bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold
Authors: Nijkamp Jurgen F. , Pop Mihai , Reinders Marcel J. T. , de Ridder Dick
Published: September 2013

Motivation: Although many tools are available to study variation and its impact in single genomes, there is a lack of algorithms for finding such variation in metagenomes. This hampers the interpretation of metagenomics sequencing datasets, which are increasingly acquired in research on the (human) microbiome, in environmental studies and in the study of processes in the production of foods and beverages. Existing algorithms often depend on the use of reference genomes, which pose a problem when a metagenome of a priori unknown strain composition is studied. In this article, we develop a method to perform reference-free detection and visual exploration of genomic variation, both within a single metagenome and between metagenomes.

Results: We present the MaryGold algorithm and its implementation, which efficiently detects bubble structures in contig graphs using graph decomposition. These bubbles represent variable genomic regions in closely related strains in metagenomic samples. The variation found is presented in a condensed Circos-based visualization, which allows for easy exploration and interpretation of the found variation.

We validated the algorithm on two simulated datasets containing three respectively seven Escherichia coli genomes and showed that finding allelic variation in these genomes improves assemblies. Additionally, we applied MaryGold to publicly available real metagenomic datasets, enabling us to find within-sample genomic variation in the metagenomes of a kimchi fermentation process, the microbiome of a premature infant and in microbial communities living on acid mine drainage. Moreover, we used MaryGold for between-sample variation detection and exploration by comparing sequencing data sampled at different time points for both of these datasets.

Availability: MaryGold has been written in C++ and Python and can be downloaded from http://bioinformatics.tudelft.nl/software

Contact:  d.deridder@tudelft.nl
Single assay-wide variance experimental (SAVE) design for high-throughput screening
Authors: Murie Carl , Barette Caroline , Lafanechère Laurence , Nadon Robert
Published: September 2013

Motivation: Advantages of statistical testing of high-throughput screens include P-values, which provide objective benchmarks of compound activity, and false discovery rate estimation. The cost of replication required for statistical testing, however, may often be prohibitive. We introduce the single assay-wide variance experimental (SAVE) design whereby a small replicated subset of an entire screen is used to derive empirical Bayes random error estimates, which are applied to the remaining majority of unreplicated measurements.

Results: The SAVE design is able to generate P-values comparable with those generated with full replication data. It performs almost as well as the random variance model t-test with duplicate data and outperforms the commonly used Z-scores with unreplicated data and the standard t-test. We illustrate the approach with simulated data and with experimental small molecule and small interfering RNA screens. The SAVE design provides substantial performance improvements over unreplicated screens with only slight increases in cost.

Contact:  robert.nadon@mcgill.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search
Authors: Wang Xiaojing , Zhang Bing
Published: September 2013

Summary: Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.

Availability and implementation:  customProDB and related documents are freely available at http://bioconductor.org/packages/2.13/bioc/html/customProDB.html.

Contact:  bing.zhang@vanderbilt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Neonatal Exposure to Sevoflurane in Mice Causes Deficits in Maternal Behavior Later in Adulthood
Authors: Takaenoki Yumiko , Satoh Yasushi , Araki Yoshiyuki , Kodama Mitsuyoshi , Yonamine Ryuji , Yufune Shinya , Kazama Tomiei
Published: September 2013

Background:

In animal models, exposure to general anesthetics induces widespread increases in neuronal apoptosis in the developing brain. Subsequently, abnormalities in brain functioning are found in adulthood, long after the anesthetic exposure. These abnormalities include not only reduced learning abilities but also impaired social behaviors, suggesting pervasive deficits in brain functioning. But the underlying features of these deficits are still largely unknown.

Methods:

Six-day-old C57BL/6 female mice were exposed to 3% sevoflurane for 6 h with or without hydrogen (1.3%) as part of the carrier gas mixture. At 7–9 weeks of age, they were mated with healthy males. The first day after parturition, the maternal behaviors of dams were evaluated. The survival rate of newborn pups was recorded for 6 days after birth.

Results:

Female mice that received neonatal exposure to sevoflurane could mate normally and deliver healthy pups similar to controls. But these dams often left the pups scattered in the cage and nurtured them very little, so that about half of the pups died within a couple of days. Yet, these dams did not show any deficits in olfactory or exploratory behaviors. Notably, pups born to sevoflurane-treated dams were successfully fostered when nursed by control dams. Mice coadministered of hydrogen gas with sevoflurane did not exhibit the deficits of maternal behaviors.

Conclusion:

In an animal model, sevoflurane exposure in the developing brain caused serious impairment of maternal behaviors when fostering their pups, suggesting pervasive impairment of brain functions including innate behavior essential to species survival.
Single-cell mutational profiling and clonal phylogeny in cancer
Authors: Potter Nicola E. , Ermini Luca , Papaemmanuil Elli , Cazzaniga Giovanni , Vijayaraghavan Gowri , Titley Ian , Ford Anthony , Campbell Peter , Kearney Lyndal , Greaves Mel
Published: September 2013

The development of cancer is a dynamic evolutionary process in which intraclonal, genetic diversity provides a substrate for clonal selection and a source of therapeutic escape. The complexity and topography of intraclonal genetic architectures have major implications for biopsy-based prognosis and for targeted therapy. High-depth, next-generation sequencing (NGS) efficiently captures the mutational load of individual tumors or biopsies. But, being a snapshot portrait of total DNA, it disguises the fundamental features of subclonal variegation of genetic lesions and of clonal phylogeny. Single-cell genetic profiling provides a potential resolution to this problem, but methods developed to date all have limitations. We present a novel solution to this challenge using leukemic cells with known mutational spectra as a tractable model. DNA from flow-sorted single cells is screened using multiplex targeted Q-PCR within a microfluidic platform allowing unbiased single-cell selection, high-throughput, and comprehensive analysis for all main varieties of genetic abnormalities: chimeric gene fusions, copy number alterations, and single-nucleotide variants. We show, in this proof-of-principle study, that the method has a low error rate and can provide detailed subclonal genetic architectures and phylogenies.
Speciation and Distribution of Arsenic in the Nonhyperaccumulator Macrophyte Ceratophyllum demersum
Authors: Mishra Seema , Wellenreuther Gerd , Mattusch Jürgen , Stärk Hans-Joachim , Küpper Hendrik
Published: September 2013

Although arsenic (As) is a common pollutant worldwide, many questions about As metabolism in nonhyperaccumulator plants remain. Concentration- and tissue-dependent speciation and distribution of As was analyzed in the aquatic plant Ceratophyllum demersum to understand As metabolism in nonhyperaccumulator plants. Speciation was analyzed chromatographically (high-performance liquid chromatography-[inductively coupled plasma-mass spectrometry]-[electrospray ionization-mass spectrometry]) in whole-plant extracts and by tissue-resolution confocal x-ray absorption near-edge spectroscopy in intact shock-frozen hydrated leaves, which were also used for analyzing cellular element distribution through x-ray fluorescence. Chromatography revealed up to 20 As-containing species binding more than 60% of accumulated As. Of these, eight were identified as thiol-bound (phytochelatins [PCs], glutathione, and cysteine) species, including three newly identified complexes: Cys-As(III)-PC2, Cys-As-(GS)2, and GS-As(III)-desgly-PC2. Confocal x-ray absorption near-edge spectroscopy showed arsenate, arsenite, As-(GS)3, and As-PCs with varying ratios in various tissues. The epidermis of mature leaves contained the highest proportion of thiol (mostly PC)-bound As, while in younger leaves, a lower proportion of As was thiol bound. At higher As concentrations, the percentage of unbound arsenite increased in the vein and mesophyll of young mature leaves. At the same time, x-ray fluorescence showed an increase of total As in the vein and mesophyll but not in the epidermis of young mature leaves, while this was reversed for zinc distribution. Thus, As toxicity was correlated with a change in As distribution pattern and As species rather than a general increase in many tissues.
Knowledge transfer, educational change and the history of education
Authors: Collins Jenny , Allender Tim
Published: September 2013

Purpose

– The purpose of this paper is to present a theoretical overview of the field of knowledge transfer and educational change and a discussion of the issues raised in the six papers in this special edition.

Design/methodology/approach

– A theoretical analysis of the field of knowledge transfer.

Findings

– The six papers consider issues such as the interplay of ideas between British and Indian educationalists, post-war debates over literacy standards, the use of curriculum materials for the process of citizen formation, the influence of international exchanges in the education of adolescents for citizenship, Vigotsky and the transfer of knowledge across time, space, culture, disciplines and networks, and the way constructions of Chinese identity within history books were shaped by knowledge processes that transcended nation states.

Originality/value

– This special issue of the History of Education Review engages with new approaches that have become available to historians in the past decade illustrating how they might be applied for the first time to key issues in the history of education across colonial and state borders. It addresses questions about the movement of knowledge across national and cultural boundaries, and examines key problems facing educators in a range of colonial and postcolonial contexts.
STAT6 polymorphisms are associated with neonatal regulatory T cells and cytokines and atopic diseases at 3 years
Authors: Casaca V. I. , Illi S. , Klucker E. , Ballenberger N. , Schedel M. , von Mutius E. , Kabesch M. , Schaub B.
Published: September 2013

Background

The transcription factor STAT6 is crucial for activation of the interleukin (IL)‐4/IL‐13 pathway and has been linked to regulatory T cells (Tregs). Associations of STAT6 polymorphisms with IgE levels were described; however, their impact on neonatal immune responses and early disease development is unknown.

Methods

STAT6 polymorphisms were genotyped in cord blood mononuclear cells by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS). Gene expression was assessed by real‐time polymerase chain reaction (PCR) and cytokines by Multiplex. At age 3 years, atopic diseases were assessed by questionnaires.

Results

STAT6 rs324011 but not rs1059513 polymorphism was associated with significant or borderline significant decreased mRNA expression of Treg‐associated genes (FOXP3, GITR, LAG3). Heterozygotes and minor allele homozygotes of rs324011 had low levels of tumor necrosis factor alpha (TNF‐α) and increased interferon gamma (IFN‐γ) (P ≤ 0.04), while heterozygotes and minor allele homozygotes of rs1059513 had increased TNF‐α and Granulocyte–macrophage colony‐stimulating factor (GM‐CSF) (P ≤ 0.05). In minor allele homozygotes of rs324011, expression of Treg‐associated genes was strongly inverse correlated with IFN‐γ (unstimulated, r = −0.7, P = 0.111; LpA stimulation, r = −0.8, P = 0.011), but not in heterozygotes or major allele homozygotes. Heterozygotes and minor allele homozygotes of rs324011 presented a lower risk of atopic dermatitis and obstructive bronchitis until age 3 years.

Conclusions

Two STAT6 polymorphisms were associated with altered immune responses already at birth. STAT6 rs324011 was associated with lower neonatal Treg and increased Th1 response. Those neonates had a lower risk of atopic dermatitis and obstructive bronchitis until 3 years. Our data suggest a role for STAT6 polymorphisms in early immune regulation and implications on early atopic disease development.
Prevalence and classification of rhinitis in preschool children in Portugal: a nationwide study
Authors: Morais‐Almeida M. , Santos N. , Pereira A. M. , Branco‐Ferreira M. , Nunes C. , Bousquet J. , Fonseca J. A.
Published: September 2013

Background

Information on rhinitis epidemiology in preschool children is scarce.

Objectives

To estimate, in children with 3–5 years of age, current rhinitis prevalence, to describe rhinitis symptoms and associated sociodemographic characteristics, and to report allergic rhinitis and its impact on asthma (ARIA) classification.

Methods

Cross‐sectional, nationwide, population‐based study including children aged 3–5 years. A multistep selection strategy was used to obtain a representative sample. Data were collected at kindergartens and parish centers by face‐to‐face interview to caregivers, using an adapted ISAAC questionnaire. ‘Current rhinitis’ (CR) was defined as the presence of ≥1 rhinitis symptom (repeated sneezing and/or itchy nose, blocked nose for >1 h, or runny nose without having a cold/flu) in the last year. Rhinitis lasting ≥4 days/week and ≥4 consecutive weeks was classified as persistent. Moderate–severe disease interfered ‘a moderate amount’ or ‘a lot’ in daily activities.

Results

Five thousand and eighteen children were included. CR prevalence was 43.4% [95% CI (42.0–44.8%); n = 2179] and that of physician‐diagnosed rhinitis was 11.7% [95% CI (10.8–12.6%); n = 588]. Of children with CR, 67% reported blocked nose, 48% rhinorrhea, and 46% sneezing/itchy nose. Considering ARIA classification, 30% of the population had mild intermittent, 3% mild persistent, 7% moderate–severe intermittent, and 3% moderate–severe persistent rhinitis. Children with CR had more current wheezing, physician‐diagnosed asthma, self‐reported food allergy, and family history of allergic disease. These characteristics were also associated with persistent and moderate–severe rhinitis.

Conclusions

This is the first nationwide population‐based study reporting rhinitis prevalence and ARIA classification in preschool children. In this age‐group, rhinitis is frequent and underdiagnosed. About 25% children with rhinitis presented moderate–severe disease.
Allergology in Europe, the blueprint
Authors: de Monchy J. G. , Demoly P. , Akdis C. A. , Cardona V. , Papadopoulos N. G. , Schmid‐Grendelmeier P. , Gayraud J.
Published: September 2013

The number of patients with allergic diseases in Europe, and thus relevant demand for health care, is continuously increasing. In this EAACI‐UEMS position paper, a rationale is given for the medical specialty of allergology. General practitioners and general paediatricians usually cannot elucidate and address all causative factors. Throughout Europe, therefore, the expertise of allergologists (allergists) is required. In collaboration with other medical professionals, they take care of allergic patients, in private practices or in specialized public centres. A well‐structured collaboration between allergists and allergy centres offers the possibility of rapid signalling of new trends developing in the population of allergic patients (e.g. in food and drug allergy). Allergy centres also can perform clinical (and basic) research, teach medical students, future allergists and provide postgraduate training. To prevent that the quality of care in one or several countries within Europe lags behind developments in other countries, the UEMS Section and Board on Allergology together with the European Academy of Allergy and Clinical Immunology advocates the status of a full specialty of allergology in each European country, with a further intention to align their activities (blueprint, curriculum and centre visitation) with the UEMS Section of Paediatrics.
The obesity–asthma link in different ages and the role of Body Mass Index in its investigation: findings from the Genesis and Healthy Growth Studies
Authors: Guibas G. V. , Manios Y. , Xepapadaki P. , Moschonis G. , Douladiris N. , Mavrogianni C. , Papadopoulos N. G.
Published: September 2013

Background

To date, an obesity/asthma link is well defined in adults; however, the nature of such a link is obscure in children, partly due to Body Mass Index (BMI) limitations as a surrogate fat mass marker in childhood. We thus opted to investigate the association of adiposity with asthma in children of different ages, using several indices to assess fat mass.

Methods

Wheeze ever/in the last 12 months (current) and physician‐diagnosed asthma were retrospectively reported via questionnaire by the parents of 3641 children, participating in two cross‐sectional studies: 1626 children aged 2–5 (the Genesis Study) and 2015 children aged 9–13 (the Healthy Growth Study). Perinatal data were recorded from the children's medical records or reported by parents. Anthropometric measurements (i.e., BMI, waist/hip circumference, biceps/triceps/subscapular/suprailiac skinfold thickness) were conducted in both cohorts; bioelectric impedance analysis (BIA) was conducted only in preadolescent children.

Results

In children aged 2–5, asthma was positively correlated with conicity index, waist/hip circumference, waist‐to‐height ratio, skinfold thickness, and skinfold‐derived percentage fat mass (P < 0.05) but not BMI or BMI‐defined overweight/obesity, after adjusting for several confounders. In children aged 9–13, asthma was positively associated with conicity index, waist circumference, waist‐to‐height ratio, skinfold thickness, skinfold‐derived percentage fat mass, BIA‐derived percentage fat mass, BMI, and BMI‐defined overweight/obesity, following adjustment (P < 0.05). Current/ever wheeze was not consistently associated with fat mass in either population.

Conclusions

Fat mass is positively linked to asthma in both 2–5 and 9–13 age spans. However, the failure of BMI to correlate with preschool asthma suggests its potential inefficiency in asthma studies at this age range.
Clinical and imaging characterization of progressive spastic dysarthria
Authors: Clark H. M. , Duffy J. R. , Whitwell J. L. , Ahlskog J. E. , Sorenson E. J. , Josephs K. A.
Published: September 2013

Background and purpose

To describe speech, neurological and imaging characteristics of a series of patients presenting with progressive spastic dysarthria as the first and predominant sign of a presumed neurodegenerative disease.

Methods

Participants were 25 patients with spastic dysarthria as the only or predominant speech disorder. Clinical features, pattern of MRI volume loss on voxel‐based morphometry and pattern of hypometabolism on F18‐fluorodeoxyglucose positron emission tomography (FDG‐PET) scan are described.

Results

All patients demonstrated speech characteristics consistent with spastic dysarthria, including strained voice quality, slow speaking rate, monopitch and monoloudness, and slow and regular speech alternating motion rates. Eight patients did not have additional neurological findings on examination. Pseudobulbar affect, upper motor neuron pattern limb weakness, spasticity, Hoffman sign and positive Babinski reflexes were noted in some of the remaining patients. Twenty‐three patients had electromyographic assessment and none had diffuse motor neuron disease or met El Escorial criteria for amyotrophic lateral sclerosis. Voxel‐based morphometry revealed striking bilateral white matter volume loss affecting the motor cortex (BA 4), including the frontoparietal operculum (BA 43) with extension into the middle cerebral peduncle. FDG‐PET showed subtle hypometabolism affecting the premotor and motor cortices in some patients, particularly in those who had a disease duration longer than 2 years.

Conclusions

A neurodegenerative disorder that begins focally with spastic dysarthria due to involvement of the motor and premotor cortex and descending corticospinal and corticobulbar pathways is characterized. The descriptive label ‘progressive spastic dysarthria’ to best capture the dominant presenting feature of the syndrome is proposed.
Cardiovascular control from cardiac and pulmonary vascular receptors
Authors: Hainsworth Roger
Published: September 2013

New Findings

What is the topic of this review?

The purpose of this review is to summarize present knowledge of the function of the afferent nerves arising from the heart and the coronary and pulmonary arteries. Although there is abundant evidence that atrial receptor stimulation influences heart rate and urine flow, with little or no effect elsewhere, and that ventricular receptors are strongly excited only by chemical stimuli, there is still the erroneous belief that they act as a homogeneous group causing cardiovascular depression.

What advances does it highlight?

Coronary receptors deserve to be recognized as a potentially important additional group of baroreceptors. Stimulation of pulmonary arterial baroreceptors at physiological pressures causes reflex vasoconstriction and could have a hitherto unacknowledged important role in cardiovascular control, for example in exercise.

Although there has been a tendency to regard cardiac and pulmonary receptors as a single population of ‘cardiopulmonary receptors’, this cannot be justified as the various receptor types all induce their own particular pattern of responses. Stimulation of atrial receptors increases activity in sympathetic nerves to the sino‐atrial node, causing tachycardia, but there is no effect on activity to the myocardium or to most blood vessels. Renal nerve activity, however, is decreased, and secretion of antidiuretic hormone is inhibited, causing diuresis. Ventricular receptors induce a powerful depressor response, but only in response to abnormal chemical stimulation and possibly to myocardial injury. Coronary arterial receptors function as baroreceptors, but have a lower threshold and a more prolonged effect than other baroreceptors. Pulmonary arterial baroreceptors induce vasoconstriction and respiratory stimulation at physiological pressures and may be of importance in mediating some of the responses to exercise, as well as in hypoxic conditions.
Deep brain stimulation and autonomic control
Authors: Lovick Thelma
Published: September 2013

New Findings

What is the topic of this review?

This article reviews data from studies on human participants and animal models showing how electrical stimulation in deep brain structures (deep brain stimulation) can influence autonomic function.

What advances does it highlight?

Focusing on the control of the cardiovascular system and bladder function, it highlights the potential for development of deep brain stimulation as a new treatment option for patients with autonomic dysfunction.

Deep brain stimulation (DBS) in humans has come of age as a tool to treat movement disorders including Parkinson's disease tremor and dystonia as well as a panoply of other disease states including headache, epilepsy, obesity, eating disorders, depression, obsessive compulsive disorder, Tourette's syndrome, addiction and chronic pain. Increasingly, practitioners of DBS are reporting autonomic side effects, which intriguingly, sometimes result in improved autonomic function. Focussing on the effects of stimulation at periaqueductal and periventricular sites on cardiovascular function and control of micturition, this review shows that data obtained from studies in animals is now being confirmed in humans. Lowering of blood pressure and improved baroreflex function can be evoked in humans by DBS at these midbrain sites as well as increased bladder capacity. The findings highlight the tantalizing possibility that DBS could be developed for treatment of dysfunctional autonomic states in humans.
Acute acetaminophen (paracetamol) ingestion improves time to exhaustion during exercise in the heat
Authors: Mauger Alexis R. , Taylor Lee , Harding Christopher , Wright Benjamin , Foster Josh , Castle Paul C.
Published: September 2013

New Findings

What is the central question of this study?

Acetaminophen (paracetamol) is an analgesic and antipyretic, which has been shown to improve self‐paced cycling performance through a reduction in pain. We sought to ascertain whether acetaminophen could improve time to exhaustion during exercise in the heat through its antipyretic action.

What is the main finding and its importance?

An acute dose of acetaminophen allowed participants to cycle significantly longer in hot conditions by a mean of 4 min (+17%). This was accompanied by significantly lower core, skin and body temperature, and participants found the exercise less of a thermal strain. These findings suggest that acetaminophen may reduce the thermal challenge of exercise in hot conditions.

Acetaminophen (paracetamol) is a commonly used over‐the‐counter analgesic and antipyretic and has previously been shown to improve exercise performance through a reduction in perceived pain. This study sought to establish whether its antipyretic action may also improve exercise capacity in the heat by moderating the increase in core temperature. On separate days, 11 recreationally active participants completed two experimental time‐to‐exhaustion trials on a cycle ergometer in hot conditions (30°C, 50% relative humidity) after ingesting a placebo control or an oral dose of acetaminophen in a randomized, double‐blind design. Following acetaminophen ingestion, participants cycled for a significantly longer period of time (acetaminophen, 23 ± 15 min versus placebo, 19 ± 13 min; P= 0.005; 95% confidence interval = 90–379 s), and this was accompanied by significantly lower core (−0.15°C), skin (−0.47°C) and body temperatures (0.19°C; P < 0.05). In the acetaminophen condition, participants also reported significantly lower ratings of thermal sensation (−0.39; P= 0.015), but no significant change in heart rate was observed (P > 0.05). This is the first study to demonstrate that an acute dose of acetaminophen can improve cycling capacity in hot conditions, and that this may be due to the observed reduction in core, skin and body temperature and the subjective perception of thermal comfort. These findings suggest that acetaminophen may reduce the thermoregulatory strain elicited from exercise, thus improving time to exhaustion.
Air expansion in a water rocket
Authors: Romanelli Alejandro , Bove Italo , González Madina Federico
Published: September 2013

We study the thermodynamics of a water rocket in the thrust phase, taking into account the expansion of the air with water vapor, vapor condensation, and the corresponding latent heat. We set up a simple experimental device with a stationary bottle and verify that the gas expansion in the bottle is well approximated by a polytropic process PVβ = constant, where the parameter β depends on the initial conditions. We find an analytical expression for β that depends only on the thermodynamic initial conditions and is in good agreement with the experimental results.
Exploring dynamical systems and chaos using the logistic map model of population change
Authors: Groff Jeffrey R.
Published: September 2013

The logistic map difference equation is encountered in the theoretical ecology literature as a mathematical model of population change for organisms with non-overlapping generations and density-dependent dynamics influenced solely by intraspecific interactions. This article presents the logistic map as a simple model suitable for introducing students to the properties of dynamical systems including periodic orbits, bifurcations, and deterministic chaos. After a brief historical and mathematical introduction to models of population change and the logistic map, the article summarizes the logistic map activities I teach in my introductory physics laboratories for non-physics majors. The logistic map laboratory introduces the many bioscience students in my courses to a foundational model in population ecology that has inspired ecologists to recognize the importance of nonlinear dynamics in real populations. Although I use this activity in courses for non-majors, the logistic map model of population change could also be taught to physics majors to introduce properties of dynamical systems while demonstrating an application of mathematical modeling outside of traditional physics.
Stationary points of the rigid body kinetic energy and the principal axes of inertia
Authors: Labinac Velimir , Jusup Marko , Legović Tarzan
Published: September 2013

We demonstrate how searching for the extrema of the rotational kinetic energy can be exploited to introduce the idea of the principal axes of inertia in a general and intuitive way. To that end, we propose a motivational starting point for a discussion with students, followed by a physical problem that, in its simplest form, can be handled using only basic calculus. Principal axes and moments of inertia arise seamlessly as solutions to the proposed problem. A numerical example is provided to emphasize key ideas. To encourage alternative ways of thinking, we also show how similar conclusions can be derived from the square of the angular momentum. A generalized procedure, appropriate for a classical mechanics course, is outlined in the Appendix.
Using computation to teach the properties of the van der Waals fluid
Authors: Swendsen Robert H.
Published: September 2013

The calculation of the thermodynamic properties of the van der Waals fluid is not trivial and most of its properties are rarely discussed because of mathematical difficulties. I describe a numerical approach that produces the full thermodynamic behavior of the van der Waals fluid with little effort. The numerical approach is particularly useful for showing the behavior of the specific heat, the isothermal compressibility, and the coefficient of thermal expansion at and near the critical point. The results of these computations show some surprising properties and give new insights into the mean-field description of the liquid-gas transition.
A digital hysteresis loop experiment
Authors: Francavilla T. L. , Claassen J. H. , Willard M. A.
Published: September 2013

A toroid with primary and secondary windings is used as a transformer to generate magnetic hysteresis curves. The primary winding is driven by a signal generator, which induces an alternating voltage in the secondary winding. Both input and output voltages are captured using a digital storage oscilloscope and processed to generate and display a hysteresis curve. We show such curves are representative of the material used as the transformer core. Data acquisition and processing steps are presented in a manner suitable for use in an undergraduate laboratory or lecture demonstration.
The shape function of a free-falling laminar jet: Making use of Bernoulli's equation
Authors: Massalha Taha , Digilov Rafael M.
Published: September 2013

The shape function of a laminar liquid jet issuing from a circular orifice and falling vertically in air under gravity is analyzed. The diameter of the jet is observed to decrease with the axial distance from the nozzle. The governing equation for variation of the jet radius with the axial coordinate is derived from a modified Bernoulli's law, including the interfacial energy density and viscous losses. The analytical solution found in terms of dimensionless group numbers agrees well with experimental data.
About photon correlations
Authors: Degiorgio V.
Published: September 2013

Some general properties of photon correlations are discussed in a simple way through an analysis of the two-detector measurement scheme. It is shown that the assumption of the discreteness of the random process leads directly to the conclusion that the zero-delay value of the correlation function is only bound to be non-negative. The adopted approach allows discussing in a more intuitive way the photon correlation properties of different optical fields, including non-classical fields presenting an apparent violation of the Cauchy-Schwarz inequality. The comparison between the two- and the single-detector experiment clarifies the role of the operator ordering in the definition of the correlation function.
Integrated testlets and the immediate feedback assessment technique
Authors: Slepkov Aaron D.
Published: September 2013

We describe how an answer-until-correct multiple-choice (MC) response format allows for the construction of fully multiple-choice examinations designed to operate much as a hybrid between standard MC and constructed-response (CR) testing. With this tool—the immediate feedback assessment technique (IF-AT)—students gain complete knowledge of the correct answer for each question during the examination and can use such information for solving subsequent test items. This feature allows for the creation of a new type of context-dependent item set: the “integrated testlet.” In an integrated testlet, certain items are purposefully inter-dependent and are thus presented in a particular order. Such integrated testlets represent a proxy of typical CR questions, but with a straightforward and uniform marking scheme that also allows for granting partial credit for proximal knowledge. As proof-of-principle, we present a case study of an IF-AT-scored midterm and final examination for an introductory physics course and discuss specific testlets possessing varying degrees of integration. In total, the polychotomously scored items are found to allow for excellent discrimination, with a mean item-total correlation measure for the combined 45 items of the two examinations of r¯′=0.41±0.13 (mean ± standard deviation) and a final examination test reliability of α = 0.82 (n = 25 items). Furthermore, partial credit is shown to be allocated in a discriminating and valid manner in these examinations. As has been found in other disciplines, the reaction of undergraduate physics students to the IF-AT is highly positive, further motivating its expanded use in formal classroom assessments.
Role of Bacterial Communities in the Natural Suppression of Rhizoctonia solani Bare Patch Disease of Wheat (Triticum aestivum L.)
Authors: Yin Chuntao , Hulbert Scot H. , Schroeder Kurtis L. , Mavrodi Olga , Mavrodi Dmitri , Dhingra Amit , Schillinger William F. , Paulitz Timothy C.
Published: September 2013

Rhizoctonia
bare patch and root rot disease of wheat, caused by
Rhizoctonia solani
AG-8, develops as distinct patches of stunted plants and limits the yield of direct-seeded (no-till) wheat in the Pacific Northwest of the United States. At the site of a long-term cropping systems study near Ritzville, WA, a decline in
Rhizoctonia
patch disease was observed over an 11-year period. Bacterial communities from bulk and rhizosphere soil of plants from inside the patches, outside the patches, and recovered patches were analyzed by using pyrosequencing with primers designed for 16S rRNA. Taxa in the class
Acidobacteria
and the genus
Gemmatimonas
were found at higher frequencies in the rhizosphere of healthy plants outside the patches than in that of diseased plants from inside the patches.
Dyella
and
Acidobacteria
subgroup Gp7 were found at higher frequencies in recovered patches.
Chitinophaga
,
Pedobacter
,
Oxalobacteriaceae
(
Duganella
and
Massilia
), and
Chyseobacterium
were found at higher frequencies in the rhizosphere of diseased plants from inside the patches. For selected taxa, trends were validated by quantitative PCR (qPCR), and observed shifts of frequencies in the rhizosphere over time were duplicated in cycling experiments in the greenhouse that involved successive plantings of wheat in
Rhizoctonia
-inoculated soil.
Chryseobacterium soldanellicola
was isolated from the rhizosphere inside the patches and exhibited significant antagonism against
R. solani
AG-8
in vitro
and in greenhouse tests. In conclusion, we identified novel bacterial taxa that respond to conditions affecting bare patch disease symptoms and that may be involved in suppression of
Rhizoctonia
root rot and bare batch disease.
Association of a
d
-Alanyl-
d
-Alanine Carboxypeptidase Gene with the Formation of Aberrantly Shaped Cells during the Induction of Viable but Nonculturable Vibrio parahaemolyticus
Authors: Hung Wei-cheng , Jane Wann-Neng , Wong Hin-chung
Published: September 2013

Vibrio parahaemolyticus
is a halophilic Gram-negative bacterium that causes human gastroenteritis. When the viable but nonculturable (VBNC) state of this bacterium was induced by incubation at 4°C in Morita minimal salt solution containing 0.5% NaCl, the rod-shaped cells became coccoid, and various aberrantly shaped intermediates were formed in the initial stage. This study examined the factors that influence the formation of these aberrantly shaped cells. The proportion of aberrantly shaped cells was not affected in a medium containing
d
-cycloserine (50 μg/ml) but was lower in a medium containing cephalosporin C (10 μg/ml) than in the control medium without antibiotics. The proportion of aberrantly shaped cells was higher in a culture medium that contained 0.5% NaCl than in culture media containing 1.0 or 1.5% NaCl. The expression of 15 of 17 selected genes associated with cell wall synthesis was enhanced, and the expression of VP2468 (
dacB
), which encodes
d
-alanyl-
d
-alanine carboxypeptidase, was enhanced the most. The proportion of aberrantly shaped cells was significantly lower in the
dacB
mutant strain than in the parent strain, but the proportion was restored in the presence of the complementary
dacB
gene. This study suggests that disturbance of the dynamics of cell wall synthesis by enhanced expression of the VP2468 gene is associated with the formation of aberrantly shaped cells in the initial stage of induction of VBNC
V. parahaemolyticus
cells under specific conditions.
Novel Gene Clusters and Metabolic Pathway Involved in 3,5,6-Trichloro-2-Pyridinol Degradation by Ralstonia sp. Strain T6
Authors: Li Jingquan , Huang Yan , Hou Ying , Li Xiangmin , Cao Hui , Cui Zhongli
Published: September 2013

3,5,6-Trichloro-2-pyridinol (TCP) is a widespread pollutant. Some bacteria and fungi have been reported to degrade TCP, but the gene clusters responsible for TCP biodegradation have not been characterized. In this study, a fragment of the reduced flavin adenine dinucleotide (FADH
2
)-dependent monooxygenase gene
tcpA
was amplified from the genomic DNA of
Ralstonia
sp. strain T6 with degenerate primers. The
tcpA
disruption mutant strain T6-Δ
tcpA
could not degrade TCP but could degrade the green intermediate metabolite 3,6-
d
i
h
ydroxy
p
yridine-2,5-
d
ione (DHPD), which was generated during TCP biodegradation by strain T6. The flanking sequences of
tcpA
were obtained by self-formed adaptor PCR.
tcpRXA
genes constitute a gene cluster. TcpR and TcpX are closely related to the LysR family transcriptional regulator and flavin reductase, respectively. T6-Δ
tcpA
-com, the complementation strain for the mutant strain T6-Δ
tcpA
, recovered the ability to degrade TCP, and the strain
Escherichia coli
DH10B-
tcpRXA
, which expressed the
tcpRXA
gene cluster, had the ability to transform TCP to DHPD, indicating that
tcpA
is a key gene in the initial step of TCP degradation and that TcpA dechlorinates TCP to DHPD. A library of DHPD degradation-deficient mutants of strain T6 was obtained by random transposon mutagenesis. The fragments flanking the Mariner transposon were amplified and sequenced, and the
dhpRIJK
gene cluster was cloned. DhpJ could transform DHPD to yield an intermediate product, 5-
a
mino-2,4,5-
t
ri
o
xo
p
entanoic
a
cid (ATOPA), which was further degraded by DhpI. DhpR and DhpK are closely related to the AraC family transcriptional regulator and the MFS family transporter, respectively.
Components of the Cultivated Red Seaweed Chondrus crispus Enhance the Immune Response of Caenorhabditis elegans to Pseudomonas aeruginosa through the
pmk-1
,
daf-2/daf-16
, and
skn-1
Pathways
Authors: Liu Jinghua , Hafting Jeff , Critchley Alan T. , Banskota Arjun H. , Prithiviraj Balakrishnan
Published: September 2013

Marine macroalgae are rich in bioactive compounds that can, when consumed, impart beneficial effects on animal and human health. The red seaweed
Chondrus crispus
has been reported to have a wide range of health-promoting activities, such as antitumor and antiviral activities. Using a
Caenorhabditis elegans
infection model, we show that
C. crispus
water extract (CCWE) enhances host immunity and suppresses the expression of quorum sensing (QS) and the virulence factors of
Pseudomonas aeruginosa
(strain PA14). Supplementation of nematode growth medium with CCWE induced the expression of
C. elegans
innate immune genes, such as
irg-1
,
irg-2
,
F49F1.6
,
hsf-1
,
K05D8.5
,
F56D6.2
,
C29F3.7
,
F28D1.3
,
F38A1.5 ZK6.7
,
lys-1
,
spp-1
, and
abf-1
, by more than 2-fold, while
T20G5.7
was not affected. Additionally, CCWE suppressed the expression of PA14 QS genes and virulence factors, although it did not affect the growth of the bacteria. These effects correlated with a 28% reduction in the PA14-inflicted killing of
C. elegans
. Kappa-carrageenan (K-CGN), a major component of CCWE, was shown to play an important role in the enhancement of host immunity. Using
C. elegans
mutants, we identified that
pmk-1
,
daf-2/daf-16
, and
skn-1
are essential in the K-CGN-induced host immune response. In view of the conservation of innate immune pathways between
C. elegans
and humans, the results of this study suggest that water-soluble components of
C. crispus
may also play a health-promoting role in higher animals and humans.
Stark Contrast in Denitrification and Anammox across the Deep Norwegian Trench in the Skagerrak
Authors: Trimmer Mark , Engström Pia , Thamdrup Bo
Published: September 2013

Environmental anaerobic ammonium oxidation (anammox) was demonstrated for the first time in 2002, using
15
N labeling, in homogenized sediment from the Skagerrak, where it accounted for up to 67% of N
2
production. We returned to some of these original sites in 2010 to make measurements of nitrogen and carbon cycling under conditions more representative of those
in situ
, quantifying anammox and denitrification, together with oxygen penetration and consumption, in intact sediment cores. Overall, oxygen consumption and N
2
production decayed with water depth, as expected, but the drop in N
2
production was relatively more pronounced. Whereas we confirmed the dominance of N
2
production by anammox (72% and 77%) at the two deepest sites (∼700 m of water), anammox was conspicuously absent from two shallower sites (∼200 m and 400 m). At the shallower sites, we could measure no anammox activity with either intact or homogeneous sediment, and quantitative PCR (16S rRNA) gave a negligible abundance of anammox bacteria in the anoxic layers. Such an absence of anammox, especially at one locale where it was originally demonstrated, is hard to reconcile. Despite the dominance of anammox at the deepest sites, anammox activity could not make up for the drop in denitrification, and assuming Redfield ratios for the organic matter being mineralized, the estimated retention of fixed N actually increased to 90% to 97% of that mineralized, whereas it was 80% to 86% at the shallower sites.
Snf1 Is a Regulator of Lipid Accumulation in Yarrowia lipolytica
Authors: Seip John , Jackson Raymond , He Hongxian , Zhu Quinn , Hong Seung-Pyo
Published: September 2013

In the oleaginous yeast
Yarrowia lipolytica
,
de novo
lipid synthesis and accumulation are induced under conditions of nitrogen limitation (or a high carbon-to-nitrogen ratio). The regulatory pathway responsible for this induction has not been identified. Here we report that the SNF1 pathway plays a key role in the transition from the growth phase to the oleaginous phase in
Y. lipolytica
. Strains with a
Y. lipolytica
snf1
(
Ylsnf1
) deletion accumulated fatty acids constitutively at levels up to 2.6-fold higher than those of the wild type. When introduced into a
Y. lipolytica
strain engineered to produce omega-3 eicosapentaenoic acid (EPA),
Ylsnf1
deletion led to a 52% increase in EPA titers (7.6% of dry cell weight) over the control. Other components of the
Y. lipolytica
SNF1 pathway were also identified, and their function in limiting fatty acid accumulation is suggested by gene deletion analyses. Deletion of the gene encoding YlSnf4, YlGal83, or YlSak1 significantly increased lipid accumulation in both growth and oleaginous phases compared to the wild type. Furthermore, microarray and quantitative reverse transcription-PCR (qRT-PCR) analyses of the
Ylsnf1
mutant identified significantly differentially expressed genes during
de novo
lipid synthesis and accumulation in
Y. lipolytica
. Gene ontology analysis found that these genes were highly enriched with genes involved in lipid metabolism. This work presents a new role for Snf1/AMP-activated protein kinase (AMPK) pathways in lipid accumulation in this oleaginous yeast.
Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada
Authors: Sonthiphand Puntipar , Cejudo Eduardo , Schiff Sherry L. , Neufeld Josh D.
Published: September 2013

The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH
3
and NH
4
+
) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO
3
−
or N
2
), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities.