bluuebunny/crossref_metadata_2025_split huggingface dataset:
Update of the BIPM comparison BIPM.RI(II)-K1.Sn-113 of activity measurements of the radionuclide 113Sn to include the 2010 results of the PTB (Germany) and the LNE-LNHB (France), and the 2011 result of the CIEMAT (Spain)
Authors: Michotte C , Ratel G , Courte S , Kossert K , Nähle O , Bobin C , Lépy M - C , Moune M , Garcia-Toraño E , Peyres V , Roteta M 
Published: May 2016

Since 1975, seven national metrology institutes (NMI) have submitted eleven samples of known activity of 113Sn to the International Reference System (SIR) for activity comparison at the Bureau International des Poids et Mesures (BIPM), with comparison identifier BIPM.RI(II)-K1.Sn-113. The values of the activity submitted were between about 0.7 MBq and 22 MBq. The present primary standardization results for the PTB, Germany and the LNE-LNHB, France, replace their earlier results of 1989 and 1992, respectively. A key comparison reference value (KCRV) has been evaluated for the first time for 113Sn. There are only three results remaining in the BIPM.RI(II)-K1.Sn-113 comparison, all the previously published ones being outdated. The degrees of equivalence between each of these three equivalent activities measured in the SIR and the KCRV have been calculated and the results are given in the form of a table. A graphical presentation is also given.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Final report. SIM comparison in mass standards SIM.M.M-K4
Authors: Becerra L O , Peña L M , Luján L , Díaz J C , Centeno L M , Loayza V , Cacais F , Olman Ramos , Rodriguez S , Garcia Fe , Garcia Fr , Leyton F , Santo C , Caceres J , Kornblit F , Leiblich J , Jacques C 
Published: May 2016

This report summarizes the results of a SIM comparison of a 1 kg mass standard carried out by 7 NMIs. The results reported by the participants are consistent with each other and they can be linked to the comparison CCM.M-K4 with satisfactory degrees of equivalence.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
The Addiction-Related Protein ANKK1 is Differentially Expressed During the Cell Cycle in Neural Precursors
Authors: España-Serrano Laura , Guerra Martín-Palanco Noelia , Montero-Pedrazuela Ana , Pérez-Santamarina Estela , Vidal Rebeca , García-Consuegra Inés , Valdizán Elsa María , Pazos Angel , Palomo Tomás , Jiménez-Arriero Miguel Ángel , Guadaño-Ferraz Ana , Hoenicka Janet 
Published: May 2016

Abstract
TaqIA is a polymorphism associated with addictions and dopamine-related traits. It is located in the ankyrin repeat and kinase domain containing 1 gene (ANKK1) nearby the gene for the dopamine D2 receptor (D2R). Since ANKK1 function is unknown, TaqIA-associated traits have been explained only by differences in D2R. Here we report ANKK1 studies in mouse and human brain using quantitative real-time PCR, Western blot, immunohistochemistry, and flow cytometry. ANKK1 mRNA and protein isoforms vary along neurodevelopment in the human and mouse brain. In mouse adult brain ANKK1 is located in astrocytes, nuclei of postmitotic neurons and neural precursors from neurogenic niches. In both embryos and adults, nuclei of neural precursors show significant variation of ANKK1 intensity. We demonstrate a correlation between ANKK1 and the cell cycle. Cell synchronization experiments showed a significant increment of ANKK1-kinase in mitotic cells while ANKK1-kinase overexpression affects G1 and M phase that were found to be modulated by ANKK1 alleles and apomorphine treatment. Furthermore, during embryonic neurogenesis ANKK1 was expressed in slow-dividing neuroblasts and rapidly dividing precursors which are mitotic cells. These results suggest a role of ANKK1 during the cell cycle in neural precursors thus providing biological support to brain structure involvement in the TaqIA-associated phenotypes.
Antimicrobial combinations: Bliss independence and Loewe additivity derived from mechanistic multi-hit models
Authors: Baeder Desiree Y. , Yu Guozhi , Hozé Nathanaël , Rolff Jens , Regoes Roland R. 
Published: May 2016

Antimicrobial peptides (AMPs) and antibiotics reduce the net growth rate of bacterial populations they target. It is relevant to understand if effects of multiple antimicrobials are synergistic or antagonistic, in particular for AMP responses, because naturally occurring responses involve multiple AMPs. There are several competing proposals describing how multiple types of antimicrobials add up when applied in combination, such as Loewe additivity or Bliss independence. These additivity terms are defined ad hoc from abstract principles explaining the supposed interaction between the antimicrobials. Here, we link these ad hoc combination terms to a mathematical model that represents the dynamics of antimicrobial molecules hitting targets on bacterial cells. In this multi-hit model, bacteria are killed when a certain number of targets are hit by antimicrobials. Using this bottom-up approach reveals that Bliss independence should be the model of choice if no interaction between antimicrobial molecules is expected. Loewe additivity, on the other hand, describes scenarios in which antimicrobials affect the same components of the cell, i.e. are not acting independently. While our approach idealizes the dynamics of antimicrobials, it provides a conceptual underpinning of the additivity terms. The choice of the additivity term is essential to determine synergy or antagonism of antimicrobials.
This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.
Perspectives on the evolutionary ecology of arthropod antimicrobial peptides
Authors: Rolff Jens , Schmid-Hempel Paul 
Published: May 2016

Antimicrobial peptides (AMPs) are important elements of the innate immune defence in multicellular organisms that target and kill microbes. Here, we reflect on the various points that are raised by the authors of the 11 contributions to a special issue ofPhilosophical Transactionson the ‘evolutionary ecology of arthropod antimicrobial peptides'. We see five interesting topics emerging. (i) AMP genes in insects, and perhaps in arthropods more generally, evolve much slower than most other immune genes. One explanation refers to the constraints set by AMPs being part of a finely tuned defence system. A new view argues that AMPs are under strong stabilizing selection. Regardless, this striking observation still invites many more questions than have been answered so far. (ii) AMPs almost always are expressed in combinations and sometimes show expression patterns that are dependent on the infectious agent. While it is often assumed that this can be explained by synergistic interactions, such interactions have rarely been demonstrated and need to be studied further. Moreover, how to define synergy in the first place remains difficult and needs to be addressed. (iii) AMPs play a very important role in mediating the interaction between a host and its mutualistic or commensal microbes. This has only been studied in a very small number of (insect) species. It has become clear that the very same AMPs play different roles in different situations and hence are under concurrent selection. (iv) Different environments shape the physiology of organisms; especially the host-associated microbial communities should impact on the evolution host AMPs. Studies in social insects and some organisms from extreme environments seem to support this notion, but, overall, the evidence for adaptation of AMPs to a given environment is scant. (v) AMPs are considered or already developed as new drugs in medicine. However, bacteria can evolve resistance to AMPs. Therefore, in the light of our limited understanding of AMP evolution in the natural context, and also the very limited understanding of the evolution of resistance against AMPs in bacteria in particular, caution is recommended. What is clear though is that study of the ecology and evolution of AMPs in natural systems could inform many of these outstanding questions, including those related to medical applications and pathogen control.This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.
UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
Authors: Smith Tom , Heger Andreas , Sudbery Ian 
Published: May 2016

AbstractUnique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughout sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalised. In particular, sequencing errors in the UMI sequence are often ignored, or else resolved in an ad-hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single cell RNA-Seq datasets. Reproducibility between iCLIP replicates and single cell RNA-Seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package (https://github.com/CGATOxford/UMI-tools).
Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia
Authors: Fromer Menachem , Roussos Panos , Sieberts Solveig K , Johnson Jessica S , Kavanagh David H , Perumal Thanneer M , Ruderfer Douglas M , Oh Edwin C , Topol Aaron , Shah Hardik R , Klei Lambertus L , Kramer Robin , Pinto Dalila , Gümüş Zeynep H , Cicek A. Ercument , Dang Kristen K , Browne Andrew , Lu Cong , Xie Li , Readhead Ben , Stahl Eli A , Parvisi Mahsa , Hamamsy Tymor , Fullard John F , Wang Ying-Chih , Mahajan Milind C , Derry Jonathan M.J. , Dudley Joel , Hemby Scott E , Logsdon Benjamin A , Talbot Konrad , Raj Towfique , Bennett David A , De Jager Phil L , Zhu Jun , Zhang Bin , Sullivan Patrick F , Chess Andrew , Purcell Shaun M , Shinobu Leslie A , Mangravite Lara M , Toyoshiba Hiroyoshi , Gur Raquel E , Hahn Chang-Gyu , Lewis David A , Haroutonian Vahram , Peters Mette A , Lipska Barbara K , Buxbaum Joseph D , Schadt Eric E , Hirai Keisuke , Roeder Kathryn , Brennand Kristen J , Katsanis Nicholas , Dominici Enrico , Devlin Bernie , Sklar Pamela 
Published: May 2016

ABSTRACTOver 100 genetic loci harbor schizophrenia associated variants, yet how these common variants confer risk is uncertain. The CommonMind Consortium has sequenced dorsolateral prefrontal cortex RNA from schizophrenia cases (n=258) and control subjects (n=279), creating the largest publicly available resource to date of gene expression and its genetic regulation; ∼5 times larger than the latest release of GTEx. Using this resource, we find that ∼20% of the schizophrenia risk loci have common variants that could explain regulation of brain gene expression. In five loci, these variants modulate expression of a single gene:FURIN, TSNARE1, CNTN4, CLCN3 or SNAP91. Experimentally altered expression of three of them,FURIN,TSNARE1, andCNTN4, perturbs the proliferation and apoptotic index of neural progenitors and leads to neuroanatomical deficits in zebrafish. Furthermore, shRNA mediated knock-down ofFURIN1in neural progenitor cells derived from human induced pluripotent stem cells produces abnormal neural migration. Although 4.2% of genes (N = 693) display significant differential expression between cases and controls, 44% show some evidence for differential expression. All fold changes are ≤ 1.33, and an independent cohort yields similar differential expression for these 693 genes (r = 0.58). These findings are consistent with schizophrenia being highly polygenic, as has been reported in investigations of common and rare genetic variation. Co-expression analyses identify a gene module that shows enrichment for genetic associations and is thus relevant for schizophrenia. Taken together, these results pave the way for mechanistic interpretations of genetic liability for schizophrenia and other brain diseases.
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning
Authors: Wang Bo , Zhu Junjie , Pierson Emma , Ramazzotti Daniele , Batzoglou Serafim 
Published: May 2016

AbstractSingle-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical to identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. Here, we propose a novel similarity-learning framework, SIMLR (single-cell interpretation via multi-kernel learning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization applications. Benchmarking against state-of-the-art methods for these applications, we used SIMLR to re-analyse seven representative single-cell data sets, including high-throughput droplet-based data sets with tens of thousands of cells. We show that SIMLR greatly improves clustering sensitivity and accuracy, as well as the visualization and interpretability of the data.
EM and component-wise boosting for Hidden Markov Models: a machine-learning approach to capture-recapture
Authors: Rankin Robert W. 
Published: May 2016

AbstractThis study introduces statistical boosting for capture-mark-recapture (CMR) models. It is a shrinkage estimator that constrains the complexity of a CMR model in order to promote automatic variable-selection and avoid over-fitting. I discuss the philosophical similarities between boosting and AIC model-selection, and show through simulations that a boosted Cormack-Jolly-Seber model often out-performs AICc methods, in terms of estimating survival and abundance, yet yields qualitatively similar estimates. This new boosted CMR framework is highly extensible and could provide a rich, unified framework for addressing many topics in CMR, such as non-linear effects (splines and CART-like trees), individual-heterogeneity, and spatial components.
Whole-genome sequencing of an advanced case of small-cell gallbladder neuroendocrine carcinoma
Authors: Li Maolan , Liu Fatao , Zhang Yijian , Wu Xiangsong , Wu Wenguang , Wang Xu-An , Zhao Shuai , Liu Shibo , Liang Haibin , Zhang Fei , Gao Yuan , Xiang Shanshan , Li Huaifeng , Lu Wei , Weng Hao , Mu Jiasheng , Shu Yijun , Bao Runfa , Jiang Lin , Hu Yunping , Gong Wei , Zhang Yun , Ma Tieliang , Zhang Kai , Liu Yun , Liu Yingbin 
Published: May 2016

AbstractThe majority of gallbladder cancer cases are discovered at later stages, which frequently leads to poor prognoses. Small-cell gallbladder neuroendocrine carcinoma (GB-SCNEC) is a relatively rare histological type of gallbladder cancer, and its survival rate is exceptionally low because of its greater malignant potential. In addition, the genomic landscape of GB-SCNEC is rarely considered in treatment decisions. We performed whole-genome sequencing on an advanced case of GB-SCNEC. By analyzing the whole-genome sequencing data of the primary cancer tissue (76.29X coverage), lymphatic metastatic cancer tissue (73.92X coverage) and matched non-cancerous tissue (35.73X coverage), we identified approximately 900 high-quality somatic single nucleotide variants (SNVs), 109 of which were shared by both the primary and metastatic tumor tissues. Somatic non-synonymous coding variations with damaging impact in HMCN1 and CDH10 were observed in both the primary and metastatic tissue specimens. A pathway analysis of the genes mapped to the SNVs revealed gene enrichment associated with axon guidance, ERBB signaling, sulfur metabolism and calcium signaling. Furthermore, we identified 20 chromosomal rearrangements that included 11 deletions, 4 tandem duplications and 5 inversions that mapped to known genes. Two gene fusions, NCAM2-SGCZ and BTG3-CCDC40 were also discovered and validated by Sanger sequencing. Additionally, we identified genome-wide copy number variations and microsatellite instability. In this study, we identified novel biological markers of GB-SCNEC that may serve as valuable prognostic factors or indicators of treatment response in patients with GB-SCNEC with lymphatic metastasis.
The relationship between transformational leadership and effort-reward imbalance
Authors: Weiß Eva-Ellen , Süß Stefan 
Published: May 2016

Purpose
– The purpose of this paper is to investigate the relationship between transformational leadership and effort-reward imbalance as well as the moderating role of overcommitment and subjective well-being. In particular, the study focuses on the transformational leadership component individualized consideration and its relationship with effort-reward imbalance.

Design/methodology/approach
– Using linear hierarchical regression analyses, the authors tested four hypotheses on a broad sample of 229 German employees.

Findings
– The results confirm the expected relationship between transformational leadership and effort-reward imbalance and that the strongest relationship exists with individualized consideration. However, there is no support for the hypothesized moderating effects.

Research limitations/implications
– First, the recruitment of the sample via fora and periodicals may bias the results. Second, the dependent and the independent variables were assessed with the same method, thus facilitating a common method bias. Third, the study underlies a cross-sectional design which does not allow drawing conclusions on causality.

Practical implications
– The findings provide implications for leaders by showing that the most effective leadership behaviours are those encompassed by the transformational leadership component individualized consideration when it comes to reducing negative health effects of adverse working conditions. Furthermore, the results suggest that overcommitment plays a major role for employees’ effort-reward imbalance and should thus be addressed by specific training measures.

Originality/value
– Researchers have devoted little attention to revealing how effort-reward imbalance can be avoided or reduced by leaders. The study attempts to fill this gap by exploring the relationship between effort-reward imbalance and transformational leadership.
The impact of supervisor humor on newcomer adjustment
Authors: Gkorezis Panagiotis , Petridou Eugenia , Lioliou Katerina 
Published: May 2016

Purpose– Substantial research has examined the pivotal role of supervisor positive humor in generating employee outcomes. To date, though, little is known about the relationship between supervisor humor and newcomers’ adjustment. The purpose of this paper is to contribute to this gap by examining the effect of supervisor positive humor on newcomers’ adjustment. In doing so, the authors highlighted relational identification with the supervisor as a mediating mechanism that explains the aforementioned association.Design/methodology/approach– Data were drawn from 117 newcomers. In order to collect the data the authors used the snowball method. Also, hierarchical regression analysis was conducted.Findings– The results demonstrated that supervisor positive humor affects employees’ relational identification with the supervisor which, in turn, positively relates to newcomers’ adjustment.Research limitations/implications– Data were collected using a cross-sectional design and, therefore, the authors cannot directly assess causality. Moreover, the authors used self-report measures which may strengthen the causal relationships.Originality/value– To the best of the knowledge, this is the first study that illustrates the role of supervisor humor in enhancing both newcomers’ relational identification and adjustment.
Making rhetoric a reality: inclusion in practice as “transformative learning”
Authors: Mercer Dave , Kenworthy Heidi , Pierce-Hayes Ian 
Published: May 2016

Purpose
– “Inclusivity” and “empowerment” are central concepts in the philosophy of nursing practice and education. Recent professional concern has focused on the need to embed compassion in healthcare cultures where practice contributes to learning. The purpose of this paper is to explore an innovative partnership approach to undergraduate placement provision for adult-general nursing students in the context of learning disability and mental health.

Design/methodology/approach
– Critical discussion focuses on evaluation of a non-clinical placement centred on the health and social care of individuals with a learning disability or mental health needs. Two projects from practice around healthy living and hate crime illustrated the value of transformative learning as a pedagogic philosophy.

Findings
– Student feedback offered insight into social and cultural processes that impact on practice-based learning, and factors promoting inclusive engagement. Such included the context of identity formation, narrative as an evidence-base for caring, and personal/emotional growth through critical reflection.

Practical implications
– Evaluation provided a platform to re-think model(s) of clinical practice learning in healthcare education derived from a non-clinical placement. There are tangible benefits for sustaining value-led practice at a time of political change in the way health services are configured and delivered.

Social implications
– When engagement with the principles of inclusivity and empowerment become part of the lived-experience of the nursing student, longer-term recognition and retention of caring, and enabling values are more likely to endure.

Originality/value
– The emotional development and skills acquired by nursing students transfer to all branches of the profession by revitalising core conditions of compassion, respect, dignity, and humanity.