bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotypic and Molecular-Phylogenetic Analysis Provide Novel Insights into the Diversity of Curtobacterium flaccumfaciens
Authors: Osdaghi Ebrahim , Taghavi S. Mohsen , Calamai Silvia , Biancalani Carola , Cerboneschi Matteo , Tegli Stefania , Harveson Robert M.
Published: May 2018

A multiphasic approach was used to decipher the phenotypic features, genetic diversity, and phylogenetic position of 46 Curtobacterium spp. strains isolated from dry beans and other annual crops in Iran and Spain. Pathogenicity tests, resistance to arsenic compounds, plasmid profiling and BOX-PCR were performed on the strains. Multilocus sequence analysis (MLSA) was also performed on five housekeeping genes (i.e., atpD, gyrB, ppk, recA, and rpoB) of all the strains, as well as five pathotype strains of the species. Pathogenicity test showed that six out of 42 strains isolated in Iran were nonpathogenic on common bean. Despite no differences found between pathogenic and nonpathogenic strains in their plasmid profiling, the former were resistant to different concentrations of arsenic, while the latter were sensitive to the same concentrations. Strains pathogenic on common bean were polyphyletic with at least two evolutionary lineages (i.e., yellow-pigmented strains versus red/orange-pigmented strains). Nonpathogenic strains isolated from solanaceous vegetables were clustered within either the strains of C. flaccumfaciens pv. flaccumfaciens or different pathovars of the species. The results of MLSA and BOX-PCR analysis were similar to each other and both methods were able to discriminate the yellow-pigmented strains from the red/orange-pigmented strains. A comprehensive study of a worldwide collection representing all five pathovars as well as nonpathogenic strains of C. flaccumfaciens is warranted for a better understanding of the diversity within this phytopathogenic bacterium.
Is gonadotropin stimulation bad for oocytes?
Authors: Lindenberg Svend , Almind Gitte J. , Lindenberg Frederikke B.
Published: May 2018

Purpose of review

Gonadotrophin in IVF increases the number of oocytes retrieved, and many doctors regard a high number of oocytes as a measurement of success in IVF. Thus, the dogma of more oocytes provides better IVF success has been broadly accepted. However, some European fertility specialists have argued against this concept, saying fewer eggs might, in some instances, be a better option for the patient.

Recent findings

The concept of ‘one size fits all’ stimulation in artificial reproductive technologies is not broadly supported by the current literature. The ovarian stimulation strategy has to be viewed in relation to cost, infrastructure and economics, expectations from the doctors and the patients, and more importantly the local legislation. Furthermore, also luteal phase, epigenetic factors and patient safety is a matter of concern. Studies show that in the fresh cycle, ovarian stimulation might have an impact on the epigenetics, quality of the embryo and increase the risk of ovarian hyper stimulation. Strategies like agonist triggering or ‘freeze all’ can help during a fresh cycle. However, there is an ongoing debate whether these strategies might increase time to pregnancy or not.

In conclusion, each fertility clinic setup has its own benefits and gonadotropin hyperstimulation in IVF has to be related to this and the specific patient demographic in the clinic; however, epigenetics and time to pregnancy are still issues open to debate.
Relationships among factors affecting advanced practice registered nurses' job satisfaction and intent to leave: A systematic review
Authors: Han Robin M. , Carter Patricia , Champion Jane Dimmitt
Published: May 2018

Background and purpose:

This systematic review explores relationships between advanced practice registered nurses' (APRN) job satisfaction and intent to leave. There exists a dearth of APRN providers compared with the ever-growing need for their services. Furthermore, the organizational costs associated with the APRN turnover are extremely high. It, therefore, behooves practice administrators to understand what factors most contribute to APRN job satisfaction and retention.

Methods:

A search of research databases CINAHL, PubMed, and PsycINFO, using keywords “Advanced Practice Registered Nurse,” “job satisfaction,” “intent to leave,” “anticipated turnover,” and “Nurse Practitioner” to yield articles included in this review.

Conclusions:

The strength of existing evidence for this topic is weak. Studies have found that extrinsic factors, such as administrative support and salary, significantly contribute to job dissatisfaction, whereas intrinsic factors, such as autonomy and finding work meaningful, most significantly contribute to job satisfaction. Additional research is needed to better understand the factors relating to APRN job satisfaction and dissatisfaction, and how those factors influence practitioners' intent to leave.

Implications for practice:

Efforts to improve APRN job satisfaction will have positive implications for provider retention, practices, and patients. Administrators should consider the job satisfaction factors identified herein when implementing practice improvement and retention efforts.
Surrogates' experiences of engaging in Physician Orders for Life-Sustaining Treatment discussions for persons with advanced dementia
Authors: Kim Hyejin , Bradway Christine , Hickman Susan E. , Ersek Mary
Published: May 2018

Background and purpose:

Little is known about surrogates' experiences of engaging in Physician Orders for Life-Sustaining Treatment (POLST) discussions. This study describes family surrogates' experiences when engaging in POLST discussions with primary care providers.

Methods:

Semistructured interviews were conducted with 10 family surrogates of individuals with advanced dementia who were enrolled in a Program of All-Inclusive Care for the Elderly or resided in a nursing home. Interviews were analyzed using directed content analysis based on the conceptual model of communication and surrogate decision making by Torke et al.

Results and conclusion:

Surrogates reported that clear explanations of clinical information and the opportunity to ask questions and reiterate what they heard were helpful in making treatment decisions. Moreover, surrogates reported feeling respected and understood when providers expressed concern for them or their family member with advanced dementia and asked them about their emotional responses to decision making. Although nine surrogates reported very positive communication with providers, one surrogate expressed discomfort with the interaction and described feeling pressured to make health care decisions.

Implications for practice:

With effective communication, family surrogates feel emotionally supported during communication and decision-making processes. Providers are encouraged to focus on developing expert communication skills for end-of-life care discussions.
Helping High School Students Explore Nursing Careers in a Summer Internship Program
Authors: Gómez Eva , Brostoff Marcie
Published: May 2018

Although nursing remains the most trusted profession in the United States, it is still challenging to attract high school students due to a perception that nursing may not be as intellectual, challenging, or prestigious as other careers in health care. Nursing professional development practitioners can create an opportunity to change this perception by engaging high school students through a summer internship program. The Student Career Opportunity Outreach Program embeds high school students in the hospital environment, enabling them to be a part of a clinical area and engage with nurses in a meaningful way. This article aims to explain the components of the summer internship program for high school students in a pediatric academic medical center and discuss findings from a survey exploring career choices pre- and postprogram as well as other outcome measures.
Pneumoperitoneum
Authors: Ramponi Denise R.
Published: May 2018

Pneumoperitoneum, usually seen as free air under the diaphragm, is a finding that can be seen on plain abdominal radiographs, signifying a leakage of air, usually from a perforation in the gastrointestinal tract. There are several other potential pathways from other body compartments for air to enter the abdominal cavity. Pneumoperitoneum does not always signify bowel rupture, as it can also result from pneumomediastinum and pneumothorax, and in patients who are being mechanically ventilated. Patient history and physical examination can assist in a preliminary diagnosis before diagnostic imaging. Plain chest/abdominal radiograph or computed tomographic scan of the abdomen can be diagnostic of pneumoperitoneum. Surgical versus nonsurgical conservative observation is determined on the basis of the cause and amount of free air.
Recognizing Measles, Mumps, and Rubella in the Emergency Department
Authors: Gadler Tracie , Martinez Nicole , Ogg-Gress Jill
Published: May 2018

Measles, mumps, and rubella have impacted millions of American lives over the last 100 years. During the last century, researchers have identified viral diseases, developed a combination vaccine, and have continued ongoing research when outbreaks have occurred. Despite the high incidence of vaccinated individuals, these highly communicable diseases continue to flourish within clusters of outbreaks throughout the United States. Emergency medicine providers play a key role in early recognition and diagnosis of the disease. The proper management and reporting reflect the emphasis on prevention of widespread outbreaks.
Assessment, Selection, Use, and Evaluation of Body-Worn Absorbent Products for Adults With Incontinence
Authors: Gray Mikel , Kent Dea , Ermer-Seltun JoAnn , McNichol Laurie
Published: May 2018

The Wound, Ostomy and Continence Nurses (WOCN) Society charged a task force with creating recommendations for assessment, selection, use, and evaluation of body-worn absorbent products. The 3-member task force, assisted by a moderator with knowledge of this area of care, completed a scoping literature review to identify recommendations supported by adequate research to qualify as evidence-based, and area of care where evidence needed to guide care was missing. Based on findings of this scoping review, the Society then convened a panel of experts to develop consensus statements guiding assessment, use, and evaluation of the effect of body-worn absorbent products for adults with urinary and/or fecal incontinence. These consensus-based statements underwent a second round of content validation using a modified Delphi technique using a different panel of clinicians with expertise in this area of care. This article reports on the scoping review and subsequent evidence-based statements, along with generation and validation of consensus-based statements that will be used to create an algorithm to aid clinical decision making.
Noise Analysis in Biochemical Complex Formation
Authors: Xu Zikai , Ghusinga Khem Raj , Singh Abhyudai
Published: May 2018

Several biological functions are carried out via complexes that are formed via multimerization of either a single species (homomers) or multiple species (heteromers). Given functional relevance of these complexes, it is arguably desired to maintain their level at a set point and minimize fluctuations around it. Here we consider two simple models of complex formation – one for homomer and another for heteromer of two species – and analyze how important model parameters affect the noise in complex level. In particular, we study effects of (i) sensitivity of the complex formation rate with respect to constituting species’ abundance, and (ii) relative stability of the complex as compared with that of the constituents. By employing an approximate moment analysis, we find that for a given steady state level, there is an optimal sensitivity that minimizes noise (quantified by fano-factor; variance/mean) in the complex level. Furthermore, the noise becomes smaller if the complex is less stable than its constituents. Finally, for the heteromer case, our findings show that noise is enhanced if the complex is comparatively more sensitive to one constituent. We briefly discuss implications of our result for general complex formation processes.
pheno-seq – linking morphological features to gene expression in 3D cell culture systems
Authors: Tirier Stephan M. , Park Jeongbin , Preußer Friedrich , Amrhein Lisa , Gu Zuguang , Steiger Simon , Mallm Jan-Philipp , Waschow Marcel , Eismann Björn , Gut Marta , Gut Ivo G. , Rippe Karsten , Schlesner Matthias , Theis Fabian , Fuchs Christiane , Ball Claudia R. , Glimm Hanno , Eils Roland , Conrad Christian
Published: May 2018

3D-culture systems have advanced cancer modeling by reflecting physiological characteristics of in-vivo tissues, but our understanding of functional intratumor heterogeneity including visual phenotypes and underlying gene expression is still limited. Single-cell RNA-sequencing is the method of choice to dissect transcriptional tumor cell heterogeneity in an unbiased way, but this approach is limited in correlating gene expression with contextual cellular phenotypes.

To link morphological features and gene expression in 3D-culture systems, we present ‘pheno-seq’ for integrated high-throughput imaging and transcriptomic profiling of clonal tumor spheroids. Specifically, we identify characteristic EMT expression signatures that are associated with invasive growth behavior in a 3D breast cancer model. Additionally, pheno-seq determined transcriptional programs containing lineage-specific markers that can be linked to heterogeneous proliferative capacity in a patient-derived 3D model of colorectal cancer. Finally, we provide evidence that pheno-seq identifies morphology-specific genes that are missed by scRNA-seq and inferred single-cell regulatory states without acquiring additional single cell expression profiles. We anticipate that directly linking molecular features with patho-phenotypes of cancer cells will improve the understanding of intratumor heterogeneity and consequently be useful for translational research.
A crowdsourced analysis to identifyab initiomolecular signatures predictive of susceptibility to viral infection
Authors: Fourati Slim , Talla Aarthi , Mahmoudian Mehrad , Burkhart Joshua G. , Klén Riku , Henao Ricardo , Aydin Zafer , Yeung Ka Yee , Ahsen Mehmet Eren , Almugbel Reem , Jahandideh Samad , Liang Xiao , Nordling Torbjörn E.M. , Shiga Motoki , Stanescu Ana , Vogel Robert ,   The Respiratory Viral DREAM Challenge Consortium, Pandey Gaurav , Chiu Christopher , McClain Micah T. , Woods Chris W. , Ginsburg Geoffrey S. , Elo Laura L. , Tsalik Ephraim L. , Mangravite Lara M. , Sieberts Solveig K.
Published: May 2018

Respiratory viruses are highly infectious; however, the variation of individuals’ physiologic responses to viral exposure is poorly understood. Most studies examining molecular predictors of response focus on late stage predictors, typically near the time of peak symptoms. To determine whether pre- or early post-exposure factors could predict response, we conducted a community-based analysis to identify predictors of resilience or susceptibility to several respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV) using peripheral blood gene expression profiles collected from healthy subjects prior to viral exposure, as well as up to 24 hours following exposure. This analysis revealed that it is possible to construct models predictive of symptoms using profiles even prior to viral exposure. Analysis of predictive gene features revealed little overlap among models; however, in aggregate, these genes were enriched for common pathways. Heme Metabolism, the most significantly enriched pathway, was associated with higher risk of developing symptoms following viral exposure.
Neonatal gut-microbiome-derived 12,13 DiHOME impedes tolerance and promotes childhood atopy and asthma
Authors: Levan S.R. , Stamnes K.A. , Lin D.L. , Fujimura K.E. , Ownby D.R. , Zoratti E.M. , Boushey H.A. , Johnson C.C. , Lynch S.V.
Published: May 2018

Neonates at risk of childhood atopy and asthma are characterized by gut microbiome perturbation and fecal enrichment of 12,13 DiHOME(1); however, the underlying mechanism and source of this metabolite remain poorly understood. Here we show that 12,13 DiHOME treatment of human dendritic cells altered peroxisome proliferator-activated receptor γ regulated gene expression and decreased immune tolerance. In mice, 12,13 DiHOME treatment prior to airway challenge exacerbated pulmonary inflammation and decreased lung regulatory T cells. Neonatal fecal metagenomic sequencing revealed putative bacterial sources of 12,13 DiHOME. In our cohort, three bacterial genes and their product, 12,13 DiHOME, are associated with increased odds of childhood atopy or asthma, suggesting that early-life gut-microbiome risk factors may shape immune tolerance and identify high-risk neonates years in advance of clinical symptoms.

One Sentence Summary

Early-life gut-microbiome risk factors may shape immune tolerance and identify neonates at high-risk of disease.
Drosophila mef2is essential for normal mushroom body and wing development
Authors: Crittenden Jill R. , Skoulakis Efthimios M. C. , Goldstein Elliott. S. , Davis Ronald L.
Published: May 2018

MEF2 (myocyte enhancer factor 2) transcription factors are found in the brain and muscle of insects and vertebrates and are essential for the differentiation of multiple cell types. We show that in the fruitflyDrosophila, MEF2 is essential for normal development of wing veins, and for mushroom body formation in the brain. In embryos mutant forD-mef2, there was a striking reduction in the number of mushroom body neurons and their axon bundles were not detectable. D-MEF2 expression coincided with the formation of embryonic mushroom bodies and, in larvae, expression onset was confirmed to be in post-mitotic neurons. With aD-mef2point mutation that disrupts nuclear localization, we find that D-MEF2 is restricted to a subset of Kenyon cells that project to the α/β, and γ axonal lobes of the mushroom bodies, but not to those forming the α’/β’ lobes. Our findings that ancestralmef2is specifically important in dopamine-receptive neurons has broad implications for its function in mammalian neurocircuits.
Enhancer control of miR-155 expression in Epstein-Barr virus infected B cells
Authors: David Wood C. , Carvell Thomas , Gunnell Andrea , Ojeniyi Opeoluwa O. , Osborne Cameron , West Michelle J.
Published: May 2018

The oncogenic microRNA-155 (miR-155) is the most frequently upregulated miRNA in Epstein-Barr virus (EBV)-positive B cell malignancies and is upregulated in other non-viral lymphomas. Both the EBV nuclear antigen 2 (EBNA2), and B cell transcription factor, interferon regulatory factor 4 (IRF4) are known to activate transcription of the host cell gene from which miR-155 is processed (miR-155HG,BIC). EBNA2 also activatesIRF4transcription indicating that EBV may upregulate miR-155 through direct and indirect mechanisms. The mechanism of transcriptional regulation ofIRF4andmiR-155HGby EBNA2 however has not been defined. We demonstrate that EBNA2 can activateIRF4andmiR-155HGexpression through specific upstream enhancers that are dependent on the Notch signaling transcription factor RBPJ, a known binding partner of EBNA2. We demonstrate that in addition to activation of themiR-155HGpromoter, IRF4 can also activatemiR-155HGvia the upstream enhancer also targeted by EBNA2. Gene editing to remove the EBNA2- and IRF4-responsivemiR-155HGenhancer located 60 kb upstream ofmiR-155HGled to reducedmiR155HGexpression in EBV-infected cells. Our data therefore demonstrate that specific RBPJ-dependent enhancers regulate the IRF4-miR-155 expression network and play a key role in the maintenance of miR-155 expression in EBV-infected B cells. These findings provide important insights that will improve our understanding of miR-155 control in B cell malignancies.

IMPORTANCE

MicroRNA-155 (miR-155) is expressed at high level in many human cancers particularly lymphomas. Epstein-Barr virus (EBV) infects human B cells and drives the development of numerous lymphomas. Two EBV-encoded genes (LMP1 and EBNA2) upregulate miR-155 expression and miR-155 expression is required for the growth of EBV-infected B cells. We show that the EBV transcription factor EBNA2 upregulates miR-155 expression by activating an enhancer upstream from the miR-155 host gene (miR-155HG) from which miR-155 is derived. We show that EBNA2 also indirectly activatesmiR-155expression through enhancer-mediated activation ofIRF4.IRF4 then activates both themiR-155HGpromoter and the upstream enhancer, independently of EBNA2. Gene editing to remove themiR-155HGenhancer leads to a reduction inmiR-155HGexpression. We therefore identify enhancer-mediated activation ofmiR-155HGas a critical step in promoting B cell growth and a likely driver of lymphoma development.
Evaluation of the GenoType MTBDRplusand MTBDRslfor the detection of drug-resistantMycobacterium tuberculosison isolates from Beijing, China
Authors: Jian Jiyong , Yang Xinyu , Yang Jun , Chen Liang
Published: May 2018

The incidence of tuberculosis (TB) and especially multidrug-resistant TB (MDR) and extreme drug resistance (XDR-TB) continue to increase alarmingly worldwide and reliable and fast diagnosis of MDR-TB and XDR-TB is essential for the adequate treatment of patients. So molecular line probe assays (LPAs) for detection of MDR-TB and XDR-TB have been endorsed by the World Health Organization (WHO). We analyzed 96 isolates from Beijing comparing culture-based drug susceptibility testing (DST) to LPAs detecting rifampicin (RFP), isoniazid (INH), and levofloxacin (LFX), amikacin (AM), capreomycin (CMP), ethambutol (EMB) resistance. Compared to phenotypic DST, the GenoType MTBDRplusand MTBDRslshowed a sensitivity of 98.7% and a specificity of 88.9% for detection of RFP resistance, 82.1% and 94.4% for INH, 89.7% and 94.4% for LFX, 60.0% and 98.7% for AM/CPM, 57.5% and 98.2% for EMB, respectively. The sensitivity and specificity of LPAs for MDR-TB and XDR-TB were 80.8%, 100% and 50.0%, 97.6%. Mutations in codon S531L of therpoBgene and S315T1 ofKatGgene were dominated in MDR-TB strains. The most frequently observed mutations were in codon A90V of thegyrAgene, A1401G of therrsgene and M306V of theembBgene, according to the MTBDRslresults. Our study showed that, in combination to phenotypic DST, application of the LPAs might be an efficient and reliable supplementary DST assay for rapid susceptibility screening of MDR-TB and XDR-TB. Using LPAs in high MDR/XDR burden countries allows for appropriate and timely treatment, which will reduce transmission rates, morbidity and improve treatment outcomes in patients.
The Biological Evaluation of Fusidic Acid and Its Hydrogenation Derivative as Antimicrobial and Anti-inflammatory Agents
Authors: Wu Pan-Pan , He Hao , Hong W. David , Wu Tong-Rong , Zhao Su-Qing , Cui Xi-Ping , Zhong Ying-Ying , Li Dong-Li , Xu Xue-Tao , Sheng Zhao-Jun , Tu Bo-Rong , Gao Min , Zhou Jun , Ward Stephen A. , O’Neill Paul M. , Zhang Kun
Published: May 2018

Fusidic acid (WU-FA-00) is the only commercially available antimicrobial from the fusidane family that has a narrow spectrum of activity against Gram-positive bacteria. Herein, the hydrogenation derivative (WU-FA-01) of fusidic acid was prepared, and both compounds were examined against a panel of six bacterial strains. In addition, their anti-inflammation properties were evaluated using a 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced mouse ear edema model. The results of the antimicrobial assay revealed that both WU-FA-00 and WU-FA-01 displayed a high level of antimicrobial activity against Gram-positive strains. Moreover, killing kinetic studies were performed, and the results were in accordance with the MIC and MBC results. We also demonstrated that the topical application of WU-FA-00 and WU-FA-01 effectively decreased TPA-induced ear edema in a dose-dependent manner. This inhibitory effect was associated with the inhibition of TPA-induced up-regulation of pro-inflammation cytokines IL-1β, TNF-α and COX-2. WU-FA-01 significantly suppressed the expression levels of p65, IκB-α, and p-IκB-α in the TPA-induced mouse ear model. Overall, our results showed that WU-FA-00 and WU-FA-01 not only had effective antimicrobial activitiesin vitro, especially to the Gram-positive bacteria, but also possessed strong anti-inflammatory effectsin vivo. These results provide a scientific basis for developing fusidic acid derivatives as antimicrobial and anti-inflammatory agents.
Restriction of chromatin accessibility is necessary for appropriate enhancer expression
Authors: Hagey Daniel W. , Klum Susanne , Zaouter Cecile , Muhr Jonas
Published: May 2018

Tissue specific gene expression underpins cell type diversity, and arises from the cooperative activities of transcription factors and the chromatin landscape. It has been previously demonstrated that enhancers with specific arrangements of transcription factor binding motifs can bring together commonly and specifically expressed factors in order to stabilize chromatin accessibility and drive spatially restricted reporter expression within different regions of the CNS. However, when reporters were used to analyse the activity of enhancers bound differentially by a common factor in the endoderm and CNS, several examples of non-tissue specific reporter expression were observed. In order to judge whether or not this may have been due to the unregulated chromatin environment of exogenously delivered enhancer reporters, here we have analysed the chromatin landscape of cells from the CNS and endodermal tissues and find that this reflects neighbouring gene expression to a greater degree than transcription factor binding. This work demonstrates that chromatin accessibility plays an essential role in defining enhancer activity in distantly related cell types.
Studies on the mechanism of membrane mediated general anesthesia
Authors: Pavel Mahmud Arif , Petersen E. Nicholas , Wang Hao , Lerner Richard A. , Hansen Scott B.
Published: May 2018

Inhaled anesthetics are a chemically diverse collection of hydrophobic molecules that robustly activate TWIK related K+ channels (TREK-1) and reversibly induce loss of consciousness. For a hundred years anesthetics were speculated to target cellular membranes, yet no plausible mechanism emerged to explain a membrane effect on ion channels. Here we show that inhaled anesthetics (chloroform and isoflurane) activate TREK-1 through disruption of palmitate-mediated localization of phospholipase D2 (PLD2) to lipid rafts and subsequent production of signaling lipid phosphatidic acid (PA). Catalytically dead PLD2 robustly blocks anesthetic TREK-1 currents in cell patch-clamp. Localization of PLD2 renders the anesthetic-insensitive TRAAK channel sensitive. General anesthetics chloroform, isoflurane, diethyl ether, xenon, and propofol disrupt lipid rafts and activate PLD2. In the whole brain of flies, anesthesia disrupts rafts and PLDnull flies resist anesthesia. Our results establish a membrane mediated target of inhaled anesthesia and suggest PA helps set anesthetic sensitivity in vivo.
Haplotype-based eQTL mapping finds evidence for complex gene regulatory regions poorly tagged by marginal SNPs
Authors: Brown Robert , Sankararaman Sriram , Pasaniuc Bogdan
Published: May 2018

Motivation

Expression quantitative trait loci (eQTLs), variations in the genome that impact gene expression, are identified through eQTL studies that test for a relationship between single nucleotide polymorphisms (SNPs) and gene expression levels. These studies typically assume an underlying additive model. Non-additive tests have been proposed, but are limited due to the increase in the multiple testing burden and are potentially biased by filtering criteria that relies on marginal association data. Here we propose using combinations of short haplotypes instead of SNPs as predictors for gene expression. Essentially, this method looks for genomic regions where haplotypes have different effect sizes. The differences in effect can be due to multiple genetic architectures such as a single SNP, a burden of rare SNPs, multiple SNPs with independent effect or multiple SNPs with an interaction effect occurring on the same haplotype.

Results

Simulations show that when haplotypes, rather than SNPs, are assigned non-zero effect sizes, our method has increased power compared to the marginal SNP method. In the GEUVADIS gene expression data, our method finds 101 more eGenes than the marginal method (5,202 vs. 5,101). The methods do not have full overlap in the eGenes that they find. Of the 5,202 eGenes found by our method, 707 are not found by the marginal method—even though it has a lower significance threshold. This indicates that many genes have regulatory architectures that are not well tagged by marginal SNPs and demonstrates the need to better model alternative archi-tectures.
ChIP-chip
Authors: Kim Tae Hoon , Dekker Job
Published: May 2018

ChIP-chip can be used to analyze protein–DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications. The relative hybridization intensity of ChIP DNA and that of the input DNA is used to determine whether the probe sequence is a potential site of protein–DNA interaction. Resolution of actual genomic sites bound by the protein is dependent on the size of the chromatin and on the genomic distance between the probes on the array. As with expression profiling using gene chips, ChIP-chip experiments require multiple replicates for reliable statistical measure of protein–DNA interactions.
Isolation of DNA from Mouse Tails without Extraction by Organic Solvents
Authors: Green Michael R. , Sambrook Joseph
Published: May 2018

This protocol describes a variation of a simple method for isolation of DNA from mouse tails that does not require extraction with phenol:chloroform. This variant is useful when processing very large numbers of samples.
Touchdown Polymerase Chain Reaction (PCR)
Authors: Green Michael R. , Sambrook Joseph
Published: May 2018

“Touchdown polymerase chain reaction (PCR)” is a method to decrease off-target priming and hence to increase the specificity of PCRs. In touchdown PCR the temperature selected for the annealing step is initially set 5°C–10°C higher than the calculated Tm of the primers. Annealing under conditions of high stringency favors the formation of perfect primer–template hybrids. In subsequent cycles, the annealing temperature is gradually decreased by a small amount so that by the end of the PCR, the annealing temperature is 2°C–5°C below the calculated Tm of the primers. By then, the target sequence will have undergone several cycles of geometric amplification and therefore becomes the dominant product of the PCR. To minimize mispriming during the early stages of the PCR, touchdown PCR should always be performed in conjunction with a hot start protocol. The use of touchdown PCR is essential when the sequence of the primer might not match that of the target—for example, if the sequence of the primer has been deduced from amino acid sequences, when the template DNA may contain several closely related targets, or when the target DNA is of a different species from that used to design the primers.
The transnational comparative study on the potential risks and efficiency of commercial banks based on the weight-limited DEA model
Authors: Wang Hao , Wang Yu , Zhao Shuang , Wang Lan-ping , An Hui
Published: May 2018

Purpose

The purpose of this paper is to calculate the bank efficiency of removing potential risks that are hidden from the extreme portfolio of bank’s assets and further compare the differences and causes of bank’s efficiency and potential risk level between China’s representative banks and OECD representative banks in 2011-2015.

Design/methodology/approach

Based on the weight-limited DEA model, this paper calculates the bank’s efficiency and further compares the differences between China’s representative banks and OECD representative banks by using commercial banks’ transnational data.

Findings

By analyzing US representative banks’ data, the authors find that the excessive expansion of the scale of banks’ investment for the non-real economy shrinks after the bubble burst and would not improve the efficiency of banks immediately. The OECD representative banks rather prefer to extreme asset portfolio so that the potential risks gradually increase, while there is a diminishing effect on investments in non-real economies to improve bank efficiency. On the other hand, China’s representative banks have the signs of reducing investment in the real estate market, but the existence of the bubble in the market led to a lagged effect on the impact of adjustment of bank asset portfolio on efficiency.

Research limitations/implications

This paper has practical significance for commercial banks to improve efficiency and reduce credit risks. This is conducive to the implementation of targeted supervision by the banking supervision department.

Practical implications

Based on the lesson that the financial crisis created by the real estate bubble burst in the USA in 2008 and the financial market active guidance of the developed economies, faced with the reality of Chinese real estate market bubble rising and the continuous improvement of Chinese financial market, this paper compares the differences between representative banks in China and OECD, and explores the causes by using the cross-country data of commercial banks.

Originality/value

By adjusting the weight of the input variables in the efficiency measurement, quantifying the risk is often overlooked by the changes in bank efficiency. This potential risk is caused by the bank’s investment preferences in the non-real economy represented by real estate and tradable financial assets.
Worker cooperatives: alternative governance for caring and precarious work
Authors: Berry Daphne , Bell Myrtle P.
Published: May 2018

Purpose

Precarious work, characterized by low wages, unpredictable schedules and hours, physical hazards, and stressful psychosocial conditions, is a significant problem in the twenty-first century US economy. It most harshly affects women, racial/ethnic minorities, and immigrants. Caring labor jobs often involve precarious work and home health aide jobs are among the most precarious of these. With an ageing population creating high demand and a decline in the number of available workers, a societal crisis looms. The purpose of this paper is to discuss a business form that could positively impact the home care work environment.

Design/methodology/approach

This paper reviews previous research to call for closer examination of worker cooperatives as a means to reduce precarious work among home health care workers.

Findings

Worker cooperatives provide opportunities for economic empowerment for impoverished and marginalized workers. Cooperative Home Care Associates, a worker cooperative in the home care industry, reports better outcomes to workers than similar conventionally governed businesses.

Research limitations/implications

This paper reviews results of a study comparing three organizational forms in the home health industry. Although there are relatively few worker cooperatives in the USA, future research should investigate this structure both where there is a low-wage labor force, and in general.

Practical implications

Better outcomes for employees in the worker cooperative suggest that this is a viable business form for workers in precarious work environments.

Social implications

The paper highlights the features of an organizational form that could help alleviate social ills caused by precarious work.

Originality/value

This paper considers the structure and function of a business form little studied in the management discipline. Based on their unique features and possibilities, worker cooperatives should be of interest to equality, diversity, and inclusion scholars; and to strategy, organizational behavior, and entrepreneurship scholars.
Confronting capital’s care fix: care through the lens of democracy
Authors: Dowling Emma
Published: May 2018

Purpose

The purpose of this paper is to propose to expand the political economic understanding of a “fix”, that is, capital’s ability to overcome crises of profitability through a displacement of its crisis tendencies, to include an analytical attention to the gendered, sexualised and racialised unwaged and underpaid (caring) labour that reproduces labour power within a capitalist economy.

Design/methodology/approach

A “care fix”, the author argues, involves attempts to manage a crisis of care in ways that do not resolve but merely displace the crisis, perpetuating the systemic imperative of capital to off-load the cost of social reproduction and care, thereby constituting a crucial dynamic of capitalist development and restructuring and resulting in the reorganisation of gendered and racialised class relations and historically contingent regimes of reproduction.

Findings

The maceration of the Fordist regime of reproduction under neoliberalism has given way to a new post-Fordist arrangement that, having exhausted its care fix, is now once again in crisis. A new care fix is currently under way, while at the same time it is being contested and redirected by the contemporary struggles over social reproduction, care and democracy.

Research limitations/implications

Consequently, the author discusses the emergence of the notion of “caring capitalism” and contrasts this with proposals for democratising care, in turn investigating these developments in the context of an ongoing crisis of political representation in Europe and offering a notion of “care municipalism” as a possible way forward.

Practical implications

The practical implications concern the possibility of democratising the care sector.

Social implications

The social implications pertain to the questions of how social, political and economic institutions shift when care is placed on their agenda.

Originality/value

The value of this paper is to make a theoretical contribution to the analysis of changing configurations of care, social reproduction and society in relation to questions of democracy.
Intra-team conflict: the moderating effect of emotional self-leadership
Authors: Flores Hector R. , Jiang Xueting , Manz Charles C.
Published: May 2018

Purpose

The aim of this paper is to present a model of the moderating role of emotional self-leadership on the cognitive conflict–affective conflict relationship and their effect on work team decision quality.

Design/methodology/approach

This paper draws upon extant theoretical and empirical research on the conflict, leadership and emotions literature works to argue for the role of emotional self-leadership as a boundary condition of the intra-team conflict–work team decision quality relationship.

Findings

Key to understanding why cognitive conflict sometimes leads to improved decision quality and sometimes it does not is the role of emotional self-leadership. Through emotional self-leadership, team members can actively anticipate, guide and focus their emotional responses to cognitive conflict and reduce their experience of affective conflict, improving team decision quality.

Research limitations/implications

Identifying and explaining the moderating role of emotional self-leadership represents important progress for reframing emotion regulation and emotional intelligence into a new theoretical lens that may yield more meaningful insights into self-managed teams’ research. If empirically supported, this moderating effect would help explain the contradictory results obtained in prior empirical studies.

Practical implications

Practitioners can diminish or avoid the negative effect of the type of conflict that lowers work team decision quality and preserve the positive effect of the type of conflict that improves work team decision quality by identifying and implementing ways to improve a work team’s level of collective emotional self-leadership.

Originality/value

This paper extends the emotions, leadership and conflict literature works into the current research on self-directed work teams’ effectiveness by bringing attention to the moderating role of emotional self-leadership and calls for empirical research on this subject.
From placemaking to sustainability citizenship
Authors: Beza Beau Bradley , Hernández-Garcia Jaime
Published: May 2018

Purpose

Placemaking is an established practice and research field. It takes on a spatial dimension created through a socio-political process where value and meaning are assigned to settings. An emerging concept, sustainability citizenship relies on social actors creating sustainable urban settings by working, sometimes, “outside” formal planning; offering an evolutionary step in the creation and understanding of community realised places. The purpose of this paper is twofold: examine one of Bogotá, Colombia’s informal settlements to explore the placemaking/sustainability citizenship relationship, and use this exploration as a means to argue the appropriateness of sustainability citizenship when investigating/realising settings in Bogotá’s informal settlements.

Design/methodology/approach

To address the paper’s aim, books, journal articles and monographs related to citizen/community participation, placemaking, citizenship (in Latin America and conceptually) and sustainability citizenship were collected and critically reviewed. Identification of these documents was achieved through a literature review of the library database at Deakin University and Pontificia Universidad Javeriana and the co-authors of this paper contributing to and reviewing submissions to the 2016 Routledge publication, Sustainability Citizenship. Field observation and engagement with the citizenry living in the informal settlements of Bogotá, Colombia were conducted at various times in 2013, 2014 and 2017.

Findings

Sustainability citizenship and placemaking are linked through their “process-driven” approach to realising places and use of the citizenry to enact change. In Bogotá, Colombia’s informal settlement of Caracoli, public spaces are created outside formal planning processes through alternative path dependencies and the resourcefulness of its citizens. Sustainability citizenship, rather than placemaking, can work outside formal planning and manoeuvre around established path dependencies, which offers an evolutionary step in the creation and understanding of community realised places in the global south.

Originality/value

This paper provides insight into the use of placemaking when explaining the realisation process of Bogotá, Colombia’s informal settlements. The paper’s contents also explore the placemaking/sustainability citizenship relationship, which in terms of the latter is a new citizenry dimension that can be used to provide new insight into the realisation process of public spaces in Bogotá’s informal settlements.
Rethinking participation: lessons from a municipal market in Athens
Authors: Vaiou Dina
Published: May 2018

Purpose

The paper aims to propose (re)thinking participation, a much-debated issue in urban studies, planning and development, both in its grass-roots and its institutional versions.

Design/methodology/approach

The paper draws from two phases of people’s participation concerning the re-use of a former municipal market in Athens, the Agora, in the neighborhood of Kypseli. The two phases represent two different approaches to “participation”: an initiative of local groups implementing participation as a site of radical possibility and an invited or induced process, in which the municipal authorities initiated the whole exercise.

Findings

The radically different starting points correspond to equally different perspectives with regard to the stakes and meanings of the respective participatory process, as well as the individuals and groups who are involved.

Originality/value

The paper approaches participation as a spatial process, producing interactions among people, creating emotional or material connections, exchanges and inevitably conflict, re-configuring (public) space and extending (urban) citizenship.
Placemaking and urban gardening: Himmelbeet case study in Berlin
Authors: Karge Toni
Published: May 2018

Purpose

This paper aims to examine urban community gardens from the urban planning perspective. The paper analyses the Berlin case study Himmelbeet and its relation to the concept of critical placemaking (Toolis, 2017) and placemaking principles of Madden and Schwartz (1999).

Design/methodology/approach

The study is based on participatory action research. It examines one specific case study in Berlin where the author volunteered for several years. The set of placemaking principles is used as an ex-post analysis tool to evaluate how the community garden meets the criteria of placemaking.

Findings

The paper shows that the urban community garden can be considered as a placemaking scheme although it was not planned with placemaking instruments. The garden’s placemaking process shows strategies to challenge issues of exclusion, disinvestment and depoliticization of public spaces and thus exemplifies the possibilities of citizen-controlled placemaking processes.

Originality/value

The paper links placemaking with urban community gardens by assessing the placemaking principles and discussing the criteria of critical placemaking. The paper also contributes to a better understanding of urban community gardens in relation to current trends of austerity and urban inequalities.
The evolving role of public libraries in South Africa in addressing information poverty
Authors: J. Strand Karla , Britz Johannes
Published: May 2018

Purpose

The purpose of this paper is to provide an overview of the historical development of libraries in South Africa against a backdrop of poverty and social inequality. In particular, this paper illustrates how the development of libraries in South Africa both reflected and influenced information poverty and has as its goal to increase awareness of the role of libraries in the alleviation of information poverty.

Design/methodology/approach

The information in this paper is based on doctoral research completed by the author who investigated the role of libraries in the alleviation of information poverty in South Africa. The methodology for the research included two case studies, interviews, examination of library records, and observation. An extensive review of the professional literature and recorded histories provided imperative context for that research and this paper.

Findings

Findings indicate that libraries can play an important role in the alleviation of information poverty in South Africa. Libraries are underutilized in this role and in order to increase their capacity in addressing information poverty, one should consider the historical circumstances behind the dispossession of library services. Understanding the development of libraries in South Africa and sociopolitical ramifications of this development can encourage and inform greater participation of libraries in the alleviation of information poverty in the future.

Originality/value

This paper compiles the work and findings of previous studies on the history of South African libraries. The information provided here offers an accessible and efficient history of libraries in South Africa. In so doing, it provides context that is invaluable to the understanding of how the development of libraries throughout time can have sociopolitical effects on the people and their circumstances. The paper also encourages increased understanding of the value and purpose of libraries in combating information poverty in South Africa.