bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
Authors: Bengtsen Tone , Holm Viktor L. , Kjølbye Lisbeth Ravnkilde , Midtgaard Søren R. , Johansen Nicolai Tidemand , Tesei Giulio , Bottaro Sandro , Schiøtt Birgit , Arleth Lise , Lindorff-Larsen Kresten 
Published: August 2019

AbstractNanodiscs are membrane mimetics that consist of a protein belt surrounding a lipid bilayer, and are broadly used for characterization of membrane proteins. Here, we investigate the structure, dynamics and biophysical properties of two small nanodiscs, MSP1D1ΔH5 and ΔH4H5. We combine our SAXS and SANS experiments with molecular dynamics simulations and previously obtained NMR and EPR data to derive and validate a conformational ensemble that represents the structure and dynamics of the nanodisc. We find that it displays conformational heterogeneity with various elliptical shapes, and with substantial differences in lipid ordering in the centre and rim of the discs. Together, our results reconcile previous apparently con2icting observations about the shape of nanodiscs, and paves the way for future integrative studies of larger complex systems such as membrane proteins embedded in nanodiscs.
Single Cell Analysis Reveals Multiple Requirements for Zinc in the Mammalian Cell Cycle
Authors: Lo Maria N. , Damon Leah J. , Tay Jian Wei , Palmer Amy E. 
Published: August 2019

AbstractDespite recognition of the fundamental role of zinc (Zn2+) for growth and proliferation, mechanisms of how Zn2+deficiency arrests these processes remain enigmatic. We induced subtle intracellular Zn2+perturbations and tracked asynchronously cycling cells throughout division using fluorescent reporters, high throughput microscopy, and quantitative analysis. We found that Zn2+deficiency induces quiescence and Zn2+resupply stimulates cell-cycle reentry. By monitoring single cells after Zn2+deprivation, we found that depending on where cells were in the cell cycle, they either went quiescent or entered the cell cycle but stalled in S phase. Stalled cells were defective in DNA synthesis and had increased DNA damage levels, suggesting a role for Zn2+in maintaining genome integrity. Finally, we found that Zn2+deficiency-induced quiescence does not require the cell-cycle inhibitor p21. Overall, our study provides new insights into when Zn2+is required during the mammalian cell cycle and the consequences Zn2+deficiency.
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes
Authors: Vakirlis Nikolaos , Carvunis Anne-Ruxandra , McLysaght Aoife 
Published: August 2019

AbstractThe origin of “orphan” genes, species-specific sequences that lack detectable homologues, has remained mysterious since the dawn of the genomic era. There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; andde novoemergence from ancestral non-genic sequences, such that homologues genuinely do not exist. The relative contribution of the two processes remains unknown. Here, we harness the special circumstance of conserved synteny to estimate the contribution of complete divergence to the pool of orphan genes. By separately comparing yeast, fly and human genes to related taxa using conservative criteria, we find that complete divergence accounts, on average, for at most a third of eukaryotic orphan and taxonomically restricted genes. We observe that complete divergence occurs at a stable rate within a phylum but at different rates between phyla, and is frequently associated with gene shortening akin to pseudogenization. Two cancer-related human genes,DEC1andDIRC1, have likely originated via this route in a primate ancestor.
Escherichia coliclonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing
Authors: Shevchenko Sofiya G. , Radey Matthew , Tchesnokova Veronika , Kisiela Dagmara , Sokurenko Evgeni V. 
Published: August 2019

ABSTRACTWhile microbiome studies have focused on diversity on the species or higher level, bacterial species in microbiomes are represented by different, often multiple strains. These strains could be clonally and phenotypically very different, making assessment of strain content vital to a full understanding of microbiome function. This is especially important with respect to antibiotic resistant strains, the clonal spread of which may be dependent on competition between them and susceptible strains from the same species. The pandemic, multi-drug resistant, and highly pathogenicE. colisubclone ST131-H30 (H30) is of special interest, as it has already been found persisting in the gut and bladder of healthy people. In order to rapidly assessE. coliclonal diversity, we developed a novel method based on deep sequencing of two loci used for sequence typing, along with an algorithm for analysis of resulting data. Using this method, we assessed fecal and urinary samples from healthy women carryingH30, and were able to uncover considerable diversity, including strains with frequencies at <1% of theE. colipopulation. We also found that even in the absence of antibiotic use,H30 could complete dominate the gut and, especially, urine of healthy carriers. Our study offers a novel tool for assessing a species’ clonal diversity (clonobiome) within the microbiome, that could be useful in studying population structure and dynamics of multi-drug resistant and/or highly pathogenic strains in their natural environments.IMPORTANCEBacterial species in the microbiome are often represented by multiple genetically and phenotypically different strains, making insight into subspecies diversity critical to a full understanding of the microbiome, especially with respect to opportunistic pathogens. However, methods allowing efficient high-throughput clonal typing are not currently available. This study combines a conventionalE. colityping method with deep amplicon sequencing to allow analysis of many samples concurrently. While our method was developed forE. coli, it may be adapted for other species, allowing for microbiome researchers to assess clonal strain diversity in natural samples. Since assessment of subspecies diversity is particularly important for understanding the spread of antibiotic resistance, we applied our method to study of a pandemic multidrug-resistantE. coliclone. The results we present suggest that this clone could be highly competitive in healthy carriers, and that the mechanisms of colonization by such clones need to be studied.
Superior Colliculus to VTA pathway controls orienting response to conspecific stimuli
Authors: Prévost-Solié Clément , Contestabile Alessandro , Espinosa Pedro , Musardo Stefano , Bariselli Sebastiano , Huber Chieko , Carleton Alan , Bellone Camilla 
Published: August 2019

AbstractSocial behaviours characterize cooperative, mutualistic aggressive or parental interactions that occurs among conspecifics. Although several neuronal substrates of social behaviour have been identified, whether defined circuits are dedicated to specific aspect of conspecific interaction is still an open question. Ventral Tegmental Area (VTA) contributes to the rewarding properties of conspecific interaction. However, how information related to conspecifics are conveyed to the VTA is still largely unknown. In this study, we identified a population of Superior Colliculus (SC) neurons projecting to the VTA which increase their activity before conspecific interaction and control orienting response towards unfamiliar conspecifics. Finally, we show that SC inputs target a subpopulation of Dopamine (DA) neurons within the VTA that in turn project to dorsolateral striatum (DLS). Our work supports the hypothesis that specialized sub-circuits are dedicated to process different aspect of social interaction.
Stress Resistance Screen in a Human Primary Cell Line Identifies Small Molecules that Affect Aging Pathways and ExtendC. elegans’Lifespan
Authors: Zhang Peichuan , Zhai Yuying , Cregg James , Ang Kenny Kean-Hooi , Arkin Michelle , Kenyon Cynthia 
Published: August 2019

AbstractIncreased resistance to environmental stress at the cellular level is correlated with the longevity of long-lived mutants and wild-animal species. Moreover, in experimental organisms, screens for increased stress resistance have yielded mutants that are long-lived. To find entry points for small molecules that might extend healthy longevity in humans, we screened ∼100,000 small molecules in a human primary-fibroblast cell line and identified a set that increased oxidative-stress resistance. Some of the hits fell into structurally-related chemical groups, suggesting that they may act on common targets. Two small molecules increasedC. elegans’stress resistance, and at least 9 extended their lifespan by ∼10-50%. Thus, screening for increased stress resistance in human cells can enrich for compounds with promising pro-longevity effects. Further characterization of these compounds, including a chalcone that promoted stress resistance independently ofNRF2, may elucidate new ways to extend healthy human lifespan.
Partial loss of CFIm25 causes aberrant alternative polyadenylation and learning deficits
Authors: Alcott Callison E. , Yalamanchili Hari Krishna , Ji Ping , van der Heijden Meike E. , Saltzman Alexander B. , Leng Mei , Bhatt Bhoomi , Hao Shuang , Wang Qi , Saliba Afaf , Tang Jianrong , Malovannaya Anna , Wagner Eric J. , Liu Zhandong , Zoghbi Huda Y. 
Published: August 2019

ABSTRACTWe previously showed that NUDT21-spanning copy-number variations (CNVs) are associated with intellectual disability (Gennarino et al., 2015). However, the patients’ CNVs also included other genes. To determine if reduced NUDT21 function alone can cause disease, we generated Nudt21+/- mice to mimic the human state of decreased expression. We found that although these mice have 50% reduced Nudt21 mRNA, they only have 30% less of its cognate protein, CFIm25. Despite this partial protein-level compensation, the Nudt21+/- mice have learning deficits and cortical hyperexcitability. Further, to determine the molecular mechanism driving neural dysfunction, we partially inhibited NUDT21 in human stem cell-derived neurons to reduce CFIm25 by 30%. This reduction in CFIm25 was sufficient to induce misregulated alternative polyadenylation (APA) and protein levels in hundreds of genes, dozens of which cause intellectual disability when mutated. Altogether, these results indicate that disruption of NUDT21-regulated APA events in the brain can cause intellectual disability.
Niobium isocyanide complexes, Nb(CNAr)6, with Ar = 2,6-dimethylphenyl (Xyl), a diamagnetic dimer containing four reductively coupled isocyanides, and Ar = 2,6-diisopropylphenyl (Dipp), a paramagnetic monomer analogous to the highly unstable hexacarbonylniobium(0)
Authors: Kucera Benjamin E. , Roberts Christopher J. , Young Victor G. , Brennessel William W. , Ellis John E. 
Published: August 2019

Treatment of bis(mesitylene)niobium(0) with 6–7 equivalents of 2,6-dimethylphenyl isocyanide (CNXyl) affords two products with the empirical formula Nb(CNXyl)
n
(n = 7 or 6), which have been shown to be the diamagnetic dimers bis[μ-N,N′,N′′,N′′′-tetrakis(2,6-dimethylphenyl)squaramidinato(2−)]bis[pentakis(2,6-dimethylphenyl isocyanide)niobium(I)], [Nb2(C9H9N)10(C36H36N4)] or [Nb(CNXyl)5]2[μ-C4(NXyl)4]·xSolvent, 1, and bis[μ-N,N′,N′′,N′′′-tetrakis(2,6-dimethylphenyl)squaramidinato(2−)]bis[tetrakis(2,6-dimethylphenyl isocyanide)niobium(I)] tetrahydrofuran trisolvate, [Nb2(C9H9N)8(C36H36N4)]·3C4H8O or [Nb(CNXyl)4]2[μ-C4(NXyl)4]·3THF (THF = tetrahydrofuran), 2. Each contains NbI bound to either five or four terminal isocyanides, respectively, and to an unprecedented bridging tetraarylsquaramidinate(2−) unit, coordinated as a bidentate ligand to each niobium center, symmetrically due to the crystallographic inversion center that coincides with the centroid of the central C4 unit. Thus, in the presence of CNXyl, the bis(mesitylene)niobium(0) is oxidized to niobium(I), resulting in the facile loss of both mesitylene groups and the reductive coupling of two CNXyl groups per niobium to provide the first examples of tetraarylsquaramidinate(2−) ligands, [cyclo-C4N4Ar4]2−, coordinated to metals. In contrast, bis(mesitylene)niobium(0) reacts with the more crowded 2,6-diisopropylphenyl isocyanide (CNDipp) to afford the paramagnetic monomer hexakis(2,6-diisopropylphenyl isocyanide)niobium(0), [Nb(C13H17N)6] or Nb(CNDipp)6, 3, the first zero-valent niobium isocyanide analog of the highly unstable Nb(CO)6, which is presently only known to exist in an argon matrix at 4.2 K.
A performance measurement system for change initiatives
Authors: Naslund Dag , Norrman Andreas 
Published: August 2019

Purpose
The purpose of this paper is to develop, implement, test and further enhance a framework for measuring organizational change initiatives.

Design/methodology/approach
The conceptual part of the framework is based on the structured analysis of existing literature. The framework was further developed during an action research (AR) study where the authors developed, implemented, evaluated and improved the measurement system for organizational change initiatives.

Findings
The academic literature is rich in conceptual articles providing required characteristics of a “good” measurement system and frameworks for how organizations should measure performance. However, academia provides less empirical evidence of how these performance measurement systems can be implemented, evaluated and improved. In this paper, the authors present a study where the developed measurement system has been implemented, evaluated and improved. The results in terms of how the actual framework worked as well as the response from the case organizations are equally positive.

Research limitations/implications
The framework has been implemented in two different, major change initiatives in one case organization. While the results are truly encouraging, the framework needs to be further tested and refined in more organizations.

Practical implications
There is a gap between academic perception and practical reality regarding how organizations should measure performance in general as well as measuring organizational change initiatives. The presented, and empirically tested, framework measures both the results of the change initiative (effectiveness) the actual change process (efficiency) as well as the perception of the change initiative and process from different key stakeholders.

Originality/value
This is the first developed, implemented and further improved measurement system for organizational change which measures both the efficiency and effectiveness of the change initiative (process).
Study of safety culture in healthcare institutions: case of an Algerian hospital
Authors: Boughaba Assia , Aberkane Salah , Fourar Youcef-Oussama , Djebabra Mébarek 
Published: August 2019

Purpose
For many years, the concept of safety culture has attracted researchers from all over the world, and more particularly in the area of healthcare services. The purpose of this paper is to measure safety culture dimensions in order to improve and promote healthcare in Algeria.

Design/methodology/approach
The used approach consists of getting a better understanding of healthcare safety culture (HSC) by measuring the perception of healthcare professionals in order to guide promotion actions. For this, the Hospital Survey on Patient Safety Culture questionnaire was used in a pilot hospital setting where it was distributed on a number of 114 health professionals chosen by stratified random sampling.

Findings
The results showed that the identified priority areas for HSC improvement help in establishing a trust culture and a non-punitive environment based on the system and not on the individual.

Originality/value
Safety is recognized as a key aspect of service quality, thus measuring the HSC can help establish an improvement plan. In Algerian health facilities, this study is considered the first to examine perceptions in this particular area. The current results provide a baseline of strengths and opportunities for healthcare safety improvement, allowing the managers of this type of facilities to take steps that are more effective.
Efficacy of physician associate delivered virtual outpatient clinic
Authors: Meehan Daniel , Balhareth Ameera , Gnanamoorthy Madhumitha , Burke John , McNamara Deborah A. 
Published: August 2019

Purpose
The capacity available to deliver outpatient surgical services is outweighed by the demand. Although additional investment is sometimes needed, better aligning resources, increasing operational efficiency and considering new processes all have a role in improving delivering these services. The purpose of this paper is to evaluate the safety of a physician associate (PA) delivered virtual outpatient department (VOPD) consultation service that was established in a General and Colorectal Surgery Department at an Irish teaching hospital.

Design/methodology/approach
A series of low-risk surgical patients were referred by senior surgeons to a PA delivered virtual clinic (VOPD). Medical records belonging to half the included patients were randomly selected for review by two doctors three months following discharge back to primary care to confirm appropriate standards of care and documentation and to audit any recorded adverse incidents or outcomes.

Findings
In total, 191 patients had been reviewed by the PA in the VOPD with 159 discharged directly back to primary care. Among the 95 medical records that were reviewed by the NCHDs, there were no recorded adverse incidents after discharge. Medical record keeping was deficient in 1 out of 95 reviewed cases.

Practical implications
Using a PA delivered VOPD consultation appears to have a role in following up patients who have undergone low-risk procedures irrespective of age or co-morbidity when selected appropriately. This may assist in reducing the demand on outpatient services by reducing unnecessary return visits, thereby increasing the capacity for new referrals.

Originality/value
While there are reported examples to date of virtual clinics, these relate to services delivered by registered medical practitioners. Here, the authors demonstrate the acceptability of this model of care in an Irish population as delivered by a PA.
Are overqualified employees bad apples? A dual-pathway model of cyberloafing
Authors: Zhang Junwei , Akhtar Muhammad Naseer , Zhang Yajun , Sun Shan 
Published: August 2019

Purpose
Drawing from cognitive and emotional perspectives, the purpose of this paper is to theorize and test a dual-pathway model in which moral disengagement and anger toward organization act as two explanatory mechanisms of the association between perceived overqualification and employee cyberloafing. The authors further proposed that the strengths of these two mediating mechanisms depend on employee moral identity.

Design/methodology/approach
The authors used hierarchical linear modeling to examine the hypotheses by analyzing a sample of 294 employees working in 71 departments in China.

Findings
Results revealed that moral disengagement and anger toward organization mediated the positive link between perceived overqualification and cyberloafing beyond the influence of social exchange. Furthermore, moral identity attenuated the association between the mediators (i.e. moral disengagement and anger) and cyberloafing and the indirect relationship between perceived overqualification and cyberloafing.

Originality/value
Extant studies have examined the effects of perceived overqualification on employee behaviors in terms of task performance, organizational citizenship behavior, proactive behavior, as well as withdrawal behavior. The study expands this line of research by empirically investigating whether and how perceived overqualification influences cyberloafing.
What makes people send gifts via social network services? A mixed methods approach
Authors: Lee So-Hyun , Choi Su-Jin , Kim Hee-Woong 
Published: August 2019

Purpose
Social network services (SNS) gifting is a new business model, but many SNS providers continue to face challenges as they explore ways to increase their revenues from gifting. The purpose of this paper is to examine the key factors involved in gift giving via SNS platforms.

Design/methodology/approach
This study adopts a mixed methods approach through qualitative and quantitative research. In the first stage (qualitative study), the authors extract factors from interviews with users of SNS gifting services. In the second stage (quantitative study), the authors interpret decisional factors explored in the first stage on the basis of customer value theory, develop a research model and empirically test it.

Findings
The results show that five factors – convenience of SNS gifting, symbolic representation of SNS gifting, relationship support of SNS gifting, pleasure of SNS gifting, and an SNS gifting norm – directly or indirectly affect SNS gifting decisions.

Research limitations/implications
This study contributes to electronic commerce research by extending the customer value theory and adding to the literature on SNS gifting and gift giving in general.

Practical implications
The study informs SNS providers regarding the promotion of SNS gifting services for revenue generation.

Originality/value
This study is among the first to comprehensively examine decision-making in SNS gifting through the lens of customer value theory.
Iranian doctoral students’ perceptions of publication in English
Authors: Rezaei Saeed , Seyri Haniye 
Published: August 2019

PurposeThe purpose of this paper is to investigate the English for publication purpose practices of doctoral students in Iran. The overall objective was to explore their motives, hurdles and strategies in academic writing.Design/methodology/approachThis case study draws on a narrative inquiry to explore nine science and engineering doctoral students’ perceptions of academic publication. The data were analyzed through a hybrid process of inductive and deductive thematic analysis.FindingsThe qualitative results showed three dominant themes, namely: motives for publication, hurdles to publication and strategies for dealing with these challenges were extracted. The main sources of motives were students’ desire to publish their works for their graduation, improve their resume, satiate the universities’ evaluation system, and finally share their knowledge worldwide. Their hurdles included: political reasons, language-related problems, center-periphery priorities and the lack of academic writing instruction. In order to overcome these hurdles, the participants employed some strategies in academic writing.Research limitations/implicationsDue to qualitative nature of this study, only nine PhD students were recruited and therefore the research results are not intended to render generalizability. Besides, only narratives were employed to collect the required data. Future researchers can use surveys to collect more data.Practical implicationsThe findings are discussed within English for academic purposes discourse and some recommendations are provided to alleviate the plights of non-native-English-speaking academic writers.Originality/valueThe methodology and the higher education context in which this paper was conducted are new to the literature.