bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of nitrogen and vapour pressure deficit on phytomer growth and development in a C4 grass
Authors: Yang Fang , Gong Xiao Ying , Liu Hai Tao , Schäufele Rudi , Schnyder Hans
Published: November 2016

Phytomers are basic morphological units of plants. Knowledge of phytomer development is essential for understanding morphological plasticity, functional–structural modelling of plant growth and the usage of leaf characteristics to indicate growth conditions at the time of production (e.g. stable isotope signals). Yet, systematic analysis on the process of phytomer development is unavailable for wild or perennial C4 grasses. Also, effects of environmental factors, such as nitrogen nutrition or vapour pressure deficit (VPD), on coordination events of developmental processes of C4 grasses have not been studied. This study investigates phytomer growth and development in Cleistogenes squarrosa, a predominant C4 grass in the Eurasian steppe, grown at low (0.63 kPa) or high (1.58 kPa) VPD with low or high nitrogen supply in controlled environments. Elongation of phytomers on marked tillers was measured daily for 13 days. Then lengths of immature and mature phytomer components (blade, sheath and internode) of all phytomers were measured following dissection. Nitrogen nutrition and VPD had no effects on coordination of growth within and between phytomers: phytomer tips emerged when phytomers reached 26 % of their final length, coincident with the acceleration phase of its elongation; blade elongation stopped when phytomers reached ∼75 % of their final length and elongation of the preceding phytomer was confined to the internode. The relationship between fraction of final phytomer length and days after tip emergence for all treatments was well described by a sigmoidal function: y = 1/{1 + exp[(1.82 − x)/1.81]}. C. squarrosa exhibited little morphological plasticity at phytomer-level in response to nitrogen supply and VPD, but a clear increase in tillering under high N supply. Also, the invariant coordination of elongation within and between phytomers was a stable developmental feature, thus the quantitative coordination rules are applicable for predicting morphological development of C. squarrosa under contrasting levels of nitrogen nutrition or VPD.
GENIUS: web server to predict local gene networks and key genes for biological functions
Authors: Puelma Tomas , Araus Viviana , Canales Javier , Vidal Elena A , Cabello Juan M , Soto Alvaro , Gutiérrez Rodrigo A
Published: November 2016

GENIUS is a user-friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest. These functions may have different levels of complexity, from specific biological processes to complex traits that involve several interacting processes. GENIUS also enriches the network with new genes related to the biological function of interest, with accuracies comparable to highly discriminative Support Vector Machine methods.

Availability and Implementation

GENIUS currently supports eight model organisms and is freely available for public use at http://networks.bio.puc.cl/genius.

Supplementary information

Supplementary data are available at Bioinformatics online.
Fiscal Policy and Debt Management with Incomplete Markets*
Authors: Bhandari Anmol , Evans David , Golosov Mikhail , Sargent Thomas J.
Published: November 2016

A Ramsey planner chooses a distorting tax on labor and manages a portfolio of securities in an economy with incomplete markets. We develop a method that uses second order approximations of Ramsey policies to obtain formulas for conditional and unconditional moments of government debt and taxes that include means and variances of the invariant distribution as well as speeds of mean reversion. The asymptotic mean of the planner's portfolio minimizes a measure of fiscal risk. We obtain analytic expressions that approximate moments of the invariant distribution and apply them to data on a primary government deficit, aggregate consumption, and returns on traded securities. For U.S. data, we find that the optimal target debt level is negative but close to zero, the invariant distribution of debt is very dispersed, and mean reversion is slow.
Four Common Setaria Species are Alternative Hosts for Clavibacter michiganensis subsp. nebraskensis, Causal Agent of Goss's Bacterial Wilt and Blight of Corn
Authors: Langemeier Craig B. , Jackson-Ziems Tamra A. , Kruger Greg R.
Published: November 2016

Goss's bacterial wilt and blight, caused by Clavibacter michiganensis subsp. nebraskensis (Cmn), has reemerged as an important disease of Zea mays (corn) in the U.S. Midwest. Results from a 2011 multistate survey indicated that Setaria spp. (foxtail) were often present in corn fields with a history of Cmn. The objective of this research was to determine if Setaria spp. that are common in the Midwest are susceptible to infection by Cmn. In the greenhouse, seedlings of four Setaria spp., including S. viridis (green foxtail), S. faberi (giant foxtail), S. verticillata (bristly foxtail), and S. pumila (yellow foxtail), and Zea mays (Golden Cross Bantam sweet corn, GCB) were inoculated with a suspension of 1.0 × 107 bacteria cells. The trial was arranged in a randomized complete block design and repeated once. Percent of symptomatic leaf area was visually estimated eight days after inoculation. S. faberi exhibited the highest levels of disease among the four Setaria spp., with disease incidence similar to what was observed on Z. mays. S. viridis was the next most susceptible. Symptoms were also observed on S. viridis, S. verticillata, and were lowest for S. pumila. Bacterial streaming was confirmed microscopically and Cmn was reisolated from the four Setaria species. Results indicate that these four Setaria spp. are susceptible to Cmn, thus serving as potential sources of inoculum.

Accepted for publication 1 February 2014. Published 28 April 2014.
Intraabdominal Surgery and Anesthesia Management
Authors: Hedley-Whyte John
Published: November 2016

Inspired Oxygenation in Surgical Patients During General Anesthesia With Controlled Ventilation: A Concept of Atelectasis. By Bendixen HH, Hedley-Whyte J, and Laver MB. New Engl J Med 1963; 269:991–996. Reprinted with permission.

The purpose of this study was to determine if the pattern of ventilation, by itself, influences oxygenation during anesthesia and surgery and examine the hypothesis that progressive pulmonary atelectasis may occur during constant ventilation whenever periodic hyperventilation is lacking, but is reversible by passive hyperinflation of the lungs. Eighteen surgical patients, ranging in age from 24 to 87 yr, without known pulmonary disease, were studied during intraabdominal procedures and one radical mastectomy. Although ventilation remained constant, changes occurred in arterial oxygen tension and in total pulmonary compliance, with an average fall of 22% in oxygen tension and 15% in total pulmonary compliance. This fall in oxygen tension supports the hypothesis that progressive mechanical atelectasis may lead to increased venous admixture to arterial blood. The influence of the ventilator pattern on atelectasis and shunting is further illustrated by the reversibility of the fall in oxygen tension that follows hyperinflation. A relation between the degree of ventilation and the magnitude of fall in arterial oxygen tension was found, where large tidal volumes appear to protect against falls in oxygen tension, while shallow tidal volumes lead to atelectasis and increased shunting with impaired oxygenation.
The Effect of Cochlear Damage on the Sensitivity to Harmonicity
Authors: Bonnard Damien , Dauman René , Semal Catherine , Demany Laurent
Published: November 2016

Objectives:

A sum of simultaneous pure tones with harmonic relationships (i.e., simple frequency ratios) is normally heard as a single sound, with a single pitch, even when its components are fully resolved in the auditory periphery. This perceptual phenomenon called “harmonic fusion” is thought to play an important role in auditory scene analysis as listeners often have to segregate simultaneous harmonic sounds with different fundamental frequencies. The present study explored the consequences of mild or moderate cochlear hearing loss for the sensitivity to harmonicity and the detection of inharmonicity.

Design:

The subjects were 12 normal-hearing (NH) listeners and 8 listeners with cochlear hearing loss amounting to 30 to 50 dB (mean: 42 dB) from 0.25 to 3 kHz. In each subject, thresholds for the detection of a change in the frequency ratio of simultaneous pure tones were measured with an adaptive forced-choice procedure. The standard frequency ratio was either harmonic (2:1, i.e., one octave) or inharmonic (0.8 or 1.2 octaves). The tones were presented at a low sensation level (at most 15 dB) within broadband noise, to minimize their cochlear interactions. In the main experimental conditions, the frequency register of the stimuli varied randomly within each trial, so that subjects were forced to process frequency ratios to achieve good performance; frequency discrimination was not sufficient. In other conditions, by contrast, frequency discrimination was sufficient to perform the task optimally.

Results:

For both groups of subjects, thresholds in the main experimental conditions were lower (i.e., better) when the standard frequency ratio was harmonic than when it was inharmonic. This effect, revealing sensitivity to harmonicity, was weak for some members of the hearing-impaired group, but could be observed even in subjects showing a very poor frequency discrimination ability. The two groups, however, differed from each other with respect to the detection of inharmonicity: for the NH group, in agreement with previous results, negative deviations from one octave (i.e., compressions of this frequency ratio) were better detected than positive deviations (stretchings); for the hearing-impaired group, on the other hand, the sign of the deviations had no effect on performance.

Conclusions:

Sensitivity to harmonicity appears to be remarkably robust. However, it can be reduced in some listeners with mild or moderate cochlear damage. Moreover, as inharmonicity detection is asymmetric for NH listeners but apparently becomes symmetric in case of cochlear damage, it may be that listeners with cochlear damage do not detect inharmonicity in the same manner as NH listeners do. In some circumstances, inharmonicity can be detected on the basis of “beat” cues available in single frequency channels; however, the subjects tested here were unlikely to use cues of this type.
Auditory Brainstem Response Altered in Humans With Noise Exposure Despite Normal Outer Hair Cell Function
Authors: Bramhall Naomi F. , Konrad-Martin Dawn , McMillan Garnett P. , Griest Susan E.
Published: November 2016

Objectives:

Recent animal studies demonstrated that cochlear synaptopathy, a partial loss of inner hair cell-auditory nerve fiber synapses, can occur in response to noise exposure without any permanent auditory threshold shift. In animal models, this synaptopathy is associated with a reduction in the amplitude of wave I of the auditory brainstem response (ABR). The goal of this study was to determine whether higher lifetime noise exposure histories in young people with clinically normal pure-tone thresholds are associated with lower ABR wave I amplitudes.

Design:

Twenty-nine young military Veterans and 35 non Veterans (19 to 35 years of age) with normal pure-tone thresholds were assigned to 1 of 4 groups based on their self-reported lifetime noise exposure history and Veteran status. Suprathreshold ABR measurements in response to alternating polarity tone bursts were obtained at 1, 3, 4, and 6 kHz with gold foil tiptrode electrodes placed in the ear canal. Wave I amplitude was calculated from the difference in voltage at the positive peak and the voltage at the following negative trough. Distortion product otoacoustic emission input/output functions were collected in each participant at the same four frequencies to assess outer hair cell function.

Results:

After controlling for individual differences in sex and distortion product otoacoustic emission amplitude, the groups containing participants with higher reported histories of noise exposure had smaller ABR wave I amplitudes at suprathreshold levels across all four frequencies compared with the groups with less history of noise exposure.

Conclusions:

Suprathreshold ABR wave I amplitudes were reduced in Veterans reporting high levels of military noise exposure and in non Veterans reporting any history of firearm use as compared with Veterans and non Veterans with lower levels of reported noise exposure history. The reduction in ABR wave I amplitude in the groups with higher levels of noise exposure cannot be accounted for by sex or variability in outer hair cell function. This change is similar to the decreased ABR wave I amplitudes observed in animal models of noise-induced cochlear synaptopathy. However, without post mortem examination of the temporal bone, no direct conclusions can be drawn concerning the presence of synaptopathy in the study groups with higher noise exposure histories.
Mannose-Binding Lectin Levels in Critically Ill Children With Severe Infections*
Authors: Madsen Erik C. , Levy Emily R. , Madden Kate , Agan Anna A. , Sullivan Ryan M. , Graham Dionne A. , Randolph Adrienne G.
Published: November 2016

Objectives:

Low mannose-binding lectin levels and haplotypes associated with low mannose-binding lectin production have been associated with infection and severe sepsis. We tested the hypothesis that mannose-binding lectin levels would be associated with severe infection in a large cohort of critically ill children.

Design:

Prospective cohort study.

Setting:

Medical and Surgical PICUs, Boston Children’s Hospital.

Patients:

Children less than 21 years old admitted to the ICUs from November 2009 to November 2010.

Interventions:

None.

Measurements and Main Results:

We measured mannose-binding lectin levels in 479 of 520 consecutively admitted children (92%) with severe or life-threatening illness. We genotyped 213 Caucasian children for mannose-binding lectin haplotype tagging variants and assigned haplotypes. In the univariate analyses of mannose-binding lectin levels with preadmission characteristics, levels were higher in patients with preexisting renal disease. Patients who received greater than 100 mL/kg of fluids in the first 24 hours after admission had markedly lower mannose-binding lectin, as did patients who underwent spinal fusion surgery. Mannose-binding lectin levels had no association with infection status at admission, or with progression from systemic inflammatory response syndrome to sepsis or septic shock. Although mannose-binding lectin haplotypes strongly influenced mannose-binding lectin levels in the predicted relationship, low mannose-binding lectin–producing haplotypes were not associated with increased risk of infection.

Conclusions:

Mannose-binding lectin levels are largely genetically determined. This relationship was preserved in children during critical illness, despite the effect of large-volume fluid administration on mannose-binding lectin levels. Previous literature evaluating an association between mannose-binding lectin levels and severe infection is inconsistent; we found no relationship in our PICU cohort. We found that mannose-binding lectin levels were lower after aggressive fluid resuscitation and suggest that studies of mannose-binding lectin in critically ill patients should assess mannose-binding lectin haplotypes to reflect preillness levels.
A Multilevel Analysis of U.S. Hospital Patient Safety Culture Relationships With Perceptions of Voluntary Event Reporting
Authors: Burlison Jonathan D. , Quillivan Rebecca R. , Kath Lisa M. , Zhou Yinmei , Courtney Sam C. , Cheng Cheng , Hoffman James M.
Published: November 2016

Objectives

Patient safety events offer opportunities to improve patient care, but, unfortunately, events often go unreported. Although some barriers to event reporting can be reduced with electronic reporting systems, insight on organizational and cultural factors that influence reporting frequency may help hospitals increase reporting rates and improve patient safety. The purpose of this study was to evaluate the associations between dimensions of patient safety culture and perceived reporting practices of safety events of varying severity.

Methods

We conducted a cross-sectional survey study using previously collected data from The Agency for Healthcare Research and Quality Hospital Survey of Patient Safety Culture as predictors and outcome variables. The dataset included health-care professionals in U.S. hospitals, and data were analyzed using multilevel modeling techniques.

Results

Data from 223,412 individuals, 7816 work areas/units, and 967 hospitals were analyzed. Whether examining near miss, no harm, or potential for harm safety events, the dimension feedback about error accounted for the most unique predictive variance in the outcome frequency of events reported. Other significantly associated variables included organizational learning, nonpunitive response to error, and teamwork within units (all P < 0.001). As the perceived severity of the safety event increased, more culture dimensions became significantly associated with voluntary reporting.

Conclusions

To increase the likelihood that a patient safety event will be voluntarily reported, our study suggests placing priority on improving event feedback mechanisms and communication of event-related improvements. Focusing efforts on these aspects may be more efficient than other forms of culture change.
The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species
Authors: Mungall Christopher J , McMurry Julie A , Köhler Sebastian , Balhoff James P. , Borromeo Charles , Brush Matthew , Carbon Seth , Conlin Tom , Dunn Nathan , Engelstad Mark , Foster Erin , Gourdine JP , Jacobsen Julius O.B. , Keith Daniel , Laraway Bryan , Lewis Suzanna E. , Nguyen Xuan Jeremy , Shefchek Kent , Vasilevsky Nicole , Yuan Zhou , Washington Nicole , Hochheiser Harry , Groza Tudor , Smedley Damian , Robinson Peter N. , Haendel Melissa A
Published: November 2016

The principles of genetics apply across the whole tree of life: on a cellular level, we share mechanisms with species from which we diverged millions or even billions of years ago. We can exploit this common ancestry at the level of sequences, but also in terms of observable outcomes (phenotypes), to learn more about health and disease for humans and all other species. Applying the range of available knowledge to solve challenging disease problems requires unified data relating genomics, phenotypes, and disease; it also requires computational tools that leverage these multimodal data to inform interpretations by geneticists and to suggest experiments. However, the distribution and heterogeneity of databases is a major impediment: databases tend to focus either on a single data type across species, or on single species across data types. Although each database provides rich, high-quality information, no single one provides unified data that is comprehensive across species, biological scales, and data types. Without a big-picture view of the data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) is an international consortium dedicated to providing computational tools that leverage a computational representation of phenotypic data for genotype-phenotype analysis, genomic diagnostics, and precision medicine on the basis of a large-scale platform of multimodal data that is deeply integrated across species and covering broad areas of disease.
All or Nothing: the False Promise of Anonymity
Authors: Walker Neil
Published: November 2016

In early 2016, the International Committee of Medical Journal Editors (ICMJE) proposed that responsible sharing of de-identified individual-level data be required for clinical trials published in their affiliated journals. There would be a delay in implementing this policy to allow for the necessary informed consents to work their way through ethical review. Meanwhile, some researchers and policy makers have conflated the notions of de-identification and anonymity. The former is a process that seeks to mitigate disclosure risk though careful application of rules and statistical analysis, while the latter is an absolute state. The consequence of confusing the process and the state is profound. Extensions to the ICMJE proposal based on the presumed anonymity of data include: sharing unconsented data; sharing data without managing access, as Open Data; and proposals to sell data. This essay aims to show that anonymity (the state) cannot be guaranteed by de-identification (the process), and so these extensions to the ICMJE proposal should be rejected on governance grounds, if no other. This is not as negative a position as it might seem, as other disciplines have been aware of these limitations and concomitant responsibilities for many years. The essay concludes with an example from social science of managed access strategies that could be adopted by the medical field.
The lexical categorization model: A computational model of left-ventral occipito-temporal cortex activation in visual word recognition
Authors: Gagl Benjamin , Richlan Fabio , Ludersdorfer Philipp , Sassenhagen Jona , Eisenhauer Susanne , Gregorova Klara , Fiebach Christian J.
Published: November 2016

To characterize the left-ventral occipito-temporal cortex (lvOT) role during reading in a quantitatively explicit and testable manner, we propose the lexical categorization model (LCM). The LCM assumes that lvOT optimizes linguistic processing by allowing fast meaning access when words are familiar and filter out orthographic strings without meaning. The LCM successfully simulates benchmark results from functional brain imaging. Empirically, using functional magnetic resonance imaging, we demonstrate that quantitative LCM simulations predict lvOT activation across three studies better than alternative models. Besides, we found that word-likeness, which is assumed as input to LCM, is represented posterior to lvOT. In contrast, a dichotomous word/non-word contrast, which is assumed as the LCM’s output, could be localized to upstream frontal brain regions. Finally, we found that training lexical categorization results in more efficient reading. Thus, we propose a ventral-visual-stream processing framework for reading involving word-likeness extraction followed by lexical categorization, before meaning extraction.
A novel restraint device for injection ofGalleria mellonellalarvae that minimises the risk of accidental operator needle stick injury
Authors: Dalton J.P. , Uy B. , Swift S. , Wiles S.
Published: November 2016

Larvae of the insectGalleria mellonellaare increasingly being used for studying pathogenic microbes and their virulence mechanisms, and as a rapid model for screening novel antimicrobial agents. The larvae (waxworms) are most frequently infected by injection of pathogenic organisms into the haemocoel through the insect’s prolegs. The mostly widely used method for restraining the waxworms for injection is by grasping them between the operator’s fingers, which puts the operator at risk of needle stick injury, an important consideration when working with highly pathogenic and/or drug-resistant microorganisms. While use of a stab proof glove can reduce this risk of injury, it does so at the loss of manual dexterity and speed, resulting in a more labour-intensive and cumbersome assay. We describe a simple cost effective device (the so-called ‘GalleriaGrabber’) for restraining waxworms for injection that keeps the operator’s fingers clear of the needle thus reducing the risk of injury.
Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis
Authors: MacManes Matthew D. , Austin Suzanne H. , Booth Andrew , Austin April , Farrar Victoria , Calisi Rebecca M.
Published: November 2016

The hypothalamic-pituitary-gonadal (HPG) axis is a key biological system required for reproduction and associated sexual behaviors to occur. In the avian reproductive model of the rock dove (Columba livia), we characterized the transcript community of each tissue of the HPG axis in both sexes, thereby significantly expanding our mechanistic insight into HPG activity. We report greater sex-biased differential expression in the pituitary as compared to the hypothalamus, with multiple genes more highly expressed in the male pituitary being related to secretory function, and multiple genes more highly expressed in the female pituitary being related to reproduction, growth, and development. We report tissue-specific and sex-biased expression in genes commonly investigated when studying reproduction, highlighting the need for sex parity in future studies. In addition, we uncover new targets of investigation in both sexes, which could potentially change our understanding of HPG function.
Feature-coding transitions to conjunction-coding with progression through human visual cortex
Authors: Cowell Rosemary A. , Serences John T.
Published: November 2016

Identifying an object and distinguishing it from similar items depends upon the ability to perceive its component parts as conjoined into a cohesive whole, but the brain mechanisms underlying this ability remain elusive. The ventral visual processing pathway in primates is organized hierarchically: Neuronal responses in its early stages are sensitive to the manipulation of simple visual features whereas neuronal responses in subsequent stages are tuned to increasingly complex stimulus attributes. It is widely assumed that feature-coding dominates in early visual cortex whereas later visual regions employ conjunction-coding in which object representations are different from the sum of their simple-feature parts. However, no study has demonstrated that putative object-level codes in higher visual cortex cannot be accounted for by feature-coding and that putative feature-codes in regions prior to ventral temporal cortex are not equally well characterized as object-level codes. Thus the existence of a transition from feature- to conjunction-coding in visual cortex remains unconfirmed, and, if a transition does occur, its location remains unknown. By employing multivariate analysis of human functional imaging data, we measure both feature-coding and conjunction-coding directly, using the same set of visual stimuli, and pit them against each other to reveal the relative dominance of one versus the other throughout cortex. We provide the first demonstration of a transition from feature-coding in early visual cortex to conjunction-coding in both inferior temporal and posterior parietal cortices. This novel method enables the use of experimentally controlled stimulus features to investigate population-level feature- and conjunction-codes throughout human cortex.
An evolving cancer instigates clonally unrelated neighboring cells to form distant metastases
Authors: Dong Jie , Darini Cedric , Kabeer Farhia , Dendievel Sarah , Min Junxia , Hambardzumyan Dolores , Gaboury Louis , Lenaerts Tom , Darrasse-Jèze Guillaume , Li Yi , Podsypanina Katrina
Published: November 2016

Based on the clonal evolution theory of cancer formation, a single cell within a tissue gains a cancer-driving mutation and thus a growth advantage. From this expanded cellular mass, another cell gains a new mutation allowing this newly mutated cell to gain new competitive advantage and to expand in number (thus clonal expansion). Another clone then emerges. Eventually all required mutations are gained, and a cancer forms. Consequently, while a primary lesion may harbor divergent subclones, all the subclones within the primary cancer as well as all metastatic growths in secondary organs share at least the very first oncogenic mutation that initiates the primary cancer. However, by tracking genetically marked mammary epithelial cells that suffered the initiating oncogenic mutation—and their neighboring mammary cells that did not-in several mouse models of human breast cancer, we found that genetically unrelated mammary epithelial cells can be colluded by neighboring mutated cells to disseminate, and that they can even undergode novotumorigenic transformation and form distant metastases. Therefore, clonally unrelated epithelial cells may contribute to cancer progression and to the heterogeneity of the systemic disease. The non-linear cancer spread has important implications in cancer prevention, treatment, and therapeutic resistance.
Inferring the role of habitat dynamics in driving diversification: evidence for a species pump in Lake Tanganyika cichlids
Authors: Janzen Thijs , Etienne Rampal S.
Published: November 2016

Geographic isolation that drives speciation is often assumed to slowly increase over time, for instance through the formation of rivers, the formation of mountains or the movement of tectonic plates. Cyclic changes in connectivity between areas may occur with the advancement and retraction of glaciers, with water level fluctuations in seas between islands or in lakes that have an uneven bathymetry. These habitat dynamics may act as a driver of allopatric speciation and propel local diversity. Here we present a parsimonious model of the interaction between cyclical (but not necessarily periodic) changes in the environment and speciation, and provide an ABC-SMC method to infer the rates of allopatric and sympatric speciation from a phylogenetic tree. We apply our approach to the posterior sample of an updated phylogeny of theLamprologini, a tribe of cichlid fish from Lake Tanganyika where such cyclic changes in water level have occurred. We find that water level changes play a crucial role in driving diversity in Lake Tanganyika. We note that if we apply our analysis to the Most Credible Consensus (MCC) tree, we do not find evidence for water level changes influencing diversity in theLamprologini, suggesting that the MCC tree is a misleading representation of the true species tree. Furthermore, we note that the signature of habitat dynamics is found in the posterior sample despite the fact that this sample was constructed using a species tree prior that ignores habitat dynamics. However, in other cases this species tree prior might erase this signature. Hence we argue that in order to improve inference of the effect of habitat dynamics on biodiversity, phylogenetic reconstruction methods should include tree priors that explicitly take into account such dynamics.
Using the Volta phase plate with defocus for cryo-EM single particle analysis
Authors: Danev Radostin , Tegunov Dimitry , Baumeister Wolfgang
Published: November 2016

Previously, we reported an in-focus data acquisition method for cryo-EM single particle analysis with the Volta phase plate (VPP) (Danev and Baumeister, 2016). Here, we extend the technique to include a small amount of defocus which enables contrast transfer function measurement and correction. This hybrid approach simplifies the experiment and increases the data acquisition speed. It also enables 3D reconstructions with resolutions in the 2 Å range, demonstrating that, in practice, there are no resolution limitations imposed by the VPP.
Dynamical modelling of the heat shock response inChlamydomonas reinhardtii
Authors: Magni Stefano , Succurro Antonella , Skupin Alexander , Ebenhöh Oliver
Published: November 2016

Global warming is exposing plants to more frequent heat stress, with consequent crop yield reduction. Organisms exposed to large temperature increases protect themselves typically with a heat shock response (HSR). To study the HSR in photosynthetic organisms we present here a data driven mathematical model describing the dynamics of the HSR in the model organismChlamydomonas reinhartii. Temperature variations are sensed by the accumulation of unfolded proteins, which activates the synthesis of heat shock proteins (HSP) mediated by the heat shock transcription factor HSF1. Our dynamical model employs a system of ordinary differential equations mostly based on mass-action kinetics to study the time evolution of the involved species. The signalling network is inferred from data in the literature, and the multiple experimental data-sets available are used to calibrate the model, which allows to reproduce their qualitative behaviour. With this model we show the ability of the system to adapt to temperatures higher than usual during heat shocks longer than three hours by shifting to a new steady state. We study how the steady state concentrations depend on the temperature at which the steady state is reached. We systematically investigate how the accumulation of HSPs depends on the combination of temperature and duration of the heat shock. We finally investigate the system response to a smooth variation in temperature simulating a hot day.
Rfx2 stabilizes Foxj1 binding at chromatin loops to enable multiciliated cell gene expression
Authors: Quigley Ian K , Kintner Chris
Published: November 2016

Cooperative transcription factor binding at cis-regulatory sites in the genome drives robust eukaryotic gene expression, and many such sites must be coordinated to produce coherent transcriptional programs. The transcriptional program leading to motile cilia formation requires members of the DNA-binding forkhead (Fox) and Rfx transcription factor families and these factors co-localize to cilia gene promoters, but it is not clear how many cilia genes are regulated by these two factors, whether these factors act directly or indirectly, or how these factors act with specificity in the context of a 3-dimensional genome. Here, we use genome-wide approaches to show that cilia genes reside at the boundaries of topological domains and that these areas have low enhancer density. We show that the transcription factors Foxj1 and Rfx2 binding occurs in the promoters of more cilia genes than other known cilia transcription factors and that while Rfx2 binds directly to promoters and enhancers equally, Foxj1 prefers direct binding to enhancers and is stabilized at promoters by Rfx2. Finally, we show that Rfx2 and Foxj1 lie at the anchor endpoints of chromatin loops, suggesting that target genes are activated when Foxj1 bound at distal sites is recruited via a loop created by Rfx2 binding at both sites. We speculate that the primary function of Rfx2 is to stabilize distal enhancers with proximal promoters by operating as a scaffolding factor, bringing key regulatory domains bound by Foxj1 into close physical proximity and enabling coordinated cilia gene expression.

Author Summary

The multiciliated cell extends hundreds of motile cilia to produce fluid flow in the airways and other organ systems. The formation of this specialized cell type requires the coordinated expression of hundreds of genes in order to produce all the protein parts motile cilia require. While a relatively small number of transcription factors has been identified that promote gene expression during multiciliate cell differentiation, it is not clear how they work together to coordinate the expression of genes required for multiple motile ciliation. Here, we show that two transcription factors known to drive cilia formation, Foxj1 and Rfx2, play complementary roles wherein Foxj1 activates target genes but tends not to bind near them in the genome, whereas Rfx2 can’t activate target genes by itself but instead acts as a scaffold by localizing Foxj1 to the proper targets. These results suggest not only a mechanism by which complex gene expression is coordinated in multiciliated cells, but also how transcriptional programs in general could be modular and deployed across different cellular contexts with the same basic promoter configuration.
Synthesis and characterization of a cadmium(II)–organic supramolecular coordination compound based on the multifunctional 2-amino-5-sulfobenzoic acid ligand
Authors: Yuan Gan-Yin , Zhang Lei , Wang Meng-Jie , Zhang Kou-Lin
Published: November 2016

Much attention has been paid by chemists to the construction of supramolecular coordination compounds based on the multifunctional ligand 5-sulfosalicylic acid (H3SSA) due to the structural and biological interest of these compounds. However, no coordination compounds have been reported for the multifunctional amino-substituted sulfobenzoate ligand 2-amino-5-sulfobenzoic acid (H2asba). We expected that H2asba could be a suitable building block for the assembly of supramolecular networks due to its interesting structural characteristics. The reaction of cadmium(II) nitrate with H2asba in the presence of the auxiliary flexible dipyridylamide ligandN,N′-bis[(pyridin-4-yl)methyl]oxamide (4bpme) under ambient conditions formed a new mixed-ligand coordination compound, namely bis(3-amino-4-carboxybenzenesulfonato-κO1)diaquabis{N,N′-bis[(pyridin-4-yl)methyl]oxamide-κN}cadmium(II)–N,N′-bis[(pyridin-4-yl)methyl]oxamide–water (1/1/4), [Cd(C7H6NO5S)2(C14H14N4O2)2(H2O)2]·C14H14N4O2·4H2O, (1), which was characterized by single-crystal and powder X-ray diffraction analysis (PXRD), FT–IR spectroscopy, thermogravimetric analysis (TG), and UV–Vis and photoluminescence spectroscopic analyses in the solid state. The central CdIIatom in (1) occupies a special position on a centre of inversion and exhibits a slightly distorted octahedral geometry, being coordinated by two N atoms from two monodentate 4bpme ligands, four O atoms from two monodentate 4-amino-3-carboxybenzenesulfonate (Hasba−) ligands and two coordinated water molecules. Interestingly, complex (1) further extends into a threefold polycatenated 0D→2D (0D is zero-dimensional and 2D is two-dimensional) interpenetrated supramolecular two-dimensional (4,4) layer through intermolecular hydrogen bonding. The interlayer hydrogen bonding further links adjacent threefold polycatenated two-dimensional layers into a three-dimensional network. The optical properties of complex (1) indicate that it may be used as a potential indirect band gap semiconductor material. Complex (1) exhibits an irreversible dehydration–rehydration behaviour. The fluorescence properties have also been investigated in the solid state at room temperature.
Synthesis and structures of 11,11,12,12-tetracyano-2,6-diiodo-9,10-anthraquinodimethane and its 2:1 cocrystals with anthracene, pyrene and tetrathiafulvalene
Authors: Ren Yi , Lee Semin , Bertke Jeffery , Gray Danielle L. , Moore Jeffrey S.
Published: November 2016

Radical salts and charge-transfer complexes (CTCs) containing tetracyanoquinodimethane (TCNQ) display electrical conductivity, which has led to the development of many TCNQ derivatives with enhanced electron-accepting properties that are applicable toward organic electronics. To expand the family of TCNQ derivatives, we report the synthesis and structures of 11,11,12,12-tetracyano-2,6-diiodo-9,10-anthraquinodimethane (abbreviated as DITCAQ), C20H6I2N4, and its charge-transfer complexes with various electron donors, namely DITCAQ–anthracene (2/1), C20H6I2N4·0.5C14H10, (I), DITCAQ–pyrene (2/1), C20H6I2N4·0.5C16H10, (II), and DITCAQ–tetrathiafulvalene (2/1), C20H6I2N4·0.5C6H4S4, (III). The molecular structure of DITCAQ consists of a 2,6-diiodo-9,10-dihydroanthracene moiety with two malononitrile substituents. DITCAQ possesses a saddle shape, since the malononitrile groups bend significantly up out of the plane of the central ring and the two benzene rings bend down out of the same plane. π–π interactions between DITCAQ and the electron-donor molecules control the degree of charge transfer in cocrystals (I), (II), and (III), which is reflected in both the dihedral angles between the terminal benzene ring and the central ring on the DITCAQ motifs, and their corresponding IR spectra.
A new antibacterial silver(I) complex incorporating 2,5-dimethylpyrazine and the anti-inflammatory diclofenac
Authors: Hamamci Alisir Sevim , Dege Necmi
Published: November 2016

AgI-containing coordination complexes have attracted attention because of their photoluminescence properties and antimicrobial activities and, in principle, these properties depend on the nature of the structural topologies. A novel two-dimensional silver(I) complex with the anti-inflammatory diclofenac molecule, namely bis{μ-2-[2-(2,6-dichloroanilino)phenyl]acetato-κ3O,O′:O}bis(μ-2,5-dimethylpyrazine-κ2N:N′)silver(I), [Ag2(C14H10Cl2NO2)2(C6H8N2)]n, (I), has been synthesized and characterized by single-crystal X-ray diffraction, revealing that the AgIions are chelated by the carboxylate groups of the anionic 2-[2-(2,6-dichloroanilino)phenyl]acetate (dicl) ligand in a μ3-η1:η2coordination mode. Each dicl ligand links three AgIatoms to generate a one-dimensional infinite chain. Adjacent chains are connected through 2,5-dimethylpyrazine (dmpyz) ligands to form a two-dimensional layer structure parallel to the crystallographicbcplane. The layers are further connected by C—H...π interactions to generate a three-dimensional supramolecular structure. Additionally, the most striking feature is that the structure contains an intramolecular C—H ...Ag anagostic interaction. Furthermore, the title complex has been tested for itsin vitroantibacterial activity and is determined to be highly effective on the studied microorganisms.
Crystal structures of three carbazole derivatives: 12-ethyl-7-phenylsulfonyl-7H-benzofuro[2,3-b]carbazole, (1), 2-(4,5-dimethoxy-2-nitrophenyl)-4-hydroxy-9-phenylsulfonyl-9H-carbazole-3-carbaldehyde, (2), and 12-phenyl-7-phenylsulfonyl-7H-benzofuro[2,3-b]carbazole, (3)
Authors: Gangadharan Rajeswari , Narayanan P. , Sethusankar K. , Saravanan Velu , Mohanakrishnan Arasambattu K.
Published: November 2016

The three title compounds, C26H19NO3S, (1), C27H20N2O8S, (2), and C30H19NO3S, (3), are carbazole derivatives, where (1) and (3) are heterocycle-containing carbazoles with a benzofuran moiety fused to a carbazole unit. In (2), a dimethoxynitrophenyl ring is attached to the carbazole moiety. In the three derivatives, a phenylsulfonyl group is attached to the N atom of the carbazole unit. Compound (1) crystallizes with two independent molecules in the asymmetric unit (AandB). The carbazole skeleton in the three compounds is essentially planar. In compound (1), the benzene ring of the phenylsulfonyl moiety is almost orthogonal to the carbazole moiety, with dihedral angles of 85.42 (9) and 84.52 (9)° in moleculesAandB, respectively. The benzene ring of the phenylsulfonyl group in compounds (2) and (3) are inclined to the carbazole moiety, making dihedral angles of 70.73 (13) and 81.73 (12)°, respectively. The S atom has a distorted tetrahedral configuration in all three compounds. In the crystals, C—H...O hydrogen bonds give rise toR22(12) inversion dimers for compound (1), and toR22(24) inversion dimers andR44(40) ring motifs for compound (2). The crystal packing in (1) also features C—H...π and π–π interactions [shortest intercentroid distance = 3.684 (1) Å], leading to supramolecular three-dimensional aggregation. In the crystal of compound (2), the combination of the various C—H...O hydrogen bonds leads to the formation of a three-dimensional network. In the crystal of compound (3), molecules are linked by C—H...O hydrogen bonds, forming chains running parallel to theaaxis, and the chains are linked by C—H...π interactions, forming corrugated sheets parallel to theabplane.
Crystal structure of a dimeric β-diketiminate magnesium complex
Authors: MacNeil Connor S. , Johnson Kevin R. D. , Hayes Paul G. , Boeré René T.
Published: November 2016

The solid-state structure of a dimeric β-diketiminate magnesium(II) complex is discussed. The compound, di-μ-iodido-bis[({4-amino-1,5-bis[2,6-bis(propan-2-yl)phenyl]pent-3-en-2-ylidene}azanido-κ2N,N′)magnesium(II)] toluene sesquisolvate, [Mg2(C29H41N2)2I2]·1.5C7H8, crystallizes as two independent molecules, each with 2/mcrystallographic site symmetry, located at Wyckoff sites 2cand 2d. These have symmetry-equivalent magnesium atoms bridged by μ-iodide ligands with very similar Mg—I distances. The two Mg atoms are located slightly below (∼0.5 Å) the least-squares plane defined by N–C—C–N atoms in the ligand scaffold, and are approximately tetrahedrally coordinated. One and one-half toluene solvent molecules are disordered with respect to mirror-site symmetry at Wyckoff sites 4iand 2a, respectively. In the former case, two toluene molecules interact in an off-center parallel stacking arrangement; the shortest C to C′ (π–π) distance of 3.72 (1) Å was measured for this interaction.
Crystal structure of 5,7,12,14-tetrahydro-5,14:7,12-bis([1,2]benzeno)pentacene-6,13-dione
Authors: Nozari Mohammad , Jasinski Jerry P. , Kaur Manpreet , Addison Anthony W. , Arabi Shamsabadi Ahmad , Soroush Masoud
Published: November 2016

The lattice of 5,7,12,14-tetrahydro-5,14:7,12-bis([1,2]benzeno)pentacene-6,13-dione, C34H20O2, at 173 K has triclinic (P-1) symmetry and crystallizes with four independent half-molecules in the asymmetric unit. Each molecule is generated from a C17H10O substructure through an inversion center at the centroid of the central quinone ring, generating a wide H-shaped molecule, with a dihedral angle between the mean planes of the terminal benzene rings in each of the two symmetry-related pairs over the four molecules of 68.6 (1) (A), 65.5 (4) (B), 62.3 (9) (C), and 65.8 (8)° (D), an average of 65.6 (1)°. This compound has applications in gas-separation membranes constructed from polymers of intrinsic microporosity (PIM). The title compound is a product of a double Diels–Alder reaction between anthracene andp-benzoquinone followed by dehydrogenation. It has also been characterized by cyclic voltammetry and rotating disc electrode polarography, FT–IR, high resolution mass spectrometry, elemental analysis, and1H NMR.
OSCAR Foundation: empowering lives through football
Authors: Varghese Elsa , Galliara Meena , Srivastava Manjari
Published: November 2016

Subject area

Social entrepreneurship, Social enterprise.

Study level/applicability

Masters Programme in Social Entrepreneurship, Social Work, Business Administration; Management Development Programme for Social Entreprenuers.

Case overview

Organisation for Social Change, Awareness and Responsibility (OSCAR) Foundation is a non-profit organisation registered in 2010 under the Bombay Public Trust Act, 1950. Born and raised in the slum colony of Ambedkar Nagar, Cuffe Parade, Ashok, the founder, grew up seeing his friends becoming a victim to many socially inappropriate behaviours due to dropping out of school. Inspired by the thought of breaking this vicious cycle, Ashok used football as a mechanism to instil essential life skills among children and youth and encouraged them to continue their education. The success of his pilot motivated him to set up OSCAR. Presently, through its various programmes, the organisation has reached out to more than 3,000 marginalised children and 500 youths and aims to reach out to 20,000 children by 2020. The case highlights the struggles of Ashok’s entrepreneurial journey and maps the new challenges in scaling up his enterprise.

Expected learning outcomes

The expected learning outcomes are as follows: to identify the characteristics of a social entrepreneur and ascertain the leadership skills required by a social entrepreneur; to scrutinise the life cycle of a social enterprise and develop insights to examine the unique risks and challenges faced at the start-up phase of the social enterprise; and to enhance the understanding of interrelationship between passion, mission focus and challenges to attain financial sustainability for a social venture.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 3: Entrepreneurship.