bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Story in Three Contexts: The Redaction of a Toseftan Pericope
Authors: Katzoff Binyamin 
Published: May 2014

The introduction of non-halakhic material into a halakhic section of a classical rabbinic work is a redactional choice that can substantially affect the interpretation of both kinds of material. Understanding the relationship between the non-halakhic material and the surrounding halakhic material can affect one's assessment of the redactor's activity. Conversely, assumptions concerning the redactor's activity can affect the interpretation of the non-halakhic material.The relationship between halakhic and non-halakhic material and the implications of that relationship for redaction critical investigations are particularly complex in the case of the Tosefta, because the latter is not a completely independent composition. Some scholars see the Tosefta as an interpretative work based on the Mishna while others argue for a degree of redactional independence. What then is the proper context for the interpretation of materials found in the Tosefta—the Tosefta itself or the Mishnah? The answer to this question will crucially affect our interpretation of the non-halakhic material included in the Tosefta and the relation of that material to the halakhic material. This article demonstrates the difficulty in determining the proper redactional context for the interpretation of Toseftan passages that contain halakhic and non-halakhic material by examining the story of Rabbi Yehuda walking behind his teachers in T. Berakhot 1.2. The reason for inserting the story can be understood in three ways, corresponding to three different definitions of the “halakhic context,” in which the Mishnah has a greater or lesser controlling influence over the Tosefta.
Shari‘a, Shi‘as and Chishtiya Revivalism: Contextualising the Growth of Sectarianism in the Tradition of the Sialvi Saints of the Punjab
Authors: KAMRAN TAHIR , SHAHID AMIR KHAN 
Published: May 2014

AbstractThis article discusses the transformation that took place within the Chishtiya silsilah after its revival in the Punjab in the eighteenth and nineteenth centuries. Within this Chishtiya revival an exclusionary streak emerged, embedded within a shari‘a-centred orientation, leading to Shi‘a and Chishti Sunni antagonism in the Punjab. As a result, the composite and all-inclusive ethos epitomised by earlier Chishti Sufis of the thirteenth century was jettisoned. Underpinning these developments was the advent of the Usuli faction among the Shi‘a of Awadh, whose influence was resonating in the Punjab by the turn of the twentieth century. The khanaqah of Sial Sharif in Sargodha district illustrates this exclusionary trend, as reflected in the texts such as the Mazhab-i Shi‘a by Khawja Qammar ud Din Sialvi.
Lattice Boltzmann Simulation of Shale Gas Transport in Organic Nano-Pores
Authors: Zhang Xiaoling , Xiao Lizhi , Shan Xiaowen , Guo Long 
Published: May 2014

AbstractPermeability is a key parameter for investigating the flow ability of sedimentary rocks. The conventional model for calculating permeability is derived from Darcy's law, which is valid only for continuum flow in porous rocks. We discussed the feasibility of simulating methane transport characteristics in the organic nano-pores of shale through the Lattice Boltzmann method (LBM). As a first attempt, the effects of high Knudsen number and the associated slip flow are considered, whereas the effect of adsorption in the capillary tube is left for future work. Simulation results show that at small Knudsen number, LBM results agree well with Poiseuille's law and flow rate (flow capacity) is proportional to the square of the pore scale. At higher Knudsen numbers, the relaxation time needs to be corrected. In addition, velocity increases as the slip effect causes non negligible velocities on the pore wall, thereby enhancing the flow rate inside the pore, i.e., the permeability. Therefore, the LBM simulation of gas flow characteristics in organic nano-pores provides an effective way of evaluating the permeability of gas-bearing shale.
Growth of Optically Active Chiral Inorganic Films through DNA Self-Assembly and Silica Mineralisation
Authors: Liu Ben , Han Lu , Duan Yingying , Cao Yunayuan , Feng Ji , Yao Yuan , Che Shunai 
Published: May 2014

AbstractThe circularly polarized reflection of nature is due to their distinct azimuthally twisted or helical character in the nanostructure of the surface films. Although many chiral inorganic powders have been successfully synthesised, the artificial synthesis of chiral inorganic films is rare. Herein, we reported a facile synthetic route for the growth of monolayered chiral film on the quaternary ammonium-modified silicon substrate. The films grew on the substrate surface because of the strong electrostatic interaction between positively charged quaternary ammonium groups and negatively charged phosphate groups of DNA, with subsequent growth to right-handed, vertically aligned, impeller-like helical architectures with left-handed two-dimensional square p4mm-structured DNA chiral packing. The DNA–silica composite films exhibited strong optical activity at 295 nm and in the range of 400–800 nm, corresponding to DNA chiral packing (absorption) and to the helical blade in the impeller (scattering), respectively. Upon removal of DNA templates, the pure inorganic impeller-like helical morphology was maintained; consequently, the scattering-based optical response was blue-shifted approximately 200 nm as a result of a decrease in the effective average refractive index. The hierarchical structures were reflected from the surfaces by cross-polarised light, which confirmed that the films were strongly birefringent, with long-range anisotropy.
Wavelength conversion and temporal compression of pulse train using dispersion oscillating fibre
Authors: Feng F. , Fatome J. , Sysoliatin A. , Chembo Y.K. , Wabnitz S. , Finot C. 
Published: May 2014

The generation of a picosecond pulse train is demonstrated taking advantage of the cross‐gain occurring in a dispersion‐oscillating fibre. The resulting frequency‐converted signal is detuned by more than 20 nm from the pump and can be temporally compressed by a factor of 2 compared with the input sinusoidal pump wave.
Social interactions dominate speed control in poising natural flocks near criticality
Authors: Bialek William , Cavagna Andrea , Giardina Irene , Mora Thierry , Pohl Oliver , Silvestri Edmondo , Viale Massimiliano , Walczak Aleksandra M. 
Published: May 2014

SignificanceThe coherent flight of bird flocks is one of nature’s most impressive aerial displays. Beyond the fact that thousands of birds fly, on average, with the same velocity, quantitative observations show that small deviations of individual birds from this average are correlated across the entire flock. By learning minimally structured models from field data, we show that these long-ranged correlations are consistent with local interactions among neighboring birds, but only because the parameters of the flock are tuned to special values, mathematically equivalent to a critical point in statistical mechanics. Being in this critical regime allows information to propagate almost without loss throughout the flock, while keeping the variance of individual velocities small.
Understanding the pharmacological properties of a metabolic PET tracer in prostate cancer
Authors: Viola-Villegas Nerissa Therese , Carlin Sean D. , Ackerstaff Ellen , Sevak Kuntal K. , Divilov Vadim , Serganova Inna , Kruchevsky Natalia , Anderson Michael , Blasberg Ronald G. , Andreev Oleg A. , Engelman Donald M. , Koutcher Jason A. , Reshetnyak Yana K. , Lewis Jason S. 
Published: May 2014

Significance
Solid tumors adapt a glycolytic phenotype for their energetic requirements, leading to acidification of the extracellular environment. Targeting this global event is important to gauge the pace of tumor growth and invasiveness, as well as to provide a basis for predicting disease response to pH-dependent chemotherapies. To realize this goal, a noninvasive method is necessary to measure tumor extracellular acidification to meet clinical needs. This study explores the utility of pH (low) insertion peptide, an acidosis-targeting peptide, as a PET-based imaging probe to provide a method for quantifying extracellular pH and its correlation to known acidity markers, such as hypoxia, carbonic anhydrase IX, and lactate dehydrogenase A, within the prostate tumor tissue.
Conjugative pili.
Authors: Christie P. J. 
Published: May 2014

Abstract

This chapter provides an overview of the biogenesis, structure and biological functions of conjugative pili. The discussion will focus mainly on the 2 more extensively characterized pili, F-pili elaborated by the Escherichia coli F plasmid and P-pili produced by E. coli plasmids of the P, N or W incompatibility (Inc) groups and the Agrobacterium tumefaciens VirB/VirD4 T-DNA transfer system.
Pilus biogenesis by the chaperone-usher pathway.
Authors: Phan G. , Waksman G. 
Published: May 2014

Abstract

Gram-negative bacteria display a variety of multi-subunit fibrillar structures on their cell surface called 'pili' or 'fimbriae'. Originally based on the filament morphology and the biogenesis machinery, pili are currently classified into five different families: (i) the curli, (ii) the type IV pili, (iii) the type III secretion system needle, (iv) the type IV secretion system pili, and (v) the chaperone-usher (CU) pili. This chapter reviews the biogenesis machinery of one of the most widespread and important microbial adhesion factor, the chaperone-usher (CU) pili, as well as its structure, function and polymerization. The CU pili are made of different subunits that polymerize to either thin flexible fibres or rigid long filaments. The main function of the CU pili is the adhesion to the host cells, mediated by a specialized pilus subunit, the adhesin, often containing a lectin domain that specifically recognizes the lining sugars of the target tissue, thereby defining the host tropism. Generally clustered under the same promoter, all the necessary components for the CU pili biogenesis are encoded within the same operon and it has been shown that multiple CU pathway clusters may be present within the same genome, extending the range of receptors the same bacterium might be able to adhere to.
Type 1 and P pili of uropathogenic Escherichia coli.
Authors: Russell C. , Mulvey M. 
Published: May 2014

Abstract

In uropathogenic Escherichia coli (UPEC), type 1 pili (T1P) and P pili enable the bacterium to bind to host epithelial cells within the urinary tract, which can lead to a urinary tract infection. This chapter reviews the genetics, structure and functions of UPEC T1P and P pili. It also describes the mechanisms by which T1P and P pili contribute to UPEC pathogenesis and host immune response.
Pili of Streptococcus pyogenes.
Authors: Scott J. R. 
Published: May 2014

Abstract

Streptococcus pyogenes, also called group A streptococcus (GAS), is one of the most common human pathogens. Although different GAS strains encode serologically different types of pili, and their structure and assembly differs, all GAS strains have their proteins necessary for synthesis and assembly of pili encoded in a single locus. Pili are composed of many copies of the backbone protein (the T antigen), linked end-to-end by a sortase family transpeptidase, or pilin polymerase. This chapter reviews the genetic organization of pili, the role of FCT genes in pilus assembly, the biological roles of pili in cell adhesion and biofilm formation, and the regulation of pilus gene expression.
Risks to human health from
Encephalitozoon
and
Enterocytozoon
carried by wild animals.
Authors: Lallo M. A. , Spadacci-Morena D. D. 
Published: May 2014

Abstract

The microsporidia are opportunistic pathogens, obligate intracellular parasites of vertebrates and invertebrates. They have been described in patients with AIDS, transplant recipients, children, travellers, seniors, contact lens wearers and patients with other immunosuppressive conditions. These organisms have long been known to be causative agents of economically important diseases in insects (silkworms and honey bees), fish, birds and mammals (lagomorpha, carnivores, rodents and primates). There are about 1300 species of microsporidia described and of the 14 species of microsporidia currently known to infect humans,
Enterocytozoon bieneusi
and
Encephalitozoon
are the most common causes of human infections and are associated with diarrhoea and systemic disease. The microsporidia that infect human beings, in particular,
Enterocytozoon
and
Encephalitozoon
are found in domestic and wild animals, and for this reason, the animals may be considered as a source of infection for humans. The waterborne, foodborne and zoonotic transmission have been demonstrated by molecular epidemiology. In this review, we present the most relevant epidemiological aspects of microsporidia simultaneously observed in humans and wildlife, in order to understand the risks from microsporidiosis in wild animals to human health.
Alternative technologies for tomato post-harvest quality preservation.
Authors: Pinheiro J. , Gonçalves E. M. , Silva C. L. M. 
Published: May 2014

Abstract

Fresh tomato (
Solanum lycopersicum
) is one of the most consumed fruits and the preservation of its quality and shelf-life extension is a continuous challenge. An understanding of fruit deterioration factors allows the investigation of new approaches to reach this objective. Fruit preservation is achieved by destroying enzymes and micro-organisms, and reducing physiological disorders, using treatments such as chlorinated water (HIPO), ozone, low or high temperatures, ultrasounds, UV-C radiation, modified atmosphere packaging, edible coatings and 1-methylcyclopropene. In this review, a description of action, advantages and disadvantages of each preservation treatment, and corresponding effects on tomato quality and safety are presented. The development of a
green
technology for tomato has advantages for all fresh chain interventions, with direct or indirect impacts on human health.
ReadXplorer—visualization and analysis of mapped sequences
Authors: Hilker Rolf , Stadermann Kai Bernd , Doppmeier Daniel , Kalinowski Jörn , Stoye Jens , Straube Jasmin , Winnebald Jörn , Goesmann Alexander 
Published: May 2014

Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data.
Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion–insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets.
Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual.
Contact: rhilker@mikrobio.med.uni-giessen.de
Supplementary information: Supplementary Data are available at Bioinformatics online.
Wide-field 12CO (J = 1–0) imaging of the nearby barred galaxy M 83 with NMA and Nobeyema 45 m telescope: Mole cular gas kinematics and star formation along the bar
Authors: Hirota Akihiko , Kuno Nario , Baba Junichi , Egusa Fumi , Habe Asao , Muraoka Kazuyuki , Tanaka Ayako , Nakanishi Hiroyuki , Kawabe Ryohei 
Published: May 2014

Abstract
We present the results of the wide-field 12CO(1–0) observations of the nearby barred galaxy M 83 carried out with the Nobeyama Millimeter Array (NMA). The interferometric data are combined with the data obtained with the Nobeyama 45 m telescope to recover the total flux. The target fields of the observations cover the molecular bar and part of the spiral arms, with a spatial resolution of ∼ 110 pc × 260 pc. By exploiting the resolution and sensitivity to extended CO emission, the impact of the galactic structures on the molecular gas content is investigated in terms of the gas kinematics and the star formation. By inspecting the gas kinematics, the pattern speed of the bar is estimated to be 57.4 ± 2.8 km s−1 kpc−1, which places the corotation radius at about 1.7 times the semi-major radius of the bar. Within the observed field, H ii regions brighter than 1037.6 erg s−1 in Hα luminosity are found to be preferentially located downstream of the CO-emitting regions. Azimuthal angular offsets between molecular gas and star forming (SF) calculated with the angular cross-correlation method confirm the trend. By comparing with a cloud orbit model based on the derived pattern speed, the angular offsets are found to be in accordance with a time delay of about 10 Myr. Finally, to test whether the arm/bar promote star formation efficiency [SFE ≡ Star Formation Rate (SFR)/H2 mass], SFR is derived with the diffuse-background-subtracted Hα and 24 μm images. The arm-to-interarm ratio of the SFE is found to lie in the range of 2 to 5, while it is ∼ 1 if no background removal is performed. The CO–SF offsets and the enhancement of the SFE in the arm/bar found in the inner region of M 83 are in agreement with the predictions of the classical galactic shock model.
Magnetic configurations related to the coronal heating and solar wind generation. I. Twist and expansion profiles of magnetic loops produced by flux emergence
Authors: Lee Hwanhee , Magara Tetsuya 
Published: May 2014

Abstract
The generation of outflows from the Sun known as solar winds is coupled with the heating of the solar corona, and both processes are operated in magnetic structures formed on the Sun. To study the magnetic configuration responsible for these processes, we use three-dimensional magnetohydrodynamic simulations to reproduce magnetic structures via flux emergence and investigate their configurations. We focus on two key quantities characterizing a magnetic configuration: the force-free parameter α and the flux expansion rate fex, the former of which represents how much a magnetic field is twisted while the latter represents how sharply a magnetic field expands. We derive distributions of these quantities in an emerging flux region. Our result shows that an emerging flux region consists of an outer part where a magnetic loop takes a large flux expansion rate but a small value of α at their photospheric footpoints, and an inner part occupied by those loops where a strong electric current flows. We also investigate the expansion profile of a magnetic loop comprising an emerging flux region. The profile is given by an exponential expansion type near the solar surface while it is given by a quadratic expansion type in an outer atmosphere. These detailed magnetic configurations obtained by this study contribute to developing a realistic model for the coronal heating and solar wind generation.
Pediatric Constipation in the Emergency Department
Authors: Freedman Stephen B. , Thull‐Freedman Jennifer , Rumantir Maggie , Eltorki Mohamed , Schuh Suzanne 
Published: May 2014

ABSTRACTObjectives:Limited knowledge exists surrounding the pharmacologic management of pediatric constipation in the emergency department (ED) setting and the success of interventions. Our primary objective was to determine whether enema administration is associated with 7‐day ED revisits for persistent symptoms. Secondary objectives focused on assessing other predictors of ED revisits.Methods:We conducted a retrospective cohort study of children <18 years old, diagnosed as having constipation (International Classification of Diseases‐10 codes F98.1 nonorganic encopresis, K59.0 constipation) in a pediatric ED in Toronto, Canada, between November 2008 and October 2010.Results:A total of 3592 visits were included; 6% (n = 225) were associated with a revisit. Children with revisits more frequently had vomiting (28% vs 17%, P = 0.001), more pain (5.7 ± 3.6 vs 4.6–3.6 of 10, P = 0.01), and underwent more blood tests (19% 05, 11%, 95% confidence interval [CI] of the difference 3%–14%] and diagnostic imaging (62% vs 47%, 95% CI of the difference 9%–22%). Children administered an enema were 1.54 times more likely to revisit the ED than those who did not receive an enema (8.6% vs 5.5%, 95% CI of the difference 1.1%–5.2%, P = 0.001). Type of enema administered varied by age (P < 0.001). Regression analysis identified the following independent predictors of revisits: diagnostic imaging (odds ratio [OR] 1.54, 95% CI 1.15–2.06), vomiting (OR 1.45, 95% CI 1.07–1.98), enema administration (OR 1.40, 95% CI 1.05–1.88), and significant medical history (OR 1.26, 95% CI 1.04–1.53).Conclusions:Enema administration and diagnostic imaging are associated with revisits in children diagnosed with constipation. Their role in the ED management of pediatric constipation requires further evaluation.
Research and the Promotion of Child Health
Authors: Koletzko Berthold , Kolacek Sanja , Phillips Alan , Troncone Riccardo , Vandenplas Yvan , Baumann Ulrich , van Goudoever Johannes , de Swarte Casper , Benninga Marc , Mearin Luisa 
Published: May 2014

ABSTRACTChildren comprise one‐fifth of Europe's population. Promoting child health and development is of key importance for society and its future. This position paper highlights opportunities of investing in gastrointestinal, liver, and nutritional research to promote child health and delineates priorities for research. Investing in child health plays a key role in the promotion of population health, well‐being, and disease prevention lifelong, with large health economic benefits. Major opportunities for improving knowledge and translational application arise from recent scientific and technological developments, for example, the long‐term impact of early environmental cues interacting with genes. Personalised approaches to therapy and prevention should be enhanced. Deciphering the microbiome and its effects on functions can help in promoting long‐term health. Epigenetic research can help to understand how early environmental factors influence later gastrointestinal and hepatic health and disease. A linked nutrition and physical activity strategy can promote health and prevent nutritional deficiencies, inactivity, and chronic noncommunicable diseases, such as diabetes, to ensure optimal health and cognition. Special attention should be devoted to populations with low socioeconomic status, migrant background, and ethnic minorities, and to critical life periods, including pregnancy, lactation, infancy, and childhood. Improved understanding of optimal nutrition and on maintaining gut and liver homeostasis throughout childhood will help prevent chronic diseases in later life.