bluuebunny/crossref_metadata_2025 huggingface dataset:
When less is more: ‘slicing’ sequencing data improves read decoding accuracy and de novo assembly quality
Authors: Lonardi Stefano , Mirebrahim Hamid , Wanamaker Steve , Alpert Matthew , Ciardo Gianfranco , Duma Denisa , Close Timothy J.
Published: May 2015

Motivation: As the invention of DNA sequencing in the 70s, computational biologists have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing.

Results: We explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to bacterial artificial chromosome (BAC) clones (in the context of the combinatorial pooling design we have recently proposed), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on ‘divide and conquer’: we ‘slice’ a large dataset into smaller samples of optimal size, decode each slice independently, and then merge the results. Experimental results on over 15 000 barley BACs and over 4000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data.

Availability and implementation: Python scripts to process slices and resolve decoding conflicts are available from http://goo.gl/YXgdHT; software Hashfilter can be downloaded from http://goo.gl/MIyZHs

Contact:  stelo@cs.ucr.edu or timothy.close@ucr.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations
Authors: Lever Mark A. , Rogers Karyn L. , Lloyd Karen G. , Overmann Jörg , Schink Bernhard , Thauer Rudolf K. , Hoehler Tori M. , Jørgensen Bo Barker
Published: May 2015

The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.
Homeostatic ‘bystander’ proliferation of human peripheral blood B cells in response to polyclonal T-cell stimulationin vitro
Authors: Jasiulewicz Aleksandra , Lisowska Katarzyna A. , Pietruczuk Krzysztof , Frąckowiak Joanna , Fulop Tamas , Witkowski Jacek M.
Published: May 2015

The mechanisms of maintenance of adequate numbers of B lymphocytes and of protective levels of immunoglobulins in the absence of antigenic (re)stimulation remain not fully understood. Meanwhile, our results presented here show that both peripheral blood naive and memory B cells can be activated strongly and non-specifically (in a mitogen-like fashion) in 5-day in vitro cultures of anti-CD3- or concanavalin A (Con A)-stimulated peripheral blood mononuclear cells of healthy people. This polyclonal, bystander activation of the B cells includes multiple divisions of most of them (assessed here by the flow cytometric technique of dividing cell tracking) and significant antibody [immunoglobulin M (IgM) and IgG] secretion. Observed proliferation of the CD19 + B cells depends on contact with stimulated T helper (T h ) cells (via CD40–CD40L interaction) and on the response of B cells to secreted interleukins IL-5, IL-10 and IL-4, and is correlated with the levels of these T h -derived molecules, while it does not involve the ligation of the BCR/CD19 complex. We suggest that the effect might reflect the situation occurring in vivo as the homeostatic proliferation of otherwise non-stimulated, peripheral B lymphocytes, providing an always ready pool for efficient antibody production to any new (or cognate) antigen challenge.
Identifying Obstructive Sleep Apnea in Administrative Data
Authors: McIsaac Daniel I. , Gershon Andrea , Wijeysundera Duminda , Bryson Gregory L. , Badner Neal , van Walraven Carl
Published: May 2015

AbstractAbstract

In approximately 5,000 patients who underwent preoperative polysomnography, 56% met criteria for a diagnosis of obstructive sleep apnea (OSA). In these patients with known or excluded OSA, none of the health administrative diagnostic codes, diagnostic procedures, or therapeutic interventions by themselves or in combination identified OSA with adequately high sensitivity and specificity. Existing studies using administrative codes to identify OSA should be interpreted with caution.

Background:

Health administrative (HA) databases are increasingly used to identify surgical patients with obstructive sleep apnea (OSA) for research purposes, primarily using diagnostic codes. Such means to identify patients with OSA are not validated. The authors determined the accuracy of case-ascertainment algorithms for identifying patients with OSA with the use of HA data.

Methods:

Clinical data derived from an academic health sciences network within a universal health insurance plan were used as the reference standard. The authors linked patients to HA data and retrieved all claims in the 2 yr before surgery to determine the presence of any diagnostic codes, diagnostic procedures, or therapeutic interventions consistent with OSA.

Results:

The authors identified 4,965 patients (2003 to 2012) who underwent preoperative polysomnogram. Of these, 4,353 patients were linked to HA data; 2,427 of these (56%) had OSA based on diagnosis by a sleep physician or the apnea hypopnea index. A claim for a polysomnogram and receipt of a positive airway pressure device had a sensitivity, specificity, and positive likelihood ratio (+LR) for OSA of 19, 98, and 10.9%, respectively. An International Classification of Diseases, Tenth Revision, code for sleep apnea in hospitalization abstracts was 9% sensitive and 98% specific (+LR, 4.5). A physician billing claim for OSA (International Classification of Diseases, Ninth Revision, 780.5) was 58% sensitive and 38% specific (+LR, 0.9). A polysomnogram and a positive airway pressure device or any code for OSA was 70% sensitive and 36% specific (+LR, 1.1).

Conclusions:

No code or combination of codes provided a +LR high enough to adequately identify patients with OSA. Existing studies using administrative codes to identify OSA should be interpreted with caution.
Behavioral Modification of Intraoperative Hyperglycemia Management with a Novel Real-time Audiovisual Monitor
Authors: Sathishkumar Subramanian , Lai Manda , Picton Paul , Kheterpal Sachin , Morris Michelle , Shanks Amy , Ramachandran Satya Krishna
Published: May 2015

AbstractAbstract

Real-time audiovisual notification is associated with a significant increase in desirable intraoperative glycemic management behavior and may help achieve tighter intraoperative glycemic control.

Background:

Hyperglycemia, defined as blood glucose (BG) levels above 200 mg/dl (11.1 mM), is associated with increased postoperative morbidity. Yet, the treatment standard for intraoperative glycemic control is poorly defined for noncardiac surgery. Little is known of the interindividual treatment variability or methods to modify intraoperative glycemic management behaviors. AlertWatch (AlertWatch, USA) is a novel audiovisual alert system that serves as a secondary patient monitor for use in operating rooms. The authors evaluated the influence of use of AlertWatch on intraoperative glycemic management behavior.

Methods:

AlertWatch displays historical patient data (risk factors and laboratory results) from multiple networked information systems, combined with the patient’s live physiologic data. The authors extracted intraoperative data for 19 months to evaluate the relationship between AlertWatch usage and initiation of insulin treatment for hyperglycemia. Outcome associations were adjusted for physical status, case duration, procedural complexity, emergent procedure, fasting BG value, home insulin therapy, patient age, and primary anesthetist.

Results:

Overall, 2,341 patients had documented intraoperative hyperglycemia. Use of AlertWatch (791 of 2,341; 33.5%) was associated with 55% increase in insulin treatment (496 of 791 [62.7%] with and 817 of 1,550 [52.7%] without AlertWatch; adjusted odds ratio [95% CI], 1.55 [1.23 to 1.95]; P < 0.001) and 44% increase in BG recheck after insulin administration (407 of 791 [51.5%] with AlertWatch and 655 of 1,550 [42.3%] in controls; adjusted odds ratio [95% CI], 1.44 [1.14 to 1.81]; P = 0.002).

Conclusion:

AlertWatch is associated with a significant increase in desirable intraoperative glycemic management behavior and may help achieve tighter intraoperative glycemic control.
Predictors of Failure of Awake Regional Anesthesia for Neonatal Hernia Repair
Authors: Frawley Geoff , Bell Graham , Disma Nicola , Withington Davinia E. , de Graaff Jurgen C. , Morton Neil S. , McCann Mary Ellen , Arnup Sarah J. , Bagshaw Oliver , Wolfler Andrea , Bellinger David , Davidson Andrew J.
Published: May 2015

AbstractAbstract

In a secondary analysis of the General Anesthesia compared to Spinal anesthesia study, data from 339 infants younger than 60 weeks postmenstrual age receiving spinal or caudal anesthesia for herniorrhaphy were examined. Failure of regional anesthesia requiring general anesthesia occurred in 10% of cases, and its only predictor was bloody tap on the first attempt at lumbar puncture.

Background:

Awake regional anesthesia (RA) is a viable alternative to general anesthesia (GA) for infants undergoing lower abdominal surgery. Benefits include lower incidence of postoperative apnea and avoidance of anesthetic agents that may increase neuroapoptosis and worsen neurocognitive outcomes. The General Anesthesia compared to Spinal anesthesia study compares neurodevelopmental outcomes after awake RA or GA in otherwise healthy infants. The aim of the study is to describe success and failure rates of RA and report factors associated with failure.

Methods:

This was a nested cohort study within a prospective, randomized, controlled, observer-blind, equivalence trial. Seven hundred twenty-two infants 60 weeks or less postmenstrual age scheduled for herniorrhaphy under anesthesia were randomly assigned to receive RA (spinal, caudal epidural, or combined spinal caudal anesthetic) or GA with sevoflurane. The data of 339 infants, where spinal or combined spinal caudal anesthetic was attempted, were analyzed. Possible predictors of failure were assessed including patient factors, technique, experience of site and anesthetist, and type of local anesthetic.

Results:

RA was sufficient for the completion of surgery in 83.2% of patients. Spinal anesthesia was successful in 86.9% of cases and combined spinal caudal anesthetic in 76.1%. Thirty-four patients required conversion to GA, and an additional 23 patients (6.8%) required brief sedation. Bloody tap on the first attempt at lumbar puncture was the only risk factor significantly associated with block failure (odds ratio = 2.46).

Conclusions:

The failure rate of spinal anesthesia was low. Variability in application of combined spinal caudal anesthetic limited attempts to compare the success of this technique to spinal alone.
A 17-Year-Old Girl With Acute Onset of Hemiparesis
Authors: Morrissey Michael , Ciorciari Anthony J. , Cunningham Sandra J.
Published: May 2015

The presentation of acute-onset hemiparesis in a teenager can be challenging and offers a wide differential diagnosis. We discuss the approach to the patient (which should begin with thorough history taking and physical examination) and advanced imaging as directed by the patient’s signs and symptoms. We report the case of an otherwise well 17-year-old girl who presented to the pediatric emergency department with a 2-day history of left-sided weakness and difficulty ambulating. Her eventual diagnosis of Balo concentric sclerosis, a rare form of multiple sclerosis, is discussed.
Loss of CDKN2A Promoter Methylation Coincides With the Epigenetic Transdifferentiation of Uterine Myosarcomatous Cells
Authors: Roncati Luca , Barbolini Giuseppe , Sartori Giuliana , Siopis Elena , Pusiol Teresa , Maiorana Antonio
Published: May 2015

Leiomyosarcoma is the most common type of uterine sarcoma and usually displays typical morphology. Heterologous leiomyosarcoma is the rarest variant, in which the tumor contains liposarcomatous, osteosarcomatous, or rhabdomyosarcomatous components. We have investigated the largest series of uterine leiomyosarcoma with a rhabdomyosarcomatous component and we have disclosed a molecular finding, which coincides to the process of transdifferentiation from smooth muscle into striated muscle phenotype. The surgical specimens of 5 rare cases of uterine leiomyosarcoma with a rhabdomyosarcomatous component were formalin fixed and paraffin embedded. In addition to hematoxylin/eosin stains, phosphotungstic acid hematoxylin staining, immunohistochemistry, and methylation-specific polymerase chain reaction the CDKN2A promoter region were performed. Leiomyosarcomatous cells were found to be strongly immunoreactive for both desmin and α-smooth muscle actin. Rhabdomyosarcomatous cells were immunoreactive for sarcomeric actin, desmin, vimentin, CD10, and p16. The methylation-specific polymerase chain reaction revealed the presence of a methylated allele and an unmethylated allele in the microdissected samples, coming from leiomyosarcomatous cells. On the contrary, 2 unmethylated alleles, molecular expression of a loss of heterozygosity, were detected in all the microdissected samples in the rhabdomyosarcomatous cells. The loss of heterozygosity methylation in the promoter region of the CDKN2A gene, occurred only in the rhabdomyosarcomatous cells with increases in both p16 and p14 expression. This event may result in an inhibition of cdk4/cdk6 activity, stabilizes the tumor suppressor protein p53, and coincides with the transdifferentiation from smooth muscle into striated muscle.
Structural constraints on the evolution of the collagen fibril: convergence on a 1014-residue COL domain
Authors: Slatter David Anthony , Farndale Richard William
Published: May 2015

Type I collagen is the fundamental component of the extracellular matrix. Its α1 gene is the direct descendant of ancestral fibrillar collagen and contains 57 exons encoding the rod-like triple-helical COL domain. We trace the evolution of the COL domain from a primordial collagen 18 residues in length to its present 1014 residues, the limit of its possible length. In order to maintain and improve the essential structural features of collagen during evolution, exons can be added or extended only in permitted, non-random increments that preserve the position of spatially sensitive cross-linkage sites. Such sites cannot be maintained unless the twist of the triple helix is close to 30 amino acids per turn. Inspection of the gene structure of other long structural proteins, fibronectin and titin, suggests that their evolution might have been subject to similar constraints.
Analytical model of reactive transport processes with spatially variable coefficients
Authors: Simpson Matthew J. , Morrow Liam C.
Published: May 2015

Analytical solutions of partial differential equation (PDE) models describing reactive transport phenomena in saturated porous media are often used as screening tools to provide insight into contaminant fate and transport processes. While many practical modelling scenarios involve spatially variable coefficients, such as spatially variable flow velocity,
v
(
x
), or spatially variable decay rate,
k
(
x
), most analytical models deal with constant coefficients. Here we present a framework for constructing exact solutions of PDE models of reactive transport. Our approach is relevant for advection-dominant problems, and is based on a regular perturbation technique. We present a description of the solution technique for a range of one-dimensional scenarios involving constant and variable coefficients, and we show that the solutions compare well with numerical approximations. Our general approach applies to a range of initial conditions and various forms of
v
(
x
) and
k
(
x
). Instead of simply documenting specific solutions for particular cases, we present a symbolic worksheet, as supplementary material, which enables the solution to be evaluated for different choices of the initial condition,
v
(
x
) and
k
(
x
). We also discuss how the technique generalizes to apply to models of coupled multispecies reactive transport as well as higher dimensional problems.
Extreme ecological response of a seabird community to unprecedented sea ice cover
Authors: Barbraud Christophe , Delord Karine , Weimerskirch Henri
Published: May 2015

Climate change has been predicted to reduce Antarctic sea ice but, instead, sea ice surrounding Antarctica has expanded over the past 30 years, albeit with contrasted regional changes. Here we report a recent extreme event in sea ice conditions in East Antarctica and investigate its consequences on a seabird community. In early 2014, the Dumont d'Urville Sea experienced the highest magnitude sea ice cover (76.8%) event on record (1982–2013: range 11.3–65.3%; mean±95% confidence interval: 27.7% (23.1–32.2%)). Catastrophic effects were detected in the breeding output of all sympatric seabird species, with a total failure for two species. These results provide a new view crucial to predictive models of species abundance and distribution as to how extreme sea ice events might impact an entire community of top predators in polar marine ecosystems in a context of expanding sea ice in eastern Antarctica.
Flavobacterium nitrogenifigens sp. nov., isolated from switchgrass (Panicum virgatum)
Authors: Kämpfer Peter , Busse Hans-Jürgen , McInroy John A. , Xu Jia , Glaeser Stefanie P.
Published: May 2015

A yellow, nitrogen-fixing bacterial strain, NXU-44T, isolated from the rhizosphere of switchgrass (Panicum virgatum) in Auburn, Alabama, USA, was studied to determine its taxonomic position. Cells of the isolate were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Flavobacterium with highest sequence similarities to the type strains of Flavobacterium ginsenosidimutans (97.9 %), Flavobacterium phragmitis (97.6 %) and Flavobacterium anhuiense (97.5 %). The 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were below 97.5 %. The fatty acid profile of strain NXU-44T consisted of the major fatty acids iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. The major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylserine, one aminolipid and two polar lipids. The quinone system was composed exclusively of menaquinone MK-6. The polyamine pattern contained the major compound sym-homospermidine and only minor amounts of other polyamines. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. These data and the differential biochemical and chemotaxonomic properties show that strain NXU-44T represents a novel species of the genus Flavobacterium for which the name Flavobacterium nitrogenifigens sp. nov. is proposed. The type strain is NXU-44T ( = LMG 28694T = CIP 110894T).
Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
Authors: Grandi Fiorella C. , Rosser James M. , Newkirk Simon J. , Yin Jun , Jiang Xiaoling , Xing Zhuo , Whitmore Leanne , Bashir Sanum , Ivics Zoltán , Izsvák Zsuzsanna , Ye Ping , Yu Y. Eugene , An Wenfeng
Published: May 2015

Long interspersed elements (LINEs), through both self-mobilization and trans-mobilization of short interspersed elements and processed pseudogenes, have made an indelible impact on the structure and function of the human genome. One consequence is the creation of new CpG islands (CGIs). In fact, more than half of all CGIs in the genome are associated with repetitive DNA, three-quarters of which are derived from retrotransposons. However, little is known about the epigenetic impact of newly inserted CGIs. We utilized a transgenic LINE-1 mouse model and tracked DNA methylation dynamics of individual germline insertions during mouse development. The retrotransposed GFP marker sequence, a strong CGI, is hypomethylated in male germ cells but hypermethylated in somatic tissues, regardless of genomic location. The GFP marker is similarly methylated when delivered into the genome via the Sleeping Beauty DNA transposon, suggesting that the observed methylation pattern may be independent of the mode of insertion. Comparative analyses between insertion- and non-insertion-containing alleles further reveal a graded influence of the retrotransposed CGI on flanking CpG sites, a phenomenon that we described as “sloping shores.” Computational analyses of human and mouse methylomic data at single-base resolution confirm that sloping shores are universal for hypomethylated CGIs in sperm and somatic tissues. Additionally, the slope of a hypomethylated CGI can be affected by closely positioned CGI neighbors. Finally, by tracing sloping shore dynamics through embryonic and germ cell reprogramming, we found evidence of bookmarking, a mechanism that likely determines which CGIs will be eventually hyper- or hypomethylated.
Quantification of GC-biased gene conversion in the human genome
Authors: Glémin Sylvain , Arndt Peter F. , Messer Philipp W. , Petrov Dmitri , Galtier Nicolas , Duret Laurent
Published: May 2015

Much evidence indicates that GC-biased gene conversion (gBGC) has a major impact on the evolution of mammalian genomes. However, a detailed quantification of the process is still lacking. The strength of gBGC can be measured from the analysis of derived allele frequency spectra (DAF), but this approach is sensitive to a number of confounding factors. In particular, we show by simulations that the inference is pervasively affected by polymorphism polarization errors and by spatial heterogeneity in gBGC strength. We propose a new general method to quantify gBGC from DAF spectra, incorporating polarization errors, taking spatial heterogeneity into account, and jointly estimating mutation bias. Applying it to human polymorphism data from the 1000 Genomes Project, we show that the strength of gBGC does not differ between hypermutable CpG sites and non-CpG sites, suggesting that in humans gBGC is not caused by the base-excision repair machinery. Genome-wide, the intensity of gBGC is in the nearly neutral area. However, given that recombination occurs primarily within recombination hotspots, 1%–2% of the human genome is subject to strong gBGC. On average, gBGC is stronger in African than in non-African populations, reflecting differences in effective population sizes. However, due to more heterogeneous recombination landscapes, the fraction of the genome affected by strong gBGC is larger in non-African than in African populations. Given that the location of recombination hotspots evolves very rapidly, our analysis predicts that, in the long term, a large fraction of the genome is affected by short episodes of strong gBGC.
Hydrogen-bonded supramolecular architecture in nonlinear optical ammonium 2,4-dinitrophenolate hydrate
Authors: Prasad A. Aditya , Meenakshisundaram S. P.
Published: May 2015

Single crystals of ammonium 2,4-dinitrophenolate hydrate (ADH) were grown by the slow evaporation solution growth technique. The structure is elucidated by single-crystal X-ray diffraction analysis and the crystal belongs to an orthorhombic system with noncentrosymmetric space groupPna21. The second harmonic generation efficiency of ADH is superior to that of the reference material KH2PO4. The X-ray study reveals that molecules are associated by weak C—H...O, O—H...N, N—H...π and π–π stacking interactions, which are responsible for the formation and strengthening of the supramolecular assembly. Inter- and intramolecular hydrogen-bonding interactions support the supramolecular architecture in the crystal packing. Three different types of architecture,i.e.column-like packing, a sandwich model of packing and a cluster network type of infrastructure, are observed. Optical studies reveal that the absorption is minimum in the visible region and the cutoff wavelength is at ∼240 nm. The band-gap energy was estimated by the application of the Kubelka–Munk algorithm. The powder X-ray diffraction pattern reveals the good crystallinity of the as-grown specimen. Investigation of the intermolecular interactions and crystal packing using Hirshfeld surface analysis, based on single-crystal X-ray diffraction, reveals that the close contacts are associated with molecular interactions. Fingerprint plots of Hirshfeld surfaces were used to locate and analyze the percentage of hydrogen-bonding interactions.
Considerations on the model-free shape retrieval of inorganic nanocrystals from small-angle scattering data
Authors: Burian Max , Fritz-Popovski Gerhard , He Meng , Kovalenko Maksym V. , Paris Oskar , Lechner Rainer T.
Published: May 2015

Some new considerations on the model-free shape retrieval of inorganic nanocrystals based on the evaluation of averaged dummy atom models obtained from small-angle X-ray scattering data are presented. Scattering curves for shapes commonly found in inorganic nanocrystal systems were computed, from which dummy atom models were reconstructed usingDAMMINandDAMAVER. Cross sectional analysis methods were applied to allow a quantitative interpretation of these models, where special focus was directed towards the measurement of discrete model dimensions. By a quantitative comparison of the obtained models with the initial geometries, the limits of the proposed evaluation techniques were tested. Further, the proposed methods were utilized to study the influence of the accessible scattering vector as well as the effect of increasing size distributions on models retrieved byDAMMINandDAMAVER. The results confirm the usefulness of theseab initioshape-retrieval methods for slightly polydisperse systems. Finally, the practicability of the proposed techniques is demonstrated on an ensemble of chemically synthesized colloidal bismuth nanocrystals.
Why crystal structure analysis works: a one-dimensional crystallography teaching tool
Authors: Pinkerton A. Alan
Published: May 2015

A teaching tool is proposed to help beginner students of crystallography understand how crystallographic calculations work. Examples of the most important methods taught in X-ray crystallography courses have been adapted to a one-dimensional hypothetical structure. All calculations can be carried out in class with a scientific calculator or by using a simple spreadsheet.
Quantitative grain-scale ferroic domain volume fractions and domain switching strains from three-dimensional X-ray diffraction data
Authors: Oddershede Jette , Majkut Marta , Cao Qinghua , Schmidt Søren , Wright Jonathan P. , Kenesei Peter , Daniels John E.
Published: May 2015

A method for the extension of the three-dimensional X-ray diffraction technique to allow the extraction of domain volume fractions in polycrystalline ferroic materials is presented. This method gives access to quantitative domain volume fractions of hundreds of independent embedded grains within a bulk sample. Such information is critical to furthering our understanding of the grain-scale interactions of ferroic domains and their influence on bulk properties. The method also provides a validation tool for mesoscopic ferroic domain modelling efforts. The mathematical formulations presented here are applied to tetragonal coarse-grained Ba0.88Ca0.12Zr0.06Ti0.94O3 and rhombohedral fine-grained (0.82)Bi0.5Na0.5TiO3–(0.18)Bi0.5K0.5TiO3 electroceramic materials. The fitted volume fraction information is used to calculate grain-scale non-180° ferroelectric domain switching strains. The absolute errors are found to be approximately 0.01 and 0.03% for the tetragonal and rhombohedral cases, which had maximum theoretical domain switching strains of 0.47 and 0.54%, respectively. Limitations and possible extensions of the technique are discussed.
Crystallization and preliminary X-ray diffraction analysis of the two distinct types of zebrafish β2-microglobulin
Authors: Chen Zhaosan , Zhang Nianzhi , Lu Shuangshuang , Tariq Mansoor , Wang Junya , Xia Chun
Published: May 2015

β2-Microglobulin (β2m) noncovalently associates with the heavy chain of major histocompatibility complex class I (MHC I) molecules, which bind foreign antigen peptides to control the cytotoxic T lymphocyte (CTL) immune response. In contrast to mammals, there are distinct types of β2ms derived from two loci in a number of teleost species. In order to clarify the structures of the β2ms, the zebrafish (Danio rerio) β2msDare-β2m-I andDare-β2m-II were expressed inEscherichia coli, purified and crystallized, and diffraction data were collected to 1.6 and 1.9 Å resolution, respectively. Both crystals belonged to space groupP212121. The unit-cell parameters were determined to bea= 38.2,b= 50.4,c= 50.9 Å forDare-β2m-I anda= 38.9,b= 52.7,c= 65.8 Å forDare-β2m-II. Each asymmetric unit was constituted of one molecule, with Matthews coefficients of 2.22 and 3.01 Å3 Da−1and solvent contents of 45 and 59% forDare-β2m-I andDare-β2m-II, respectively. These two β2m structures will provide relevant information for further studies of the structures of the MHC I complex.
A preliminary X-ray study of 3-deoxy-D-manno-oct-2-ulosonic acid 8-phosphate phosphatase (YrbI) fromBurkholderia pseudomallei
Authors: Park Jimin , Lee Daeun , Kim Mi-Sun , Kim Dae Yong , Shin Dong Hae
Published: May 2015

3-Deoxy-D-manno-oct-2-ulosonic acid 8-phosphate phosphatase (YrbI), the third enzyme in the pathway for the biosynthesis of 3-deoxy-D-manno-oct-2-ulosonic acid (KDO), hydrolyzes KDO 8-phosphate to KDO and inorganic phosphate. YrbI belongs to the haloacid dehalogenase (HAD) superfamily, which is a large family of magnesium-dependent phosphatase/phosphotransferase enzymes. In this study, YrbI fromBurkholderia pseudomallei, the causative agent of melioidosis, has been cloned, expressed, purified and crystallized. Synchrotron X-ray data were also collected to 2.25 Å resolution. The crystal belonged to the primitive orthorhombic space groupP212121, with unit-cell parametersa= 63.7,b= 97.5,c= 98.0 Å. A full structural determination is in progress to elucidate the structure–function relationship of this protein.
Structure of the MarR family protein Rv0880 fromMycobacterium tuberculosis
Authors: Gao Yun-Rong , Feng Na , Chen Tao , Li De-Feng , Bi Li-Jun
Published: May 2015

Rv0880 from the pathogenMycobacterium tuberculosisis classified as a MarR family protein in the Pfam database. It consists of 143 amino acids and has an isoelectric point of 10.9. Crystals of Rv0880 belonged to space groupP1, with unit-cell parametersa= 54.97,b= 69.60,c= 70.32 Å, α = 103.71, β = 111.06, γ = 105.83°. The structure of the MarR family transcription regulator Rv0880 was solved at a resolution of 2.0 Å with anRcrystandRfreeof 21.2 and 24.9%, respectively. The dimeric structure resembles that of other MarR proteins, with each subunit comprising a winged helix–turn–helix domain connected to an α-helical dimerization domain.
Crystallization and preliminary X-ray diffraction analysis of the Csu pili CsuC–CsuA/B chaperone–major subunit pre-assembly complex fromAcinetobacter baumannii
Authors: Pakharukova Natalia , Tuittila Minna , Paavilainen Sari , Zavialov Anton
Published: May 2015

The attachment of many Gram-negative pathogens to biotic and abiotic surfaces is mediated by fimbrial adhesins, which are assembledviathe classical, alternative and archaic chaperone–usher (CU) pathways. The archaic CU fimbrial adhesins have the widest phylogenetic distribution, yet very little is known about their structure and mechanism of assembly. To elucidate the biogenesis of archaic CU systems, structural analysis of the Csu fimbriae, which are used byAcinetobacter baumanniito form stable biofilms and cause nosocomial infection, was focused on. The major fimbriae subunit CsuA/B complexed with the CsuC chaperone was purified from the periplasm ofEscherichia colicells co-expressing CsuA/B and CsuC, and the complex was crystallized in PEG 3350 solution using the hanging-drop vapour-diffusion method. Selenomethionine-labelled CsuC–CsuA/B complex was purified and crystallized under the same conditions. The crystals diffracted to 2.40 Å resolution and belonged to the hexagonal space groupP6422, with unit-cell parametersa=b= 94.71,c = 187.05 Å, α = β = 90, γ = 120°. Initial phases were derived from a single anomalous diffraction (SAD) experiment using the selenomethionine derivative.
Protein production, crystallization and preliminary crystallographic analysis of the four N-terminal immunoglobulin domains of Down syndrome cell adhesion molecule 1
Authors: Cheng Linna , Li Shu-Ang , Yu Yamei , Chen Qiang
Published: May 2015

Down syndrome cell adhesion molecule 1 (Dscam1), a member of the immunoglobulin (Ig) superfamily, plays important roles in both the nervous and the immune systems. Via alternative RNA splicing,DrosophilaDscam1 encodes a vast family of Ig-containing proteins that exhibit isoform-specific homophilic binding. Whether different Dscam1 isoforms adopt the same dimerization mode is under debate, and the detailed mechanism of Dscam1 specificity remains unclear. In this study, eight different isforms of Dscam1 Ig1–4 have been cloned, overexpressed, purified to homogeneity and crystallized. X-ray data were collected to 1.9–4.0 Å resolution. These structures will provide the opportunity to perform extensive structural comparisons of different Dscam1 isoforms and provide insight into its specificity.
Expression, purification, crystallization and preliminary X-ray analysis of CttA, a putative cellulose-binding protein fromRuminococcus flavefaciens
Authors: Venditto Immacolata , Bule Pedro , Thompson Andrew , Sanchez-Weatherby Juan , Sandy James , Ferreira Luis M. A. , Fontes Carlos M. G. A. , Najmudin Shabir
Published: May 2015

A number of anaerobic microorganisms produce multi-modular, multi-enzyme complexes termed cellulosomes. These extracellular macromolecular nanomachines are designed for the efficient degradation of plant cell-wall carbohydrates to smaller sugars that are subsequently used as a source of carbon and energy. Cellulolytic strains from the rumens of mammals, such asRuminococcus flavefaciens, have been shown to have one of the most complex cellulosomal systems known. Cellulosome assembly requires the binding of dockerin modules located in cellulosomal enzymes to cohesin modules located in a macromolecular scaffolding protein. Over 220 genes encoding dockerin-containing proteins have been identified in theR. flavefaciensgenome. The dockerin-containing enzymes can be incorporated into the primary scaffoldin (ScaA), which in turn can bind to adaptor scaffoldins (ScaB or ScaC) and subsequently to anchoring scaffoldin (ScaE), thereby attaching the whole complex to the cell surface. However, unlike other cellulosomes such as that fromClostridium thermocellum, theRuminococcusspecies lack a specific carbohydrate-binding module (CBM) on ScaA which recruits the entire complex onto the surface of the substrate. Instead, a cellulose-binding protein, CttA, comprising two putative tandem novel carbohydrate-binding modules and a C-terminal X-dockerin module, which can bind to the cohesin of ScaE, may mediate the attachment of bacterial cells to cellulose. Here, the expression, purification and crystallization of the carbohydrate-binding modular part of the CttA fromR. flavefaciensare described. X-ray data have been collected to resolutions of 3.23 and to 1.61 Å in space groupsP3121 orP3221 andP21, respectively. The structure was phased using bound iodide from the crystallization buffer by SAD experiments.
Influence of palm oil, canola oil and blends on characteristics of fried plantain crisps
Authors: Mba Ogan I. , Dumont Marie-Josée , Ngadi Michael
Published: May 2015

Purpose

– The purpose of this paper is to study the influence of crude palm oil (PO), canola oil (CO) and their blends on characteristics of fried plantain crisps at two different stages of ripening.

Design/methodology/approach

– Plantain (Musa paradisiaca L.) samples were peeled, sliced into 3 mm slices, blanched at 70 °C for 3 min and dried. The slices were deep fried at 180 °C for different times.

Findings

– There was no significant difference (p
>
0.05) in the moisture loss rate and the crispiness of the crisps produced using PO and CO. Significant differences (p
<
0.05) existed in the fat uptake and color properties of the crisps fried in the two oils. PO fried crisps absorbed 15 percent less oil in the unripe crisps samples and 21 percent less oil in the fully ripened crisps than CO. The browning index showed that the PO crisps had greater color changes than the crisps fried using CO. The difference between the crisps from 50:50 blends of PO: CO and CO was not statistically significant, while 70:30 blends improved the qualities of the crisps better than CO alone. Analysis of kinetics data showed that moisture loss, oil uptake and browning index followed a first-order kinetics model.

Originality/value

– Understanding the interactions between ripening and processing methods is enhanced and use of crude PO for industrial deep-fat frying is encouraged.
Paying to see a bug on my food
Authors: de-Magistris Tiziana , Pascucci Stefano , Mitsopoulos Dimitrios
Published: May 2015

Purpose

– The purpose of this paper is to examine the role of the European Novel Food Regulation (ENFR) on consumers’ acceptance of and willingness to pay (WTP) for radical food innovations. The research question is focussed on determining whether the ENFR is hampering the market potential of insect-based food products in the European Union (EU). The authors position this question within the domain of regulatory barriers related to food innovations.

Design/methodology/approach

– Using a choice experiment, the authors assess the presence and relevance of these failures through the analysis of consumers’ acceptance and WTP for insect-based food products with different product attributes directly imposed by the ENFR. Namely, the authors assess the effect of the visualization of insects in the product, the use of logo, and nutritional information.

Findings

– The results show that consumers prefer and are willing to pay a premium price for insect-based products with a nutritional health claim and logo, but they are not willing to pay for a product with a visualized insect.

Originality/value

– This paper highlights the risk of regulatory failures for novel foods in the EU, such as insect-based food products due to the ENFR.
How knowledgeable are high school students about food safety? Results from a predominantly minority Chicago charter school
Authors: Burke Anne , Dworkin Mark
Published: May 2015

Purpose

– High school students are at an age where food handling may occur for themselves and as entry level workers in food service. An estimated 21 percent of food and beverage service workers are aged 16-19 years. The purpose of this paper is to determine baseline food safety knowledge and associated factors among high school students.

Design/methodology/approach

– A convenience sample of 231 Chicago high school students was approached to participate in a 34-question survey to obtain information about their food safety knowledge, behaviors, and personal hygiene. Frequencies of correct answers to each knowledge question were examined to determine knowledge gaps. Bivariate analyses were performed to identify student variables associated with knowledge score and regression models were used to examine the associations between eligible factors and knowledge score.

Findings

– Among the 195 participating students, 70 percent described themselves as Hispanic/Latino and 15 percent as non-Hispanic Black. In all, 12 percent of the students had restaurant employment experience. The overall student mean knowledge score was 37 percent. Students demonstrated substantial knowledge gaps regarding the temperatures for cooking, mechanisms for thawing food, cross-contamination, and vulnerable populations for foodborne disease. In the final linear regression model, Hispanic ethnicity and experience cooking seafood were significantly associated with lower knowledge score and experience cooking meat and cooking alone were significantly associated with higher knowledge score (p
<
0.05).

Research limitations/implications

– Students demonstrated substantial knowledge gaps regarding the temperatures for cooking, mechanisms for thawing food, cross-contamination, and vulnerable populations for foodborne disease. In the final linear regression model, Hispanic ethnicity and experience cooking seafood were significantly associated with lower knowledge score and experience cooking meat and cooking alone were significantly associated with higher knowledge score (p
<
0.05).

Originality/value

– These data demonstrate substantial knowledge gaps in a predominantly minority high school student population. Given that high school students are a substantial proportion of the food service workforce, they are especially important to target for food safety education.
Factors influencing the decisions to buy and consume functional food
Authors: Kraus Artur
Published: May 2015

Purpose

– The purpose of this paper is to identify the most important characteristics of functional foods and the motives behind its consumption.

Design/methodology/approach

– The data were collected in the direct interview. The sample (n=200) consisted of 137 women and 63 men at the age of 18-60 years. The research tool was a questionnaire divided into four sections. The first one included quality attributes. The second one included healthful properties, functional components and carriers. The third one concerned the motives for purchasing functional food and included the consequences and values. In the fourth section the participants were asked about gender, age and education.

Findings

– Among the quality attributes the research reveals six principal components package of information on healthful properties and nutritional value of the product, attributes of taste, health and safety, practical packaging, freshness, purity and naturalness. In terms of health benefits, two components were distinguished prevention of health problems, strengthening of the body and improvement of its functions. Among functional components, the following were distinguished vitamins and minerals, dietary fibre and Omega-3 fatty acids. As the best carriers the following were recognized: cereal products, dairy products, meat products; mixtures of fruits and vegetables. As the most important consequences motivating people to consume functional food the following were recognized: the health effects of proper nutrition resulting from consciousness raising actions promoting health; and the joy of eating and improvement of the appearance. When it comes to the most important motivating factors, good health, long harmonious life and self-esteem were included. The means to achieve these goals are to be responsible for health.

Originality/value

– The key factors determining the functional product and motivating for consumption of functional food may establish a basis for actions related to development and consumption of the food. The understanding of the factors that consumers take into account when choosing functional food will help in shaping the optimal strategies for product development. Learning about the basic motivating factors in consumption may be helpful in the development of healthy nutrition education and promotion programmes. The research may provide valuable support for actions related to food products promotion and marketing.
Adult obesity, food access, and eating habits in Italy: an empirical analysis
Authors: Bimbo Francesco , Bonanno Alessandro , Viscecchia Rosaria
Published: May 2015

Purpose

– Improving access to healthy foods is currently on the European Union health policy agenda, as a means to mitigate obesity. The purpose of this paper is to analyze the relationship between access to food stores and adult BMI in Italy, accounting also for the synergic role of individuals’ eating habits.

Design/methodology/approach

– To study the relationship between access to different food outlets, eating habits, and adult BMI in Italy, the authors combine three years of individual-level data with region-level food stores’ density measures and account for store location endogeneity using a Generalized Method of Moment estimator.

Findings

– While large stores and specialty fruit and vegetable stores show a BMI decreasing effect, local/convenience stores show little to no effect on adult BMI. The effect of access on adult BMI varies conditionally on dietary habits, since access to food outlets and healthy eating can have a synergic impact on reducing Italian adults’ BMI.

Originality/value

– The authors highlight how, the effectiveness of policies aimed to curb obesity may vary according with the food environment consumers live in as well as on individuals’ eating habits.
The effect of workplace diversity management in a highly male-dominated culture
Authors: Kim Hye Kyoung , Lee Ung Hee , Kim Young Hyung
Published: May 2015

Purpose

– The purpose of this paper is to, first, examine gender differences in response to the presence of diversity management and in the level of organizational commitment, second, to investigate the influence of diversity management practices on organizational commitment, and third, to examine the relationships among gender, diversity management, organizational commitment, and job performance in a more highly male-dominated culture.

Design/methodology/approach

– Based on a review of the literature, this empirical study uses a survey and statistical analysis, including t-tests and regressions, to test the hypotheses.

Findings

– The major findings are as follows: first, female workers reported a more favorable perception of diversity management practices than did male workers. However, there was no difference between female and male workers in organizational commitment. Second, diversity management was positively and significantly related to organizational commitment. Finally, the results show that gender was not related to in-role performance, while diversity management and organizational commitment were positively related to in-role performance.

Originality/value

– The significance of this study lies in its investigation of the effect of diversity management on employees’ attitude and behavior and the gender differences in the perception of diversity management and organizational commitment in a highly male-dominated society. In addition, since Korean companies have become more performance oriented (House et al., 2004), finding the positive relationship between diversity management practices and job performance can also suggest one way for all organizations to increase their employees’ task performance for their continuous development.