bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of multiple probes on the hybridization of target DNA on surfaces
Authors: Welling Ryan C. , Knotts Thomas A.
Published: January 2015

DNA microarrays have disruptive potential in many fields including genetics and medicine, but the technology has yet to find widespread clinical use due to poor reliability. Microarrays work on the principle of hybridization and can only be as dependable as this process is reliable. As such, a significant amount of theoretical research has been done to understand hybridization on surfaces on the molecular level. Previous simulations of a target strand with a single, surface-tethered probe molecule have yielded valuable insights, but such is an ideal system and little is known about the effects of multiple probes—a situation that more closely approximates the real system. This work uses molecular simulation to determine the specific differences in duplex stability between one, three, six, and nine tethered probes on a surface. The results show that it is more difficult for a single target to hybridize to a probe as the number of probes on the surface increases due to crowding effects; however, once hybridized, the duplex is more stable than when fewer probes are present. The data also indicate that hybridization of a target to a probe on the face of a group of probes is more stable than hybridization to probes at the edge or center locations. Taken as a whole, the results offer new insights into the cause of the poor reproducibility exhibited by microarrays.
Bistability in a self-assembling system confined by elastic walls: Exact results in a one-dimensional lattice model
Authors: Pȩkalski J. , Ciach A. , Almarza N. G.
Published: January 2015

The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk. Exact and asymptotic expressions for the local density and for the effective potential between the confining surfaces are obtained for a one-dimensional lattice model introduced by J. Pȩkalski et al. [J. Chem. Phys. 138, 144903 (2013)]. The simple asymptotic formulas are shown to be in good quantitative agreement with exact results for slits containing at least 5 layers. We observe that the incommensurability of the system size and the average distance between the clusters or layers in the bulk leads to structural deformations that are different for different values of the chemical potential μ. The change of the type of defects is reflected in the dependence of density on μ that has a shape characteristic for phase transitions. Our results may help to avoid misinterpretation of the change of the type of defects as a phase transition in simulations of inhomogeneous systems. Finally, we show that a system confined by soft elastic walls may exhibit bistability such that two system sizes that differ approximately by the average distance between the clusters or layers are almost equally probable. This may happen when the equilibrium separation between the soft boundaries of an empty slit corresponds to the largest stress in the confined self-assembling system.
In silico infrared and Raman spectroscopy under pressure: The case of CaSnO3 perovskite
Authors: Maul J. , Erba A. , Santos I. M. G. , Sambrano J. R. , Dovesi R.
Published: January 2015

The CaSnO3 perovskite is investigated under geochemical pressure, up to 25 GPa, by means of periodic ab initio calculations performed at B3LYP level with local Gaussian-type orbital basis sets. Structural, elastic, and spectroscopic (phonon wave-numbers, infrared and Raman intensities) properties are fully characterized and discussed. The evolution of the Raman spectrum of CaSnO3 under pressure is reported to remarkably agree with a recent experimental determination [J. Kung, Y. J. Lin, and C. M. Lin, J. Chem. Phys. 135, 224507 (2011)] as regards both wave-number shifts and intensity changes. All phonon modes are symmetry-labeled and bands assigned. The single-crystal total spectrum is symmetry-decomposed into the six directional spectra related to the components of the polarizability tensor. The infrared spectrum at increasing pressure is reported for the first time and its main features discussed. All calculations are performed using the Crystal14 program, taking advantage of the new implementation of analytical infrared and Raman intensities for crystalline materials.
A structural study of a two-dimensional electrolyte by Monte Carlo simulations
Authors: Aupic Jana , Urbic Tomaz
Published: January 2015

Properties of superconducting and superfluid thin films, modeled as a two-dimensional classic Coulomb fluid, are connected to the molecular structure of the system. Monte Carlo simulations to explore structural properties and ordering in the classical two-dimensional Coulomb fluid were performed. The density dependence of translational order parameters at various temperatures and cluster distribution below and above the Kosterlitz-Thouless line were studied, and the percolation temperature threshold was determined. Results show that one could detect the insulator-conductor transition by observing the translational order parameters, average cluster number, or mean cluster size besides dielectric constant and dipole moment of the system.
Numerical modelling of underwater detonation of non-ideal condensed-phase explosives
Authors: Schoch Stefan , Nikiforakis Nikolaos
Published: January 2015

The interest in underwater detonation tests originated from the military, since the expansion and subsequent collapse of the explosive bubble can cause considerable damage to surrounding structures or vessels. In military applications, the explosive is typically represented as a pre-burned material under high pressure, a reasonable assumption due to the short reaction zone lengths, and complete detonation of the unreacted explosive. Hence, numerical simulations of underwater detonation tests have been primarily concerned with the prediction of target loading and the damage incurred rather than the accurate modelling of the underwater detonation process. The mining industry in contrast has adopted the underwater detonation test as a means to experimentally characterise the energy output of their highly non-ideal explosives depending on explosive type and charge configuration. This characterisation requires a good understanding of how the charge shape, pond topography, charge depth, and additional charge confinement affect the energy release, some of which can be successfully quantified with the support of accurate numerical simulations. In this work, we propose a numerical framework which is able to capture the non-ideal explosive behaviour and in addition is capable of capturing both length scales: the reaction zone and the pond domain. The length scale problem is overcome with adaptive mesh refinement, which, along with the explosive model, is validated against experimental data of various TNT underwater detonations. The variety of detonation and bubble behaviour observed in non-ideal detonations is demonstrated in a parameter study over the reactivity of TNT. A representative underwater mining test containing an ammonium-nitrate fuel-oil ratestick charge is carried out to demonstrate that the presented method can be readily applied alongside experimental underwater detonation tests.
Ferroelectric instabilities and enhanced piezoelectric response in Ce modified BaTiO3 lead-free ceramics
Authors: Brajesh Kumar , Kalyani Ajay Kumar , Ranjan Rajeev
Published: January 2015

The crystal structure, ferroelectric, and piezoelectric behaviors of the Ba(Ti1−xCex)O3 solid solution have been investigated at close composition intervals in the dilute concentration regime. Ce concentration as low as 2 mol. % induces tetragonal-orthorhombic instability and coexistence of the phases, leading to enhanced high-field strain and direct piezoelectric response. Detailed structural analysis revealed tetragonal + orthorhombic phase coexistence for x = 0.02, orthorhombic for 0.03 ≤ x ≤ 0.05, and orthorhombic + rhombohedral for 0.06 ≤ x ≤ 0.08. The results suggest that Ce-modified BaTiO3 is a potential lead-free piezoelectric material.
Numerical study on the power extraction performance of a flapping foil with a flexible tail
Authors: Wu J. , Shu C. , Zhao N. , Tian F.-B.
Published: January 2015

The numerical study on the power extraction performance of a flapping foil with a flexible tail is performed in this work. A NACA0015 airfoil is arranged in a two-dimensional laminar flow and imposed with a synchronous harmonic plunge and pitch rotary motion. A flat plate that is attached to the trailing edge of the foil is utilized to model a tail, and so they are viewed as a whole for the purpose of power extraction. In addition, the tail either is rigid or can deform due to the exerted hydrodynamic forces. To implement numerical simulations, an immersed boundary-lattice Boltzmann method is employed. At a Reynolds number of 1100 and the position of the pitching axis at third chord, the influences of the mass and flexibility of the tail as well as the frequency of motion on the power extraction are systematically examined. It is found that compared to the foil with a rigid tail, the efficiency of power extraction for the foil with a deformable tail can be improved. Based on the numerical analysis, it is indicated that the enhanced plunging component of the power extraction, which is caused by the increased lift force, directly contributes to the efficiency improvement. Since a flexible tail with medium and high masses is not beneficial to the efficiency improvement, a flexible tail with low mass together with high flexibility is recommended in the flapping foil based power extraction system.
First-principles study of carbon impurities in CuInSe2 and CuGaSe2, present in non-vacuum synthesis methods
Authors: Bekaert J. , Saniz R. , Partoens B. , Lamoen D.
Published: January 2015

A first-principles study of the structural and electronic properties of carbon impurities in CuInSe2 and CuGaSe2 is presented. Carbon is present in organic molecules in the precursor solutions used in non-vacuum growth methods for CuInSe2 and CuGaSe2 based photovoltaic cells. These growth methods make more efficient use of material, time, and energy than traditional vacuum methods. The formation energies of several carbon impurities are calculated using the hybrid HSE06 functional. CCu acts as a shallow donor, CIn and interstitial C yield deep donor levels in CuInSe2, while in CuGaSe2 CGa and interstitial C act as deep amphoteric defects. So, these defects reduce the majority carrier (hole) concentration in p-type CuInSe2 and CuGaSe2 by compensating the acceptor levels. The deep defects are likely to act as recombination centers for the photogenerated charge carriers and are thus detrimental for the performance of the photovoltaic cells. On the other hand, the formation energies of the carbon impurities are high, even under C-rich growth conditions. Thus, few C impurities will form in CuInSe2 and CuGaSe2 in thermodynamic equilibrium. However, the deposition of the precursor solution in non-vacuum growth methods presents conditions far from thermodynamic equilibrium. In this case, our calculations show that C impurities formed in non-equilibrium tend to segregate from CuInSe2 and CuGaSe2 by approaching thermodynamic equilibrium, e.g., via thorough annealing.
Expression and function of transcription factor AP-2γ in early embryonic development of porcine parthenotes
Authors: Lee Sung-Hyun , Kwon Jung-Woo , Choi Inchul , Kim Nam-Hyung
Published: January 2015

Transcription factor AP-2γ (TFAP2C) is a member of the transcription factor activating enhancer binding protein (AP) family. In the present study we determined the temporal and spatial expression patterns of TFAP2C in porcine parthenotes during preimplantation development. Porcine TFAP2C transcripts were expressed at all stages of preimplantation development, with highest expression at the 8-cell stage. In contrast with the mouse, TFAP2C protein was not restricted to the trophectoderm and was also detected in the ICM in blastocyst stage porcine parthenotes. In knockdown (KD) experiments, most TFAP2C-depleted embryos were arrested before the compacted 8-cell stage. This developmental failure is attributed to abnormal expression of genes involved in cell adhesion, tight junction biogenesis and cell proliferation. Interestingly, although the conserved region 4 (CR4) of the porcine OCT4 5′ upstream regionlacked the AP2C-binding motif, OCT4 transcript levels were elevated in porcine TFAP2C-KD 8-cell embryos, suggesting TFAP2C may be involved in the regulation of OCT4 in porcine embryos through other mechanisms. In summary, the results suggest that TFAP2C is necessary for the transition from de novo transcript synthesis by activation to compaction and further development, and the different expression patterns of TFAP2C in porcine embryos may reflect species-specific functions during preimplantation embryo development.
Model-driven discovery of underground metabolic functions in
Escherichia coli
Authors: Guzmán Gabriela I. , Utrilla José , Nurk Sergey , Brunk Elizabeth , Monk Jonathan M. , Ebrahim Ali , Palsson Bernhard O. , Feist Adam M.
Published: January 2015

Significance

Organisms have evolved to take advantage of their environment. Enzymes drive this adaptability by displaying flexibility in terms of substrate specificity and catalytic promiscuity. This enzyme promiscuity has been observed in a limited number of laboratory experiments; however, a larger underground network of reactions may occur within a cell below the level of detection. It is not until a cell’s metabolic capabilities are probed that these novel functions come to light. In this study, a workflow is presented for probing promiscuous activity at the genome scale. This workflow combines genome-scale reconstructions of metabolic networks with gene KOs and adaptive laboratory evolution. Such tools become increasingly important when designing drugs targeting pathogenic bacteria or engineering enzymes and bacteria for biotechnology applications.
Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant
Authors: Kawato Tatsuya , Mizohata Eiichi , Shimizu Yohei , Meshizuka Tomohiro , Yamamoto Tomohiro , Takasu Noriaki , Matsuoka Masahiro , Matsumura Hiroyoshi , Kodama Tatsuhiko , Kanai Motomu , Doi Hirofumi , Inoue Tsuyoshi , Sugiyama Akira
Published: January 2015

The streptavidin/biotin interaction has been widely used as a useful tool in research fields. For application to a pre-targeting system, we previously developed a streptavidin mutant that binds to an iminobiotin analog while abolishing affinity for natural biocytin. Here, we design a bivalent iminobiotin analog that shows 1000-fold higher affinity than before, and determine its crystal structure complexed with the mutant protein.
Structural insights into stereospecific reduction of α, β-unsaturated carbonyl substrates by old yellow enzyme from Gluconobacter oxydans
Authors: Yin Bo , Deng Jian , Lim Lirong , Yuan Y Adam , Wei Dongzhi
Published: January 2015

We report the crystal structure of old yellow enzyme (OYE) family protein Gox0502 (a.a 1–315) in free form at 3.3 Å. Detailed structural analysis revealed the key residues involved in stereospecific determination of Gox0502, such as Trp66 and Trp100. Structure-based computational analysis suggested the bulky side chains of these tryptophan residues may play important roles in product stereoselectivity. The introduction of Ile or Phe or Tyr mutation significantly reduced the product diastereoselectivity. We hypothesized that less bulky side chains at these critical residues could create additional free space to accommodate intermediates with different conformations. Notably, the introduction of Phe mutation at residue Trp100 increased catalytic activity compared to wild-type Gox0502 toward a set of substrates tested, which suggests that a less bulky Phe side chain at residue W100F may facilitate product release. Therefore, Gox0502 structure could provide useful information to generate desirable OYEs suitable for biotechnological applications in industry.
In vitro reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in Rhodococcus jostii RHA1
Authors: Yamanashi Tomoya , Kim Seung-Young , Hara Hirofumi , Funa Nobutaka
Published: January 2015

The β-ketoadipate pathway is a major pathway involved in the catabolism of the aromatic compounds in microbes. The recent progress in genome sequencing has led to a rapid accumulation of genes from the β-ketoadipate pathway in the available genetic database, yet the functions of these genes remain uncharacterized. In this study, the protocatechuate branch of the β-ketoadipate pathway of Rhodococcus jostii was reconstituted in vitro. Analysis of the reaction products of PcaHG, PcaB, and PcaL was achieved by high-performance liquid chromatography. These reaction products, β-ketoadipate enol-lactone, 3-carboxy-cis,cis-muconate, γ-carboxymuconolactone, muconolactone, and β-ketoadipate, were further characterized using LC-MS and nuclear magnetic resonance. In addition, the in vitro reaction of PcaL, a bidomain protein consisting of γ-carboxy-muconolactone decarboxylase and β-ketoadipate enol-lactone hydrolase activities, was demonstrated for the first time. This work provides a basis for analyzing the catalytic properties of enzymes involved in the growing number of β-ketoadipate pathways deposited in the genetic database.
Water extract of Cinnamomum cassia suppresses angiogenesis through inhibition of VEGF receptor 2 phosphorylation
Authors: Kim Eok-Cheon , Kim Hye Jin , Kim Tack-Joong
Published: January 2015

Angiogenesis, the process of new blood vessel formation, has been a major target for cancer therapy. Antiangiogenic herbal medicines are useful in the treatment of cancer. In this study, we found that a water extract of Cinnamomum cassia (CCWE) was a potent inhibitor of angiogenesis. In cultured human umbilical vein endothelial cells, CCWE suppressed vascular endothelial growth factor (VEGF)-induced proliferation, migration, invasion, tube formation, and intracellular signaling events such as phosphorylation of ERK, p38 and VEGFR2, and activation of matrix metalloproteinase. Furthermore, CCWE inhibited VEGF-induced vessel sprouting of rat aorta ex vivo. These findings might be of particular interest for drug development because VEGF signaling is a potential target for treatment of angiogenesis-associated diseases.
Expression and characterization of Streptomyces coelicolor serine/threonine protein kinase PkaE
Authors: Urabe Hiroaki , Ogawara Hiroshi , Motojima Kiyoto
Published: January 2015

We identified and characterized a new eukaryotic-type protein kinase (PkaE) from Streptomyces coelicolor A3 (2) M145. PkaE, consisting of 510 amino acid residues, is a cytoplasmic protein kinase and contains the catalytic domain of eukaryotic protein kinases in the N-terminal region. Recombinant PkaE was found to be autophosphorylated at threonine residues only. The disruption of chromosomal pkaE resulted in the overproduction of the actinorhodin-related blue pigment antibiotics. pkaE was expressed during the late growth phase in S. coelicolor A3 (2) M145, which corresponded to the production time of blue pigments. This result indicated that PkaE acts as a negative regulator for production of the secondary metabolites. In addition, PkaE was able to phosphorylate KbpA, a regulator involved in the AfsK–AfsR regulatory pathway.
Activity of temocillin in a murine model of urinary tract infection due to Escherichia coli producing or not producing the ESBL CTX-M-15
Authors: Soubirou J. F. , Rossi B. , Couffignal C. , Ruppé E. , Chau F. , Massias L. , Lepeule R. , Mentre F. , Fantin B.
Published: January 2015

Objectives

Temocillin is a 6α-methoxy derivative of ticarcillin that is resilient to ESBLs. Prospective data about its in vivo activity remain scarce. Our aims were: (i) to evaluate the activity of temocillin in a urinary tract infection (UTI) model due to ESBL-producing Escherichia coli and compare it with that of imipenem; and (ii) to define in vivo susceptibility breakpoints.

Methods

Mice were infected with a susceptible E. coli CFT073-RR or its transconjugant (CFT073-RR Tc) harbouring a blaCTX-M-15-carrying plasmid, using an ascending UTI model. Therapeutic regimens were chosen in order to reproduce percentage of time of free drug concentrations above MIC (fT>MIC) obtained in humans with standard regimens of temocillin (200 mg/kg every 2 h for 2 g every 12 h) or imipenem (100 mg/kg every 2 h for 1 g every 8 h). Additional regimens of temocillin (200 mg/kg every 4 and 6 h) with reduced fT>MIC were studied.

Results

MICs of temocillin and imipenem were 4/8 and 0.5/0.5 mg/L, for CFT073-RR and CFT073-RR Tc, respectively. In vivo, when given every 2 h (fT>MIC = 82% and 70%), temocillin was bactericidal and as effective as imipenem in kidneys against both strains without selecting resistant mutants. Temocillin remained active even when given every 4 h, generating an fT>MIC of 41% and 35%, which corresponded to a breakpoint of 16 mg/L in humans with the standard regimen.

Conclusions

Our observations support the consideration of a standard regimen of temocillin as an alternative to carbapenems for the treatment of UTI due to CTX-M-producing E. coli strains with an MIC of 16 mg/L or less.
Local Elites in the Greek East
Authors: Schuler Christof
Published: January 2015

Roman rule in the provinces relied on cities, which were required to control their surrounding territory and had relative independence in all local matters. These cities also served as models of the Roman way of life and provided a framework for integrating the provincial population into the Roman imperial system. Rome relied on the wealthy local elite. In this regard, the eastern provinces did not differ substantively from Italy and the West, but there were important divergences (such as the existence of the polis and the politai, who enjoyed freedom and self-governance), which this chapter analyzes and outlines in full. The chapter stresses the importance of how the social prestige of elite groups and their families was advertised to contemporaries through a varied array of rituals and oral communications, and how inscribed monuments played a key role as permanent symbols of elite status within contemporary discourse.
The Rise of Christianity
Authors: Mazzoleni Danilo
Published: January 2015

This chapter analyzes Christian epigraphy, that is, epigraphic documents connected with early Christian communities, from the beginnings of Christianity to the end of the sixth century. Texts written in Latin constitute the largest group of Christian inscriptions and are the main focus. Funerary inscriptions are by far the most numerous type, but there are also many dedications, building inscriptions, votive, exegetical, and devotional texts, as well as texts of good augury that throw light on the rise of Christianity .
Sexualities
Authors: Rupp Leila J. , Thomsen Carly
Published: January 2015

This chapter explores the ways that feminist theorists, from both social constructionist and poststructural perspectives, have addressed the question of what sexuality is. We suggest that core to all kinds of feminist thinking about sexuality is that it cannot be understood simply as a fixed biological essence and that it involves power dynamics, as captured by the phrase sexual politics. Yet there is no agreement among feminist theorists about the questions of whether women’s sexuality is fundamentally different than men’s, or whether women’s experiences of sexuality are characterized more by danger or pleasure. We take up these debates to think through the history and future of feminist theories of sexuality.
Basic Number Representation and Beyond
Authors: Roggeman Chantal , Fias Wim , Verguts Tom
Published: January 2015

We discuss recent computational network models of elementary number processing. One key issue to emerge from this work is a crucial distinction between symbolic and non-symbolic number representation, and the related distinction between number-selective and number-sensitive coding. Empirical predictions from the models were tested, and are here summarized. Another issue is the relation with task-based decision making mechanisms. In both lab and real-life settings, representations are seldomly accessed in a task-neutral manner, rather subjects are usually presented with a task. A related theme is the functional association between number representations and working memory. In these issues also, both modeling and neuroimaging work is summarized. To conclude, we propose that the combined modeling-neuroimaging approach should be extended to tackle more complex questions about number processing (e.g. fractions, development, dyscalculia).
Liberalism and American Political Development
Authors: Ericson David F.
Published: January 2015

We need to go beyond Louis Hartz’sThe Liberal Tradition in America, not only in terms of how we think of liberalism but also in terms of how we think of and, more importantly, do American political development. Hartz’s conception of liberalism was too reified to capture the richness of American policy debates and his historical narrative does not tell us much about politicaldevelopment. Yet, his initial premise of a consensual liberal tradition that has structured policy debates remains a good starting point for thinking about and doing American political development. Several recent studies offer excellent templates for conducting research that integrates the roles of liberal ideas and illiberal purposes in explaining specific policy outcomes.
Performing Pannkotis Identity in Haiti
Authors: Butler Melvin L.
Published: January 2015

This chapter focuses on transnational networks of Pentecostal practice. It explores the use of “Pannkotis” to identify musical practice among a variety of Haitian churches, including some tied historically to Protestant and Pentecostal organizations in the United States. It also discusses the author’s roles as a Western ethnomusicologist and a Pentecostal believer, reflecting on the power shifts in transnational engagement that shared faith can engender: the author was often not only a learner about Haitian Pentecostals themselves, but also a religious learner with them; at other times, by virtue of the “portable” religious capital of the author’s status as a Pentecostal minister, he was placed as a musical and religious teacher. The chapter points provocatively to the discontinuities the author experienced as an ethnomusicologist because of the understandings and beliefs he shared as a coreligionist with Haitian Pentecostals.
Negotiations of Faith and Space in Memphis Music
Authors: Ryan Jennifer
Published: January 2015

This chapter traces the demarcation of sacred and secular space among Christian blues musicians in Memphis’s tourist music strip, Beale Street, drawing attention to the way in which the performative dynamics of sacred musical practices—particularly the ecstasy of Pentecostal worship—are mirrored in Beale Street (commercial, secular) performances by Christian blues players. However, these blues players negotiate the meanings of this circulation by individually rethinking strong notions of sacred and secular space. The chapter roots this individual redrawing of boundaries—as the blues players recognize their circulation between sacred and secular spaces—in African American theologies, in which direct and personal access to and reflection on God is a key value.
Walter Benjamin’s Esteem for Carl Schmitt
Authors: Bredekamp Horst
Published: January 2015

This chapter shows why Carl Schmitt’s philosophical theories retained their fascination and conceptual force for young intellectuals in postwar Germany. Publication of a letter Walter Benjamin had written to Schmitt in 1930, which revealed his esteem for Schmitt, was a catalyst for philosophers such as Jacob Taubes, who had distanced himself from Schmitt. Taubes’s research into the two men’s relationship helped to overcome the postwar construction of a clear-cut distinction between good and bad, shedding new light on the work of both philosophers and the intellectual atmosphere of the Weimar period. Benjamin’s and Schmitt’s works convey a strong mutual influence, especially throughout the 1930s, implicitly revealed in Benjamin’s appropriation of Schmitt’s concept of the “state of exception.” The appeal of Schmitt’s theory for Benjamin lay in its suggestive force about the roles of aesthetics and avant-garde.
Imam Warith Deen Mohammed
Authors: Mitchell Aneesa
Published: January 2015

This essay focuses on Warith Deen Mohammed’s early life and his leadership of the Nation of Islam (NOI). Warith Deen Mohammed inherited the mantle of NOI leadership from his father in 1975. The essay provides a background on NOI through 1975, particularly how it shaped the image of Islam and Muslims in America for much of the twentieth century and attracted African Americans who embraced Islam as an alternative to “white” religions. It then explores the evolution of Imam Warith Deen Mohammed and his community, with emphasis on how his childhood molded him and the significance of what he accomplished between 1933 and 1974. Furthermore, it examines the rise of mainstream Islam and universalism under Warith Deen Mohammed’s leadership, as well as his transformation from community leader to representative of American Muslims in 1981–2008 and his family life and dynamics before concluding with an assessment of the NOI today
Reevaluation of Acetylcholinesterase Staining for the Diagnosis of Hirschsprung Disease and Allied Disorders
Authors: Budianto Iskandar R. , Obata Satoshi , Kinoshita Yoshiaki , Yoshimaru Koichiro , Yanagi Yusuke , Miyata Junko , Nagata Kouji , Ieiri Satoshi , Taguchi Tomoaki
Published: January 2015

Objectives:

Acetylcholinesterase (AChE) staining has become the gold standard for definitively diagnosing Hirschsprung disease (HD), although some pitfalls have been reported. We reevaluated a large series at our institute in order to validate the accuracy of AChE staining for detecting HD.

Methods:

A retrospective study of the rectal mucosal specimens of all of the children with suspected HD during a 13‐year period was performed. The specimens were stained according to the modified Karnovsky‐Roots method for AChE staining. The final diagnosis, prognosis, and management after the histopathological diagnosis were analyzed with a questionnaire sent to the patient's original hospital.

Results:

Three hundred and fifty‐eight specimens were collected. One hundred twenty‐two (34%) specimens were diagnosed as HD, 198 (55%) as nonHD, 25 (7%) as “undetermined,” and 13 (4%) as “inappropriate.” The non‐HD group contained 190 (96%) specimens with a normal appearance and 8 (4%) specimens with suspected intestinal neuronal dysplasia (IND). Three hundred and six of 358 questionnaires were returned. The final diagnosis showed that no specimens first diagnosed as HD were identified as non‐HD and vice versa, for a sensitivity and specificity of 100%. Four cases were finally diagnosed as chronic idiopathic intestinal pseudo‐obstruction (CIIP) in the non‐HD group. All of the patients with HD underwent radical surgery. Most non‐HD patients were managed conservatively, although some continued to have constipation.

Conclusions:

AChE staining is an accurate tool for differentiating between HD and non‐HD with high sensitivity and specificity. CIIP can be included in cases of non‐HD; therefore, careful follow‐up is mandatory.
Acute Upper Gastrointestinal Bleeding in Childhood
Authors: Thomson Mike A. , Leton Neme , Belsha Dalia
Published: January 2015

Background/Aims:

Upper gastrointestinal bleeding (UGIB) is a rare and potentially life‐threatening condition in childhood. In adults with UGIB, validated scoring systems exist, but these are not applicable to children. The aim of this study was to construct a clinical scoring system to accurately predict the need for endoscopic haemostatic intervention.

Methods:

A retrospective data collection occurred during a 3‐year period at a tertiary children's hospital. A total of 69 patients who had had endoscopic assessment were divided into group 1 (no intervention required) and group 2 (intervention required). A wide range of clinical parameters were collated including preexisting conditions, melaena, haematemesis and degree, transfusion requirement, parameters of hypovolaemia, presenting haemoglobin (Hb), Hb drop during 24 hours, platelet count, coagulation indices, liver function tests, and urea/electrolytes.

Results:

Parameters that reached statistical significance for endoscopic intervention (group 1 vs group 2) were the presence of significant preexisting condition, melaena, large haematemesis, heart rate (HR) >20 mean HR for age, prolonged capillary refill time (CRT), Hb drop of >20 g/L, need for fluid bolus, need for blood transfusion (Hb < 80 g/L), and need for other blood products. Using these parameters, a number of scoring models were tested, and the most predictive resulted in a scoring system constructed with a total of 24 and a cutoff for intervention of 8. According to this design, there were 4 false‐negatives in the interventional group with 3 false‐positives in the noninterventional group. This resulted in a positive predictive value (PPV) of 91.18% (95% confidence interval [CI] 76.3–98.04), negative predictive value (NPV) of 88.57% (95% CI 73.24–96.73), sensitivity of 88.7% (95% CI 73.24–96.73), and specificity of 91.18% (95% CI 76.3–98.04).

Conclusions:

In our study population, we were able to formulate a scoring system with reasonable PPV and NPV to predict the need for endoscopic intervention in acute UGIB in children. Prospective evaluation is now required.
Intestinal Inflammation and Impact on Growth in Children With Cystic Fibrosis
Authors: Dhaliwal Jasbir , Leach Steven , Katz Tamarah , Nahidi Lily , Pang Tamara , Lee J.M. , Strachan Roxanne , Day Andrew S. , Jaffe Adam , Ooi Chee Y.
Published: January 2015

Objective:

The aim of the study was to evaluate and compare faecal markers of intestinal inflammation in children with cystic fibrosis (CF), and determine whether intestinal inflammation adversely affects the nutritional phenotype.

Methods:

Faecal samples for markers of intestinal inflammation, calprotectin, S100A12, and osteoprotegerin, were collected from children with CF, healthy controls (HCs), and Crohn disease (CD). Associations between inflammatory markers and clinical and nutritional indices were determined in subjects with CF.

Results:

Twenty‐eight children with CF (mean [standard deviation (SD)] 8.4 [3.3] years old, 22 pancreatic insufficient [PI]), 47 HC, and 30 CD were recruited. Mean (SD) faecal calprotectin in CF (94.3 [100.6] mg/kg) was greater than HC (26.7 [15.4] mg/kg, P < 0.0001), but lower than CD (2133 [2781] mg/kg, P = 0.0003). Abnormal faecal calprotectin was found in subjects only with PI (17/22 (77%), P = 0.001). There was no difference in faecal mean (SD) S100A12 (0.8 [0.9] vs 1.5 [2.2] mg/kg, P = 0.14) and osteoprotegerin concentrations (72.7 [52.2] vs 62.5 [0.0] pg/mL, P = 0.2) between CF and HC. Patients with CD had significantly elevated S100A12 and osteoprotegerin compared with CF and HC. Faecal calprotectin inversely correlated with both weight (r = −0.5, P = 0.003) and height z scores (r = −0.6, P = 0.002) in CF.

Conclusions:

The pattern of intestinal inflammation in CF is unique and distinct from inflammatory bowel disease, with elevated faecal calprotectin but normal faecal S100A12 and osteoprotegerin concentrations. The severity of intestinal inflammation, based on faecal calprotectin, significantly correlates with poor growth.
Monotherapy With Infliximab Versus Combination Therapy in the Maintenance of Clinical Remission in Children With Moderate to Severe Crohn Disease
Authors: Kierkuś Jarosław , Iwańczak Barbara , Wegner Agnieszka , Dadalski Maciej , Grzybowska‐Chlebowczyk Urszula , Łazowska Izabella , Maślana Jolanta , Toporowska‐Kowalska Ewa , Czaja‐Bulsa Grażyna , Mierzwa Grażyna , Korczowski Bartosz , Czkwianianc Elżbieta , Żabka Alicja , Szymańska Edyta , Krzesiek Elżbieta , Więcek Sabina , Sładek Małgorzata
Published: January 2015

Objectives:

The aim of the present study was to compare the efficacy and safety of 2 protocols of maintenance therapy with infliximab (IFX) and an immunomodulatory agent in pediatric patients with Crohn disease (CD): withdrawal of immunomodulators versus continuation of immunosuppressants.

Methods:

The present multicenter randomized open‐label trial included 99 patients with CD (ages 14.5 ± 2.6 years) who were administered IFX (5 mg/kg body weight) along with an immunomodulatory agent (azathioprine 1.5–3 mg/kg body weight per day, methotrexate 10–25 mg/week). After 10 weeks of the induction therapy, 84 responders were centrally randomized into 1 of the following groups: group I (n = 45) in which IFX and an immunomodulatory agent were continued up to week 54 and group II (n = 39) in which the immunomodulatory agent was discontinued after 26 weeks.

Results:

The induction therapy was reflected by a significant decrease in Pediatric Crohn's Disease Activity Index (PCDAI) and Simplified Endoscopic Activity Score for Crohn's Disease (SES‐CD) values. After the maintenance phase, the analyzed groups did not differ significantly in terms of the clinical response loss rates and final PCDAI and SES‐CD scores. Furthermore, no significant intragroup differences were documented between mean PCDAI scores determined at the end of induction and maintenance phases. Intensification/modification of the treatment was required in 13 of 45 (29%) and 11 of 39 (28%) patients of groups I and II, respectively. A total of 9 serious adverse events were documented; none of the patients died during the trial.

Conclusions:

Twenty‐six weeks likely represent the safe duration of combined IFX/immunomodulatory therapy in our sample of pediatric patients with CD.
Sensory Processing Difficulties in Toddlers With Nonorganic Failure‐to‐Thrive and Feeding Problems
Authors: Yi Sook‐Hee , Joung Yoo‐Sook , Choe Yon Ho , Kim Eun‐Hye , Kwon Jeong‐Yi
Published: January 2015

Objectives:

Failure‐to‐thrive is defined as an abnormally low weight and/or height for age. The term “nonorganic failure‐to‐thrive” (NOFT) has been used to describe “failure‐to‐thrive” without an obvious cause underlying the growth failure. The purpose of the present study was to compare sensory processing abilities between toddlers with NOFT and feeding problems and age‐matched controls.

Methods:

Toddlers with NOFT and feeding problems (N = 16) were recruited from the pediatric feeding clinic in a tertiary university hospital, and age‐matched controls (N = 16) were recruited from community volunteers. They were evaluated for sensory processing ability using an Infant/Toddler Sensory Profile (ITSP), and for development of cognition, motor skills, and language using the Bayley Scales of Infant Development II and Sequenced Language Scale for Infants. Behavior at mealtime was evaluated using the Behavioral Pediatrics Feeding Assessment Scale.

Results:

In the NOFT with feeding problems group, atypical performances were more frequently observed in 3 of 5 ITSP section items (tactile, vestibular, and oral) compared with those in the control group. Significant delayed development of cognition, motor skills, and language was observed in the NOFT with feeding problems group compared with that in the control group. In addition, children who showed 1 or more atypical performances in ITSP had delayed development in cognition, motor skills, and language.

Conclusions:

Sensory processing problems were more commonly observed in toddlers with feeding problems and growth deficiency. The present study could provide a preliminary evidence for a possible impact of the sensory processing problems on the feeding difficulties in toddlers with NOFT. Future large studies should be conducted to clarify the relation between sensory processing difficulties and feeding problems in toddlers.
Clinical Relevance of Esophageal Baseline Impedance Measurement
Authors: Tambucci Renato , Thapar Nikhil , Saliakellis Efstratios , Pescarin Matilde , Quitadamo Paolo , Cristofori Fernanda , Lindley Keith J. , Borrelli Osvaldo
Published: January 2015

Objective:

The clinical relevance of esophageal baseline impedance (BI) remains to be determined. In the present study, we explored the impact of gastroesophageal reflux disease (GERD) and esophageal dysmotility on BI.

Methods:

A total of 18 children with esophageal atresia, 26 children with GERD, and 17 controls prospectively underwent esophagogastroduodenoscopy and pH–impedance monitoring. BI was measured in both proximal and distal esophagus. Gastroesophageal reflux (GER) and bolus transit indicators were defined according to published criteria.

Results:

Patients with esophageal atresia showed significantly lower proximal and distal BI values (952 [716–1811] Ω; 895 [284–1189] Ω; respectively) compared with those with GERD (3015 [2368–3975] Ω; 2231 [1770–3032] Ω, P < 0.001 and <0.001, respectively) and controls (3699 [3194–4358] Ω; 3522 [2927–3994] Ω, P < 0.001 and <0.001, respectively). Using linear regression, proximal BI strongly correlated with total bolus transit time (r2 = 0.61, P < 0.001) and bolus presence time (BPT; r2 = 0.63, P < 0.001). Distal BI weakly correlated with acid exposure time (r2 = 0.16, P < 0.01) and longstanding reflux episodes (r2 = 0.17, P < 0.01), and strongly correlated with total bolus transit time (r2 = 0.53, P < 0.001) and BPT (r2 = 0.58, P < 0.001). By logistic regression, BPT predicted low proximal BI values (odds ratio [OR] 1.052; P < 0.05), whereas both GER indicators (acid exposure time: OR 1.56, P < 0.05; longstanding reflux episodes: OR 2.8, P < 0.05) and BPT (OR 1.66, P < 0.01) predicted low distal BI values.

Conclusions:

Along the length of esophagus, both bolus transit variables and GER significantly affect BI. This suggests that BI may merely mirror phenomena occurring within the esophageal lumen or wall, limiting its value as a discrete clinical entity to replace variables already used for assessing both GERD and esophageal dysmotility.
Crystal growth of bullet-shaped magnetite in magnetotactic bacteria of theNitrospiraephylum
Authors: Li Jinhua , Menguy Nicolas , Gatel Christophe , Boureau Victor , Snoeck Etienne , Patriarche Gilles , Leroy Eric , Pan Yongxin
Published: January 2015

Magnetotactic bacteria (MTB) are known to produce single-domain magnetite or greigite crystals within intracellular membrane organelles and to navigate along the Earth's magnetic field lines. MTB have been suggested as being one of the most ancient biomineralizing metabolisms on the Earth and they represent a fundamental model of intracellular biomineralization. Moreover, the determination of their specific crystallographic signature (e.g. structure and morphology) is essential for palaeoenvironmental and ancient-life studies. Yet, the mechanisms of MTB biomineralization remain poorly understood, although this process has been extensively studied in several cultured MTB strains in theProteobacteriaphylum. Here, we show a comprehensive transmission electron microscopy (TEM) study of magnetic and structural properties down to atomic scales on bullet-shaped magnetites produced by the uncultured strain MYR-1 belonging to theNitrospiraephylum, a deeply branching phylogenetic MTB group. We observed a multiple-step crystal growth of MYR-1 magnetite: initial isotropic growth forming cubo-octahedral particles (less than approx. 40 nm), subsequent anisotropic growth and a systematic final elongation along [001] direction. During the crystal growth, one major {111} face is well developed and preserved at the larger basal end of the crystal. The basal {111} face appears to be terminated by a tetrahedral–octahedral-mixed iron surface, suggesting dimensional advantages for binding protein(s), which may template the crystallization of magnetite. This study offers new insights for understanding magnetite biomineralization within theNitrospiraephylum.
Functional identity and diversity of animals predict ecosystem functioning better than species-based indices
Authors: Gagic Vesna , Bartomeus Ignasi , Jonsson Tomas , Taylor Astrid , Winqvist Camilla , Fischer Christina , Slade Eleanor M. , Steffan-Dewenter Ingolf , Emmerson Mark , Potts Simon G. , Tscharntke Teja , Weisser Wolfgang , Bommarco Riccardo
Published: January 2015

Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of speciesper se.
Clostridium oryzae sp. nov., from soil of a Japanese rice field
Authors: Horino Haruka , Ito Miyuki , Tonouchi Akio
Published: January 2015

An obligately anaerobic bacterial strain designated KC3T was isolated from a rice straw-degrading culture, for which soil of a Japanese rice field was used as the inoculum. Cells of strain KC3T were determined to be non-cellulolytic, Gram-stain-positive, non-motile, ellipsoidal, spore-forming rods, 0.8–1×4–25 µm. Endospores were formed at a terminal position in elongated cells (12–25 µm, mean 15 µm). The temperature range for growth was 20–50 °C, with an optimum at 37 °C. The pH range for growth was 5.0–7.5, with an optimum at pH 6.0 (slightly acidophilic). Strain KC3T fermented cellobiose to lactate, butyrate, acetate, formate, hydrogen and carbon dioxide. The major cellular fatty acids (>10 %) were C14 : 0, C16 : 0 and C19 : 0 cyclo 11,12 dimethylacetal. The DNA G+C content of strain KC3T was 37.5 mol%. 16S rRNA gene sequence analysis revealed that strain KC3T shared low sequence similarity (<93 %) with type strains of the genus

Clostridium

sensu stricto (Clostridium rRNA cluster I). Analyses of the DNA gyrase A and ATP synthase beta subunit sequences supported the affiliation of strain KC3T to the genus

Clostridium

sensu stricto. The evidence presented here indicates that strain KC3T represents a novel species of the genus

Clostridium

, for which the name Clostridium oryzae sp. nov. is proposed. The type strain of Clostridium oryzae is KC3T ( = DSM 28571T = NBRC 110163T).