published: August 2015

Apart from sharing the basic cellular features of otherBacteria, the cyanobacteria possess unique and diagnostic characteristics that will be briefly described here, but less extensively than in the 1989 edition ofBergey's Manual of Systematic Bacteriology. The cell wall in cyanobacteria is of a Gram‐negative type. Cell division in most unicellular and colonial cyanobacteria and some filamentous forms is by binary fission. Regarding cell exterior and motility, fimbriae (or pili) occur abundantly with diverse patterns in many cyanobacteria. Although not all thylakoids in cyanobacteria appear to be invaginations of the cytoplasmic membrane, there are orderly “attachment points” or “thylakoid centers” associated with the periphery of the cytoplasm or the cytoplasmic membrane. In the cytoplasm of cyanobacteria there are many other components and “inclusions”, most of which can be visualized readily using various preparative techniques for transmission electron microscopy. They include glycogen granules, cyanophycin granules, carboxysomes (polyhedral bodies), polyphosphate (volutin) granules, and gas vacuoles. Heterocysts, akinetes, and hormogonia are some of the specialized cells and differentiation in Cyanobacteria. The chief physiological/biochemical characteristic of cyanobacteria, distinguishing them from all other procaryotes, is the dual photosystem that allows the use of H2O as photoreductant with the consequent liberation of O2. Two courses for the delimitation of genera have been followed by cyanobacterial specialists: (a) to retain “small” genera or (b) to gather many species into fewer genera.

Cyanobacteria / General Characteristics of the Cyanobacteria
Oxygenic Photosynthetic Bacteria
Authors: Castenholz Richard W.
Published: August 2015

The oxygenic photosynthetic procaryotes comprise a single phylogenetic branch within the domain Bacteria (Eubacteria). In this chapter, it is concluded that the three described genera of the chl
a/b
‐containing oxygenic procaryotes (
Prochloron
,
Prochlorothrix
, and
Prochlorococcus
) fall within three distinct polyphyletic branches of the cyanobacterial tree according to 16S rDNA sequence analyses, and are, therefore, more closely related to a number of typical cyanobacteria than to each other. Thus, the synthesis of a second type of light‐harvesting chlorophyll, or the lack of phycobiliproteins or phycobilisomes within the cyanobacteria, should not be considered as a major phylogenetic divergence.

Cyanobacteria / Oxygenic Photosynthetic Bacteria
Mollicutes
Authors: Brown Daniel R. , May Meghan , Bradbury Janet M. , Johansson Karl‐Erik
Published: August 2015

Mol'li.cutes or Mol.li.cu'tes. L. adj.mollissoft, pliable; L. fem. n.cutisskin; N.L. fem. pl. n.Mollicutesclass with pliable cell boundary.

Tenericutes / Mollicutes
Solirubrobacterales
Authors: Whitman William B. , Suzuki Ken‐ichiro
Published: August 2015

So.li.ru.bro.bac'te.ra.les. N.L. masc. n.
Solirubrobacter
type genus of the order; suff. ‐
ales
ending to denote an order; N.L. fem. pl. n.
Solirubrobacterales
the
Solirubrobacter
order.

Actinobacteria \ Thermoleophilia \ Solirubrobacterales
Clostridiales
Authors: Rainey Fred A.
Published: August 2015

Clos.tri'di.a'les. N.L. neut. n.
Clostridium
type genus of the order; suff. ‐
ales
ending denoting an order; N.L. fem. pl. n.
Clostridiales
the order
Clostridium
.

Firmicutes / “Clostridia” / Clostridiales
Halanaerobiales
corrig
Authors: Oren Aharon
Published: August 2015

Hal.an.ae.ro.bi.a'les. N.L. fem. pl. n.
Halanaerobiaceae
type family of the order; ‐
ales
ending to denote an order; N.L. fem. pl. n.
Halanaerobiales
the
Halanaerobiaceae
order.

Firmicutes / “Clostridia” / Halanaerobiales
Sphingomonadales ord. nov
Authors: Yabuuchi Eiko , Kosako Yoshimasa
Published: August 2015

Sphing.o.mon.a.da' les
. M.L. fem. n.
Sphingomonas
type genus of the order; ‐
ales
ending to denote an order; M.L. fem. pl. n.
Sphingomonadales
the order of
Sphingomonas
.

Proteobacteria / Alphaproteobacteria / Sphingomonadales
Alteromonadales ord. nov.
Authors: Bowman John P. , McMeekin Thomas A.
Published: August 2015

Al.ter.o.mon.a.da' les
. M.L. fem. n.
Alteromonas
the type genus of the order; L. suff. ‐
ales
ending which denotes an order; M.L. fem. n.
Alteromonadales
the
Alteromonas
order.

Proteobacteria / Gammaproteobacteria / Alteromonadales
Spirochaetales
Authors: Paster Bruce J.
Published: August 2015

Spi.ro.chae.ta'les. N.L. fem. n.
Spirochaeta
type genus of the order; ‐
ales
suffix to denote an order; N.L. fem. pl. n.
Spirochaetales
the
Spirochaeta
order.

Spirochaetes / Spirochaetia / Spirochaetales
Synergistales
Authors:   Editorial Board
Published: August 2015

Syn.er.gist'al.es. N.L.. masc. n.
Synergistes
–type genus of the order; suff. –
ales
ending to denote order; N.L. fem. pl. n.
Synergistales
the order of the genus
Synergistes
.

Synergistetes / Synergistia / Synergistales
Aquificae phy. nov.
Authors: Reysenbach Anna‐Louise
Published: August 2015

A.qui.fi' cae
. M.L. fem. pl. n.
Aquificales
type order of the phylum; dropping the ending to denote a phylum; M.L. fem. pl. n.
Aquificae
the phylum of
Aquificales
.

Aquificae
Robust adaptive consensus tracking for higher‐order multi‐agent uncertain systems with nonlinear dynamics via distributed intermittent communication protocol
Authors: Wang Bohui , Wang Jingcheng , Zhang Langwen , Zhang Bin
Published: August 2015

This paper considers the robust adaptive consensus tracking for higher‐order multi‐agent uncertain systems with nonlinear dynamics via distributed intermittent communication protocol. The main contribution of this work is solving the robust consensus tracking problem without the assumption that the topology among followers is strongly connected and fixed. The focus is the problem of actuator with occasional failure inputs and communication resources constraints. A novel distributed intermittent communication framework is proposed via adaptive approach. In this framework, the underlying communication topologies switch among several directed graphs with a limited directed spanning tree rooted at a leader agent. Furthermore, by introducing a strategy of actuator fault compensation inputs, a combination of robust consensus tracking protocol is designed by the different adaptive feedback controllers. It is proved that the robust adaptive consensus tracking can be achieved by using local states information of neighboring agents if the communication retention rate condition is satisfied. Two examples are presented to demonstrate the effectiveness of the proposed approach. Copyright © 2015 John Wiley & Sons, Ltd.
Unusual Circularly Polarized Photocatalytic Activity in Nanogapped Gold–Silver Chiroplasmonic Nanostructures
Authors: Hao Changlong , Xu Liguang , Ma Wei , Wu Xiaoling , Wang Libing , Kuang Hua , Xu Chuanlai
Published: August 2015

Gold‐gap‐silver nanostructures (GGS NSs) with interior nanobridged gaps are enantioselectively fabricated. Guided by l/d‐cysteine, the GGS‐L/D (L/D represents l/d‐cysteine) NSs show reversed plasmon‐induced circular dichroism (CD) signals in the visible region. It is found that the nanogap plays a key role in the plasmonic CD of GGS NSs and the chiroptical response can be tailored by adjusting the amount of cysteine. The anisotropy factor of GGS‐L/D NSs with a 0.5 nm interior gap at 430 nm is as high as ≈0.01. The circularly polarized photocatalytic activity of GGS NSs is examined. It is shown that upon irradiation with left‐circularly polarized light, the catalytic efficiency of GGS‐L NSs is 73‐fold and 17‐fold higher than that of Au nanoparticles (NPs) and Au@Ag core–shell NPs, respectively. Upon irradiation with right‐circularly polarized light, the catalytic activity of GGS‐D NSs is about 71 times and 17 times higher than that of Au NPs and Au@Ag core–shell NPs, respectively. These unique chiral NSs with high plasmonic response can be applied to enantioselective catalysis.
Comparing the prognostic value of risk stratifying models for patients with lower‐risk myelodysplastic syndromes: Is one model better?
Authors: Zeidan Amer M. , Sekeres Mikkael A. , Wang Xiao‐Feng , Al Ali Najla , Garcia‐Manero Guillermo , Steensma David P. , Roboz Gail , Barnard John , Padron Eric , DeZern Amy , Maciejewski Jaroslaw P. , List Alan F. , Komrokji Rami S. ,   on Behalf of the MDS Clinical Research Consortium (Funded by Edward P. Evans Foundation)
Published: August 2015

Some patients classified as having lower‐risk (LR)‐disease by the International Prognostic Scoring System (IPSS) fare more poorly than predicted. We examined the prognostic utility of IPSS, the MD Anderson LR‐Prognostic System (LR‐PSS), and the revised IPSS (IPSS‐R) in a large cohort of patients classified as having IPSS LR‐MDS in the MDS Clinical Research Consortium database. Actual overall survival (OS) was assessed in patients with IPSS LR‐MDS (i.e. low and intermediate‐1) using Kaplan–Meier methods. Harrell's c index (HCI) and Akaike information criteria (AIC) were used to compare the models. Median OS of 1,140 eligible patients was 47 months (95% CI, 44–52). Median follow‐up was 62 months. HCI values indicating the discriminatory power of the models (higher is better) were better for LR‐PSS (0.74, 95% CI, 0.70–0.78) than IPSS‐R (0.64, 95% CI, 0.60–0.67) and IPSS (0.64, 95% CI, 0.60–0.68). Similarly, AIC values indicating the goodness of the fit were better for LR‐PSS than IPSS‐R and IPSS (8,110, 8,147, and 8,150, respectively, lower is better). LR‐PSS assigned 25.1% and 37.4% of patients with IPSS LR‐MDS into LR‐PSS Category 3 and IPSS‐R Categories ≥Intermediate, respectively. Of 291 patients (25.5%) who survived ≤24 months from diagnosis, only 37.1% and 45% were classified as LR‐PSS category 3 and IPSS‐R categories ≥Intermediate, respectively (P = 0.06). While both LR‐PSS and IPSS‐R distinguish groups with varied survival outcome among patients with IPSS LR‐MDS, both tools fail to identify a significant subset with poor OS. Future studies should assess whether patients identified as at increased risk will benefit from earlier interventions with disease‐modifying therapies. Am. J. Hematol. 90:1036–1040, 2015. © 2015 Wiley Periodicals, Inc.
Clinical features of pulmonary arterial hypertension in patients receiving dasatinib
Authors: Shah Neil P. , Wallis Nicola , Farber Harrison W. , Mauro Michael J. , Wolf Robert A. , Mattei Daniele , Guha Mausumee , Rea Delphine , Peacock Andrew
Published: August 2015

The prognosis of most leukemia patients treated with BCR‐ABL tyrosine kinase inhibitors (TKIs) is favorable, and a more precise understanding of serious and potentially irreversible treatment‐related toxicities is essential to properly inform treatment choice. Few cases of pulmonary arterial hypertension (PAH) have been reported in patients with leukemia treated with dasatinib, a second‐generation BCR‐ABL TKI. To better understand characteristics and outcomes of dasatinib‐treated patients with PAH, all clinical cases of PAH confirmed by right‐heart catheterization in the Bristol‐Myers Squibb pharmacovigilance database (N = 41), including 22 previously unpublished cases, were examined for previous treatments for leukemia, patient characteristics, time to PAH onset, and outcomes. Our analysis shows that compared with PAH due to other etiologies, dasatinib‐related PAH is atypical, in that it is associated with partial to complete reversibility upon treatment discontinuation. The incidence of dasatinib‐related PAH appears to be low. Most PAH cases were observed in patients who had received prior treatments for leukemia. No specific patient attributes appear to be associated with an increased risk of developing PAH while receiving dasatinib. Symptoms of PAH in dasatinib‐treated leukemia patients should prompt a thorough workup, including consideration of confirmatory right‐heart catheterization. In cases of confirmed PAH, dasatinib should be discontinued. Am. J. Hematol. 90:1060–1064, 2015. © 2015 Wiley Periodicals, Inc.
Clinical and molecular characterization of seven Egyptian families with autosomal recessive robinow syndrome: Identification of four novel ROR2 gene mutations
Authors: Aglan Mona , Amr Khalda , Ismail Samira , Ashour Adel , Otaify Ghada A. , Mehrez Mennat Allah I. , Aboul‐Ezz Eman H. A. , El‐Ruby Mona , Mazen Inas , Abdel‐Hamid Mohamed S. , Temtamy Samia A.
Published: August 2015

Robinow syndrome (RS) is a rare genetic disorder characterized by limb shortening, genital hypoplasia, and craniofacial/orodental abnormalities. The syndrome follows both autosomal dominant and recessive patterns of inheritance with similar phenotypic presentation and overlapping features. Autosomal recessive Robinow syndrome (ARRS) is caused by mutations in the ROR2 gene. Here, we present the clinical, radiological and molecular findings of 11 Egyptian patients from 7 unrelated consanguineous families with clinical features of ARRS. Mutation analyses of ROR2 gene identified five pathogenic mutations distributed all over the gene. The identified mutations included four novel (G326A, D166H, S677F, and R528Q) and one previously reported (Y192D). Our results extend the number of ROR2 mutations identified so far, suggest a founder effect in the Egyptian population, and emphasize the important role of genetic testing in proper counseling and patients' management. © 2015 Wiley Periodicals, Inc.
Jacobsen syndrome: Advances in our knowledge of phenotype and genotype
Authors: Favier Remi , Akshoomoff Natacha , Mattson Sarah , Grossfeld Paul
Published: August 2015

In 1973, the Danish geneticist Petrea Jacobsen described a three‐generation family in which the proband carried a presumed terminal deletion at the end of the long arm of chromosome 11 (11q). This patient had dysmorphic features, congenital heart disease, and intellectual disability. Since Dr. Jacobsen's initial report, over 200 patients with Jacobsen syndrome have been reported, suggesting that Jacobsen syndrome is a contiguous gene disorder. With the advent of high resolution deletion mapping and the completion of the human genome sequencing project, a comprehensive genotype/phenotype analysis for Jacobsen syndrome became possible. In this article, we review research describing individual causal genes in distal 11q that contribute to the overall Jacobsen syndrome clinical phenotype. Through a combination of human genetics and the use of genetically engineered animal models, causal genes have been identified for the clinical problems in JS that historically have caused the greatest morbidity and mortality: congenital heart disease, the Paris–Trousseau bleeding disorder, intellectual disability, autism, and immunodeficiency. Insights gained from these studies are being applied for future drug development and clinical trials, as well as for a potential strategy for the prevention of certain forms of congenital heart disease. The results of these studies will likely not only improve the prognostic and therapeutic approaches for patients with Jacobsen syndrome, but also for the general population afflicted with these problems. © 2015 Wiley Periodicals, Inc.
Inter‐individual variation in weaning among rhesus macaques (Macaca mulatta): Serum stable isotope indicators of suckling duration and lactation
Authors: Reitsema Laurie J. , Partrick Katherine A. , Muir Andrew B.
Published: August 2015

Weaning is a transition in early development with major implications for infant survival and well‐being, and for maternal lifetime reproductive success. The particular strategy a primate mother adopts in rearing her offspring represents a negotiation between her ability to invest and her need to invest, and can be considered adaptive and influenced by biological and social factors. Any investigation into how and why maternal weaning strategies differ among non‐human primates is limited by the precision of the measurement tool used to assess infants' weaning ages. Stable carbon and nitrogen isotope analysis of soft tissues (e.g., hair, nails, feces, urine, blood) offers an objective means of monitoring the weaning status of infants. In this study, we assess stable isotope ratios in blood serum from 14 captive rhesus macaque dyads (Macaca mulatta) at infant ages 2, 5, 6, 7, 8, and 10 months to estimate the timing of weaning events. Male infants wean earlier than female infants. Infants with the lowest birth weights wean latest. Most infants wean upon reaching 2.5 times their birth weights, sooner than when weaning elsewhere has been predicted for captive cercopithecine primates. The longest weaning periods (ca. 10 months) are observed among infants of small mothers. The shortest weaning period, between 2 and 5 months, was among the lowest ranking dyad. Parity and mothers' ages had no discernible effect on the timing of weaning events. The stable carbon and nitrogen isotope values of dams during lactation are significantly different than those of a non‐lactating adult female outgroup, raising questions about the suitability and selection of adult comparative baselines in studies where lactating mothers cannot be sampled longitudinally (e.g., bioarchaeology; paleontology). Am. J. Primatol. 78:1113–1134, 2016. © 2015 Wiley Periodicals, Inc.