bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of the fossils in molecular clocks: an example using chelid turtles
Authors: Holley Juan Alfredo , Basso Néstor Guillermo , Sterli Juliana 
Published: January 2018

Background. The clade Chelidae (Testudines, Pleurodira) is a group of fresh water turtles with representatives in Australasia and South America. Its diversity of extant and fossil species is characterized by two recognized morphotypes: the long-necked and the short-necked chelids. So far, the phylogenies constructed over Chelidae differ depending on the information source. While morphology recovers one monophyletic group of long-necked chelids (with South American and Australasian species), the molecular data split the group into South American and Australasian chelids, both as monophyletic sister groups and containing long-necked species. The consequences of this conflict imply the emergence of long-necked chelids (i) one time before the final breakup of Southern Gondwana (≅ 35 Mya) or (ii) independently after this event.
Methods. Using BEAST, a set of molecular clock analyses was performed. Seven of these analyses correspond to the molecular hypothesis and thirteen to the morphological hypothesis. So, ten fossils were used as calibration points in different combinations for each hypothesis. The results were statistically compared performing ANOVA and the global similarity was inspected by a hierarchical cluster analysis (HCA).
Results. Molecular hypothesis: all the analyses produced an age of the origin of Chelidae, and rising of long neck, older than 35 Mys. Divergence times in the South American clade were generally older than the observed in the Australasian clade. The result of the HCA was: analyses 2, 4 and 5 form a group and the analyses 3, 6 and 7 form another group; the analysis 1 is close related to this last. Morphological hypothesis: the origin of the clade of long-necked chelids predated the 35 Mys in all the analyses except one; however the Chelodina group resulted younger than this age in all the analyses. The HCA yielded two main groups of molecular clock analyses (1, 3, 7, 8, 9, 13 and 2, 4, 6, 10, 11, 12) and one analysis (5) clearly separated of these two. The ANOVA resulted in significant differences for all estimated nodes in both phylogenetic hypotheses.
Discussion. Our set of molecular clock analyses suggests an early diversification of the chelid turtles and the raising of the long-necked chelids before the final breakup of Southern Gondwana. However, the appearance of this trait one time or as evolutionary convergence still depends on which phylogenetic scenario is taken into account. Furthermore, our results indicate that the number of calibration points not necessarily improve the precision of estimated nodes. Instead the “quality” of the fossils used as calibrations and its position in the phylogeny, have appreciable impact not only over this parameter, but also over the global evolutionary rate along the tree.
A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments
Authors: Bokulich Nicholas A , Rideout Jai Ram , Kopylova Evguenia , Bolyen Evan , Patnode Jessica , Ellett Zach , McDonald Daniel , Wolfe Benjamin , Maurice Corinne F , Dutton Rachel J , Turnbaugh Peter J , Knight Rob , Caporaso J Gregory 
Published: January 2018

Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms.
Results: We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtime up to two-fold and achieve high-precision genus-level assignments; an evaluation of classification methods that highlights differences in performance with different marker genes and at different levels of taxonomic resolution; and an extensible framework for evaluating and optimizing new classification methods, which we hope will serve as a model for standardized and reproducible bioinformatics methods evaluations.
Conclusions: Our new methods are accessible in QIIME 1.9.0, and our evaluation framework will support ongoing optimization of classification methods to complement rapidly evolving short-amplicon sequencing and bioinformatics technologies. Static versions of all of the analysis notebooks generated with this framework, which contain all code and analysis results, can be viewed at http://bit.ly/srta-012 .
Urban heat island effect on cicada densities in metropolitan Seoul
Authors: Nguyen Hoa Q. , Andersen Desiree K. , Kim Yuseob , Jang Yikweon 
Published: January 2018

Background
Urban heat island (UHI) effect, the ubiquitous consequence of urbanization, is considered to play a major role in population expansion of numerous insects. Cryptotympana atrata and Hyalessa fuscata are the most abundant cicada species in the Korean Peninsula, where their population densities are higher in urban than in rural areas. We predicted a positive relationship between the UHI intensities and population densities of these two cicada species in metropolitan Seoul.

Methods
To test this prediction, enumeration surveys of cicada exuviae densities were conducted in 36 localities located within and in the vicinity of metropolitan Seoul. Samples were collected in two consecutive periods from July to August 2015. The abundance of each species was estimated by two resource-weighted densities, one based on the total geographic area, and the other on the total number of trees. Multiple linear regression analyses were performed to identify factors critical for the prevalence of cicada species in the urban habitat.

Results
C. atrata and H. fuscata were major constituents of cicada species composition collected across all localities. Minimum temperature and sampling period were significant factors contributing to the variation in densities of both species, whereas other environmental factors related to urbanization were not significant. More cicada exuviae were collected in the second rather than in the first samplings, which matched the phenological pattern of cicadas in metropolitan Seoul. Cicada population densities increased measurably with the increase in temperature. Age of residential complex also exhibited a significantly positive correlation to H. fuscata densities, but not to C. atrata densities.

Discussion
Effects of temperature on cicada densities have been discerned from other environmental factors, as cicada densities increased measurably in tandem with elevated temperature. Several mechanisms may contribute to the abundance of cicadas in urban environments, such as higher fecundity of females, lower mortality rate of instars, decline in host plant quality, and local adaptation of organisms, but none of them were tested in the current study.

Conclusions
In sum, results of the enumeration surveys of cicada exuviae support the hypothesis that the UHI effect underlies the population expansion of cicadas in metropolitan Seoul. Nevertheless, the underlying mechanisms for this remain untested.
Selectivity of Nanoporous MnO2 and TiO2 Membranes for Residual Contaminants in Treated Wastewater
Authors: Giwa Adewale , Jung Sung M. , Ahmed Menatalla , Fang Wenjing , Kong Jing , Hasan Shadi W. 
Published: January 2018

AbstractTreated effluent from an electrically enhanced membrane bioreactor (eMBR) was filtered through MnO2 or TiO2 nanoporous membranes for the removal of residual heavy metals, bacteria, and biological oxygen demand (BOD). The fresh and spent membranes were characterized via energy‐dispersive X‐ray spectroscopy (EDAX), zeta potential analysis, and thermogravimetric analysis (TGA). Water analysis was performed by means of UV/Vis spectrophotometry. For most contaminants, eMBR‐TiO2 showed highest removal efficiency compared to MnO2 because of the combined adhesion and photocatalytic effects of TiO2. Meanwhile, eMBR‐MnO2 provided higher removal efficiency for Fe.
In Vitro Induction of Hepatocyte Synthesis of the Acute Phase Reactant Mouse Serum Amyloid P-Component by Macrophages and IL 1
Authors: Le Phong T , Mortensen Richard F 
Published: January 2018

Abstract
The in vitro culture conditions for the induction and synthesis of the mouse acute phase reactant, serum amyloid P-component (SAP), were established using isolated hepatocytes. SAP synthesis was five to eight times greater with hepatocytes isolated from mice during the acute phase of inflammation vs. hepatocytes obtained from untreated mice. The induction of SAP synthesis in normal hepatocytes for LPS-unresponsive mice was macrophage dependent. Activated macrophages provided the most “helper” activity for SAP production. Partially purified mouse IL 1 from the P388D1 macrophage line also induced SAP synthesis. Only four IL 1 units/ml were required for optimal SAP induction. The addition of IL 1 in the presence of elicited macrophages provided an additive effect on hepatocyte SAP synthesis. The SAP-inducing activity of IL 1 copurified with its thymocyte-stimulating activity and was associated with a 11 to 25-Kd MW polypeptide. Phenylglyoxal treatment of IL 1 inactivated its thymocyte stimulating activity but not its SAP inducing potential. Inhibition of m-RNA synthesis, protein synthesis, N-glycosylation, and protein secretion effectively prevented in vitro hepatocyte SAP production.
Antioxidant Effects on Cell-Mediated Immunity
Authors: Meeker Harry C , Eskew Mary Lou , Scheuchenzuber William , Scholz Richard W , Zarkower Arian 
Published: January 2018

Abstract
Experiments were performed to determine the effects of dietary selenium and/or vitamin E deficiency on cell-mediated cytotoxicity in the mouse. Natural killer cell-mediated cytotoxicity (NKCC) was depressed after 8 wk on diets deficient in selenium and/or vitamin E. In contrast, antibody-dependent cell-mediated cytotoxicity (ADCC) was not affected by 8 wk of dietary deficiency of selenium and/or vitamin E. T-lymphocyte-mediated cytotoxicity (TCMC) was found to be depressed by combined selenium-vitamin E deficiency after 7 weeks on diets.
1α,25 Dihydroxyvitamin D3 and Mononuclear Phagocytes: Enhancement of Mouse Macrophage and Human Monocyte Hydrogen Peroxide Production Without Alteration of Tumor Cytolysis
Authors: Gluck W Larry , Weinberg J Brice 
Published: January 2018

Abstract
1α,25 dihydroxyvitamin D3 (1,25 D3) is known to interact with hematopoietic cells. The purpose of this study was to determine the effect of 1,25 D3 on hydrogen peroxide (H2O2) production and tumor cell killing by mouse peritoneal macrophages and human blood monocytes. Enhanced monocyte and macrophage phorbol myristate acetate (PMA)-stimulated H2O2 production was observed at concentrations of 0.13 to 130 nM 1,25 D3 and and was maximal at 1.3 nM. At concentrations of 100 U/ml, gamma interferon (IFN-γ) alone had a similar effect but, in combination with 1,25 D3, there was no cooperative effect. At concentrations ranging from 0.13 to 130 nM, 1,25 D3 failed to augment tumor cell lysis by macrophages from peptone-injected normal or bacillus Calmette-Guerin (BCG)-infected mice, or by blood monocytes from normal humans. Our results indicate that 1,25 D3 can activate the monocyte and macrophage for H2O2 secretion without concomitant activation for tumor cell killing.
Inhibition of NK and ADCC Activity by Antibodies Against Purified Cytoplasmic Granules From Rat LGL Tumors
Authors: Reynolds Craig W , Reichardt Della , Henkart Maryanna , Millard Paul , Henkart Pierre 
Published: January 2018

Abstract
Highly purified preparations of cytoplasmic granules from transplantable rat large granular lymphocyte (LGL) tumor lines (rat natural killer (RNK) tumors) were used to immunize rabbits. Antibodies from these animals gave two precipitin lines with granule extracts in Ouchterlony experiments. They reacted with at least four different bands on nitrocellulose blots of SDS gels of LGL granule proteins. By immunofluorescence, specifically adsorbed antigranule antibodies did not recognize LGL or T cell surface antigens but reacted with the cytoplasmic granules in permeabilized RNK tumor cells as well as with normal rat LGL. These same antisera showed little or no reactivity with a panel of other cells, including peripheral blood T cells, thymocytes, macrophages, and EL-4 tumor cells. F(ab′)2 preparations of these antigranule antibodies completely blocked granule-mediated lysis of both SRBC and nucleated targets, while control F(ab′)2 preparations from rabbits immunized with EL-4 granules or TNP-KLH showed no significant inhibition of this cytolytic activity at the same antibody concentration. Anti-granule F(ab′)2 preparations specifically inhibited (&gt;75%) rat natural killer (NK) and antibody-dependent cellular cytotoxicity (ADCC) activities in a dose-dependent manner but did not effect cytotoxic T cell activity. Pretreatment of either effectors or targets by these antibodies had no effect. Anti-granule F(ab′)2 preparations, at concentrations showing strong inhibition of lysis, did not inhibit the binding of LGL to YAC-1 or Ab-coated P815 targets. These results demonstrate that a granule component(s) is necessary for the lytic activity of LGL in both NK and ADCC and provide the first direct evidence that a secretory event involving these granules is part of the lytic process.
Pulmonary Interstitial Macrophages: Isolation and Flow Cytometric Comparisons With Alveolar Macrophages and Blood Monocytes
Authors: Dethloff L A , Lehnert B E 
Published: January 2018

Abstract
Pulmonary interstitial macrophages (IM) were isolated from rat lungs by an Fcγ receptor-based affinity technique coupled with multiparameter flow cytometry. Single cell suspensions obtained by collagenase digestion of extensively perfused and lavaged lungs were applied to carpets of opsonized sheep red blood cells (SRBC-IgG) bound to plastic tissue culture flasks. At 0-4°, optimal binding of lung cells occurred within 60 min at plating densities of 1-2 × 106 lung cells/cm2 when the SRBC substrate was opsonized with 10 μg/ml anti-SRBC IgG. Nonadherent cells were removed by gently rinsing the plates and adherent cells were recovered by lysing the SRBC-IgG substrata. By light microscopy, the mixture of adherent cells was comprised of mononuclear cells (~ 54%), many of which appeared to be macrophages, lymphocytes (~20%), polymorphonuclear leukocytes (~15%), plasma cells (~8%), eosinophils (~2%), and mast cells (~0.5%). The cells which adhered to the SRBC-IgG monolayers were further resolved into subpopulations by multiparameter flow cytometry and sorted according to their electro-optical characteristics. One subpopulation appeared morphologically to be macrophages, and &gt;90% of these cells readily phagocytized SRBC-IgG in vitro. Peroxidase staining of this population was minimal, indicating that these cells were not blood monocytes (BM). Using a method by which alveolar macrophages (AM) were prelabeled with SRBC-IgG in situ, we demonstrated that alveolar macrophages constituted only ~5% of the total adherent cell population. We concluded from these observations that the macrophage population harvested in this manner were neither BM nor AM, but, rather, were harvested from the lung’s interstitial compartment. Flow cytometric analyses indicated that the IM exhibited electro-optical characteristics intermediate between those of BM and AM, which is consistent with the concept of the lung’s interstitium as a maturation compartment for the BM prior to migration into the alveolar compartment. However, the IM more closely resembled the BM than the AM, indicating that if the IM is in fact a precursor to the AM population, substantial maturation or differentiation must occur subsequent to its migration into the alveolar compartment. This isolation technique will be useful for harvesting highly purified IM for in vitro investigations.
Phorbol Myristate Acetate Induced Oxidation of 2′,7′-Dichlorofluorescin by Neutrophils From Patients With Chronic Granulomatous Disease
Authors: Hassan Nassef F , Campbell Donald E , Douglas Steven D 
Published: January 2018

Abstract
The oxidative metabolic burst of stimulated human polymorphonuclear leukocytes (PMNs) has been evaluated by the measurement of oxygen consumption, chemiluminescence, and oxygen radicals (O2-, H2O2,OH-) derived from activation of the hexose monophosphate shunt (HMPS). PMNs from patients with chronic granulomatous disease (CGD) are shown to lack functional NADPH oxidase and undetectable oxygen radical generation. However, using single cell analysis by flow cytometry and 2′,7′-dichlorofluorescin (DCFH) oxidation by H2O2, significant DCFH oxidation by the PMA stimulated CGD PMNs was observed. Furthermore, 1mM potassium cyanide enhanced DCFH oxidation by control and CGD PMNs. DCFH oxidation by cells from an obligate heterozygous mother of an X-linked CGD patient was intermediate. These observations suggest that a PMA induced oxidase enzyme is present in CGD cells.
The Human Promyelocytic Leukemia Cell (HL-60 Cell) β-Adrenergic Receptor
Authors: Sager G , Bang B E , Pedersen M , Aarbakke J 
Published: January 2018

Abstract
We have characterized the β-adrenergic receptor binding site and the β-adrenergic cAMP response of the HL-60 cell. The hydrophilic ligand [3H]-(–)-CGP-12177 was specifically and reversibly bound to one single class of binding sites (Kd 220 pM and Bmax 1,970 sites/cell). The adrenergic agonists inhibited the specific radioligand binding. The order of potency was isoproterenol &gt; epinephrine &gt; norepinephrine. The β-2 selective antagonist ICI 118551 had a binding affinity 3 orders of potency higher than the β-1 selective antagonist, atenolol. The adrenergic agonists elevated the cAMP accumulation in a concentration-dependent mode. The order of potency was isoproterenol &gt; epinephrine &gt; norepinephrine. Both the binding and the functional studies revealed stereospecificity and reversibility. The present data show that HL-60 cells possess β-2 adrenergic receptors functionally coupled to adenylate cyclase.
Modulation of c-fms Proto-Oncogene Expression in Human Blood Monocytes and Macrophages
Authors: Radzun Heinz J , Kreipe Hans , Heidorn Klaus , Parwaresch Mohammad R 
Published: January 2018

Abstract
The gene product of the c-fms proto-oncogene is a transmembrane protein with tyrosine-kinase activity that is obviously related to the receptor for the colony-stimulating-factor CSF-1. By Northern blot analysis, we investigated the expression of the cellular counterpart of v-fms in purified normal human blood mononuclear cells and different macrophage populations. The proto-oncogene c-fms expression was demonstrable in blood monocytes but not in blood lymphocytes. Short-term cultivated blood monocytes exhibited an increased expression of c-fms in comparison to freshly isolated blood monocytes, possibly due to a temporary down regulation of c-fms during the separation procedure of blood monocytes. A comparably high rate of fms-RNA expression was found in most of the analyzed samples of resident peritoneal macrophages, while resident alveolar macrophages showed a considerably lower level of c-fms expression. In this, alveolar macrophages resembled long-term cultivated adherent blood monocytes, which showed a down regulation of c-fms expression. By correlating these data obtained by Northern blot analysis with phenotypic properties of the analyzed monocyte/macrophage populations, it is concluded that different levels of c-fms expression in monocytes/macrophages correspond to their stage of differentiation and maturity.
3-Deaza-Adenosine Inhibition of Stimulus-Response Coupling in Human Polymorphonuclear Leukocytes
Authors: Fantone Joseph C , Duque Ricardo E , Davis Bruce H , Phan Sem H 
Published: January 2018

Abstract
In an effort to define better the functional role of S-adenosyl-methionine-mediated methylation reactions in modulating polymorphonuclear (PMN) functional responses to chemotactic stimuli, we investigated the effects of 3-deaza-adenosine (3-DZA), a known inhibitor of methylation reactions in phagocytic cells, on formyl methionyl-leucyl-phenylalanine (FMLP)-induced responses in human PMN leukocytes. Using the fluorescent cyanine dye 3,3′-dipropylthiocarbocyanine (di-S-C3-(5)) as an optical probe of membrane potential we observed that 3-DZA at concentrations that inhibit FMLP-induced O2− production does not significantly alter FMLP-induced changes in transmembrane potential. Additional studies showed an inhibitory effect of 3-DZA on FMLP-induced PMN pinocytosis and to a lesser degree on FMLP-induced degranulation. However, pretreatment of PMNs with 3-DZA did not alter FMLP-induced changes in Quin-2 fluorescence, an indicator of changes in intracellular calcium levels. These findings demonstrate a dissociation between chemotactic factor-induced cell membrane depolarization, changes in intracellular calcium, and specific neutrophil functional responses and suggest that chemotactic factor-induced changes in transmembrane potential and intracellular calcium are independent of chemotactic factor-induced methylation reactions. Furthermore, 3-DZA did not alter phorbol myristate acetate induced O2− production or fluid pinocytosis indicating a stimulus specificity for the inhibitory effects of this agent on O2− production.
Endocytic and Secretory Repertoire of the Lipid-Loaded Macrophage
Authors: Montgomery Ruth R , Cohn Zanvil A 
Published: January 2018

Abstract
We have studied the effects of intracellular lipid storage on macrophage function. Mouse peritoneal macrophages were lipid loaded by three regimens modeling loading through the scavenger receptor [acetylated low density lipoprotein (Ac-LDL) cells], by extracellular matrix-bound LDL [low density lipoprotein complexed with dextran sulfate (DS-LDL) cells], and by conditions of reduced cholesterol acceptors in the medium [low serum, oleic acid, Ac-LDL (LS/OI) cells]. Significantly increased cholesterol levels in all three regimens were measured by cholesterol determination and Oil Red O staining of fixed cells. Upid-laden cells were equal to control macrophages in binding and ingesting immunoglobulin-coated sheep erythrocytes, reflecting Fc-mediated endocytosis. The lipid-laden cells were compared to control cells for secretory functions of macrophages that could be important in the atherosclerotic artery. They were still capable of producing all secretory products examined, but the quantities of H2O2 and arachidonic acid metabolites were reduced in some cases, and fibrinolytic activity appeared to be increased. Western blot analysis showed a five-fold increase in the release of tumor necrosis factor by DS-LDL-loaded cells. We suggest that the location of intracellular lipid pools as well as the type of lipids (and/or lipid complexes) ingested may determine the extent of functional changes.