bluuebunny/crossref_metadata_2025 huggingface dataset:
Dance/Movement Therapy and Breast Cancer Care
Authors: Serlin Ilene A. , Goldov Nancy , Hansen Erika
Published: December 2017

Breast cancer causes the second highest mortality rate for any type of cancer. The illness, treatment, and side-effects can impact a woman’s identity, body image, and ability to function. Medical dance/movement therapy (MDMT) is a holistic therapeutic method uniquely suited to working with women with breast cancer. This chapter describes MDMT as an intervention that, through a safe and supportive environment that encourages creativity, can help develop psycho, social, and spiritual dimensions of women’s lives at a time when their life trajectory has been interrupted. It explores ways in which MDMT can enable women to rebuild their sense of self and their worlds. Arguments are put forward that create new meaning-making systems, confronting existential issues, and experiencing personal transformation through movement which can lead to enhanced wellbeing. A review of relevant literature is included to illustrate some key ideas of this work at individual, group, and ritual/community levels.
Subjective and Neurophysiological Perspectives on Emotion Perception from Dance
Authors: Grosbras Marie-Helene , Reason Matthew , Tan Haodan , Kay Rosie , Pollick Frank E.
Published: December 2017

Emotional engagement and aesthetic appreciation can be prime motivations for engaging with dance. Dance can therefore offer a valuable tool for the neuroscientific study of emotion processing. This idea underpinned the project Watching Dance, which investigated the neural correlates of subjective emotional response. Participants watched a four-minute video of contemporary dance involving two dancers and three music segments. Subjective emotional response was measured by continuous rating with a slider on an analogue scale, and structured interviews prompted participants to reflect on their ratings. The neural correlates were measured using functional brain imaging complemented by a brain interference study to investigate a causal link between regional brain activity and the subjective emotional response. A pattern of emotional rating emerged that was strongly influenced by both music and movement, as confirmed by the qualitative investigation. A direct link was established between posterior parietal cortex activity and emotional reaction to dance.
Writing Body Stories
Authors: Roberts June Gersten
Published: December 2017

Gerry Tuvey’s Body Stories project maps the life journey of her dancing body through the scars and memories of illness, injury, and surgery. Through solo dance performance, visual art, and video installation, Body Stories witnesses injury as physical knowledge. The author, writing as collaborative artist and video maker, reflects on Body Stories with a particular focus on four dance videos made for projection in the performance installation (three of which accompany this book). The fourth is a four-minute performance video of Turvey’s Body Stories performance at Huddersfield Art Gallery in 2013. The text reflects on positive wellbeing experiences found through participating in autobiographic storytelling, and explores sites for locating wellbeing within the videos, which offer absorbing, visceral framings of Turvey’s body, revealing both her vulnerability and her physical power. The chapter describes the concept of haptic visuality, delving into various video strategies that enhance, question, and recolour the pallet of subjective wellbeing.
Moving Systems
Authors: Schaub-Moore Claire
Published: December 2017

Every year, secondary schools face large numbers of drop-outs. To approach the inherent social and educational challenges, this two-year study applied a multidisciplinary understanding to the aspect of ‘individual learning’—in particular, on how current and past life experiences affect a young person’s capacity to learn, understand, communicate, and relate. In this study, three different semistructured ‘movement’-oriented interventions were offered to twenty-six ‘difficult’ pupils of an eighth grade at a German Hauptschule, their teachers, and their families. The results of the research project were very promising. All pupils passed their examinations and were able to continue with further education or training.
Body Memory and its Recuperation through Movement
Authors: Panhofer Heidrun
Published: December 2017

Departing from the Cartesian theory of body–mind duality, this chapter concerns the concept of body memory as it emerges from embodiment approaches. Building on concepts such as ‘kinetic melodies’ and the embodied mind, it advocates ‘thinking in movement’. Uniting minds and bodies has far-reaching implications for research and practice in dance and dance movement psychotherapy, hence a simple methodology of how to access the knowledge of the body is described. A process of writing–moving–writing invites the mover to focus on a significant moment to explore, and then bring it to movement. The mover is invited to work with ‘somatic modes of attention’, focusing on any extero- and interoceptive sensations. Clinical applications of the technique are discussed. The chapter aims to encourage educators, therapists, and researchers in dance and movement to make use of their knowing and remembering bodies, thus contributing to a global kind of knowledge in their field.
Authentic Movement as a Practice for Wellbeing
Authors: Bacon Jane
Published: December 2017

Practitioners working with the somatic practice of Authentic Movement often employ a holistic notion of wellbeing that includes psyche, soma, and spirit. This approach is widely believed to be crucial to the sense of wellbeing often generated. Authentic Movement, developed in the 1950s by Mary Starks Whitehouse, is an expressive and improvised movement practice based originally on the theories of C. G. Jung, to help individuals find their ‘authentic’ moving self. This is often a deeply liberating and transforming experience. In Authentic Movement, appropriate strategies are developed to engage the body as a moving container, as well as articulation strategies for bringing moving experiences into language. These allow the participant to experience a sense of ‘authenticity’ that is beyond current ego consciousness. This chapter aims to explore Authentic Movement as a philosophy to understand more fully how this practice might help transform trauma and engender wellbeing.
Authentic Movement and the Relationship of Embodied Spirituality to Health and Wellbeing
Authors: Avstreih Zoe
Published: December 2017

This chapter explores the possibility of a relationship between spiritual practices and some of the many facets of wellbeing. It considers the distinction between religion and spirituality with reference to the literature. It discusses Authentic Movement, an inner-directed movement process rooted in the intersection of dance/movement therapy and Jungian depth psychology, and the concept of embodied spirituality in which the relationship between the mover and the witness is explored. In particular, it explores the relationship of this practice to health and the increased sense of wellbeing that stems from a direct experience of the sacred, which supports a deepening sense of connection to one’s true self.
Suppression of Meloidogyne incognita by the Entomopathogenic Fungus Lecanicillium muscarium
Authors: Hussain Manzoor , Zouhar Miloslav , Ryšánek Pavel
Published: December 2017

The entomopathogenic fungus Lecanicillium muscarium (Petch) Zare and Gams is currently being developed as a biocontrol agent against insect pests, as well as some plant-pathogenic fungi and bacteria. Data about its activity against plant-parasitic nematodes exist, but are relatively limited. To expand this understanding, we investigated the biocontrol efficiency of three isolates of L. muscarium (Lm) against the root knot nematode, Meloidogyne incognita, in both in vitro and in vivo conditions. In our experiments, the maximum number of nematode eggs, juveniles (J2s), females, and egg masses that were parasitized were quantified after a 72-h exposure to the fungus. The isolate Lm1 was designated as the best biocontrol agent against nematode eggs as well as J2s. It showed the highest colonization of eggs and significantly decreased egg hatching events. The results from two additional isolates, Lm2 and Lm3, were also significant (P = 0.05) but less pronounced than those observed with Lm1. L. muscarium treatments had significant (P = 0.05) positive effects on plant shoot and root growth compared with the growth of control plants. These results suggest the effectiveness of the fungus may be due to either the infection of eggs and J2s, or the production of secondary metabolites that induced plant defense mechanisms and lead to systemic resistance. Our study demonstrates that L. muscarium could be used as a potential biocontrol agent against root knot nematodes.
Academic Support Programs Utilized for Nursing Students at Risk of Academic Failure: A Review of the Literature
Authors: Freeman Julie C. , All Anita
Published: December 2017

AIM

The purpose of the literature review is to evaluate and discuss the various types of academic support programs used for at-risk nursing students to identify those that are most effective.

BACKGROUND

Nurse educators are concerned about students admitted to nursing programs who are unable to successfully complete the program.

METHOD

To determine the format and efficacy of academic support programs, the literature review addressed the identification of at-risk students and academic support programs applicable to all student groups.

RESULTS

Nurse educators need to develop and implement plans to support and retain students in order to address the impending nursing shortage.

CONCLUSION

Replacing a student lost to academic failure is difficult. Although utilized in different manners, academic support programs are an effective retention strategy.
Nursing Living-Learning Communities and Student Retention: A Qualitative Study
Authors: Bauer Renee N. , Kiger Susan
Published: December 2017

BACKGROUND

Living-learning communities have been known to promote student performance and a sense of collegiality. Most studies on this topic have utilized quantitative methods.

AIM

This qualitative comparison case study examined personal experiences associated with residing in a living-learning community. The study was conducted to explore findings associated with promoting student retention. A secondary goal was to explore student experiences with mentoring.

METHOD

Data were collected using taped recordings of live interviews at two universities that have nursing-themed housing. The targeted sample size was 14.

RESULTS

Themes that emerged from the data were mutual support, importance of the resident assistant, and self-determination.

CONCLUSION

Nursing students enjoy themed housing and especially desire the resident assistant to be a nursing student.
A Crisis in Competency: The Strategic and Ethical Imperative to Assessing New Graduate Nurses’ Clinical Reasoning
Authors: Kavanagh Joan M. , Szweda Christine
Published: December 2017

AIM

The aim of the study was to assess entry-level competency and practice readiness of newly graduated nurses.

BACKGROUND

Literature on success of new graduates focuses primarily on National Council of State Boards of Nursing Licensure Examination (NCLEX-RN) pass rates, creating a false and incomplete picture of practice readiness.

METHOD

Posthire and prestart Performance-Based Development System assessments were administered to more than 5,000 newly graduated nurses at a large midwestern academic medical center between July 2010 and July 2015.

RESULTS

Aggregate baseline data indicate that only 23 percent of newly graduated nurses demonstrate entry-level competencies and practice readiness.

CONCLUSION

New data suggest that we are losing ground in the quest for entry-level competency. Graduates often are underprepared to operate in the complex field of professional practice where increased patient acuity and decreased length of stay, coupled with a lack of deep learning in our academic nursing programs, have exacerbated a crisis in competency.
Administrator Perspectives of Advantages and Challenges of Employing Part-Time Faculty in Nursing Education Programs: Two Sides of the Same Coin
Authors: Meyer Jacqueline Rose
Published: December 2017

AIM

The purpose of this qualitative research was to explore perspectives of administrators (n = 581) regarding advantages and challenges of employing part-time nurse faculty (PTNF) in schools of nursing in the United States.

BACKGROUND

The nursing faculty shortage has resulted in increased reliance on PTNF who are clinical experts but often inexperienced as educators. A broader evidence base is necessary to develop effective strategies to support and retain these faculty members.

METHOD

Deans and directors of schools of nursing were invited to complete an online survey with two open-ended questions about the use of PTNF.

RESULTS

Five themes emerged from the qualitative descriptive analysis: clinical practice as primary role, diversity of educational approaches, effects on full-time faculty role, economic impact, and contracted educator role. Both positive and negative aspects of each theme were identified.

CONCLUSION

Results of this study support specific efforts to provide professional development and support to PTNF.
Ventilator-Free Day Outcomes Can Be Misleading
Authors: Bodet-Contentin Laetitia , Frasca Denis , Tavernier Elsa , Feuillet Fanny , Foucher Yohann , Giraudeau Bruno
Published: December 2017

Introduction:

Acute respiratory distress syndrome often requires invasive mechanical ventilation, with both mortality and mechanical ventilation duration as outcomes of interest. The concept of ventilator-free days has been proposed as an outcome combining these two outcomes. Here we analyzed the construction of the ventilator-free day outcome and provided a hypothetical scenario to alert physicians that such an outcome can lead to misleading interpretations.

Methods:

We proposed the isoventilator-free day curve concept and, using an analytical development, illustrated how a median ventilator-free day value can actually result from very different combinations of death rates and mechanical ventilation durations. We also used a hypothetical example to compare the Student t test, Wilcoxon rank-sum test, and Gray test (which accounts for death as a competing event with extubation) in comparing exposition to mechanical ventilation.

Results:

A median ventilator-free day value of 10 days may mean that 10% of the patients died while survivors were ventilated during a median of 14 days or that 40% died while survivors were ventilated during a median of 5 days. Changing the time horizon affected the Student t test but not the Wilcoxon rank-sum result. The Gray test was more relevant than both the Student t test and Wilcoxon rank-sum test in identifying differences in groups showing highly different mechanical ventilation duration, despite equal median ventilator-free days. This approach was also illustrated using real data.

Conclusions:

Use of ventilator-free days as an outcome appears to have many drawbacks. Suitable methods of analyzing time to extubation should be preferred.
Sudden Cardiac Death in Hypertrophic Cardiomyopathy
Authors: Adamczak Daria M. , Oko-Sarnowska Zofia
Published: December 2017

Hypertrophic cardiomyopathy (HCM) is a heart disease characterized by hypertrophy of the left ventricular myocardium and is most often caused by mutations in sarcomere genes. The structural and functional abnormalities are not explained by flow-limiting coronary artery disease or loading conditions. The disease affects at least 0.2% of the population worldwide and is the most common cause of sudden cardiac death in young people and competitive athletes because of fatal ventricular arrhythmia. In some patients, however, HCM has a benign course. Therefore, it is of utmost importance to properly evaluate patients and single out those who would benefit from an implanted cardioverter defibrillator. In this article, we review and summarize the sudden cardiac death risk stratification algorithms, methods of preventing death due to HCM, and novel factors that may improve the existing prediction models.
Mandibular Reconstruction Using a Customized Three-Dimensional Titanium Implant Applied on the Lingual Surface of the Mandible
Authors: Jo You-Young , Kim Seong-Gon , Kim Min-Keun , Shin Sung-Ho , Ahn Janghoon , Seok Hyun
Published: December 2017

A patient had a right mandibular defect due to resection of an ameloblastoma. Previously, the defect had been reconstructed by an iliac bone graft, and subsequently, a titanium mesh with xenograft was used. However, it was not successfully reconstructed. For the recovery of mandible continuity and rehabilitation of jaw movement, we manufactured a customized 3-dimensional titanium implant by computer-aided design and manufacturing and electron beam melting technology. This implant was designed to have a porous body structure and lingual plate. The customized implant was accurately inserted in the bony defect. As a result, the patient showed a normal range of mouth opening and jaw movement. New bone migration was observed in the porous structure of the implant. Although there was a slight plate exposure and lack of alveolar bone formation, the customized 3D titanium implant successfully reconstructed the mandibular discontinuous defect and recovered jaw movement.
Mucosal Dehiscence After Alveolar Bone Graft in Cleft
Authors: Amodeo Giulia , Scopelliti Domenico
Published: December 2017

Cleft lip and palate patient represent a challenging experience for the surgeon. This kind of patients had to be followed by a multidisciplinary team from the beginning to the end to avoid the deformation sequelae. During the several surgical procedures, the bone graft represents a possible procedure that, through the new procedure, could be avoided. Unfortunately, patient treated following the previous procedure must be submitted to alveolar bone graft to coordinate the arch, to restore the maxillary integrity, to allow the correct dentition.
When Can We Predict the Outcome of an Electroconvulsive Therapy Course in Adolescents?
Authors: Maoz Hagai , Nitzan Uri , Goldwyn Yiftach , Krieger Israel , Bloch Yuval
Published: December 2017

Objective

There is a dearth of up-to-date literature regarding electroconvulsive therapy (ECT) in adolescents, and the question of when to pronounce course failure has not been properly addressed. The current study aims to evaluate trajectories of clinical status throughout ECT courses in adolescent patients.

Methods

We retrieved detailed data of 36 patients who received ECT in our treatment center. Clinical records were retrospectively assessed and evaluated every 6 ECT sessions to quantify Clinical Global Impressions-Improvement (CGI-I) scores.

Results

The mean number of sessions per course was 24.4 ± 14.2. The mean CGI-I score at the conclusion of the ECT courses was 2.47 ± 1.19. At the end of the acute treatment stage, 26 patients (72.2%) were much or very much improved, based on CGI-I scores. Only 5 patients exhibited a significant response after 6 sessions or fewer, whereas 21 patients (56.6%) improved after 12 sessions. Pearson correlations between CGI-I scores throughout the course of ECT showed no significant correlation between CGI-I scores after 6 sessions and the final CGI-I scores. However, a significant correlation was found between CGI-I scores after 12 sessions and the final CGI-I score.

Conclusions

An improvement in the clinical status of adolescents treated by ECT might occur only after a substantial number of sessions. An early lack of response does not necessarily predict a failed ECT course.
ICTV Virus Taxonomy Profile: Partitiviridae
Authors: Vainio Eeva J. , Chiba Sotaro , Ghabrial Said A. , Maiss Edgar , Roossinck Marilyn , Sabanadzovic Sead , Suzuki Nobuhiro , Xie Jiatao , Nibert Max ,   ICTV Report Consortium
Published: December 2017

The Partitiviridae is a family of small, isometric, non-enveloped viruses with bisegmented double-stranded (ds) RNA genomes of 3–4.8 kbp. The two genome segments are individually encapsidated. The family has five genera, with characteristic hosts for members of each genus: either plants or fungi for genera Alphapartitivirus and Betapartitivirus, fungi for genus Gammapartitivirus, plants for genus Deltapartitivirus and protozoa for genus Cryspovirus. Partitiviruses are transmitted intracellularly via seeds (plants), oocysts (protozoa) or hyphal anastomosis, cell division and sporogenesis (fungi); there are no known natural vectors. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Partitiviridae, which is available at www.ictv.global/report/partitiviridae.
Vibrio cholerae genomic diversity within and between patients
Authors: Levade Inès , Terrat Yves , Leducq Jean-Baptiste , Weil Ana A. , Mayo-Smith Leslie M. , Chowdhury Fahima , Khan Ashraful I. , Boncy Jacques , Buteau Josiane , Ivers Louise C. , Ryan Edward T. , Charles Richelle C. , Calderwood Stephen B. , Qadri Firdausi , Harris Jason B. , LaRocque Regina C. , Shapiro B. Jesse
Published: December 2017

Cholera is a severe, water-borne diarrhoeal disease caused by toxin-producing strains of the bacterium Vibrio cholerae. Comparative genomics has revealed ‘waves’ of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent of V. cholerae genetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterized V. cholerae genomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti. To capture within-patient diversity, we isolated multiple (8 to 20) V. cholerae colonies from each of eight patients, sequenced their genomes and identified point mutations and gene gain/loss events. We found limited but detectable diversity at the level of point mutations within hosts (zero to three single nucleotide variants within each patient), and comparatively higher gene content variation within hosts (at least one gain/loss event per patient, and up to 103 events in one patient). Much of the gene content variation appeared to be due to gain and loss of phage and plasmids within the V. cholerae population, with occasional exchanges between V. cholerae and other members of the gut microbiota. We also show that certain intra-host variants have phenotypic consequences. For example, the acquisition of a Bacteroides plasmid and non-synonymous mutations in a sensor histidine kinase gene both reduced biofilm formation, an important trait for environmental survival. Together, our results show that V. cholerae is measurably evolving within patients, with possible implications for disease outcomes and transmission dynamics.
Diagnostic utility of telomere length measurement in a hospital setting
Authors: Alder Jonathan K. , Hanumanthu Vidya Sagar , Strong Margaret A. , DeZern Amy E. , Stanley Susan E. , Takemoto Clifford M. , Danilova Ludmila , Applegate Carolyn D. , Bolton Stephen G. , Mohr David W. , Brodsky Robert A. , Casella James F. , Greider Carol W. , Jackson J. Brooks , Armanios Mary
Published: December 2017

Very short telomere length (TL) provokes cellular senescence in vitro, but the clinical utility of TL measurement in a hospital-based setting has not been determined. We tested the diagnostic and prognostic value of TL measurement by flow cytometry and fluorescence in situ hybridization (flowFISH) in individuals with mutations in telomerase and telomere maintenance genes, and examined prospectively whether TL altered treatment decisions for patients with bone marrow failure. TL had a definable normal range across populations with discrete lower and upper boundaries. TL above the 50th age-adjusted percentile had a 100% negative predictive value for clinically relevant mutations in telomere maintenance genes, but the lower threshold for diagnosis was age-dependent. The extent of deviation from the age-adjusted median correlated with the age at diagnosis of a telomere syndrome as well as the predominant complication. Mild short telomere defects manifested in adults as pulmonary fibrosis-emphysema, while severely short TL manifested in children as bone marrow failure and immunodeficiency. Among 38 newly diagnosed patients with bone marrow failure, TL shorter than the 1st age-adjusted percentile enriched for patients with germline mutations in inherited bone marrow failure genes, such as RUNX1, in addition to telomere maintenance genes. The TL result modified the hematopoietic stem cell donor choice and/or treatment regimen in one-fourth of the cases (9 of 38,24%). TL testing by flowFISH has diagnostic and predictive value in definable clinical settings. In patients with bone marrow failure, it altered treatment decisions for a significant subset.
Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Celiac Disease Patients and Controls
Authors: Bodkhe Rahul , Shetty Sudarshan A. , Dhotre Dhiraj P. , Verma Anil K. , Bhatia Khushbo , Mishra Asha , Kaur Gurvinder , Pande Pranav , Bangarusamy Dhinoth K. , Santosh Beena P. , Perumal Rajadurai C. , Ahuja Vineet , Shouche Yogesh S. , Makharia Govind K.
Published: December 2017

Recent studies on celiac disease (CeD) have shown the role of gut microbiota alterations in CeD pathogenesis. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific taxa between pre-diseases and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to faecal samples indicating larger disruption of microbiota at disease site. Increased abundance of specific Helicobacter ASVs were observed in duodenum of CeD when compared to FDR (p < 0.01). In case of fecal samples CeD microbiome and Actinomyces. In addition, predicted functional metagenome showed reduced ability of gluten that ecosystem level diversity measures (except in the duodenum) were not significantly different is characterized by reduced abundance of beneficial taxa such as Akkermansia, Ruminococcus degradation by CeD faecal microbiota in comparison to FDRs and controls.
Patterns of selection reveal shared molecular targets over short and long evolutionary timescales
Authors: Li Jing , Vázquez-García Ignacio , Persson Karl , González Asier , Yue Jia-Xing , Barré Benjamin , Hall Michael N. , Long Anthony D. , Warringer Jonas , Mustonen Ville , Liti Gianni
Published: December 2017

Standing andde novogenetic variants can both drive adaptation to environmental changes, but their relative contributions and interplay remain poorly understood. Here we investigated the dynamics of drug adaptation in yeast populations with different levels of standing variation by experimental evolution coupled with time-resolved sequencing and phenotyping. We found a doubling of standing variation alone boost the adaptation by 64.1% and 51.5% in hydroxyuea and rapamycin respectively. The causative standing andde novovariants were selected on shared targets ofRNR4in hydroxyurea andTOR1, TOR2in rapamycin. The standing andde novoTOR variants map to different functional domains and act via distinct mechanisms. Interestingly, standing TOR variants from two domesticated strains exhibited opposite resistance effects, reflecting lineage-specific functional divergence. This study provides a dynamic view on how standing andde novovariants interactively drive adaptation and deepens our understanding of clonally evolving diseases.
Shared and distinct transcriptomic cell types across neocortical areas
Authors: Tasic Bosiljka , Yao Zizhen , Smith Kimberly A. , Graybuck Lucas , Nguyen Thuc Nghi , Bertagnolli Darren , Goldy Jeff , Garren Emma , Economo Michael N. , Viswanathan Sarada , Penn Osnat , Bakken Trygve , Menon Vilas , Miller Jeremy , Fong Olivia , Hirokawa Karla E. , Lathia Kanan , Rimorin Christine , Tieu Michael , Larsen Rachael , Casper Tamara , Barkan Eliza , Kroll Matthew , Parry Seana , Shapovalova Nadiya V. , Hirchstein Daniel , Pendergraft Julie , Kim Tae Kyung , Szafer Aaron , Dee Nick , Groblewski Peter , Wickersham Ian , Cetin Ali , Harris Julie A. , Levi Boaz P. , Sunkin Susan M , Madisen Linda , Daigle Tanya L. , Looger Loren , Bernard Amy , Phillips John , Lein Ed , Hawrylycz Michael , Svoboda Karel , Jones Allan R. , Koch Christof , Zeng Hongkui
Published: December 2017

Neocortex contains a multitude of cell types segregated into layers and functionally distinct regions. To investigate the diversity of cell types across the mouse neocortex, we analyzed 12,714 cells from the primary visual cortex (VISp), and 9,035 cells from the anterior lateral motor cortex (ALM) by deep single-cell RNA-sequencing (scRNA-seq), identifying 116 transcriptomic cell types. These two regions represent distant poles of the neocortex and perform distinct functions. We define 50 inhibitory transcriptomic cell types, all of which are shared across both cortical regions. In contrast, 49 of 52 excitatory transcriptomic types were found in either VISp or ALM, with only three present in both. By combining single cell RNA-seq and retrograde labeling, we demonstrate correspondence between excitatory transcriptomic types and their region-specific long-range target specificity. This study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct regions of the mouse cortex.
Estrogen receptor inhibition enhances cold-induced adipocyte beiging and glucose sensitivity
Authors: Lapid Kfir , Lim Ajin , Berglund Eric D. , Graff Jonathan M.
Published: December 2017

Low estrogen states, exemplified by postmenopausal women, are associated with increased adiposity and metabolic dysfunction. We recently reported a paradox, in which a conditional estrogen receptor-alpha (ERα) mutant mouse shows a hyper-metabolic phenotype with enhanced brown/beige cell formation (“browning/beiging”). These observations led us to consider that although systemic deficiency of estrogen or ERα in mice results in obesity and glucose intolerance at room-temperature, cold-exposure might induce enhanced browning/beiging and improve glucose metabolism. Remarkably, studying cold-exposure in mouse models of inhibited estrogen signaling - ERαKO mice, ovariectomy, and treatment with the ERα antagonist Fulvestrant - supported this notion. ERα/estrogen deficient mice demonstrated enhanced cold-induced beiging, reduced adiposity and increased glucose sensitivity. Fulvestrant was also effective in diet-induced obesity settings. Mechanistically, ERα inhibition sensitized cell-autonomous beige cell differentiation and stimulation, including β3-adrenoreceptor-dependent adipocyte beiging. Taken together, our findings highlight a therapeutic potential for obese/diabetic postmenopausal patients.
Building Large Updatable Colored de Bruijn Graphs via Merging
Authors: Muggli Martin D , Alipanahi Bahar , Boucher Christina
Published: December 2017

MOTIVATION: There exists several massive genomic and metagenomic data collection efforts, including GenomeTrakr and MetaSub, which are routinely updated with new data. To analyze such datasets, memory-efficient methods to construct and store the colored de Bruijn graph have been developed. Yet, a problem that has not been considered is constructing the colored de Bruijn graph in a scalable manner that allows new data to be added without reconstruction. This problem is important for large public datasets as scalability is needed but also the ability to update the construction is also needed. RESULTS: We create a method for constructing and updating the colored de Bruijn graph on a very-large dataset through partitioning the data into smaller subsets, building the colored de Bruijn graph using a FM-index based representation, and succinctly merging these representations to build a single graph. The last step, merging succinctly, is the algorithmic challenge which we solve in this paper. We refer to the resulting method as VariMerge. We validate our approach, and show it produces a three-fold reduction in working space when constructing a colored de Bruijn graph for 8,000 strains. Lastly, we compare VariMerge to other competing methods --- including Vari, Rainbowfish, Mantis, Bloom Filter Trie, the method by Almodaresi(2019) and Multi-BRWT --- and illustrate that VariMerge is the only method that is capable of building the colored de Bruijn graph for 16,000 strains in a manner that allows additional samples to be added. Competing methods either did not scale to this large of a dataset or cannot allow for additions without reconstruction. AVAILABILITY: Our software is available under GPLv3 at https://github.com/cosmo-team/cosmo/tree/VARI-merge.
Evaluating stably expressed genes in single cells
Authors: Lin Yingxin , Ghazanfar Shila , Strbenac Dario , Wang Andy , Patrick Ellis , Lin Dave , Speed Terence , Yang Jean YH , Yang Pengyi
Published: December 2017

Background

Single-cell RNA-seq (scRNA-seq) profiling has revealed remarkable variation in transcription, suggesting that expression of many genes at the single-cell level are intrinsically stochastic and noisy. Yet, on cell population level, a subset of genes traditionally referred to as housekeeping genes (HKGs) are found to be stably expressed in different cell and tissue types. It is therefore critical to question whether stably expressed genes (SEGs) can be identified on the single-cell level, and if so, how their expression stability can be assessed? We have developed a computational framework for ranking expression stability of genes in single cells. Here we evaluate the proposed framework and characterize SEGs derived from two scRNA-seq datasets that profile early human and mouse development.

Results

Here, we show that gene expression stability indices derived from the early human and mouse development scRNA-seq datasets are highly reproducible and conserved across species. We demonstrate that SEGs identified from single cells based on their stability indices are considerably more stable than HKGs defined previously from cell populations across 10 diverse biological systems. Our analyses indicate that SEGs are inherently more stable at the single-cell level and their characteristics reminiscent of HKGs, suggesting their potential role in sustaining essential functions in individual cells.

Conclusions

SEGs identified in this study have immediate utility both for understanding variation/stability of single-cell transcriptomes and for practical applications including scRNA-seq data normalization, the proposed framework can be applied to identify genes with stable expression in other scRNA-seq datasets.
Shifts in diversification rates and host jump frequencies shaped the diversity of host range amongSclerotiniaceaefungal plant pathogens
Authors: Navaud Olivier , Barbacci Adelin , Taylor Andrew , Clarkson John P. , Raffaele Sylvain
Published: December 2017

The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within theSclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in theSclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Consistent with previous reports on oomycete parasites, our findings suggest that host jump and radiation, possibly combined with low speciation rates, could associate with the emergence of generalist pathogens. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.
Learning from mistakes: Accurate prediction of cell type-specific transcription factor binding
Authors: Keilwagen Jens , Posch Stefan , Grau Jan
Published: December 2017

Computational prediction of cell type-specific, in-vivo transcription factor binding sites is still one of the central challenges in regulatory genomics, and a variety of approaches has been proposed for this purpose.

Here, we present our approach that earned a shared first rank in the “ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge” in 2017. This approach employs features derived from chromatin accessibility, binding motifs, gene expression, genomic sequence and annotation to train classifiers using a supervised, discriminative learning principle. Two further key aspects of this approach are learning classifier parameters in an iterative training procedure that successively adds additional negative examples to the training set, and creating an ensemble prediction by averaging over classifiers obtained for different training cell types.

In post-challenge analyses, we benchmark the influence of different feature sets and find that chromatin accessiblity and binding motifs are sufficient to yield state-of-the-art performance for in-vivo binding site predictions. We also show that the iterative training procedure and the ensemble prediction are pivotal for the final prediction performance.

To make predictions of this approach readily accessible, we predict 682 peak lists for a total of 31 transcription factors in 22 primary cell types and tissues, which are available for download at https://www.synapse.org/#!Synapse:syn11526239, and we demonstrate that these may help to yield biological conclusions. Finally, we provide a user-friendly version of our approach as open source software at http://jstacs.de/index.php/Catchitt.

Contact

grau@informatik.uni-halle.de
Network analysis of mass spectrometry imaging data from colorectal cancer identifies key metabolites common to metastatic development
Authors: Inglese Paolo , Strittmatter Nicole , Doria Luisa , Mroz Anna , Speller Abigail , Poynter Liam , Dannhorn Andreas , Kudo Hiromi , Mirnezami Reza , Goldin Robert D , Nicholson Jeremy K , Takats Zoltan , Glen Robert C
Published: December 2017

A deeper understanding of inter-tumor and intra-tumor heterogeneity is a critical factor for the advancement of next generation strategies against cancer. The heterogeneous morphology exhibited by solid tumors is mirrored by their metabolic heterogeneity. Defining the basic biological mechanisms that underlie tumor cell variability will be fundamental to the development of personalized cancer treatments. Variability in the molecular signatures found in local regions of cancer tissues can be captured through an untargeted analysis of their metabolic constituents. Here we demonstrate that DESI mass spectrometry imaging (MSI) combined with network analysis can provide detailed insight into the metabolic heterogeneity of colorectal cancer (CRC). We show that network modules capture signatures which differentiate tumor metabolism in the core and in the surrounding region. Moreover, module preservation analysis of network modules between patients with and without metastatic recurrence explains the inter-subject metabolic differences associated with diverse clinical outcomes such as metastatic recurrence.

Significance

Network analysis of DESI-MSI data from CRC human tissue reveals clinically relevant co-expression ion patterns associated with metastatic susceptibility. This delineates a more complex picture of tumor heterogeneity than conventional hard segmentation algorithms. Using tissue sections from central regions and at a distance from the tumor center, ion co-expression patterns reveal common features among patients who developed metastases (up of > 5 years) not preserved in patients who did not develop metastases. This offers insight into the nature of the complex molecular interactions associated with cancer recurrence. Presently, predicting CRC relapse is challenging, and histopathologically like-for-like cancers frequently manifest widely varying metastatic tendencies. Thus, the methodology introduced here more robustly defines the risk of metastases based on tumor biochemical heterogeneity.

Author contributions

P.I., Z.T., R.C.G.: designed the study, developed the workflow, analyzed the data, interpreted the results, wrote the paper; N.S. collected the MS, performed the H…E staining, wrote the paper; L.D.: interpreted the results, wrote the paper; A.M.: collected the MS; A.S.: histological assessment; L.P.: collected the tissue specimens and clinical metadata; A.D.: collected the MS; H.K.: performed the H…E staining; R.M.: collected the tissue specimens and clinical metadata. R.G.: histological assessment; J.K.N: designed the study, edited the paper.
Evolutionary plasticity in the innate immune function of Akirin
Authors: Polanowska Jolanta , Chen Jia-Xuan , Soulé Julien , Omi Shizue , Belougne Jerome , Taffoni Clara , Pujol Nathalie , Selbach Matthias , Zugasti Olivier , Ewbank Jonathan J.
Published: December 2017

Eukaryotic gene expression requires the coordinated action of transcription factors, chromatin remodelling complexes and RNA polymerase. The conserved nuclear protein Akirin plays a central role in immune gene expression in insects and mammals, linking the SWI/SNF chromatin-remodelling complex with the transcription factor NFκB. Although nematodes lack NFκB, Akirin is also indispensable for the expression of defence genes in the epidermis of Caenorhabditis elegans following natural fungal infection. Through a combination of reverse genetics and biochemistry, we discovered that in C. elegans Akirin has conserved its role of bridging chromatin-remodellers and transcription factors, but that the identity of its functional partners is different since it forms a physical complex with NuRD proteins and the POU-class transcription factor CEH-18. In addition to providing a substantial step forward in our understanding of innate immune gene regulation in C. elegans, our results give insight into the molecular evolution of lineage-specific signalling pathways.
Shell Nigeria’s Global Memorandum of Understanding and corporate-community accountability relations
Authors: Egbon Osamuyimen , Idemudia Uwafiokun , Amaeshi Kenneth
Published: December 2017

Purpose

The purpose of this paper is to examine whether Shell Nigeria’s Global Memorandum of Understanding (GMoU) promotes corporate-community accountability as a basis for fostering sustainable community development in the Niger Delta.

Design/methodology/approach

Shell Nigeria’s GMoU stand-alone reports were analysed through the lenses of accountability and transparency theoretical frameworks to explore the extent to which GMoU, as a corporate social responsibility (CSR) initiative, is dialogically embedded and practised. Meaning-oriented content analysis was deductively used to isolate pertinent themes and generate findings from the background theoretical literature.

Findings

The authors find that Shell discursively appropriates the meaning of accountability and transparency in a manner that allows it to maintain its social legitimacy and the asymmetric power relations between itself and host communities whilst restricting communities’ agency to hold it accountable. Shell does this by interpreting the notion of participation restrictively, selectively deploying the concept of transparency and accountability and subtly exerting excessive control over the GMoU. Thus, the GMoU’s potential to contribute to sustainable community development and positive corporate-community relation is unlikely tenable.

Originality/value

Accountability and transparency are core and critical to corporate-community relations and for achieving community development CSR objectives, but are often taken for granted or ignored in the CSR literature on the Niger Delta of Nigeria. This paper addresses this gap in the literature by using accountability and transparency lenses to unpick GMoU model and contribute to studies on CSR practices by oil multinational corporations (MNCs) in developing countries. Indeed, the use of these lenses to explore CSR process offers new insights as to why CSR practices have failed to contribute to sustainable community development despite increased community spending by oil MNCs.
Transparency fallacy
Authors: Gold Stefan , Heikkurinen Pasi
Published: December 2017

Purpose

The purpose of this paper is to focus on the research question of how stakeholder claims for transparency work as a means to support responsibility in the international supply chain.

Design/methodology/approach

This theoretical study analyses the relationship between stakeholder claims for corporate transparency and responsible business in the global context, and develops a conceptual model for further theoretical and empirical work.

Findings

The study finds that the call for corporate transparency is insufficient as a means to increase responsibility within international supply chains. The erroneous belief that stakeholder claims for transparency will lead to responsible behaviour is identified as the “transparency fallacy”. The fallacy emerges from the denial of opacity in organisations and the blindness to the conditions of international supply chains (including complexity, distance, and resistance) that work against attempts to increase transparency.

Research limitations/implications

Acknowledging the limits of the transparency mechanism in both management theory and practice is necessary in order to advance responsible business in the international arena. Being conceptual in nature, the generic limitations of the type of research apply.

Practical implications

While acknowledging opacity, corporate managers and stakeholders should focus on changing the supply chain conditions to support responsible behaviour. This includes reducing complexity, distance, and resistance in the supply network.

Originality/value

This study contests the commonly assumed link between corporate transparency and responsibility, and sheds light on the limits and unintended consequences of stakeholder attempts to impose transparency on business organisations.