bluuebunny/crossref_metadata_2025 huggingface dataset:
Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
Authors: Ahlgren Nathan A , Ren Jie , Lu Yang Young , Fuhrman Jed A , Sun Fengzhu
Published: October 2016

Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host taxonomy from among ∼32 000 prokaryotic genomes for 1427 virus isolate genomes whose true hosts are known. The background-subtracting measure $d_2^*$ at k = 6 gave the highest host prediction accuracy (33%, genus level) with reasonable computational times. Requiring a maximum dissimilarity score for making predictions (thresholding) and taking the consensus of the 30 most similar hosts further improved accuracy. Using a previous dataset of 820 bacteriophage and 2699 bacterial genomes, $d_2^*$ host prediction accuracies with thresholding and consensus methods (genus-level: 64%) exceeded previous Euclidian distance ONF (32%) or homology-based (22-62%) methods. When applied to metagenomically-assembled marine SUP05 viruses and the human gut virus crAssphage, $d_2^*$-based predictions overlapped (i.e. some same, some different) with the previously inferred hosts of these viruses. The extent of overlap improved when only using host genomes or metagenomic contigs from the same habitat or samples as the query viruses. The $d_2^*$ ONF method will greatly improve the characterization of novel, metagenomic viruses.
East Asian observations of low-latitude aurora during the Carrington magnetic storm
Authors: Hayakawa Hisashi , Iwahashi Kiyomi , Tamazawa Harufumi , Isobe Hiroaki , Kataoka Ryuho , Ebihara Yusuke , Miyahara Hiroko , Kawamura Akito Davis , Shibata Kazunari
Published: October 2016

A magnetic storm around 1859 September 2, caused by a so-called Carrington flare, was the most intense in the history of modern scientific observations, and hence is considered to be a benchmark event concerning space weather. The magnetic storm caused worldwide observations of auroras, even at very low latitudes, such as Hawaii, Panama, or Santiago. Available magnetic-field measurements at Bombay, India, showed two peaks: the main was the Carrington event, which occurred in day time in East Asia; a second storm after the Carrington event occurred at night in East Asia. In this paper, we present results from surveys of aurora records in East Asia, which provide new information concerning the aurora activity of this important event. We found some new East Asian records of low-latitude aurora observations caused by a storm which occurred after the Carrington event. The size of the aurora belt of the second peak of the Carrington magnetic storm was even wider than that of usual low-latitude aurora events.
Foamy-like endogenous retroviruses are extensive and abundant in teleosts
Authors: Ruboyianes Ryan , Worobey Michael
Published: October 2016

Recent discoveries indicate that the foamy virus (FV) (Spumavirus) ancestor may have been among the first retroviruses to appear during the evolution of vertebrates, demonstrated by foamy endogenous retroviruses present within deeply divergent hosts including mammals, coelacanth, and ray-finned fish. If they indeed existed in ancient marine environments hundreds of millions of years ago, significant undiscovered diversity of foamy-like endogenous retroviruses might be present in fish genomes. By screening published genomes and by applying PCR-based assays of preserved tissues, we discovered 23 novel foamy-like elements in teleost hosts. These viruses form a robust, reciprocally monophyletic sister clade with sarcopterygian host FV, with class III mammal endogenous retroviruses being the sister group to both clades. Some of these foamy-like retroviruses have larger genomes than any known retrovirus, exogenous or endogenous, due to unusually long gag-like genes and numerous accessory genes. The presence of genetic features conserved between mammalian FV and these novel retroviruses attests to a foamy-like replication biology conserved for hundreds of millions of years. We estimate that some of these viruses integrated recently into host genomes; exogenous forms of these viruses may still circulate.
Long-chain ω-6 plasma phospholipid polyunsaturated fatty acids and association with colon adenomas in adult men: a cross-sectional study
Authors: Pickens Charles A. , Albuquerque Pereira Mariana de Fátima , Fenton Jenifer I.
Published: October 2016

Dietary lipid intake can be associated with an increased risk for colorectal cancer depending on its composition. Carcinogenesis alters lipid metabolism to facilitate cell growth and survival. For instance, metabolites of polyunsaturated fatty acids (PUFAs) are associated with increasing colon cell proliferation. Moreover, precancerous colon lesions (i.e. adenomas) increase the risk for colorectal cancer. In this study, we investigated associations between plasma PUFAs and the number of colon polyps and polyp type (i.e. hyperplastic and adenoma). Healthy male participants (n=126) of 48–65 years of age were recruited before a routine colonoscopy screening. Plasma phospholipid (PPL) PUFAs were isolated by means of solid phase extraction and methylated. Fatty acid methyl esters were analyzed using gas chromatography. Factor analysis was used to cluster PUFAs into groups, and then generated factors and individual PUFAs were analyzed using polytomous logistic regression. In our age-adjusted and smoking-adjusted polytomous logistic regression, for each unit increase in PPL docosatetraenoic acid (DTA), individuals were 1.43 (1.00–2.06) and 1.33 (0.99–1.80) times more likely to have hyperplastic polyps and adenomas rather than no polyps, respectively. In our factor analysis, high PPL ω-6 PUFA and trans-fatty acid loading scores were associated with increased odds of adenoma presence rather than no polyps. Increases in long-chain PPL ω-6 PUFAs are associated with an increased risk for adenomas. As relative levels of DTA increase in PPLs, individuals had increased odds of having hyperplastic polyps and adenomas. Elevated conversion of ω-6 PUFAs to longer-chain ω-6s such as DTA may indicate altered PUFA metabolism at the tissue level.
Extraocular Sebaceous Carcinoma—A Clinicopathologic Reassessment
Authors: Candelario Nicole M. , Sánchez Julio E. , Sánchez Jorge L. , Martín-García Rafael F. , Rochet Nicole M.
Published: October 2016

Sebaceous carcinoma is an aggressive adnexal neoplasm with sebaceous differentiation. Few reports have described the histopathologic characteristics of the sebaceous carcinoma occurring extraocularly. Seventy-two cases of extraocular sebaceous carcinoma were identified from the database of a Dermatopathology Laboratory from January 1, 2007 to May 31, 2013. More cases occurred in men (60%), with a mean age at diagnosis of 65.8 years (range 39–99 years). Neoplasms were histopathologically classified as well-differentiated (22%), moderately differentiated (67%), and poorly differentiated (11%). Sixty-seven percent (67%) of cases demonstrated a squamoid growth pattern and thirty-three percent (33%) demonstrated a basaloid growth pattern. A majority of the neoplasms histopathologically classified as well-differentiated (94%) and moderately differentiated (65%) demonstrated a squamoid growth pattern. Ten percent (10%) of cases exhibited cystic histopathologic changes. The histopathological features reported in this study aid in the understanding of extraocular sebaceous carcinoma and its eventual diagnosis and classification.
FUNDUS AUTOFLUORESCENCE FINDINGS IN EARLY CHLOROQUINE MACULOPATHY
Authors: Bergholz Richard , Rossel Mirjam , Schroeter Jan , Dutescu Ralf M. , Salchow Daniel J.
Published: October 2016

Background/Purpose:

Toxic maculopathy is a rare but severe complication of chloroquine intake. Although the phenotype of established maculopathy was analyzed in detail, few data exist on the ophthalmologic findings in the early stage.

Methods:

The authors present 4 female patients with unequivocal signs of chloroquine maculopathy (bilateral [peri-]central scotoma in the visual fields, structural alterations of the macula in the optical coherence tomography) but normal or atypical findings as to fundus autofluorescence imaging.

Results:

In all patients, optical coherence tomography showed perifoveal thinning and subtle alterations of the outer retinal layers. In one patient, the latter was limited to the pericentral region, whereas it showed a more diffuse distribution in two other patients. One patient showed a combination of pericentral and diffuse damage. Multifocal electroretinography was recorded in three patients and revealed the typical (peri-)central amplitude reductions.

Conclusion:

A normal fundus autofluorescence does not rule out toxic maculopathy. Optical coherence tomography and multifocal electroretinography seem to be more sensitive in the early stage of the disease. In case of typical complaints and visual fields, the optical coherence tomography has to be evaluated for subtle alterations of the outer retina. Their presence justifies the cessation of the drug. Multifocal electroretinography may be of special value in these problematic cases.
BILATERAL CHOROIDAL NEOVASCULARIZATION IN A PATIENT WITH BETA-THALASSEMIA MAJOR AND ITS MANAGEMENT
Authors: Kiarudi Mohammad Yaser , Fadakar Kaveh , Mousavi Ebrahim
Published: October 2016

Purpose:

To describe a case of bilateral choroidal neovascularization in a patient with beta-thalassemia major and an interventional therapeutic attempt.

Method:

Retrospective case report.

Result:

A known case of beta-thalassemia major presented with gradual vision loss. Fundoscopy revealed bilateral macular edema accompanied by intraretinal hemorrhages. Optical coherence tomography and fluorescein angiography were compatible with the diagnosis of choroidal neovascularization. No signs of angioid streaks or other related abnormalities were noticed in examination and imaging. The patient was treated with intravitreal bevacizumab, and visual acuity improved within 6 months of follow-up.

Conclusion:

Bilateral choroidal neovascularization can be a presenting pathology in patients with beta-thalassemia major. Anti–vascular endothelial growth factor is a promising treatment option.
A Case of a Spontaneous Self-resolving Retrobulbar Hemorrhage Following 3,4-Methylenedioxy-methamphetamine Use
Authors: Chervenkoff Jordan V. , Rajak Saul N. , Selva Dinesh , Davis Garry
Published: October 2016

This case report discusses the case of a 23-year-old male patient who experienced retrobulbar pain, diplopia, proptosis, and mild lower eyelid bruising after consuming 3,4-methylenedioxy-methamphetamine. The symptoms settled over 10 days and vision returned to normal without intervention. The authors discuss the differential diagnosis relevant to the presenting complaints and propose several mechanisms linking 3,4-methylenedioxy-methamphetamine use to spontaneous nontraumatic intraorbital hematoma.
Relationship of Psychosocial Resources With Allostatic Load: A Systematic Review
Authors: Wiley Joshua F. , Bei Bei , Bower Julienne E. , Stanton Annette L.
Published: October 2016

Objective

Allostatic load (AL) represents cumulative wear-and-tear on the body and is operationalized as a multisystem index of biomarkers. Allostatic load is associated with morbidities and mortality, leading to a growing body of literature that uses AL as an outcome in its own right. Psychosocial resources (PSRs), such as mastery and social support, may influence health outcomes in part via AL, and the current review seeks to characterize the relations between PSRs and AL.

Methods

A systematic review was conducted by searching PubMed, CINAHL Plus, PsycINFO, Scopus, and Embase for studies examining the relation between PSR(s) and AL in humans. From 1,417 abstracts screened, 60 full-text articles were reviewed, and 24 studies met inclusion criteria.

Results

Mixed evidence exists for a relationship between PSRs and AL. Most (14/24) studies used a cross-sectional design, and only one study investigated whether a PSR predicted change in AL. Compared to cross-sectional studies, longitudinal studies were more likely to report a significant relationship (8/14 versus 8/10, respectively). Studies with statistically significant main or moderated effects had larger sample sizes than those reporting null effects. Whether a study reported a significant main or moderated relationship did not differ by whether psychological (8/11) or social (10/16) resources were assessed.

Conclusions

Evidence for a relationship between PSRs and AL is equivocal, and obtained significant relationships are generally small in magnitude. Gaps in the current literature and directions for future research are discussed. Longitudinal studies are needed that repeatedly assess PSRs and AL.
Physicians and Students Take to the Streets to Ask: What Do People Want From Their Health Care?
Authors: DiGioia Kimberly , Nair Mohit , Shields Morgan , Saini Vikas
Published: October 2016

With the aim of better understanding what the public (as opposed to “patients”) wants from health care, this study asked people on the street, “What does the right health care mean to you?” Responses ranged from “Caring about me more than just in the appointment” to “That everyone should see exactly what medical treatment costs.” A qualitative analysis revealed that all responses fell into 2 overarching categories: health care at the interpersonal level and health care at the system level. Approximately 66.7% of responses included system-level factors, whereas 59% of responses included interpersonal-level factors. We conclude that the public is cognizant of and concerned about issues that also concern patients and others working to improve health care and, thus, should be engaged in the process to design care in a way that meets their needs and preferences before they become ill or interact with the delivery system.
Computed Tomographic Appearance of Organizing Pneumonia in an Oncologic Patient Population
Authors: Long Niamh M. , Plodkowski Andrew J. , Schor-Bardach Rachel , Geyer Alexander I. , Zheng Junting , Moskowitz Chaya S. , Ginsberg Michelle S.
Published: October 2016

Objective

The aims of this study were to describe the computed tomographic features of organizing pneumonia (OP) in an oncologic patient population and to also identify features associated with lung cancer and patients undergoing hematopoietic stem cell transplant (HSCT).

Methods

In retrospective computed tomographies from 151 patients with pathologically confirmed OP between January 2009 and September 2014, number of lesions, location, size, margin type, and consistency, as well as volume of lymphadenopathy and the presence and size of pleural effusions, were recorded. Associated malignancy was noted.

Results

Organizing pneumonia most commonly presented as a diffuse process (n = 62, 41%), frequently occupied both a central and peripheral location (n = 79, 53%), and commonly presented with a solid appearance (n = 67, 44%) or with ground glass opacity (n = 80, 53%). Pleural effusions were seen in 68 patients (45%). Organizing pneumonia less frequently contained air bronchograms, cavitation, necrosis, surrounding ground glass opacity, or adjacent bronchiectasis. In patients with lung cancer (n = 25, 17%), OP more likely presented as discrete lesions and occupied a peripheral location as compared with patients with other malignancies (Ps = 0.025 and 0.002). In HSCT patients (n = 29, 19%), a diffuse process was more commonly seen than in non-HSCT patients (P = 0.038).

Conclusions

Organizing pneumonia more commonly presents as discrete lesions with a peripheral location in patients with lung cancer and as a diffuse process in patients who had undergone HSCT.
A novel mechanism of “metal gel-shift” by histidine-rich Ni2+-binding Hpn protein fromHelicobacter pyloristrain SS1
Authors: Mahadev Shelake Rahul , Ito Yuki , Masumoto Junya , Morita Eugene Hayato , Hayashi Hidenori
Published: October 2016

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) is a universally used method for determining approximate molecular weight (MW) in protein research. Migration of protein that does not correlate with formula MW, termed “gel shifting” appears to be common for histidine-rich proteins but not yet studied in detail. We investigated “gel shifting” in Ni2+-binding histidine-rich Hpn protein cloned fromHelicobacter pyloristrain SS1. Our data demonstrate two important factors determining “gel shifting” of Hpn, polyacrylamide-gel concentration and metal binding. Higher polyacrylamide-gel concentrations resulted in faster Hpn migration. Irrespective of polyacrylamide-gel concentration, preserved Hpn-Ni2+complex migrated faster (3-4 kDa) than apo-Hpn, phenomenon termed “metal gel-shift” demonstrating an intimate link between Ni2+binding and “gel shifting”. To examine this discrepancy, eluted samples from corresponding spots on SDS-gel were analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS). The MW of all samples was the same (6945.66±0.34 Da) and identical to formula MW with or without added mass of Ni2+. MALDI-TOF-MS of Ni2+-treated Hpn revealed that monomer bound up to six Ni2+ions non-cooperatively, and equilibrium between protein-metal species was reliant on Ni2+availability. This corroborates with gradually increased heterogeneity of apo-Hpn band followed by compact "metal-gel shift" band on SDS-PAGE. In view of presented data metal-binding and “metal-gel shift” models are discussed.
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Authors: Paulson Joseph N. , Chen Cho-Yi , Lopes-Ramos Camila M. , Kuijjer Marieke L , Platig John , Sonawane Abhijeet R. , Fagny Maud , Glass Kimberly , Quackenbush John
Published: October 2016

Although ultrahigh-throughput RNA-Sequencing has become the dominant technology for genome-wide transcriptional profiling, the vast majority of RNA-Seq studies typically profile only tens of samples, and most analytical pipelines are optimized for these smaller studies. However, projects are generating ever-larger data sets comprising RNA-Seq data from hundreds or thousands of samples, often collected at multiple centers and from diverse tissues. These complex data sets present significant analytical challenges due to batch and tissue effects, but provide the opportunity to revisit the assumptions and methods that we use to preprocess, normalize, and filter RNA-Seq data – critical first steps for any subsequent analysis. We find analysis of large RNA-Seq data sets requires both careful quality control and that one account for sparsity due to the heterogeneity intrinsic in multi-group studies. An R package instantiating our method for large-scale RNA-Seq normalization and preprocessing, YARN, is available atbioconductor.org/packages/yarn.

Highlights

Overview of assumptions used in preprocessing and normalization

Pipeline for preprocessing, quality control, and normalization of large heterogeneous data

A Bioconductor package for the YARN pipeline and easy manipulation of count data

Preprocessed GTEx data set using the YARN pipeline available as a resource
Population diversity jeopardizes the efficacy of antibiotic cycling
Authors: Jiao Yunxin J. , Baym Michael , Veres Adrian , Kishony Roy
Published: October 2016

Treatment strategies that anticipate and respond to the evolution of pathogens are promising tools for combating the global rise of antibiotic resistance1–3. Mutations conferring resistance to one drug can confer positive or negative cross-resistance to other drugs4. The sequential use of drugs exhibiting negative cross-resistance has been proposed to prevent or slow down the evolution of resistance5–8, although factors affecting its efficacy have not been investigated. Here we show that population diversity can disrupt the efficacy of negative cross-resistance-based therapies. By testing 3317 resistantStaphylococcus aureusmutants against multiple antibiotics, we show that first-step mutants exhibit diverse cross-resistance profiles: even when the majority of mutants show negative cross-resistance, rare positive cross-resistant mutants can appear. Using a drug pair showing reciprocal negative cross-resistance, we found that selection for resistance to the first drug in small populations can decrease resistance to the second drug, but identical selection conditions in large populations can increases resistance to the second drug through the appearance of rare positive cross-resistant mutants. We further find that, even with small populations and strong bottlenecks, resistance to both drugs can increase through sequential steps of negative cross-resistance cycling. Thus, low diversity is necessary but not sufficient for effective cycling therapies. While evolutionary interventions are promising tools for controlling antibiotic resistance, they can be sensitive to population diversity and the accessibility of evolutionary paths, and so must be carefully designed to avoid harmful outcomes.
Quantifying predator dependence in the functional response of generalist predators
Authors: Novak Mark , Wolf Christopher , Coblentz Kyle , Shepard Isaac
Published: October 2016

A longstanding debate concerns whether functional responses are best described by prey-dependent versus ratio-dependent models. Theory suggests that ratio dependence can explain many food web patterns left unexplained by simple prey-dependent models. However, for logistical reasons, ratio dependence and predator dependence more generally have seen infrequent empirical evaluation and then only so in specialist predators, which are rare in nature. Here we develop an approach to simultaneously estimate the prey-specific attack rates and predator-specific interference rates of predators interacting with arbitrary numbers of prey and predator species. We apply the approach to field surveys and two field experiments involving two intertidal whelks and their full suite of potential prey. Our study provides strong evidence for the presence of weak predator dependence that is closer to being prey dependent than ratio dependent over manipulated and natural ranges of species abundances. It also indicates how, for generalist predators, even the qualitative nature of predator dependence can be prey-specific.

Author contributions

CW contributed to method development, KC and IS performed the caging experiment, and MN conceived of the study, carried out the fieldwork and analyses, and wrote the manuscript.
Metabolomic and proteomic analyses of a quiescentEscherichia colicell factory reveal the mechanisms behind its production efficiency
Authors: Thomson Nicholas M. , Shirai Tomokazu , Chiapello Marco , Kondo Akihiko , Mukherjee Krishnan J. , Sivaniah Easan , Summers David K. , Numata Keiji
Published: October 2016

1

Quiescent (Q-Cell)Escherichia colicultures can be created by using the signalling molecule indole to halt cell division of anhnsmutant strain. This uncouples metabolism from cell growth and allows for more efficient use of carbon feedstocks. However, the reason for the increased productivity of cells in this state was previously unknown. We show here that Q-cells can maintain metabolic activity in the absence of growth for up to 24 h, leading to four times greater per-cell productivity of a model metabolite, 3-hydroxybutyrate (3HB), than a control. Metabolomic data show that by disrupting the proton-motive force, indole interrupts the tricarboxylic acid cycle, leading to the accumulation of metabolites in the glycolysis pathway that are excellent starting points for high-value chemical production. By comparing protein expression patterns between wild-type and Q-cell cultures we show that Q-cells overexpress stress response proteins, which prime them to tolerate the metabolic imbalances incurred through indole addition. Quiescent cultures produced half the cell biomass of control cultures lacking indole, but were still able to produce 39.4 g.L-1of 3HB compared to 18.6 g.L-1in the control. Therefore, Q-cells have high potential as a platform technology for the efficient production of a wide range of commodity and high value chemicals.
Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration
Authors: Ramesh Vidya , Bayam Efil , Cernilogar Filippo M. , Bonapace Ian M. , Schulze Markus , Riemenschneider Markus J. , Schotta Gunnar , Götz Magdalena
Published: October 2016

In order to understand whether early epigenetic mechanisms instruct the long-term behavior of neural stem cells (NSCs) and their progeny, we examinedUhrf1(ubiquitin-like PHD ring finger-1; also known as Np95), as it is highly expressed in NSCs of the developing brain and rapidly down-regulated upon differentiation. Conditional deletion ofUhrf1in the developing cerebral cortex resulted in rather normal proliferation and neurogenesis but severe postnatal neurodegeneration. During development, deletion ofUhrf1lead to global DNA hypomethylation with a strong activation of the intracisternal A particle (IAP) family of endogenous retroviral elements, accompanied by an increase in 5-hydroxymethylcytosine. Down-regulation of Tet enzymes rescued the IAP activation inUhrf1conditional knockout (cKO) cells, suggesting an antagonistic interplay betweenUhrf1andTeton IAP regulation. As IAP up-regulation persists into postnatal stages in theUhrf1cKO mice, our data show the lack of means to repress IAPs in differentiating neurons that normally never expressUhrf1. The high load of viral proteins and other transcriptional deregulation ultimately led to postnatal neurodegeneration. Taken together, these data show that early developmental NSC factors can have long-term effects in neuronal differentiation and survival. Moreover, they highlight how specific the consequences of widespread changes in DNA methylation are for certain classes of retroviral elements.
Post-transcriptional control of executioner caspases by RNA-binding proteins
Authors: Subasic Deni , Stoeger Thomas , Eisenring Seline , Matia-González Ana M. , Imig Jochen , Zheng Xue , Xiong Lei , Gisler Pascal , Eberhard Ralf , Holtackers René , Gerber André P. , Pelkmans Lucas , Hengartner Michael O.
Published: October 2016

Caspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent of post-transcriptional control of caspases. Here, we describe four conserved RNA-binding proteins (RBPs)—PUF-8, MEX-3, GLD-1, and CGH-1—that sequentially repress the CED-3 caspase in distinct regions of the Caenorhabditis elegans germline. We demonstrate that GLD-1 represses ced-3 mRNA translation via two binding sites in its 3′ untranslated region (UTR), thereby ensuring a dual control of unwanted cell death: at the level of p53/CEP-1 and at the executioner caspase level. Moreover, we identified seven RBPs that regulate human caspase-3 expression and/or activation, including human PUF-8, GLD-1, and CGH-1 homologs PUM1, QKI, and DDX6. Given the presence of unusually long executioner caspase 3′ UTRs in many metazoans, translational control of executioner caspases by RBPs might be a strategy used widely across the animal kingdom to control apoptosis.
Interrogating the relevance of mitochondrial apoptosis for vertebrate development and postnatal tissue homeostasis
Authors: Tuzlak Selma , Kaufmann Thomas , Villunger Andreas
Published: October 2016

“Programmed cell death or ‘apoptosis’ is critical for organogenesis during embryonic development and tissue homeostasis in the adult. Its deregulation can contribute to a broad range of human pathologies, including neurodegeneration, cancer, or autoimmunity…” These or similar phrases have become generic opening statements in many reviews and textbooks describing the physiological relevance of apoptotic cell death. However, while the role in disease has been documented beyond doubt, facilitating innovative drug discovery, we wonder whether the former is really true. What goes wrong in vertebrate development or in adult tissue when the main route to apoptotic cell death, controlled by the BCL2 family, is impaired? Such scenarios have been mimicked by deletion of one or more prodeath genes within the BCL2 family, and gene targeting studies in mice exploring the consequences have been manifold. Many of these studies were geared toward understanding the role of BCL2 family proteins and mitochondrial apoptosis in disease, whereas fewer focused in detail on their role during normal development or tissue homeostasis, perhaps also due to an irritating lack of phenotype. Looking at these studies, the relevance of classical programmed cell death by apoptosis for development appears rather limited. Together, these many studies suggest either highly selective and context-dependent contributions of mitochondrial apoptosis or significant redundancy with alternative cell death mechanisms, as summarized and discussed here.
Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
Authors: Killian J. Keith , Dorssers Lambert C.J. , Trabert Britton , Gillis Ad J.M. , Cook Michael B. , Wang Yonghong , Waterfall Joshua J. , Stevenson Holly , Smith William I. , Noyes Natalia , Retnakumar Parvathy , Stoop J. Hans , Oosterhuis J. Wolter , Meltzer Paul S. , McGlynn Katherine A. , Looijenga Leendert H.J.
Published: October 2016

Testicular germ cell tumors (TGCTs) share germline ancestry but diverge phenotypically and clinically as seminoma (SE) and nonseminoma (NSE), the latter including the pluripotent embryonal carcinoma (EC) and its differentiated derivatives, teratoma (TE), yolk sac tumor (YST), and choriocarcinoma. Epigenomes from TGCTs may illuminate reprogramming in both normal development and testicular tumorigenesis. Herein we investigate pure-histological forms of 130 TGCTs for conserved and subtype-specific DNA methylation, including analysis of relatedness to pluripotent stem cell (ESC, iPSC), primordial germ cell (PGC), and differentiated somatic references. Most generally, TGCTs conserve PGC-lineage erasure of maternal and paternal genomic imprints and DPPA3 (also known as STELLA); however, like ESCs, TGCTs show focal recurrent imprinted domain hypermethylation. In this setting of shared physiologic erasure, NSEs harbor a malignancy-associated hypermethylation core, akin to that of a diverse cancer compendium. Beyond these concordances, we found subtype epigenetic homology with pluripotent versus differentiated states. ECs demonstrate a striking convergence of both CpG and CpH (non-CpG) methylation with pluripotent states; the pluripotential methyl-CpH signature crosses species boundaries and is distinct from neuronal methyl-CpH. EC differentiation to TE and YST entails reprogramming toward the somatic state, with loss of methyl-CpH but de novo methylation of pluripotency loci such as NANOG. Extreme methyl-depletion among SE reflects the PGC methylation nadir. Adjacent to TGCTs, benign testis methylation profiles are determined by spermatogenetic proficiency measured by Johnsen score. In sum, TGCTs share collective entrapment in a PGC-like state of genomic-imprint and DPPA3 erasure, recurrent hypermethylation of cancer-associated targets, and subtype-dependent pluripotent, germline, or somatic methylation.
LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
Authors: Tan Shengjun , Cardoso-Moreira Margarida , Shi Wenwen , Zhang Dan , Huang Jiawei , Mao Yanan , Jia Hangxing , Zhang Yaqiong , Chen Chunyan , Shao Yi , Leng Liang , Liu Zhonghua , Huang Xun , Long Manyuan , Zhang Yong E.
Published: October 2016

In a broad range of taxa, genes can duplicate through an RNA intermediate in a process mediated by retrotransposons (retroposition). In mammals, L1 retrotransposons drive retroposition, but the elements responsible for retroposition in other animals have yet to be identified. Here, we examined young retrocopies from various animals that still retain the sequence features indicative of the underlying retroposition mechanism. In Drosophila melanogaster, we identified and de novo assembled 15 polymorphic retrocopies and found that all retroposed loci are chimeras of internal retrocopies flanked by discontinuous LTR retrotransposons. At the fusion points between the mRNAs and the LTR retrotransposons, we identified shared short similar sequences that suggest the involvement of microsimilarity-dependent template switches. By expanding our approach to mosquito, zebrafish, chicken, and mammals, we identified in all these species recently originated retrocopies with a similar chimeric structure and shared microsimilarities at the fusion points. We also identified several retrocopies that combine the sequences of two or more parental genes, demonstrating LTR-retroposition as a novel mechanism of exon shuffling. Finally, we found that LTR-mediated retrocopies are immediately cotranscribed with their flanking LTR retrotransposons. Transcriptional profiling coupled with sequence analyses revealed that the sense-strand transcription of the retrocopies often lead to the origination of in-frame proteins relative to the parental genes. Overall, our data show that LTR-mediated retroposition is highly conserved across a wide range of animal taxa; combined with previous work from plants and yeast, it represents an ancient and ongoing mechanism continuously shaping gene content evolution in eukaryotes.
The producer-consumer classification gap and its effects on music festival success
Authors: Kuijken Bram , Leenders Mark A.A.M. , Wijnberg Nachoem M. , Gemser Gerda
Published: October 2016

Purpose

Producers and consumers – who represent opposing sides of the market – have different frames of reference, which may result in differences in classification of the same products. The authors aim to demonstrate that “classification gaps” have a negative effect on the performance of products and that these effects play a role in different stages of consumers’ decision process.

Design/methodology/approach

The data collection consisted of three comprehensive parts covering production and consumption in the music festival market in The Netherlands. The first part focused on festival organizers who were asked to classify their own music festival in terms of musical genres. In total, 70 festival organizers agreed to participate. The second part measured the genre classification of 540 consumers. In the third part, the authors interviewed 1,554 potential visitors of music festivals in The Netherlands about their awareness of the festival and if they considered visiting or actually visited the festival.

Findings

This paper provides empirical evidence that a classification gap between the production side and the consumption side of the market has negative effects on music festival performance. In addition, the authors found that this is in part because of lower activation of potential consumers in the marketplace.

Practical implications

An important practical implication of this study is that – in general – producers should be aware that classification gaps can occur – even if they are sure about the classification of their products – and that this can have serious consequences. The category membership of products is often seen as a given, whereas it cannot be assumed that the classification perceived by different economic groups is the same – as demonstrated in this paper.

Originality/value

This paper demonstrates that a fundamental – but understudied – disconnect between the two opposing sides of the market (i.e. producers and consumers) regarding the classification of the same products can have negative effects on performance of these products.
Understanding the selfie phenomenon: current insights and future research directions
Authors: Lim Weng Marc
Published: October 2016

Purpose

This paper aims to define the conceptual boundary of the selfie and to discuss the role of the selfie in the social media marketplace.

Design/methodology/approach

This paper extensively reviews and draws themes from the extant literature on consumer identities in the social media marketplace to explain the selfie phenomenon and to identify potentially fruitful directions for further research.

Findings

Current insights into the selfie phenomenon can be understood from socio-historical, technological, social media, marketing and ethical perspectives.

Research limitations/implications

Despite the limitations of a general review (e.g. absence of empirical data and analysis), this paper identifies multiple avenues to extend existing lines of inquiry on the selfie phenomenon. Thus, this paper should encourage further research on the topic in the academic and scientific community.

Practical implications

The selfie can be used as a marketing tool to improve marketing performance and accomplish marketing-related goals.

Originality/value

This paper sheds light on how marketing academics and practitioners can better understand the impact of the selfie in the social media marketplace.
Brand selfies: consumer experiences and marketplace conversations
Authors: Presi Caterina , Maehle Natalia , Kleppe Ingeborg Astrid
Published: October 2016

Purpose

The purpose of this paper is to explore the brand selfie phenomenon on two different levels. On the level of consumer brand experiences, the focus is on how brand selfie practices add new features to brand experiences and consumer–brand relationships. On the level of marketplace brand image, the authors explore how consumers contribute to marketplace conversations by posting brand selfies in social media and how this practice shapes and changes brand image.

Design/methodology/approach

The researchers conducted an extensive search on different social media platforms to collect various types of brand selfies. The authors approach brand selfies as rich visual texts and their analysis comprises four key steps: descriptive analysis, response analysis, formal analysis and polytextual thematic analysis.

Findings

On the level of consumer brand experiences, the findings illuminate how different types of brand selfies extend the brand experience in space and time and transfer it into the hybrid space of the consumer-defined social networks. On the level of marketplace brand image, it is illustrated how brand selfies contribute to the process of co-creating brand meaning in the social media.

Originality/value

The study proposes a typology of brand selfie assemblages showing how consumers contribute to the visual production and consumption of brand meanings. The brand selfie is a unique material and expressive reality enabling us to theorise new perspectives on how consumers consume brands and how aggregates of brand selfie production and dissemination affect marketplace dynamics.
Insight into the motivation of selfie postings: impression management and self-esteem
Authors: Pounders Kathrynn , Kowalczyk Christine M. , Stowers Kirsten
Published: October 2016

Purpose

Social media enables consumers to regularly express themselves in a variety of ways. Selfie-postings are the new tool for self-presentation, particularly among millennials. The purpose of this paper is to identify the motivations associated with selfie-postings among female millennials.

Design/methodology/approach

The exploratory study consisted of 15 in-depth interviews with women who were 19-30 years of age. The analysis of data was facilitated by an iterative constant comparison method between data, emerging concepts and extant literature.

Findings

Textual analysis reveals impression management to be pivotal in understanding the consumer selfie-posting process. Other sub-themes include happiness and physical appearance. In addition, self-esteem was revealed as a motivator and an outcome.

Research limitations/implications

The study was limited to females who were 19-30 years of age. Future research should include males and a wider age group and focus on empirical testing of the identified themes.

Practical implications

This research sheds light on the motivation and outcomes associated with selfie-postings. Implications for marketers and advertisers include a better understanding of how to engage consumers to post content in the form of selfies with brands and products.

Originality/value

This paper fulfils an identified need to explore the growing trend of selfie-postings and contributes to academic literature in consumer behavior by identifying the motivations of selfie-postings.
Classifying the narrated #selfie: genre typing human-branding activity
Authors: Eagar Toni , Dann Stephen
Published: October 2016

Purpose

This paper explores the purposive use of the selfie in the construction of personal narratives that develop and support an individual’s human brand. Selfies were divided into archetypical clusters of “genres” that reflected the combined story told through Instagram image and accompanying text captions.

Design/methodology/approach

The analysis drew a randomized sample of 1,000 images with accompanying text from a large capture of 3,300 English language captioned selfies. Coding for semantic and semiotic data used a three-wave technique to overcome interpretive limitations.

Findings

Based on their structural characteristics, seven genre types emerged from the coded sample set. These primary genres of selfie meta-narratives are autobiography, parody, propaganda, romance, self-help, travel diary and coffee-table book.

Research limitations/implications

The research is limited in generalization to the Instagram photo-sharing app platform by design. Samples were taken from the app due both to its popularity and its capacity to annotate images. Selfies conducted in non-public, non-annotation-based apps may produce alternative genres and classifications.

Practical implications

The paper presents a genre classification to examine how selfies are used to “show, not tell” a portion of the consumer’s life story. Brands, firms and marketers can apply genres to examine the selfie types that best connect with the identity of their brands and consumers, based on how their consumers communicate within the Instagram network.

Social implications

Selfies are an oft pathologized and moralized aspect of consumer conduct. We present a view of the selfie as a deliberate, consciously considered communication approach to maintaining social bonds between friends, family and wider audience. Selfies are presented as a combined effect of consumption of a social media service (Instagram) and the co-production of valued content (the selfie) that recognizes the individual as an active constructor of their digital self.

Originality/value

The paper outlines a novel framework of selfie genres to classify the deliberate human-brand narratives expressed in selfies. By taking a narrative perspective to the Instagram selfie practice, the genre type captures the combined effect of the mimesis and diegesis, where the mimesis showing of self is contextualized with the diegesis of the provided captions to capture an intentional storytelling act of image and text.
From liberation to control: understanding the selfie experience
Authors: Kedzior Richard , Allen Douglas E.
Published: October 2016

Purpose

This paper aims to serve as an integrative literature review that organizes the burgeoning literature and findings related to possible impacts of the selfie phenomenon on consumers.

Design/methodology/approach

This is a conceptual paper.

Findings

The current empirical scholarly work supports two conflicting perspectives on the impact of selfies: the selfie experience as a source of empowerment and the selfie as embodiment of societal control and expression of existing power-relations. While the two perspectives are seemingly discordant, in fact, they pertain to different levels of analysis – individual and social, respectively.

Originality/value

While the empowerment aspect of the selfie experience has been well-documented in existing literature, the mechanisms of control and disempowerment have remained underconceptualized. This research paper offers a framework which addresses this omission and theorizes ways in which the selfie phenomenon perpetuates societal control and maintains power-relations.
The importance of employee brand understanding, brand identification, and brand commitment in realizing brand citizenship behaviour
Authors: Piehler Rico , King Ceridwyn , Burmann Christoph , Xiong Lina
Published: October 2016

Purpose

This study aims to develop comprehensive definitions, conceptualizations and measures of four internal brand management (IBM) outcomes, namely, brand understanding, brand identification, brand commitment and brand citizenship behaviour (BCB). In doing so, it also aims to propose a model, which considers the relationships across these outcomes.

Design/methodology/approach

Data were collected via an online survey of 375 employees who work in service organizations, sourced from an Australian, Web-based market research list.

Findings

In addition to the indirect effect of brand understanding on BCB via affective IBM outcomes (i.e. brand identification and brand commitment), the study exposes a direct effect of brand understanding on BCB. Therefore, the study shows that BCB is affected by cognitive and affective antecedents.

Research limitations/implications

Because this study focuses on IBM outcomes, future studies could propose and test relevant antecedents and moderators. As the empirical basis of this study comes primarily from the tourism and hospitality industry in one domestic market, the study should be replicated in other industries and countries to ensure the generalizability of the identified relationships.

Practical implications

This study not only delivers IBM outcome measures but also empirically validates that employees’ understanding of the brand is a foundation for affective and behavioural IBM outcomes. Therefore, managers, especially in service organizations, should provide sufficient IBM practices to enable such brand understanding.

Originality/value

This study contributes to IBM literature by developing comprehensive definitions, conceptualizations and measures of four important IBM outcomes. This study is the first to include brand understanding, brand identification, brand commitment and BCB simultaneously.