bluuebunny/crossref_metadata_2025 huggingface dataset:
SPONTANEOUS CLOSURE OF MACULAR HOLE IN A PATIENT WITH MACULAR TELANGIECTASIA TYPE 2
Authors: Nalcı Hilal , Batıoğlu Figen , Demirel Sibel , Özmert Emin
Published: August 2018

Purpose:

To present a case of macular hole associated with macular telangiectasia Type 2 (Mac-Tel 2) which underwent spontaneous closure.

Methods:

A 58-year-old woman is admitted with complaints of blurred and distorted vision. Optical coherence tomography, fundus autofluorescence, and optical coherence tomography angiography were performed for diagnosis and follow-up.

Results:

Optical coherence tomography revealed hyporeflective cavitations in both eyes, and full-thickness macular hole covered with internal limiting membrane drape in the left eye. Fundus autofluorescence showed loss of hypoautofluorescence in temporal parafoveal area in the right eye, and centrally in the left one. Vascular irregularities were detected in optical coherence tomography angiography images. The patient was diagnosed as Mac-Tel 2. During the follow-up, the macular hole underwent a process of spontaneous closure, starting as bridging at the level of external limiting membrane and outer nuclear layer followed by further repairment and organization of the outer plexiform layer, accompanied with visual gain.

Conclusion:

Spontaneous closure of macular hole in patients with Mac-Tel 2 is a rare entity. We hypothesize that extension or proliferation of Muller cells, which leads to reconstruction of normal foveal structure, is the main mechanism for this phenomenon.
Female Sport Participation Effect on Long-Term Health-Related Quality of Life
Authors: Stracciolini Andrea , Amar-Dolan Laura , Howell David R. , Alex Taylor , Berkner Paul , Sandstrom Noah J. , Peluso Mark , Kurtz Mathew , Mannix Rebekah , Meehan William P.
Published: August 2018

Background:

Female participation in sport has grown substantially over the last 4 decades.

Objectives:

We investigated the association between sports participation and (1) later-life health outcomes and (2) later-life quality-of-life (QoL) measures among female college alumni.

Methods:

We conducted a cross-sectional study of female alumni between the ages of 40 and 70 years. Participants completed a questionnaire that included QoL measures assessing general health, negative consequences of alcohol use, mental health, and other self-reported health outcomes. We divided alumni into athletes and nonathletes. Between-group comparisons of health outcomes were adjusted for age; QoL measures were adjusted for age, exercise habits, cigarette smoking, alcohol use, and comorbidities.

Results:

Questionnaires were sent to 47 836 alumni, 3702 (8%) responded. Forty-four percent of female respondents participated in collegiate sports. After adjusting for age, female respondents who participated in collegiate sports were more likely to exercise >3×/week (61.8% vs 50.2%; P ≤ 0.001), view themselves in good/great health (91% vs 85%; P < 0.001), and less likely to have ever smoked (13.6% vs 25.3%; P ≤ 0.001) or used recreational drugs (7.5% vs 9.5%; P = 0.018). A smaller proportion of female athletes reported hypertension (5.5% vs 13.5%; P ≤ 0.001), high cholesterol (9.9% vs 17.0%; P < 0.001), and obesity (3.1% vs 6.8%; P = 0.001) compared with nonathletes. Participation in sports was, however, associated with decreased mobility (R
2 = 0.1826; P = 0.002) and increased anxiety (R
2 = 0.039; P = 0.016) QoL scores.

Conclusions:

Sports participation for female collegiate athletes was associated with mostly positive health outcomes, but also with lower mobility and increased anxiety QoL scores.
National Survey on the Management of Wilms Tumor
Authors: Elgendy Ahmed , Shehata Sherif , Medhat Zaki Ahmed , Shehata Sameh
Published: August 2018

This study aims to investigate the management of Wilms tumor by the Egyptian pediatric surgical association (EPSA) consultants. After approval of the EPSA executive board, a questionnaire was distributed individually to all consultants attending the general assembly of EPSA 2017 annual congress. Of 88 consultants, responses were received from 61. Palpable abdominal mass was indicated by 72.13% of respondents as the commonest presenting symptom. Concerning the imaging requested, computed tomography was reported by 80.33%. Approximately 62.30% of respondents perform 1 to 3 cases annually. Regarding timing of surgery, upfront resection was the most frequently reported by 62.30%. A total of 77.05% perform lymph node sampling during surgeries. Nephron-sparing surgery was adopted by only 26.23%, whereas none of the respondents reported the use of minimally invasive surgery for management. Overall, 93.44% of surgeons ask for a visit every 3 months in the first year postoperatively. Upfront nephrectomy is the commonest procedure for Wilms tumor in the current practice of EPSA consultants, whereas there is consensus against minimally invasive surgery. Surgical guidelines for nephron-sparing surgery are still incomplete and need to be tabulated. This study urges for a nationwide retrospective analysis to establish a uniform protocol with international reference to be adopted in Egypt.
Characteristics of Adults Managing Vitamins/Supplements and Prescribed Medications–Who Is Using, Not Using, and Abandoning Use of Pillboxes?
Authors: Bartlett Ellis Rebecca J. , Ganci Aaron , Head Katharine J. , Ofner Susan
Published: August 2018

Purpose:

Evidence suggests pillboxes are effective for improving medication adherence. However, prior descriptive studies about pillbox use are limited to studies of older adults or condition-specific studies. This study describes characteristics of adults with chronic conditions and their use of pillboxes.

Methods:

A survey questionnaire link was posted on a social media recruitment page from August 2016 to April 2017.

Results:

The sample of 179 people was middle-age (47.7 ± 15.4 years), predominantly white (90.4%), educated (>93% educated beyond high school), female (n = 148; men n = 26), married/partner (58.2%), and working full time (55.9%). Pillboxes were used by 66% (n = 118) of the sample at some point; 22.9% reported pillbox abandonment. Compared with people who never used a pillbox, current pillbox users were older (53.2 ± 14.3 vs 42.0 ± 14.4 years; P < .001) and took more vitamins/supplements (3.9 ± 3.8 vs 2 ± 1.8, P = .002) and prescribed medications (4.2 ± 2.2 vs 2.6 ± 1.9, P < .001). Adherence did not differ between groups; pillbox users were more likely to refill medications before running out compared with those abandoning use, P < .001.

Conclusion:

Age and number of medications may affect pillbox use. Future research should explore barriers to continued use of pillboxes and uptake in younger populations.
Maximizing Recovery From Concussions for Youth Participating in Sports and Recreational Activities
Authors: Murata Nathan M. , Oshiro Ross , Furutani Troy , Tsushima William T.
Published: August 2018

Concussions have become a public health issue. This public health concern has drawn the attention of many states in which laws were created to address concussions safety, recognition of signs and symptoms, immediate removal, medical clearance, and return-to-play protocols. Most state legislation focused on student athletes participating in organized sports. However, the rise in concussion can be directly attributed to children, youth, and adolescents participating in nonsports-related events. Maximizing recovery from a concussion involves implementing education programs that focus on recognition of symptoms, treatment, and return-to-learn options. Treatment strategies used to address concussed youth include physical and cognitive rest and minimizing external stimuli that can increase symptoms. Because learning is a direct outcome for all youth, a return-to-learn protocol based on a collaborative school-based team approach is suggested.
Breast Implant Mycobacterial Infections: An Epidemiologic Review and Outcome Analysis
Authors: Al-Halabi Becher , Viezel-Mathieu Alex , Shulman Zachary , Behr Marcel A. , Fouda Neel Omar
Published: August 2018

Background:

Epidemiologic evidence of periprosthetic mycobacterial infections is limited. The recent boom in cosmetic surgery tourism has been associated with a rise of surgical-site infections in returning patients. This review aims to explore available data, examine trends of documented periprosthetic mycobacterial infections, and analyze outcomes of management techniques.

Methods:

A search in the Biosis, Embase, LILACS, MEDLINE, and Web of Science databases from inception until December of 2017 for “Breast Implants” and “Mycobacterial Infections” and equivalents was performed. Data were pooled after two screening rounds following full-text retrieval and cross-referencing.

Results:

Forty-one reports describing 171 female patients who had breast prosthesis–related mycobacterial infections were identified. Bibliometric case-based analysis revealed a rise of periprosthetic mycobacterial infections in developing countries since the start of the millennium. The mean patient’s age was 37.9 years and the majority of patients had undergone bilateral breast augmentation. Most patients presented with breast pain or tenderness, after an average incubation period of 9 months. Mycobacterium fortuitum was isolated from 90 cases (52.6 percent). Immediate explantation with or without delayed reimplantation was the most commonly used surgical strategy, complemented by combination antimicrobial therapy for an average of 4.6 months. The mean follow-up time was 39.7 months, during which recurrence was observed in 21 of 171 patients (12.3 percent).

Conclusions:

The emergence of periprosthetic mycobacterial infections in relation to cosmetic medical tourism alerts clinicians to the importance of educating the public about the associated risks. In addition, this study identifies risk factors associated with recurrence of periprosthetic mycobacterial infections.
A bispecific immunotweezer prevents soluble PrP oligomers and abolishes prion toxicity
Authors: Bardelli Marco , Frontzek Karl , Simonelli Luca , Hornemann Simone , Pedotti Mattia , Mazzola Federica , Carta Manfredi , Eckhardt Valeria , D’Antuono Rocco , Virgilio Tommaso , González Santiago F. , Aguzzi Adriano , Varani Luca
Published: August 2018

Antibodies to the prion protein, PrP, represent a promising therapeutic approach against prion diseases but the neurotoxicity of certain anti-PrP antibodies has caused concern. Here we describe scPOM-bi, a bispecific antibody designed to function as a molecular prion tweezer. scPOM-bi combines the complementarity-determining regions of the neurotoxic antibody POM1 and the neuroprotective POM2, which bind the globular domain (GD) and flexible tail (FT) respectively. We found that scPOM-bi confers protection to prion-infected organotypic cerebellar slices even when prion pathology is already conspicuous. Moreover, scPOM-bi prevents the formation of soluble oligomers that correlate with neurotoxic PrP species. Simultaneous targeting of both GD and FT was more effective than concomitant treatment with the individual molecules or targeting the tail alone, possibly by preventing the GD from entering a toxic-prone state. We conclude that simultaneous binding of the GD and flexible tail of PrP results in strong protection from prion neurotoxicity and may represent a promising strategy for anti-prion immunotherapy.

Author summary

Antibody immunotherapy is considered a viable strategy against prion disease. We previously showed that antibodies against the so-called globular domain of Prion Protein (PrP) can cause PrP dependent neurotoxicity; this does not happen for antibodies against the flexible tail of PrP, which therefore ought to be preferred for therapy.

Here we show that simultaneous targeting of both globular domain and flexible tail by a bispecific, combination of a toxic and a non-toxic antibody, results in stronger protection against prion toxicity, even if the bispecific is administered when prion pathology is already conspicuous.

We hypothesize that neurotoxicity arises from binding to specific “toxicity triggering sites” in the globular domain. We designed our bispecific with two aims: i) occupying one such site and preventing prion or other factors from docking to it and ii) binding to the flexible tail to engage the region of PrP necessary for neurotoxicity.

We also show that neurotoxic antibodies cause the formation of soluble PrP oligomers that cause toxicity on PrP expressing cell lines; these are not formed in the presence of prion protective antibodies. We suggest that these soluble species might play a role in prion toxicity, similarly to what is generally agreed to happen in other neurodegenerative disorders.
Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH
Authors: Fernando Eustace Y. , Mcllroy Simon Jon , Nierychlo Marta , Herbst Florian-Alexander , Schmid Markus C. , Wagner Michael , Nielsen Jeppe Lund , Nielsen Per Halkjær
Published: August 2018

Enhanced biological phosphorus removal (EBPR) is a globally important biotechnological process and relies on the massive accumulation of phosphate within special microorganisms.CandidatusAccumulibacter conform to classical physiology model for polyphosphate accumulating organisms and are widely believed to be the most important player for the process in full-scale EBPR systems. However, it was impossible till now to quantify the contribution of specific microbial clades to EBPR. In this study, we have developed a new tool to directly link the identity of microbial cells to the absolute quantification of intracellular poly-P and other polymers underin situconditions, and applied it to eight full-scale EBPR plants. BesidesCa. Accumulibacter, members of the genusTetrasphaerawere found to be important microbes for P accumulation, and in six plants they were the most important. As theseTetrasphaeracells did not exhibit the classical phenotype of poly-P accumulating microbes, our entire understanding of the microbiology of the EBPR process has to be revised. Furthermore, our new single-cell approach can now also be applied to quantify storage polymer dynamics in individual populationsin situin other ecosystems and might become a valuable tool for many environmental microbiologists.
Persistent activity in primate auditory cortex evoked by sensory stimulation
Authors: Cooke James E. , Lee Julie J. , Bartlett Edward L. , Wang Xiaoqin , Bendor Daniel
Published: August 2018

Persistent activity, the elevated firing of a neuron after the termination of a stimulus, is hypothesized to play a critical role in working memory. This form of activity is therefore typically studied within the context of a behavioural task that includes a working memory component. Here we investigated whether persistent activity is observed in sensory cortex and thalamus in the absence of any explicit behavioural task. We recorded spiking activity from single units in the auditory cortex (fields A1, R and RT) and thalamus of awake, passively-listening marmosets. We observed persistent activity that lasted for hundreds of milliseconds following the termination of the acoustic stimulus, in the absence of a task. Persistent activity was observed following both adapting and sustained responses during the stimulus and showed similar stimulus tuning to these evoked responses. Persistent activity was also observed following suppression in firing during the stimulus. These response types were observed across all cortical fields tested, but were largely absent from thalamus. As well as being of shorter duration, thalamic persistent activity emerged following a longer latency than in cortex, indicating that persistent activity may be generated within auditory cortex during passive listening. Given that these responses were observed in the absence of a explicit behavioural task, persistent activity in sensory cortex may have functional importance beyond storing task-relevant information in working memory.
Tree Shape-based approaches for the Comparative study of Cophylogeny
Authors: Avino Mariano , Ng Garway T. , He Yiying , Renaud Mathias S. , Jones Bradley R. , Poon Art F. Y.
Published: August 2018

Cophylogeny is the congruence of phylogenetic relationships between two different groups of organisms due to their long-term interaction, such as between host and pathogen species. Discordance between host and pathogen phylogenies may occur due to pathogen host-switch events, pathogen speciation within a host species, and extinction. Here, we investigated the use of tree shape distance measures to quantify the degree of cophylogeny for the comparative analysis of host-pathogen interactions across taxonomic groups.

We firstly implemented a coalescent model to simulate pathogen phylogenies within a fixed host tree, given the cospeciation probability, migration rate between hosts, and pathogen speciation rate within hosts.

Next, we used simulations from this model to evaluate 13 distance metrics between these trees and the host tree, including Robinson-Foulds distance and two kernel distances that we developed for labeled and unlabeled trees, which use branch lengths and can accommodate trees of different sizes. Finally, we used these distance metrics to revisit actual datasets from published cophylogenetic studies across all taxonomic groups, where authors described the observed associations as representing a high or low degree of cophylogeny.

Our simulation analyses demonstrated that some metrics are more informative than others with respect to specific coevolution parameters. For example, the Sim metric was the most responsive to variation in coalescence rates, whereas the unlabeled kernel metric was the most responsive to cospeciation probabilities. We also determined that distance metrics were more informative about the model parameters when the underlying parameter values did not assume extreme values,e.g.,rapid host switching. When applied to real datasets, projection of these trees’ associations into a parameter space defined by the 13 distance metrics revealed some clustering of studies reporting low concordance. This suggested that different investigators are describing concordance in a consistent way across biological systems, and that these expert subjective assessments can be at least partly quantified using distance metrics.

Our results support the hypothesis that tree distance measures can be useful for quantifying host and pathogen cophylogeny. This motivates the usage of distance metrics in the field of coevolution and supports the development of simulation-based methods,i.e.,approximate Bayesian computation, to estimate coevolutionary parameters from the discordant shapes of host and pathogen trees. [tree shape; cophylogeny; codivergence; coevolution; host switching; tree metrics; kernel]
Fluorescence-Based Detection of Fusion State on a Cryo-EM Grid using Correlated Cryo-Fluorescence and Cryo-Electron Microscopy
Authors: Metskas Lauren Ann , Briggs John A. G.
Published: August 2018

Correlated light and electron microscopy (CLEM) has become a popular technique for combining the protein-specific labeling of fluorescence with electron microscopy, both at room and cryogenic temperatures. Fluorescence applications at cryo-temperature have typically been limited to localization of tagged protein oligomers due to known issues of extended triplet state duration, spectral shifts, and reduced photon capture through cryo-CLEM objectives. Here, we consider fluorophore characteristics and behaviors that could enable more extended applications. We describe how dialkylcarbocanine DiD and its autoquenching by resonant energy transfer can be used to distinguish the fusion state of a lipid bilayer at cryo-temperatures. By adapting an established fusion assay to work under cryo-CLEM conditions, we identified areas of fusion between influenza virus-like particles and fluorescently labeled lipid vesicles on a cryo-EM grid. This result demonstrates that cryo-CLEM can be used to localize functions in addition to tagged proteins, and that fluorescence autoquenching by resonant energy transfer can be incorporated successfully into cryo-CLEM approaches. In the case of membrane fusion applications, this method provides both an orthogonal confirmation of functional state independent of the morphological description from cryo-EM and a way to bridge room-temperature kinetic assays and the cryo-EM images.
Reconstructing the history of polygenic scores using coalescent trees
Authors: Edge Michael D. , Coop Graham
Published: August 2018

1

Genome-wide association studies (GWAS) have revealed that many traits are highly polygenic, in that their within-population variance is governed in part by small-effect variants at many genetic loci. Standard population-genetic methods for inferring evolutionary history are ill-suited for polygenic traits—when there are many variants of small effect, signatures of natural selection are spread across the genome and subtle at any one locus. In the last several years, several methods have emerged for detecting the action of natural selection on polygenic scores, sums of genotypes weighted by GWAS effect sizes. However, most existing methods do not reveal the timing or strength of selection. Here, we present a set of methods for estimating the historical time course of a population-mean polygenic score using local coalescent trees at GWAS loci. These time courses are estimated by using coalescent theory to relate the branch lengths of trees to allele-frequency change. The resulting time course can be tested for evidence of natural selection. We present theory and simulations supporting our procedures, as well as estimated time courses of polygenic scores for human height. Because of its grounding in coalescent theory, the framework presented here can be extended to a variety of demographic scenarios, and its usefulness will increase as both GWAS and ancestral recombination graph (ARG) inference continue to progress.
Interleukin-1 receptor antagonist mediates type I interferon-driven susceptibility to Mycobacterium tuberculosis
Authors: Ji Daisy X. , Chen Katherine J. , Mukaida Naofumi , Kramnik Igor , Darwin K. Heran , Vance Russell E.
Published: August 2018

The bacterium Mycobacterium tuberculosis (Mtb) causes tuberculosis (TB) and is responsible for more human mortality than any other single pathogen1. Although ~1.7 billion people are infected with Mtb2, most infections are asymptomatic. Progression to active disease occurs in ~10% of infected individuals and is predicted by an elevated type I interferon (IFN) response3–8. Type I IFNs are vital for antiviral immunity, but whether or how they mediate susceptibility to Mtb has been difficult to study, in part because the standard C57BL/6 (B6) mouse model does not recapitulate the IFN-driven disease that appears to occur in humans3–5,8. Here we examined B6. Sst1S congenic mice that carry the C3H “sensitive” allele of the Sst1 locus that renders them highly susceptible to Mtb infections9,10. We found that B6.Sst1S mice exhibit markedly increased type I IFN signaling, and that type I IFNs were required for the enhanced susceptibility of B6. Sst1S mice to Mtb. Type I IFNs affect the expression of hundreds of genes, several of which have previously been implicated in susceptibility to bacterial infections11,12. Nevertheless, we found that heterozygous deficiency in just a single IFN target gene, IL-1 receptor antagonist (IL-1Ra), is sufficient to reverse IFN-driven susceptibility to Mtb. As even a partial reduction in IL-1Ra levels led to significant protection, we hypothesized that IL-1Ra may be a plausible target for host-directed anti-TB therapy. Indeed, antibody-mediated neutralization of IL-1Ra provided therapeutic benefit to Mtb-infected B6. Sst1S mice. Our results illustrate how the diversity of inbred mouse strains can be exploited to better model human TB, and demonstrate that IL-1Ra is an important mediator of type I IFN-driven susceptibility to Mtb infections in vivo.
Ubiquity of collective irregular dynamics in balanced networks of spiking neurons
Authors: Ullner Ekkehard , Politi Antonio , Torcini Alessandro
Published: August 2018

We revisit the dynamics of a prototypical model of balanced activity in networks of spiking neurons. A detailed investigation of the thermodynamic limit for fixed density of connections (massive coupling) shows that, when inhibition prevails, the asymptotic regime is not asynchronous but rather characterized by a self-sustained irregular, macroscopic (collective) dynamics. So long as the connectivity is massive, this regime is found in many different setups: leaky as well as quadratic integrate-and-fire neurons; large and small coupling strength; weak and strong external currents.
Collective irregular dynamics in balanced networks of leaky integrate-and-fire neurons
Authors: Politi Antonio , Ullner Ekkehard , Torcini Alessandro
Published: August 2018

We extensively explore networks of weakly unbalanced, leaky integrate-and-fire (LIF) neurons for different coupling strength, connectivity, and by varying the degree of refractoriness, as well as the delay in the spike transmission. We find that the neural network does not only exhibit a microscopic (single-neuron) stochastic-like evolution, but also a collective irregular dynamics (CID). Our analysis is based on the computation of a suitable order parameter, typically used to characterize synchronization phenomena and on a detailed scaling analysis (i.e. simulations of different network sizes). As a result, we can conclude that CID is a true thermodynamic phase, intrinsically different from the standard asynchronous regime.
Evidence against the microbicidal action of neutrophil extracellular traps (NETs)
Authors: Semplici F. , Segal A. W.
Published: August 2018

Neutrophil extracellular traps (NETs) are fibrillary structures composed of extruded nuclear chromatin decorated with granule proteins (mostly neutrophil elastase, cathepsin G and myeloperoxidase). It has been reported that NETs are able to kill bacteria and fungi based upon the observation that smaller number of organisms are obtained in plating assays after they are incubated with NETs than if the DNA is pre-digested with DNase. It is possible that the microbial killing is apparent rather than real, and occurs because the organisms are aggregated on the DNA structure, and that the plating assay results were simply misinterpreted. The present study shows that digestion of DNA after incubation of NETs with the microbes restores their numbers to preincubation levels indicating that the apparent killing is an artefact of the assay.
The Role of Gdf5 Regulatory Regions on Development of Hip Morphology and Susceptibility to Osteoarthritis and Dislocation
Authors: Kiapour Ata M. , Cao Jiaxue , Young Mariel , Capellini Terence D.
Published: August 2018

Given GDF5 involvement in hip development, and osteoarthritis (OA) and developmental hip dysplasia (DDH) risk, here we sought to assess the role(s) of GDF5 and its regulatory sequence on the development of hip morphology linked to injury risk. The brachypodism (bp) mouse, which harbors a Gdf5 inactivating mutation, was used to survey how Gdf5 loss of function impacts the development of hip morphology. Two transgenic Gdf5 reporter BAC lines were used to assess the spatiotemporal expression of Gdf5 regulatory sequences. Each BAC line was also used to assess the functional roles of upstream and downstream sequence on hip morphology. bp/bp mice had shorter femora with smaller femoral heads and necks as well as larger alpha angles, smaller anterior offsets, and smaller acetabula, compared to bp/+ mice (p<0.04). Regulatory sequences downstream of Gdf5 drove strong prenatal (E17) expression and low postnatal (6 months) expression across regions of femoral head and acetabulum. Conversely, upstream regulatory sequences drove very low expression at E17 and no detectable expression at 6 months. Importantly, downstream, but not upstream Gdf5 regulatory sequences fully restored all the key morphologic features disrupted in bp/bp mice. Hip morphology is profoundly affected by Gdf5 absence, and downstream regulatory sequences mediate its effects by controlling Gdf5 expression during development. This downstream region contains numerous enhancers harboring risk variants related to hip OA, DDH, and dislocation. We posit that subtle alterations to morphology driven by changes in downstream regulatory sequence underlie this locus’ role in hip injury risk.
Qualitative modeling of signaling networks in replicative senescence by selecting optimal node and arc sets
Authors: Sakellaropoulos Theodore , Binenbaum Ilona , Lefaki Maria , Chatziioannou Aristotelis , Chondrogianni Niki , Alexopoulos Leonidas G.
Published: August 2018

Signaling networks are an important tool of modern systems biology and drug development. Here, we present a new methodology to qualitatively model signaling networks by combining experimental data and prior knowledge about protein connectivity. Unlike other methods, our approach does not focus solely on selecting which reactions are involved but also on whether a protein is present. This allows the user to model more complicated experiments and incorporate more knowledge into the model. To demonstrate the capabilities of our method we compared the signaling networks of young and replicative senescent human primary HFL-1 fibroblasts, whose differences are expected to be due mainly to changes in the expression of the proteins rather than the reactions involved. The resulting networks indicate that, compared to young cells, aged cells are not as responsive to insulin stimulation and activate pathways that establish and maintain senescence.

Author summary

Cells have developed a complex network of biochemical reactions to monitor their environment and react to changes. Although multiple pathways, tuned to identify specific stimuli, have been discovered, it is generally understood that the signaling process typically involves multiple pathways and is context depended. Consequently, reconstructing the signaling network utilized by cells at any given moment is not a trivial task. In this article, we report on a novel logic-based method for identifying signaling network by combining experimental data with prior knowledge about the connectivity of the involved proteins. Unlike other methods proposed so far, our method uses data to evaluate the presence or absence of reactions and proteins alike. We reconstructed and compared the signaling network of human primary HFL-1 fibroblasts as they undergo replicative senescence in the presence of 6 different stimuli. The resulting networks indicate that, compared to young cells, senescent cells are not responsive to insulin stimulation and activate pathways that are known to establish and maintain senescence.
Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study
Authors: Emad Amin , Sinha Saurabh
Published: August 2018

Reconstruction of transcriptional regulatory networks (TRNs) is a powerful approach to unravel the gene expression programs involved in healthy and disease states of a cell. However, these networks are usually reconstructed independent of the phenotypic properties of the samples and therefore cannot identify regulatory mechanisms that are related to a phenotypic outcome of interest. In this study, we developed a new method called InPheRNo to identify ‘phenotype-relevant’ transcriptional regulatory networks. This method is based on a probabilistic graphical model whose conditional probability distributions model the simultaneous effects of multiple transcription factors (TFs) on their target genes as well as the statistical relationship between target gene expression and phenotype. Extensive comparison of InPheRNo with related approaches using primary tumor samples of 18 cancer types from The Cancer Genome Atlas revealed that InPheRNo can accurately reconstruct cancer type-relevant TRNs and identify cancer driver TFs. In addition, survival analysis revealed that the activity level of TFs with many target genes could distinguish patients with good prognosis from those with poor prognosis.
Coordination complexes of chromium(0) with a series of 1,3-diphenyl-6-arylfulvenes
Authors: Peloquin Andrew J. , Smith Madelyn B. , O'Connell Bryce J. , Ghiassi Kamran B. , Balaich Gary J. , Iacono Scott T.
Published: August 2018

The synthesis and structural properties of a series of chromium tricarbonyl `piano-stool' complexes bearing substituted pentafulvene ligands were studied. The complexes, tricarbonyl(1,3,6-triphenylfulvene)chromium(0) benzene hemisolvate, [Cr(C24H18)(CO)3]·0.5C6H6 (I), tricarbonyl[1,3-diphenyl-6-(3-vinylphenyl)fulvene]chromium(0), [Cr(C26H20)(CO)3] (II), and tricarbonyl[1,3-diphenyl-6-(pyren-1-yl)fulvene]chromium(0), [Cr(C34H22)(CO)3] (III), each have a distorted octahedral geometry, with the fulvene coordinated in a π–η2:π–η2:π–η2 fashion. Significant deviation of the exocyclic fulvene double bond from the cyclopentadiene plane accompanies coordination. Evidence of non-covalent π–π interactions was observed in both (I) and (III), with centroid-to-centroid distances ranging from 3.330 (8) to 3.494 (8) Å.
Crystal structure and Hirshfeld surface analysis of (2E)-3-(2,4-dichlorophenyl)-1-(2,5-dichlorothiophen-3-yl)prop-2-en-1-one
Authors: Murthy T. N. Sanjeeva , Atioğlu Zeliha , Akkurt Mehmet , Chidan Kumar C. S. , Veeraiah M. K. , Quah Ching Kheng , Siddaraju B. P.
Published: August 2018

The molecular structure of the title compound, C13H6Cl4OS, consists of a 2,5-dichlorothiophene ring and a 2,4-dichlorophenyl ring linked via a prop-2-en-1-one spacer. The dihedral angle between the 2,5-dichlorothiophene ring and the 2,4-dichlorophenyl ring is 12.24 (15)°. The molecule has an E configuration about the C=C bond and the carbonyl group is syn with respect to the C=C bond. The molecular conformation is stabilized by intramolecular C—H...Cl contacts, producing S(6) and S(5) ring motifs. In the crystal, the molecules are linked along the a-axis direction through face-to-face π-stacking between the thiophene rings and the benzene rings of the molecules in zigzag sheets lying parallel to the bc plane along the c axis. The intermolecular interactions in the crystal packing were further analysed using Hirshfield surface analysis, which indicates that the most significant contacts are Cl...H/ H...Cl (20.8%), followed by Cl...Cl (18.7%), C...C (11.9%), Cl...S/S...Cl (10.9%), H...H (10.1%), C...H/H...C (9.3%) and O...H/H...O (7.6%).
10-Methyl-9,11-annulated dibenzobarrelene
Authors: Devassia Tomson , Mathew Eason M. , Sithambaresan M. , Unnikrishnan P. A. , Kurup M. R. Prathapachandra
Published: August 2018

In the title compound (systematic name: 8-methyl-16-oxapentacyclo[6.6.5.01,18.02,7.09,14]nonadeca-2,4,6,9(14),10,12,18-heptaen-15-one), C19H14O2, the benzene rings form a dihedral angle of 64.84 (7)°. In the crystal, π–π stacking interactions, with a centroid–centroid distance of 3.7695 (8) Å, and weak C—H...π interactions link molecules along the b-axis direction.
The influence of the cultural entrepreneur on the performance of cultural and creative firms
Authors: Orihuela-Gallardo Francisca , Fernández-Alles Mariluz , Ruiz-Navarro José
Published: August 2018

Purpose

The purpose of this paper is to analyse the influence of the profile of cultural entrepreneurs (CE), in terms of their demographic characteristics and resources, on the performance of cultural and creative firms (CCFs).

Design/methodology/approach

Departing from demographic theory and resource-based view, two hypotheses have been formulated and empirically tested, using a multiple regression model, with a sample of 80 Spanish CCFs. The CCF performance has been measured through two objective (employment growth and profitability) and one subjective/perceptual measurements (satisfaction of the CE with the attainment of objectives).

Findings

With respect to the demographic variables, a negative relationship between the CE’s age and employment growth, and a partial positive influence of the CE’s prior experience on employment growth and the subjective measurement of performance have been found. Regarding to the CE’s resources, the empirical evidence shows that there is no direct relationship between the CE’s possession of any resources studied − financial, knowledge and social connections − and CCF performance.

Originality/value

This work makes three important contributions as it analyses the CE and focuses on CCF management, a topic little discussed in the entrepreneurship literature. Second, there is an analysis of some of the variables pertaining to the entrepreneur’s demographic profile that have been applied to top management teams and in a more or less isolated way in the entrepreneurship area. And, finally, a multidimensional measurement is used to explain the CCF performance.
Optimization of the carbon nanotubes synthesis in arc discharge systems
Authors: Raniszewski Grzegorz
Published: August 2018

Purpose

The purpose of this paper is to focus on the influence of electromagnetic field during the arc discharge carbon nanotubes synthesis. It proposes modeling of electromagnetic field distribution to calculate forces in the area of arcing. The paper presents the influence of this field on the final product of the synthesis.

Design/methodology/approach

A short literature review of the arc discharge systems supported by electromagnetic field is presented. The technical solution of the coil placement is discussed. An experimental research is described. The research system constructed preceded by a series of measurements and modeling is analyzed.

Findings

The paper describes the significant meaning of the electromagnetic field during the synthesis. The electromagnetic field forces the slow rotation of the carbon plasma column where carbon nanotubes are formed. It leads to the improvement in yield.

Research limitations/implications

Because the research is limited to one type of geometry of the reactor, the results may vary in different reactors. However, the influence of the electromagnetic field is confirmed. Therefore, researchers are encouraged to investigate the influence of the electromagnetic coil in the applied systems.

Practical implications

The systems with a coil inside the reactor require the application of complex cooling systems or/and additional screens. The work proposes a technical solution based on the coil placed outside the reactor. Therefore, it simplifies the construction and increases the yield.

Social implications

The high yield of the high-quality nanotubes opens new technical possibilities for electronics and electrical engineering.

Originality/value

The paper identifies a connection between the electromagnetic field, the arc discharge movement, plasma jet, carbon nanotubes containing deposit and the yield.
Tackling everyday risks through climate adaptive organic farming
Authors: Rahmawati Hepi , Lestari Anastasia Maylinda Titi
Published: August 2018

Purpose

With the shifting patterns of rain and dry periods as a result of global climate change, the people of Gunungkidul have to deal with extreme conditions, such as crop failure, ponds and artificial lakes drying up at an alarming rate due to high evaporation. The paper aims to discuss these issues.

Design/methodology/approach

Participatory disaster and risks assessment and action planning were carried out to identify how communities perceive risks and identify priorities of actions. Farmers agreed to implement climate adaptive farming which combines organic farming, biological pest control and drought-resistant seedlings from local varieties.

Findings

The processes to adaptation required collective actions, paradigm shift and it also constitutes trial and error processes. Acceptance to innovation is mostly one of the major challenges. Working with “contact” farmers and “advance” farmers is the key to the community organizing strategy for innovation and adaptation.

Research limitations/implications

This case study is limited to the adaptation program funded by Indonesia Climate Change Trust Fund in four farmer groups in Purwosari Sub-District, GunungKidul district and Yogyakarta province, Indonesia.

Practical implications

Trainings and direct assistance to climate adaptive farming have benefitted the farmers that they are able to increase the farming production and reduce the risk of crop failure.

Social implications

The demonstration plot has strengthened farmer groups’ social modalities by working together to shift from traditional into adaptive farming.

Originality/value

This case study described how farmers have shifted from traditional practice into climate adaptive farming.
Barriers to the adoption of value management in developing countries
Authors: Aghimien Douglas Omoregie , Oke Ayodeji Emmanuel , Aigbavboa Clinton Ohis
Published: August 2018

Purpose

The purpose of this paper is to determine the barriers to the adoption of value management (VM) in the construction industry of developing countries with a view to providing possible measures in avoiding these barriers and increasing the usage of the system within the construction industry.

Design/methodology/approach

The level of knowledge and adoption of VM practices, as well as the barriers to its adoption in the construction industry were assessed through a survey design. Construction professionals were sampled from the six geo-political zones in Nigeria through the use of a structured questionnaire. Factor analysis was conducted on data gathered on the barriers of VM.

Findings

The study revealed a moderate level of knowledge of VM among construction professionals. This implies that the problem of VM is not that of awareness, but readiness to adopt the system. The study also reveals that the barriers to the adoption of VM can be categorised under the general stakeholder’s barriers, training and education barriers, client barriers and government/top management barriers.

Practical implications

This study was conducted across the six geo-political zones of the country as against common practice of selecting a particular region or states to represent the entire country. The findings therefore show a true reflection of the barriers to VM adoption in the country and its recommendations can to a large extent promote the adoption of VM in the country and also other developing countries where construction projects are executed through similar method, style and approach.

Originality/value

This paper highlights the possible barriers to the adoption of VM in Nigeria construction industry and provides ways to avoiding these barriers in order to achieve better quality construction and value for money.
Lubrication regime analysis for spherical pump
Authors: Guan Dong , Hilton Harry H. , Yang Zhengwei , Jing Li , Lu Kuan
Published: August 2018

Purpose

This paper aims to investigate the lubrication regime in spherical pump, especially under different structural parameters and operational conditions.

Design/methodology/approach

A ball-on-plane configuration is adopted to represent the contact model between spherical piston and cylinder cover. The governing equations, which include the Reynolds and elasticity equations, are solved and validated by Jin–Dowson model. Both minimum film thickness and lambda ratio (ratio of minimum fluid film thickness to combined surface roughness of the piston and cylinder cover) of the equivalent model are obtained using an established model.

Findings

The results indicate that piston diameter and radial clearance are the two main factors affecting the pump lubrication regime. Other related parameters such as rotation speed of the piston, load, viscosity of working medium, material matching and surface roughness of piston and cylinder cover also have different impacts on the lubrication regime of the spherical pump.

Originality/value

These results emphasize the importance of the design and manufacturing parameters on the tribological performance of spherical pumps and these are also helpful in improving the spherical pump lubrication regime and enlarging its life cycle. This is to certify that to the best of the authors’ knowledge, the content of this manuscript is their own work. This manuscript has only been submitted to this journal and never been published elsewhere. The authors certify that the intellectual content of this manuscript is the product of their own work and that all the assistance received in preparing this manuscript and sources has been acknowledged.
Frictional characteristic of sintered iron in high temperature
Authors: Wang Yanzhong , Guo Chao
Published: August 2018

Purpose

This paper aims to study the change rule of sintered iron friction properties under high temperature and establish the model to predict the friction coefficient.

Design/methodology/approach

The morphological measurements of sintered iron material with four different oxidation degrees are carried out. A prediction model of friction coefficient in high temperature oxide growth stage for sintered iron material is established based on the theory of flash temperature and adhesion friction. The relationship between friction coefficient and the key parameters is found through the test fitting.

Findings

The surface topography changes with oxidative wear. The wear debris will be compacted and sintered again to form a composite oxide layer with the temperature increasing. The validity and accuracy of proposed model are tested using the friction coefficient and temperature experiments. Results are in reasonable agreement with those obtained using values of load commonly used.

Originality/value

The significance lies in the change mechanism of high temperature friction characteristic is clarified. Three friction stages related to temperature of dry friction are put forward for sintered iron, and a meaningful reference is provided by the established model for high-temperature performance design of sintered iron friction material.
Managing bioethanol supply chain resiliency: a risk-sharing model to mitigate yield uncertainty risk
Authors: Ye Fei , Hou Gang , Li Yina , Fu Shaoling
Published: August 2018

Purpose

The purpose of this paper is to propose a risk-sharing model to coordinate the decision-making behavior of players in a cassava-based bioethanol supply chain under random yield and demand environment, so as to mitigate the yield and demand uncertainty risk and improve the bioethanol supply chain resiliency and performance.

Design/methodology/approach

The decision-making behavior under three models, namely, centralized model, decentralized model and risk-sharing model, are analyzed. An empirical test of the advantages and feasibility of the proposed risk-sharing model, as well as the test of yield uncertainty risk, risk-sharing coefficients and randomly fluctuating cassava market price on the decision-making behavior and performances are provided.

Findings

Though the proposed risk-sharing model cannot achieve the supply chain performance in the centralized model, it does help to encourage the farmers and the company to increase the supply of cassava and achieve the Pareto improvement of both players compared to the decentralized model. In particular, these improvements will be enlarged as the yield uncertainty risk is higher.

Practical implications

The findings will help decision makers in the bioethanol supply chain to understand how to mitigate the yield uncertainty risk and improve the supply chain resiliency under yield and demand uncertainty environment. It will also be conducive to ensure the supply of feedstock and the development of the bioethanol industry.

Originality/value

The proposed risk-sharing model incorporates the yield uncertainty risk, the random market demand and the hierarchical decision-making behavior structure of the bioethanol supply chain in the model.