bluuebunny/crossref_metadata_2025_split huggingface dataset:
A marker-free co-selection strategy for high efficiency human genome engineering
Authors: Agudelo Daniel , Bozoyan Lusiné , Duringer Alexis , Huard Caroline C. , Carter Sophie , Loehr Jeremy , Synodinou Dafni , Drouin Mathieu , Salsman Jayme , Dellaire Graham , Laganière Josée , Doyon Yannick 
Published: March 2017

ABSTRACTTargeted genome editing using engineered nucleases facilitates the creation ofbona fidecellular models for biological research and may be applied to human cell-based therapies. Broadly applicable and versatile methods for increasing the levels of gene editing in cell populations remain highly desirable due to the variable efficiency between distinct genomic loci and cell types. Harnessing the multiplexing capabilities of CRISPR-Cas9 and Cpf1 systems, we designed a simple and robust co-selection strategy for enriching cells harboring either nuclease-driven non-homologous end joining (NHEJ) or homology-directed repair (HDR) events. Selection for dominant alleles of the endogenous sodium-potassium pump (Na+,K+-ATPase) that render cells resistant to ouabain is used to enrich for custom modifications at another unlinked locus of interest, effectively increasing the recovery of engineered cells. The process was readily adaptable to transformed and primary cells, including hematopoietic stem and progenitor cells (HSPCs). The use of universal CRISPR reagents and a commercially available small molecule inhibitor streamlines the incorporation of marker-free genetic changes in human cells.
Destructive disinfection of infected brood prevents systemic disease spread in ant colonies
Authors: Pull Christopher D. , Ugelvig Line V. , Wiesenhofer Florian , Tragust Simon , Schmitt Thomas , Brown Mark J.F. , Cremer Sylvia 
Published: March 2017

AbstractSocial insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour – “destructive disinfection” – to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen’s non-contagious incubation period, relying on chemical ‘sickness cues’ emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation.
Genotoxin-induced transcriptional repression regulates selective protein aggregation
Authors: Mathew Veena , Tam Annie S. , Milbury Karissa L. , Hofmann Analise K. , Hughes Christopher S. , Morin Gregg B. , Loewen Christopher J. R. , Stirling Peter C. 
Published: March 2017

AbstractUpon genotoxic stress, dynamic relocalization events control DNA repair, and alterations of the transcriptome and proteome enabling stress recovery. How these events may influence one another is only partly known. Beginning with a cytological screen for genome maintenance proteins that move under stress, we find that, upon alkylation stress, the splicing factor Hsh155 localizes to both intranuclear and cytoplasmic protein quality control aggregates. Under stress, an ordered sequestration of Hsh155 occurs at nuclear and then cytoplasmic aggregates in a manner that is regulated by molecular chaperones. This dynamic behavior is preceded by a decrease in splicing efficiency. While DNA replication stress signaling is not required for Hsh155 sequestration, Hsh155 aggregation is cell cycle and TOR pathway dependent. Indeed, loss of a TORC1 regulated ribosomal protein gene transcription factor Sfp1 allows general aggregate formation but prevents Hsh155 recruitment. Together, our analyses suggest a model in which some proteins evicted from chromatin undergoing transcriptional remodeling during stress are targeted to protein quality control sites.
Reconstructing Promoter Activity From Lux Bioluminescent Reporters
Authors: Iqbal Mudassar , Doherty Neil , Page Anna M.L. , Qazi Saara N.A. , Ajmera Ishan , Lund Peter A. , Kypraios Theodore , Scott David J. , Hill Philip J. , Stekel Dov J. 
Published: March 2017

AbstractThe bacterial Lux system is used as a gene expression reporter. It is fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for bacterial cells, it has been adapted for eukaryotic cells, and can be used for whole cell biosensors, or in real time with live animals without the need for slaughter. However, correct interpretation of bioluminescent data is limited: the bioluminescence is different from gene expression because of nonlinear molecular and enzyme dynamics of the Lux system. We have developed a modelling approach that, for the first time, allows users of Lux assays to infer gene transcription levels from the light output. We show examples where a decrease in bioluminescence would be better interpreted as a switching off of the promoter, or where an increase in bioluminescence would be better interpreted as a longer period of gene expression. This approach could benefit all users of Lux technology.
Orienting the causal relationship between imprecisely measured traits using genetic instruments
Authors: Hemani Gibran , Tilling Kate , Smith George Davey 
Published: March 2017

AbstractInference of the causal structure that induces correlations between two traits can be achieved by combining genetic associations with a mediation-based approach, as is done in the causal inference test (CIT) and others. However, we show that measurement error in the phenotypes can lead to mediation-based approaches inferring the wrong causal direction, and that increasing sample sizes has the adverse effect of increasing confidence in the wrong answer. Here we introduce an extension to Mendelian randomisation, a method that uses genetic associations in an instrumentation framework, that enables inference of the causal direction between traits, with some advantages. First, it is less susceptible to bias in the presence of measurement error; second, it is more statistically efficient; third, it can be performed using only summary level data from genome-wide association studies; and fourth, its sensitivity to measurement error can be evaluated. We apply the method to infer the causal direction between DNA methylation and gene expression levels. Our results demonstrate that, in general, DNA methylation is more likely to be the causal factor, but this result is highly susceptible to bias induced by systematic differences in measurement error between the platforms. We emphasise that, where possible, implementing MR and appropriate sensitivity analyses alongside other approaches such as CIT is important to triangulate reliable conclusions about causality.
Category-selective human brain processes elicited in fast periodic visual stimulation streams are immune to temporal predictability
Authors: Quek Genevieve L. , Rossion Bruno 
Published: March 2017

AbstractRecording direct neural activity when periodically inserting exemplars of a particular category in a rapid visual stream of other objects offers an objective and efficient way to quantify perceptual categorization and characterize its spatiotemporal dynamics. However, since periodicity entails predictability, perceptual categorization processes identified within this framework may be partly generated or modulated by temporal expectations. Here we present a stringent test of the hypothesis that temporal predictability generates or modulates category-selective neural processes. In Experiment 1, we compare neurophysiological responses to periodic and nonperiodic (i.e., unpredictable) variable face stimuli in a fast (12 Hz) visual stream of nonface objects. In Experiment 2, we assess potential responses to rare (10%) omissions of periodic face events (i.e., violations of periodicity) in the same fast visual stream. Overall, our observations indicate that long duration category(face)-selective processes elicited in a fast periodic stream of visual objects are immune to temporal predictability. These observations do not support a predictive coding framework interpretation of category-change detection in the human brain and have important implications for understanding human perceptual categorization in a rapidly changing (i.e., dynamic) visual scene.
Farm entry and exit from US agriculture
Authors: Katchova Ani L. , Ahearn Mary Clare 
Published: March 2017

Purpose
The purpose of this paper is to use a linked-farm approach and a cohort approach to estimate farm entry and exit rates using the US Census of Agriculture. The number of new farms entering agriculture was re-estimated and adjusted upward since not all new and beginning farmers are known to US Department of Agriculture.

Design/methodology/approach
In addition to a linked-farm approach (linking farms over time), a cohort approach (farms that started operating in the same year) is used to determine exit rates conditional on the number of years a farm has been operating. Linear forecasting, moving-average forecasting, and using data from a later Census are used to re-estimate the number of new farms in their first year of operating.

Findings
Using the linked-farm approach, an average annual entry rate of 7.5 percent and exit rate of 8.5 percent is estimated for 2007 to 2012, which vary based on the farmer’s lifecycle. The cohort approach shows that exit rates are lower than 4 percent for the first 40 years of operating a farm business and then exit rates gradually increase. Revised estimates of approximately 70-80,000 new farms entering each year are calculated, which are considerably higher numbers than the 30-40,000 new farm entrants participating in the Census of Agriculture.

Originality/value
The linked-farm and cohort approaches are used to provide updated estimates for farm entry and exit using new Census data and to make comparisons with previous years. To the authors’ knowledge, this is the first study to provide revised estimates for new farm entrants into US agriculture.
Historical developments in agricultural finance and the genesis of America’s farm credit system
Authors: Turvey Calum G. 
Published: March 2017

Purpose
The purpose of this paper is to provide a review of major historical developments in agricultural finance, with particular emphasis on agricultural credit. It reviews the development of Raiffeisen and related banks that emerged in Germany and Europe throughout the nineteenth century and how the cooperative banking system made its way into the banking system of the USA in the early twentieth century. The paper emphasizes the role of the state in the developing of agricultural credit, especially with respect to farm mortgages, securitization, and bond structures.

Design/methodology/approach
This paper presents a historical synthesis of historical literature on agricultural credit.

Findings
This paper shows the direct linkage between the developments in Raiffeisen credit cooperatives and the Farm Credit System (FCS) and details the emergence of the land banks, farm credit banks, agricultural bonds and the role of joint-stock banks in agricultural credit policy.

Originality/value
In total, 2016 marks the 100th anniversary of the passing of the 1916 Federal Farm Loan Act which set in motion the USs’ first Government Sponsored Enterprise and catalyzed the formation of the FCS as it operates today to provide credit to farmers and rural communities on a cooperative basis. Although there are a few wonderful books written on certain aspects of the FCS the story of how the FCS was initiated and the many struggles it faced up to the 1933 Act has not been told often enough. This paper tells the story of the evolution of agricultural credit that ultimately led to the formation of the FCS.
Culture and context matter: gender in international business and management
Authors: Eden Lorraine , Gupta Susan Forquer 
Published: March 2017

Purpose
The purpose of this paper is to argue that culture and context (policy and environment) are key factors affecting gender inequalities within and across countries.

Design/methodology/approach
This paper applies conceptual and descriptive statistics.

Findings
The authors found evidence of increasing gender equality in the workplace, but only for rich countries. Gender inequalities persist in the poorest countries, and the gap between rich and poor countries appears to be widening not narrowing.

Research limitations/implications
This paper demonstrates the need for a comprehensive research program on gender and international business.

Practical implications
The authors provided useful statistics that could possibly be picked up by newspapers. The paper also highlights the need for a more sustained research program on gender and development.

Social implications
This paper demonstrates that the public perception of increasing gender equality applies only in very high development (rich) countries. In fact, gender inequality rises as economic development levels decline across countries, and the gap between very high and low countries has widened over the past 15 years.

Originality/value
The empirical findings with respect to gender inequality across United Nations Development Program country categories over time are, to the best of the authors’ knowledge, novel and original. Relating the gender inequality gap to culture and context highlights the roles that social issues and the environment play in affecting gender inequality across countries and across time.
An empirical competence-capability model of supply chain resilience
Authors: Mandal Santanu 
Published: March 2017

PurposeThis paper aims to investigate the influence of supply and demand competence on supply chain (SC) resilience and its impact on a firm’s operational and relational performance. While the former competence refers to production and supply management-related activities, the latter refers to distribution and demand management-related activities. Within this framework, process compliance, i.e. how well SC management processes are internally executed by the firm’s employees, is observed as an enabler (moderator) on the relationship between SC competence and SC resilience. Further the model also explores the moderating influence of environmental uncertainty (EU) on the linkage between SC resilience and firm performance.Design/methodology/approachData were collected through a Web-based cross-sectional survey from SC professionals working in different industries at various designations. Further, the collected data were analyzed using partial least squares for hypotheses’ testing.FindingsThe findings suggest a positive influence of demand- and supply-side competences on SC resilience. Supply chain resilience was also found to have a positive influence on operational and relational performance. Further, process compliance was found to positively moderate the relationship between the competences and resilience. Lastly, the relationship between resilience and performance was found to gain momentum in the presence of EU.Research limitations/implicationData were collected from a single respondent per firm. Hence, future research should attempt to collect data from multiple respondents for increased generalization.Originality/valueThe study holds significance for academicians and practitioners, as it investigates the importance of supply- and demand-side competences on the development of SC resilience and its impact on performance. This investigation showed that building resilience in a SC is dependent on the degree to which firms are process-compliant. Further, it was empirically proved that resilience’s positive influence on performance increases more with the presence of uncertainties.
Residential satisfaction and housing modifications
Authors: Carrasco Sandra , Ochiai Chiho , Okazaki Kenji 
Published: March 2017

Purpose
This study focuses on residents’ perceptions of the permanent houses built by various implementing agencies on the Calaanan site as part of post-Typhoon Washi resettlement in the city of Cagayan de Oro. This research aims to make a comparative analysis of the communities’ pre- and post-disaster situation, their satisfaction with the housing provided and the factors influencing housing modification.

Design/methodology/approach
The paper analyzes the data obtained from a questionnaire survey of residents, interviews with stakeholders involved in resettlement, observation survey and graphic documentation between July and August 2014.

Findings
The analysis of residents’ perspectives revealed that their building of extensions to houses was a response to a lack of consideration of their needs and of local environmental and cultural patterns in the planning and construction of permanent housing.

Originality/value
The findings are used to develop points to consider to gain a better understanding of residents’ adaptation to their environment. These points may be useful in improving future resettlement projects in a country permanently exposed to disasters.
Executing strategy through comprehensive performance measurement systems
Authors: Micheli Pietro , Mura Matteo 
Published: March 2017

PurposeThe purpose of this paper is to investigate the mediating role of comprehensive performance measurement systems (PMS) – i.e. measurement systems that comprise financial and non-financial indicators, and which also consist of indicators related to different aspects of an organisation’s operations – in the relationship between strategy and company performance.Design/methodology/approachSurvey data of top managers of large European companies were collected and analysed by means of exploratory factor analyses and hierarchical regressions in order to validate the proposed hypotheses.FindingsThis research shows that different strategies lead to the use of different types of performance indicators. Also, it finds that the utilisation of a comprehensive PMS enables the implementation of both differentiation and cost-leadership strategies. Specifically, a comprehensive PMS positively mediates the effect of differentiation strategy on organisational and innovative performance, and of cost-leadership strategy on organisational performance.Research limitations/implicationsFurther research could be undertaken in other contexts and consider additional factors, such as the structure, maturity and different uses of PMS, and the cost of measuring performance. Qualitative studies could examine the role of PMS in dynamic environments, as well as the evolution of PMS during strategic transitions.Practical implicationsGreater consideration should be given to the utilisation of different types of performance indicators when implementing and re-formulating strategy.Originality/valueThis study clarifies the links between strategy and performance measurement, and it is the first to identify the mediating effect of comprehensive PMS between strategy and company performance.
Driving green supply chain management performance through supplier selection and value internalisation
Authors: Roehrich Jens K. , Hoejmose Stefan U. , Overland Victoria 
Published: March 2017

PurposeThe purpose of this paper is to apply self-determination theory (SDT) to green supply chain management (GSCM) and explore how green supplier selection (GSS) drives GSCM performance and how realisation of improved GSCM performance is contingent upon SDT mechanisms of autonomy, competence and relatedness.Design/methodology/approachThis study draws on 18 semi-structured interviews and secondary data from a Germany-based first-tier aircraft interior manufacturer and its six key suppliers. The focal company was selected because it is recognised as having achieved high GSCM standards in the aerospace industry.FindingsThe study draws out the importance of GSS, distinguishing between new and legacy suppliers, and offers significant insights into how suppliers’ motivation and downstream GSCM criteria can be internalised in second-tier suppliers to drive GSCM performance.Practical implicationsGSS should be considered not only for new suppliers but also at an ongoing basis for legacy suppliers. Focal companies must realise the importance of motivating supply chain partners to realise GSCM practices and need to first build-up autonomy before focussing on competence and relatedness sub-dimensions.Originality/valueThe authors make a significant contribution to the GSCM literature by conducting a study of first-tier-second-tier relationships, thus moving beyond the buyer-supplier relationships investigated in extant studies. The results theoretically and empirically draw out key factors in GSS and supplier motivation in engaging with GSCM practices, thus driving GSCM performance.
Family planning services for incarcerated women: models for filling an unmet need
Authors: Sufrin Carolyn , Baird Sara , Clarke Jennifer , Feldman Elizabeth 
Published: March 2017

Purpose
Incarcerated women around the globe are predominantly of reproductive age. Most of these women have been pregnant before, and many want to be sexually active and avoid pregnancy upon release. Yet few of these women are on a regular method of contraception. Providing contraceptive services for women in custody benefits individual and public health goals of reducing unintended pregnancy. This policy briefing reviews evidence for an unmet need for family planning in the correctional setting, and policy implications for expanding services. The paper aims to discuss these issues.

Design/methodology/approach
The authors describe four model programs in the USA with established contraceptive services on site, highlighting practical steps other facilities can implement.

Findings
Correctional facilities health administrators, providers, advocates, and legislators should advance policies which should counsel women on family planning and should make a range of contraceptive methods available before release, while remaining sensitive to the potential pressure these women may feel to use birth control in this unique environment.

Practical implications
Family planning services for incarcerated women benefits individuals, facilities, and the community.

Social implications
Policies which enable correctional facilities to provide comprehensive family planning to incarcerated women – including reproductive life goals counseling and contraceptive method provision – promote equity in access to critical reproductive health services and also provide broad scale population level benefits in preventing unintended pregnancy or enabling counseling for healthy pregnancies for a group of women who often have limited access to such services.

Originality/value
This policy briefing highlights an area of health care in prisons and jails which gets little attention in research and in policy circles: family planning services for incarcerated women. In addition to reviewing the importance of such services for this population, the authors also highlight model family planning programs in correctional facilities. These provide actionable insights for other administrators and providers.