bluuebunny/crossref_metadata_2025 huggingface dataset:
The pacemaker role of thalamic reticular nucleus in controlling spike-wave discharges and spindles
Authors: Fan Denggui , Liao Fucheng , Wang Qingyun
Published: July 2017

Absence epilepsy, characterized by 2–4 Hz spike-wave discharges (SWDs), can be caused by pathological interactions within the thalamocortical system. Cortical spindling oscillations are also demonstrated to involve the oscillatory thalamocortical rhythms generated by the synaptic circuitry of the thalamus and cortex. This implies that SWDs and spindling oscillations can share the common thalamocortical mechanism. Additionally, the thalamic reticular nucleus (RE) is hypothesized to regulate the onsets and propagations of both the epileptic SWDs and sleep spindles. Based on the proposed single-compartment thalamocortical neural field model, we firstly investigate the stimulation effect of RE on the initiations, terminations, and transitions of SWDs. It is shown that the activations and deactivations of RE triggered by single-pulse stimuli can drive the cortical subsystem to behave as the experimentally observed onsets and self-abatements of SWDs, as well as the transitions from 2-spike and wave discharges (2-SWDs) to SWDs. In particular, with increasing inhibition from RE to the specific relay nucleus (TC), rich transition behaviors in cortex can be obtained through the upstream projection path, RE→TC→Cortex. Although some of the complex dynamical patterns can be expected from the earlier single compartment thalamocortical model, the effect of brain network topology on the emergence of SWDs and spindles, as well as the transitions between them, has not been fully investigated. We thereby develop a spatially extended 3-compartment coupled network model with open-/closed-end connective configurations, to investigate the spatiotemporal effect of RE on the SWDs and spindles. Results show that the degrees of activations of RE1 can induce the rich spatiotemporal evolution properties including the propagations from SWDs to spindles within different compartments and the transitions between them, through the RE1→TC1→Cortex1 and Cortex1→Cortex2→Cortex3 projecting paths, respectively. Overall, those results imply that RE possesses the pacemaker function in controlling SWDs and spindling oscillations, which computationally provide causal support for the involvement of RE in absence seizures and sleep spindles.
Effects of oxygen partial pressure and annealing on dispersive optical nonlinearity in NiO thin films
Authors: Chouhan Romita , Baraskar Priyanka , Agrawal Arpana , Gupta Mukul , Sen Pranay K. , Sen Pratima
Published: July 2017

We report annealing induced sign reversal of dispersive optical nonlinearity in ion beam sputtered NiO thin films deposited at 30% and 70% oxygen partial pressures. In the Ultraviolet-visible spectra of the samples, the transmission peak corresponding to d-d transitions is observed near 2 eV. A shift in this peak towards higher energy was observed when the same films were annealed at 523 K. The near resonant photoinduced transitions produced giant nonlinear optical susceptibilities of both third- and fifth- orders when the annealed film was irradiated by a continuous wave 632.8 nm He-Ne laser. The role of the thermo-optic effect has been examined critically. Experimental studies further reveal that the oxygen partial pressure influences the growth direction of the grains in the thin films. The well known Z-scan experimental procedure has been followed for measurements of optical nonlinearities in all the NiO films. The nonlinear refractive indices of both the as-deposited and annealed NiO thin films are defined in terms of the thermo-optic coefficients (dndT)T=T0 and (d2ndT2)T=T0.
Transport phenomena of electrons at the carbon nanotube interface with molecular adsorption
Authors: Kokabu Takuya , Takashima Kengo , Inoue Shuhei , Matsumura Yukihiko , Yamamoto Takahiro
Published: July 2017

The electric conductance of carbon-nanotube (CNT) films is affected by gas adsorption. Previous studies have shown that the adsorption of gas molecules on the CNT/CNT interface is the key to the changing CNT-film conductance. However, it is still unclear how the gas molecules affect the electric conduction of the CNT/CNT interface or its electron transport properties. We present here a study on the effects of gas-molecule adsorption on the CNT/CNT interface using a fluctuation-induced tunneling (FIT) model of the CNT-film electrical conduction. We demonstrated that the CNT-film conduction follows the FIT model, and the subsequently estimated electrostatic potential between the CNT/CNT interfaces was in good agreement with estimates from density functional theory simulations. Since the FIT model treats the CNT/CNT interface as a parallel-plate capacitor, we propose a modified FIT model that accounts for the change in the dielectric constant at the CNT/CNT interface due to the adsorption of gas molecules. This model well explained the electric-conductance change of the CNT film with respect to the gas pressure. Finally, we found that the adsorbed gas molecules affected the local dielectric constant at the CNT/CNT interface.
Characterising resource use and potential inefficiencies during large-fire suppression in the western US
Authors: Katuwal Hari , Dunn Christopher J. , Calkin David E.
Published: July 2017

Currently, limited research on large-fire suppression effectiveness suggests fire managers may over-allocate resources relative to values to be protected. Coupled with observations that weather may be more important than resource abundance to achieve control objectives, resource use may be driven more by risk aversion than efficiency. To explore this potential, we investigated observed percentage of perimeter contained and self-reported containment values, the exposure index, and patterns of resource use during the containment and control phases of fire response. Fireline production capacity of responding resources typically exceeds final fire perimeter, often by an order of magnitude or more. Additionally, on average, 21% of total incident resource productive capacity was observed on the fire during the control phase, that is, after the fires cease to grow. Our results suggest self-reported percentage containment significantly underestimates actual percentage of perimeter contained throughout an incident, with reported values averaging only 70% contained at actual fire cessation. Combined, these results suggest a fire manager’s risk perception influences resource use and may unnecessarily expose responders to fireline hazards. These results suggest a considerable opportunity to improve large-fire management efficiency by balancing the likelihood and consequences of fire escape against the opportunity cost of resource use.
Towards enhanced risk management: planning, decision making and monitoring of US wildfire response
Authors: Dunn Christopher J. , Calkin David E. , Thompson Matthew P.
Published: July 2017

Wildfire’s economic, ecological and social impacts are on the rise, fostering the realisation that business-as-usual fire management in the United States is not sustainable. Current response strategies may be inefficient and contributing to unnecessary responder exposure to hazardous conditions, but significant knowledge gaps constrain clear and comprehensive descriptions of how changes in response strategies and tactics may improve outcomes. As such, we convened a special session at an international wildfire conference to synthesise ongoing research focused on obtaining a better understanding of wildfire response decisions and actions. This special issue provides a collection of research that builds on those discussions. Four papers focus on strategic planning and decision making, three papers on use and effectiveness of suppression resources and two papers on allocation and movement of suppression resources. Here we summarise some of the key findings from these papers in the context of risk-informed decision making. This collection illustrates the value of a risk management framework for improving wildfire response safety and effectiveness, for enhancing fire management decision making and for ushering in a new fire management paradigm.
Group augmentation, collective action, and territorial boundary patrols by male chimpanzees
Authors: Langergraber Kevin E. , Watts David P. , Vigilant Linda , Mitani John C.
Published: July 2017

Significance

Many animals, especially humans, carry out activities collectively because the benefits of doing so exceed those that can be achieved individually. But how can collective action evolve when individuals receive the benefits of cooperation regardless of whether they pay the costs of participation? Collective action may be especially difficult to achieve when groups are large, because each individual’s contribution has a small effect on the outcome. We show that group augmentation theory helps explain one of the most striking examples of collective action in nonhuman primates, territorial boundary patrolling by male chimpanzees: Males bear the short-term costs of patrolling even when they have little to gain immediately because patrolling enhances group size, increasing the male’s chances of future reproduction.
Contrastive studies of cohesion and their impact on our knowledge of translation (English-German)
Authors: Steiner Erich
Published: July 2017

This article starts from the claim that knowledge about contrastive systems of cohesion and textual instantiations of these systems between English and German is important for translation, but that this knowledge is still fragmentary and insufficiently supported by empirical studies. This claim will be followed by three generalizing assumptions about contrastive differences in English-German cohesion which relate to (1) different degrees of local encoding of ambiguity in texts in terms of co-reference, (2) different degrees of registerial distinctions along the written-spoken and formal-informal distinctions, and (3) different orientations of discourses along the explicitness and information-density dimensions. These assumptions are being tested in corpus-based work in our group, and the currently available results will be summarized. The summary will be followed by a discussion and exemplification of implications for translation in both directions between English and German. As will be seen, an awareness of the main differences between English and German cohesion, between registers within these two languages and between written and spoken modes in particular are an important background for guiding translation strategies.
Imdeduya
Authors: Senft Gunter
Published: July 2017

This volume presents five variants of the Imdeduya myth: two versions of the actual myth, a short story, a song and John Kasaipwalova’s English poem “Sail the Midnight Sun”. This poem draws heavily on the Trobriand myth which introduces the protagonists Imdeduya and Yolina and reports on Yolina’s intention to marry the girl so famous for her beauty, on his long journey to Imdeduya’s village and on their tragic love story. The texts are compared with each other with a final focus on the clash between orality and scripturality. Contrary to Kasaipwalova’s fixed poetic text, the oral Imdeduya versions reveal the variability characteristic for oral tradition. This variability opens up questions about traditional stability and destabilization of oral literature, especially questions about the changing role of myth – and magic – in the Trobriand Islanders' society which gets more and more integrated into the by now “literal” nation of Papua New Guinea.
Pragmatic function impairment and Alzheimer’s dementia
Authors: Schatz Sara , González-Rivera Melvin
Published: July 2017

Pragmatic competence includes the capacity to express illocutionary force and successfully achieve perlocutionary effects, in order to guarantee fully functional communication exchanges. Alzheimer’s Disease is characterized by a constellation of limitations derived from progressive cognitive impairment, which is usually viewed as a global uniform phenomenon. In this paper it is argued that looking independently at the loss and recovery of pragmatic function related to illocutionary and perlocutionary abilities can be a productive way of understanding the progressive deterioration of communicative capacities by patients or their improvement under targeted treatment.
Annexin A2 supports pulmonary microvascular integrity by linking vascular endothelial cadherin and protein tyrosine phosphatases
Authors: Luo Min , Flood Elle C. , Almeida Dena , Yan LunBiao , Berlin David A. , Heerdt Paul M. , Hajjar Katherine A.
Published: July 2017

Relative or absolute hypoxia activates signaling pathways that alter gene expression and stabilize the pulmonary microvasculature. Alveolar hypoxia occurs in disorders ranging from altitude sickness to airway obstruction, apnea, and atelectasis. Here, we report that the phospholipid-binding protein, annexin A2 (ANXA2) functions to maintain vascular integrity in the face of alveolar hypoxia. We demonstrate that microvascular endothelial cells (ECs) from Anxa2−/− mice display reduced barrier function and excessive Src-related tyrosine phosphorylation of the adherens junction protein vascular endothelial cadherin (VEC). Moreover, unlike Anxa2+/+ controls, Anxa2−/− mice develop pulmonary edema and neutrophil infiltration in the lung parenchyma in response to subacute alveolar hypoxia. Mice deficient in the ANXA2-binding partner, S100A10, failed to demonstrate hypoxia-induced pulmonary edema under the same conditions. Further analyses reveal that ANXA2 forms a complex with VEC and its phosphatases, EC-specific protein tyrosine phosphatase (VE-PTP) and Src homology phosphatase 2 (SHP2), both of which are implicated in vascular integrity. In the absence of ANXA2, VEC is hyperphosphorylated at tyrosine 731 in response to vascular endothelial growth factor, which likely contributes to hypoxia-induced extravasation of fluid and leukocytes. We conclude that ANXA2 contributes to pulmonary microvascular integrity by enabling VEC-related phosphatase activity, thereby preventing vascular leak during alveolar hypoxia.
Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span
Authors: Misharin Alexander V. , Morales-Nebreda Luisa , Reyfman Paul A. , Cuda Carla M. , Walter James M. , McQuattie-Pimentel Alexandra C. , Chen Ching-I , Anekalla Kishore R. , Joshi Nikita , Williams Kinola J.N. , Abdala-Valencia Hiam , Yacoub Tyrone J. , Chi Monica , Chiu Stephen , Gonzalez-Gonzalez Francisco J. , Gates Khalilah , Lam Anna P. , Nicholson Trevor T. , Homan Philip J. , Soberanes Saul , Dominguez Salina , Morgan Vince K. , Saber Rana , Shaffer Alexander , Hinchcliff Monique , Marshall Stacy A. , Bharat Ankit , Berdnikovs Sergejs , Bhorade Sangeeta M. , Bartom Elizabeth T. , Morimoto Richard I. , Balch William E. , Sznajder Jacob I. , Chandel Navdeep S. , Mutlu Gökhan M. , Jain Manu , Gottardi Cara J. , Singer Benjamin D. , Ridge Karen M. , Bagheri Neda , Shilatifard Ali , Budinger G.R. Scott , Perlman Harris
Published: July 2017

Little is known about the relative importance of monocyte and tissue-resident macrophages in the development of lung fibrosis. We show that specific genetic deletion of monocyte-derived alveolar macrophages after their recruitment to the lung ameliorated lung fibrosis, whereas tissue-resident alveolar macrophages did not contribute to fibrosis. Using transcriptomic profiling of flow-sorted cells, we found that monocyte to alveolar macrophage differentiation unfolds continuously over the course of fibrosis and its resolution. During the fibrotic phase, monocyte-derived alveolar macrophages differ significantly from tissue-resident alveolar macrophages in their expression of profibrotic genes. A population of monocyte-derived alveolar macrophages persisted in the lung for one year after the resolution of fibrosis, where they became increasingly similar to tissue-resident alveolar macrophages. Human homologues of profibrotic genes expressed by mouse monocyte-derived alveolar macrophages during fibrosis were up-regulated in human alveolar macrophages from fibrotic compared with normal lungs. Our findings suggest that selectively targeting alveolar macrophage differentiation within the lung may ameliorate fibrosis without the adverse consequences associated with global monocyte or tissue-resident alveolar macrophage depletion.
Heart Rate Variability and Cognitive Function In Middle-Age Adults: The Coronary Artery Risk Development in Young Adults
Authors: Zeki Al Hazzouri Adina , Elfassy Tali , Carnethon Mercedes R , Lloyd-Jones Donald M , Yaffe Kristine
Published: July 2017

BACKGROUND

Low heart rate variability (HRV), a marker of cardiac autonomic dysfunction, has been associated with major risk factors of cognitive impairment. Yet, the direct association of HRV with cognitive function remains relatively unexplored, particularly in midlife.

METHODS

In 2005, 2 measures of short-term HRV, the SD of normal-to-normal intervals (SDNN) and the root mean square of successive differences (RMSSD), were calculated for participants of the Coronary Artery Risk Development in Young Adults study, and then categorized into quartiles. Five years later, 3 cognitive tests were administered for verbal memory (“Rey Auditory-Verbal Learning Test”, RAVLT, range 0–15), processing speed (“Digit Symbol Substitution Test”, DSST, range 0–133), and executive function (“Stroop interference”).

RESULTS

Two thousand one hundred and eighteen participants (57.7% female, 42.2% Black) with a mean baseline age of 45.3 years were included in this analysis. In demographic-adjusted models, compared to participants with quartile 1 SDNN (lowest quartile), participants in the upper quartiles of SDNN scored better on the DSST (quartile 4: β = 1.83 points better, P = 0.03; and quartile 3: β = 1.95 points better, P = 0.03) and on the stroop (quartile 3: β = 1.19 points better, P < 0.05; and quartile2: β = 1.44 points better, P = 0.02). After adjusting for behavioral and cardiovascular risk factors, higher quartile SDNN remained significantly associated with better stroop score (quartile 3: β = 1.21 points better, P = 0.04; and quartile 2: β = 1.72 points better, P < 0.01) but not with DSST. There was no association between quartile of RMSSD and cognitive function, from fully adjusted models.

CONCLUSIONS

Our findings suggest that higher quartile SDDN is associated with better executive function in midlife, above, and beyond cardiovascular risk factors.
Coccidioidomycosis A Cause of Sarcoidosis
Authors: Kuberski Tim , Yourison Isaac
Published: July 2017

Background

Sarcoidosis is a granulomatous disease of unknown etiology and coccidioidomycosis is a granulomatous fungal infection endemic to the southwestern United States. Clinical observations on patients with sarcoidosis and coccidioidomycosis simultaneously led to the hypothesis that sarcoidosis can be caused by the fungus Coccidioides.

Methods

Two patients with sarcoidosis and coccidioidomycosis were studied, one prospectively (ie, a patient with sarcoidosis was predicted to develop coccidioidomycosis) and the other retrospectively (ie, a patient with coccidioidomycosis develops sarcoidosis). In addition, a literature review found 5 patients with these 2 diseases, and they were analyzed to establish an archived relationship between the 2 entities. In addition, polymerase chain reaction (PCR) testing for Coccidioides deoxyribonucleic acid (DNA) was performed on tissue from 15 Arizona patients diagnosed with sarcoidosis.

Results

Patient 1 was diagnosed with sarcoid in Arizona and followed prospectively. There was no evidence for coccidioidomycosis at diagnosis. This patient was observed for 8 years before he was documented to have disseminated coccidioidomycosis. Patient 2 was retrospectively studied. He was diagnosed with disseminated coccidioidomycosis, but after 3 years, while on antifungal therapy, he developed respiratory failure. A lung biopsy was consistent with sarcoidosis with no evidence of Coccidioides; cultures, histopathology, and serology were all negative. Paradoxically, PCR testing for Coccidioides DNA on tissue taken at the time of the sarcoidosis diagnosis were all negative, including Patient 2 who had proven coccidioidomycosis.

Conclusions

The 2 study patients and 5 case reports from the literature support the hypothesis that Coccidioides can cause sarcoidosis in Arizona. There are similar reports in the literature that Histoplasma can be associated with sarcoidosis. Based on these observations, we propose that sarcoidosis can be caused by endemic fungi in different areas of the United States, coccidioidomycosis in the Southwest and histoplasmosis in the Midwest.
Accurate Immune Repertoire Sequencing Reveals Malaria Infection Driven Antibody Lineage Diversification in Young Children
Authors: Wendel Ben S. , He Chenfeng , Qu Mingjuan , Wu Di , Hernandez Stefany M. , Ma Ke-Yue , Liu Eugene W. , Xiao Jun , Crompton Peter D. , Pierce Susan K. , Ren Pengyu , Chen Keke , Jiang Ning
Published: July 2017

Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important to the understanding of the repertoire response to infections and vaccinations. Here, we describe an accurate and high-coverage repertoire sequencing method, MIDCIRS, which uses as few as 1,000 naïve B cells. Using it, we studied age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12 – 47 months old) with 4-8 ml of blood draws. Unexpectedly, we discovered high levels of somatic hypermutation (SHM) in infants as young as three months old. Antibody clonal lineage analysis revealed that both infants and toddlers increase SHM levels upon infection and memory B cells isolated from pre-malaria samples in malaria-experienced individuals continue to induce SHMs upon malaria rechallenge. These results highlight the vast potential of antibody repertoire diversification in infants and toddlers that has not been realized previously.
Speed breeding: a powerful tool to accelerate crop research and breeding
Authors: Watson Amy , Ghosh Sreya , Williams Matthew J. , Cuddy William S. , Simmonds James , Rey María-Dolores , Hatta M. Asyraf Md , Hinchliffe Alison , Steed Andrew , Reynolds Daniel , Adamski Nikolai , Breakspear Andy , Korolev Andrey , Rayner Tracey , Dixon Laura E. , Riaz Adnan , Martin William , Ryan Merrill , Edwards David , Batley Jacqueline , Raman Harsh , Rogers Christian , Domoney Claire , Moore Graham , Harwood Wendy , Nicholson Paul , Dieters Mark J. , DeLacy Ian H. , Zhou Ji , Uauy Cristobal , Boden Scott A. , Park Robert F. , Wulff Brande B. H. , Hickey Lee T.
Published: July 2017

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand [1]. This slow improvement rate is attributed partly to the long generation times of crop plants. Here we present a method called ‘speed breeding’, which greatly shortens generation time and accelerates breeding and research programs. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum), and pea (Pisum sativum) and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully-enclosed controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies, and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent and potential for adaptation to larger-scale crop improvement programs. Cost-saving through LED supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing, and genomic selection, accelerating the rate of crop improvement.
GEM: A manifold learning based framework for reconstructing spatial organizations of chromosomes
Authors: Zhu Guangxiang , Deng Wenxuan , Hu Hailin , Ma Rui , Zhang Sai , Yang Jinglin , Peng Jian , Kaplan Tommy , Zeng Jianyang
Published: July 2017

Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, Chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning framework, called GEM (Genomic organization reconstructor based on conformationalEnergy andManifold learning), to elucidate the underlying 3D spatial organizations of chromosomes from Hi-C data. Unlike previous chromatin structure reconstruction methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances between distal genomic loci, GEM is able to reconstruct an ensemble of chromatin conformations by directly embedding the neigh-boring affinities from Hi-C space into 3D Euclidean space based on a manifold learning strategy that considers both the fitness of Hi-C data and the biophysical feasibility of the modeled structures, which are measured by the conformational energy derived from our current biophysical knowledge about the 3D polymer model. Extensive validation tests on both simulated interaction frequency data and experimental Hi-C data of yeast and human demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also reconstructed accurate chromatin structures that agreed well with the hold-out or independent Hi-C data and sparse geometric restraints derived from the previous fluorescencein situhybridization (FISH) studies. In addition, as GEM can generate accurate spatial organizations of chromosomes by integrating both experimentally-derived spatial contacts and conformational energy, we for the first time extended our modeling method to recover long-range genomic interactions that are missing from the original Hi-C data. All these results indicated that GEM can provide a physically and physiologically valid 3D representations of the organizations of chromosomes and thus serve as an effective and useful genome structure reconstructor.
DddY is a bacterial dimethylsulfoniopropionate lyase representing a new cupin enzyme superfamily with unknown primary function
Authors: Lei Lei , Alcolombri Uria , Tawfik Dan S
Published: July 2017

Dimethylsulfide (DMS) is released at rates of >107tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms, release DMS via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known belonging to different superfamilies and exhibiting highly variable levels of DMSP lyase activity. DddY shows the highest activity among all reported bacterial lyases yet is poorly characterized. Here, we describe the characterization of recombinant DddY is from different marine bacteria. We found that DddY activity demands a transition metal ion cofactor. DddY also shares two sequence motifs with other bacterial lyases assigned as cupin-like enzymes, DddQ, DddL, DddK, and DddW. These cupin motif residues are essential for DddY activity, as for the other cupin DMSP lyases, and all these enzymes are characterized by a common metal-chelator inhibitor (TPEN). Analysis of all sequences carrying these cupin motifs defined a superfamily: Cupin-DLL (DMSP lyases and lyase-like). The DMSP lyase families are sporadically distributed suggesting that DMSP lyases evolved within this superfamily independently along multiple lineages. However, the specific activity levels, genomic context analysis, and systematic profiling of substrate selectivity as described in the accompanying paper, indicate that for only some of these families, most distinctly DddY and DddL, DMSP lyase is the primary, native activity. In other families, foremost DddQ, DMSP lyase seems to be merely a promiscuous activity. The native function of DddQ, and of nearly all members of this newly identified Cupin-DLL superfamily, remains unknown.

Abbreviations

DMSP

dimethylsulfoniopropionate

DMS

dimethylsulfide

cupin-DLL

cupin DMSP lyase and lyase-like

Funding

Financial support by the Estate of Mark Scher, and the Sasson & Marjorie Peress Philanthropic Fund, are gratefully acknowledged. D.S.T. is the Nella and Leon Benoziyo Professor of Biochemistry.
A computational modelling framework to quantify the effects of passaging cell lines
Authors: Jin Wang , Penington Catherine J , McCue Scott W , Simpson Matthew J
Published: July 2017

In vitrocell culture is routinely used to grow and supply a sufficiently large number of cells for various types of cell biology experiments. Previous experimental studies report that cell characteristics evolve as the passage number increases, and various cell lines can behave differently at high passage numbers. To provide insight into the putative mechanisms that might give rise to these differences, we performin silicoexperiments using a random walk model to mimic thein vitrocell culture process. Our results show that it is possible for the average proliferation rate to either increase or decrease as the passaging process takes place, and this is due to a competition between the initial heterogeneity and the degree to which passaging damages the cells. We also simulate a suite of scratch assays with cells from near–homogeneous and heterogeneous cell lines, at both high and low passage numbers. Although it is common in the literature to report experimental results without disclosing the passage number, our results show that we obtain significantly different closure rates when performingin silicoscratch assays using cells with different passage numbers. Therefore, we suggest that the passage number should always be reported to ensure that the experiment is as reproducible as possible. Furthermore, our modelling also suggests some avenues for further experimental examination that could be used to validate or refine our simulation results.
Genome-wide Association Study of Clinical Features in the Schizophrenia Psychiatric Genomics Consortium: Confirmation of Polygenic Effect on Negative Symptoms
Authors: Bigdeli Tim B. , Peterson Roseann E. , Ripke Stephan , Bacanu Silviu-Alin , Amdur Richard L. , Gejman Pablo V. , Levinson Douglas F. , Riley Brien P. , Clair David St. , Rietschel Marcella , Walters James T.R. , Ophoff Roel A. , McQuillin Andrew , Gurling Hugh , Rujescu Dan , Sullivan Patrick F. , Kirov George , Pato Michele T. , Pato Carlos N. , Andreassen Ole A. , Owen Michael J. , O'Donovan Michael C. , Corvin Aiden , Malhotra Anil K , Mowry Bryan J. , Esko Tõnu , Werge Thomas , Kendler Kenneth S. ,   Schizophrenia Working Group of the Psychiatric Genomics Consortium, Fanous Ayman H.
Published: July 2017

Schizophrenia is a clinically heterogeneous disorder. Proposed revisions inDSM - 5included dimensional measurement of different symptom domains. We sought to identify common genetic variants influencing these dimensions, and confirm a previous association between polygenic risk of schizophrenia and the severity of negative symptoms. The Psychiatric Genomics Consortium study of schizophrenia comprised 8,432 cases of European ancestry with available clinical phenotype data. Symptoms averaged over the course of illness were assessed using theOPCRIT, PANSS, LDPS, SCAN, SCID, and CASH. Factor analyses of each constituentPGCstudy identified positive, negative, manic, and depressive symptom dimensions. We examined the relationship between the resultant symptom dimensions and aggregate polygenic risk scores indexing risk of schizophrenia. We performed genome - wide association study (GWAS) of each quantitative traits using linear regression and adjusting for significant effects of sex and ancestry. The negative symptom factor was significantly associated with polygene risk scores for schizophrenia, confirming a previous, suggestive finding by our group in a smaller sample, though explaining only a small fraction of the variance. In subsequentGWAS, we observed the strongest evidence of association for the positive and negative symptom factors, withSNPsinRFX8on 2q11.2 (P = 6.27×10-8) and upstream ofWDR72 / UNC13Con 15q21.3 (P= 7.59×10-8), respectively. We report evidence of association of novel modifier loci for schizophrenia, though no single locus attained established genome - wide significance criteria. As this may have been due to insufficient statistical power, follow - up in additional samples is warranted. Importantly, we replicated our previous finding that polygenic risk explains at least some of the variance in negative symptoms, a core illness dimension.
Ecological suicide in microbes
Authors: Ratzke Christoph , Denk Jonas , Gore Jeff
Published: July 2017

The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment, such as the cooperative breakdown of complex nutrients in microbes [1]–[3] or the construction of elaborate architectures in social insects [4]. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, eg by resource depletion or the production of toxic byproducts [5]. Here we find an extreme type of negative interactions, in which bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances – like antibiotics – can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We find ecological suicide in a wide variety of microbes, suggesting that it could play a significant role in microbial ecology and evolution.
Is methodology destiny? Religiosity and charitable giving
Authors: Li Yan
Published: July 2017

Purpose

The purpose of this paper is to examine whether people who engage in religious activities are more generous in terms of both religious and secular giving.

Design/methodology/approach

Bivariate probit (BVP) and bivariate tobit (BVT) analyses show that religious people have a greater propensity to give and higher levels of giving to both religious and secular charitable organizations. The bivariate systems permit a test of the correlation across the different giving decisions, and the correlation between religious and secular giving is found to be highly significant.

Findings

Religiosity positively influences both religious and secular donations. After controlling for this correlation, the impacts of religiosity on religious and secular giving are more efficient estimates but smaller than expected.

Originality/value

As a result of these methodological shortcomings, the causal relationship between religiosity and charitable giving is far from clear. To overcome those problems, this study uses BVP and BVT models to control for the potential correlation between religious giving and secular giving by the same individual and then draws appropriate interpretations. This study adds a firmer theoretical foundation to the existing literature.
Applying critical realism in spirituality at work research
Authors: McGhee Peter , Grant Patricia
Published: July 2017

Purpose

This study aims to demonstrate how critical realism (CR) can be used in spirituality at work (SAW) research and to provide a practical example of CR in SAW research.

Design/methodology/approach

CR is a philosophical meta-theory that allows the stratification of spirituality into different levels of reality, advocates for research methods matching the ontology of the level investigated and provides complementary methods of exploring this phenomenon’s causal power in social contexts. The authors present a study where CR was used to explain how and why SAW influences ethics in organisational contexts.

Findings

The results demonstrate that CR provides a useful approach to bridging the positivist-interpretivist difference in SAW research. Moreover, a CR approach helped explain the underlying conditions and causal mechanisms that power SAW to influence ethical decision-making and behaviour in the workplace.

Originality/value

While CR has been applied in the management literature, negligible SAW research has used this approach. That which exists is either conceptual or does not discuss methods of data analysis, or describe how critical realist concepts resulted in their findings. This paper addresses that lacuna. CR also provides value, as an alternative approach to SAW research, in that it allows the use of both quantitative and qualitative methods as complementary, not confrontational methods while providing a more integrated and deeper view of SAW and its effects.
A study of emergent organizing and technological affordances after a natural disaster
Authors: Lai Chih-Hui
Published: July 2017

Purpose

Drawing on the model of technology-in-practice and the literature on bona fide approaches and technological affordances, the purpose of this paper is to argue that collectives involved in emergency response may exhibit similar and different usage patterns for technology due to the combined influence of the temporal development of the response actions and the existing and newly enacted organizational, social, and technological structures.

Design/methodology/approach

To enrich the argument about the inter-related influence on response organizations’ use of technology across phases of the disaster response, this research uses a multi-method and longitudinal case study of citizen-based response organizations after Hurricane Sandy.

Findings

Findings show that technologies were used similarly by response organizations immediately after the hurricane, whereas the later use of technologies exhibited variations. Moreover, Twitter was used consistently for diverse purposes across the phases of the disaster response, whereas Facebook usage among organizations first diverged and then converged two months after the hurricane. The organizations’ different patterns of social media use also reflected the construction and reconstruction of resource networks for relief operations over time.

Research limitations/implications

This study integrates multiple theoretical frameworks in explaining the processes and outcomes of technology use for collectives in emergency response, which presents an example of bridging and enriching the theoretical constructs from the areas of technology adaptation and emergency management.

Practical implications

Findings of this study provide practical knowledge about the mechanisms of integrating multiple information systems into the building of resilient social systems for emergency response.

Social implications

Findings of this study enrich social understanding about how the use of technologies for collective activity in emergency situations can go beyond one-time events and lay the foundation for long-term resilient emergency management.

Originality/value

The originality of this study lies in its mixed-method and longitudinal design, which allows for the examination of the timing, circumstances, and outcomes of citizen-based response organizations’ technology use.
Concurrent deposition path planning and structural topology optimization for additive manufacturing
Authors: Liu Jikai , Yu Huangchao
Published: July 2017

Purpose

Structural performance of additively manufactured parts is deposition path-dependent because of the induced material anisotropy. Hence, this paper aims to contribute a novel idea of concurrently performing the deposition path planning and the structural topology optimization for additively manufactured parts.

Design/methodology/approach

The concurrent process is performed under a unified level set framework that: the deposition paths are calculated by extracting the iso-value level set contours, and the induced anisotropic material properties are accounted for by the level set topology optimization algorithm. In addition, the fixed-geometry deposition path optimization problem is studied. It is challenging because updating the zero-value level set contour cannot effectively achieve the global orientation control. To fix this problem, a level set-based multi-step method is proposed, and it is proved to be effective.

Findings

The proposed concurrent design method has been successfully applied to designing additively manufactured parts. The majority of the planned deposition paths well match the principle stress direction, which, to the largest extent, enhances the structural performance. For the fixed geometry problems, fast and smooth convergences have been observed.

Originality/value

The concurrent deposition path planning and structural topology optimization method is, for the first time, developed and effectively implemented. The fixed-geometry deposition path optimization problem is solved through a novel level set-based multi-step method.
Multi-objective optimization of dimensional accuracy, surface roughness and hardness of hybrid investment cast components
Authors: Garg Parlad Kumar , Singh Rupinder , Ahuja IPS
Published: July 2017

Purpose

The purpose of this paper is to optimize the process parameters to obtain the best dimensional accuracy, surface finish and hardness of the castings produced by using fused deposition modeling (FDM)-based patterns in investment casting (IC).

Design/methodology/approach

In this paper, hip implants have been prepared by using plastic patterns in IC process. Taguchi design of experiments has been used to study the effect of six different input process parameters on the dimensional deviation, surface roughness and hardness of the implants. Analysis of variance has been used to find the effect of each input factor on the output. Multi-objective optimization has been done to find the combined best values of output.

Findings

The results proved that the FDM patterns can be used successfully in IC. A wax coating on the FDM patterns improves the surface finish and dimensional accuracy. The improved dimensional accuracy, surface finish and hardness have been achieved simultaneously through multi-objective optimization.

Research limitations/implications

A thin layer of wax is used on the plastic patterns. The effect of thickness of the layer has not been considered. Further research is needed to study the effect of the thickness of the wax layer.

Practical implications

The results obtained by the study would be helpful in making decisions regarding machining and/or coating on the parts produced by this process.

Originality/value

In this paper, multi-objective optimization of dimensional accuracy, surface roughness and hardness of hybrid investment cast components has been performed.
Deposition-induced effects of isotactic polypropylene and polycarbonate composites during fused deposition modeling
Authors: Zhou Ying-Guo , Su Bei , Turng Lih-sheng
Published: July 2017

Purpose

Although the feasibility and effectiveness of the fused deposition modeling (FDM) method have been proposed and developed, studies of applying this technology to various materials are still needed for researching its applicability, especially with regard to polymer blends and composites. The purpose of this paper is to study the deposition-induced effect and the effect of compatibilizers on the mechanical properties of polypropylene and polycarbonate (PP/PC) composites.

Design/methodology/approach

For this purpose, three different deposition modes for PP/PC composites with or without compatibilizers were used for the FDM method and tested for tensile properties. Also, parts with the same materials were made by injection molding and used for comparison. In addition, different deposition speeds were used to investigate the different deposition-induced effects. Furthermore, the behavior of the mechanical properties was clarified with scanning electron microscope images of the fracture surfaces.

Findings

The research results suggest that the deposition orientation has a significant influence on the mechanical behavior of PP/PC composite FDM parts. The results also indicate that there is a close relationship between the mechanical properties and morphological structures which are deeply influenced by compatibilization. Compared with injection molded parts, the ductility of the FDM parts can be dramatically improved due to the formation of fibrils and micro-fibrils by the deposition induced during processing.

Originality/value

This is the first paper to investigate a PP/PC composite FDM process. The results of this paper verified the applicability of PP/PC composites to FDM technology. It is also the first time that the deposition-induced effect during FDM has been investigated and studied.
Semantic fluency in deaf children who use spoken and signed language in comparison with hearing peers
Authors: Marshall C. R. , Jones A. , Fastelli A. , Atkinson J. , Botting N. , Morgan G.
Published: July 2017

Background

Deafness has an adverse impact on children's ability to acquire spoken languages. Signed languages offer a more accessible input for deaf children, but because the vast majority are born to hearing parents who do not sign, their early exposure to sign language is limited. Deaf children as a whole are therefore at high risk of language delays.

Aims

We compared deaf and hearing children's performance on a semantic fluency task. Optimal performance on this task requires a systematic search of the mental lexicon, the retrieval of words within a subcategory and, when that subcategory is exhausted, switching to a new subcategory. We compared retrieval patterns between groups, and also compared the responses of deaf children who used British Sign Language (BSL) with those who used spoken English. We investigated how semantic fluency performance related to children's expressive vocabulary and executive function skills, and also retested semantic fluency in the majority of the children nearly 2 years later, in order to investigate how much progress they had made in that time.

Methods & Procedures

Participants were deaf children aged 6–11 years (N = 106, comprising 69 users of spoken English, 29 users of BSL and eight users of Sign Supported English—SSE) compared with hearing children (N = 120) of the same age who used spoken English. Semantic fluency was tested for the category ‘animals’. We coded for errors, clusters (e.g., ‘pets’, ‘farm animals’) and switches. Participants also completed the Expressive One‐Word Picture Vocabulary Test and a battery of six non‐verbal executive function tasks. In addition, we collected follow‐up semantic fluency data for 70 deaf and 74 hearing children, nearly 2 years after they were first tested.

Outcomes & Results

Deaf children, whether using spoken or signed language, produced fewer items in the semantic fluency task than hearing children, but they showed similar patterns of responses for items most commonly produced, clustering of items into subcategories and switching between subcategories. Both vocabulary and executive function scores predicted the number of correct items produced. Follow‐up data from deaf participants showed continuing delays relative to hearing children 2 years later.

Conclusions & Implications

We conclude that semantic fluency can be used experimentally to investigate lexical organization in deaf children, and that it potentially has clinical utility across the heterogeneous deaf population. We present normative data to aid clinicians who wish to use this task with deaf children.