bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep profiling reveals substantial heterogeneity of integration outcomes in CRISPR knock-in experiments
Authors: Canaj Hera , Hussmann Jeffrey A. , Li Han , Beckman Kyle A. , Goodrich Leeanne , Cho Nathan H. , Li Yucheng J. , Santos Daniel A. , McGeever Aaron , Stewart Edna M. , Pessino Veronica , Mandegar Mohammad A. , Huang Cindy , Gan Li , Panning Barbara , Huang Bo , Weissman Jonathan S. , Leonetti Manuel D. 
Published: November 2019

AbstractCRISPR/Cas technologies have transformed our ability to add functionality to the genome by knock-in of payload via homology-directed repair (HDR). However, a systematic and quantitative profiling of the knock-in integration landscape is still lacking. Here, we present a framework based on long-read sequencing and an integrated computational pipeline (knock-knock) to analyze knock-in repair outcomes across a wide range of experimental parameters. Our data uncover complex repair profiles, with perfect HDR often accounting for a minority of payload integration events, and reveal markedly distinct mis-integration patterns between cell-types or forms of HDR templates used. Our analysis demonstrates that the two sides of a given double-strand break can be repaired by separate pathways and identifies a major role for sequence micro-homology in driving donor mis-integration. Altogether, our comprehensive framework paves the way for investigating repair mechanisms, monitoring accuracy, and optimizing the precision of genome engineering.
Seed mass and plant origin interact to determine species germination patterns
Authors: Veselá Andrea , Dostálek Tomáš , Rokaya Maan , Münzbergová Zuzana 
Published: November 2019

AbstractOngoing changes in temperature and precipitation regime may have strong impact on vulnerable life-history stages such as germination. Differences in germination patterns among species and populations may reflect their adaptation to conditions of their origin or may be determined by the phylogenetic constrains. These two effects are, however, rarely separated. All the germination patterns may also be modified by seed mass.We studied 40 populations of 14 species ofImpatienscoming from Himalayas. Germination of seeds of different origin was tested in four target temperatures, three simulating original conditions plus a warmer climate change scenario. We also studied effect of shorter stratification and warmer temperature in combination as another possible effect of climate change.Original and target climate interacted and had strong impact on total germination, but not on germination speed and seed dormancy. Interaction between seed mass and original climate indicated different germination strategies in light and heavy seeds. Only seed mass was affected by phylogenetic relationships among the species, while germination response (with exception of T50) was driven primarily by climate of origin.This study is the first to show that the effect of seed mass interacts with original climate in determining species germination patterns under changing climate. The differences in seed mass are thus likely crucial for species ability to adapt to novel conditions as seed mass, unlike seed germination patterns, is strongly phylogenetically constrained. Further studies exploring how seed mass modifies species germination under changing climate are needed to confirm generality of these findings.
Extremely widespread parthenogenesis and a trade-off between alternative forms of reproduction in mayflies (Ephemeroptera)
Authors: Liegeois Maud , Sartori Michel , Schwander Tanja 
Published: November 2019

AbstractStudying alternative forms of reproduction in natural populations is of fundamental importance for understanding the costs and benefits of sex. Mayflies are one of the few animal groups where sexual reproduction co-occurs with different types of parthenogenesis, providing ideal conditions for identifying benefits of sex in natural populations. Here, we establish a catalogue of all known mayfly species capable of reproducing by parthenogenesis, as well as mayfly species unable to do so. Overall, 1.8% of the described species reproduce parthenogenetically, which is an order of magnitude higher than reported in other animal groups. This frequency even reaches 47.8% if estimates are based on the number of studied rather than described mayfly species. In terms of egg-hatching success, sex is a more successful strategy than parthenogenesis, and we found a trade-off between the efficiency of sexual and parthenogenetic reproduction across species. This means that improving the capacity for parthenogenesis may come at the cost of being less able to reproduce sexually, even in facultative parthenogens. Such a trade-off can help explain why facultative parthenogenesis is extremely rare among animals despite its potential to combine the benefits of sexual and parthenogenetic reproduction. We argue that parthenogenesis is frequently selected in mayflies in spite of this probable trade-off because their typically low dispersal ability and short and fragile adult life may frequently generate situations of mate limitation in females. Mayflies are currently clearly underappreciated for understanding the benefits of sex under natural conditions.
The left angular gyrus is causally involved in information buffering and context formation: evidence from a narrative reading task
Authors: Branzi Francesca M. , Pobric Gorana , Jung JeYoung , Lambon Ralph Matthew A. 
Published: November 2019

AbstractThe role of the left angular gyrus (Ag) in semantic processing remains unclear. In this study, we used transcranial magnetic stimulation (TMS) to test the hypothesis that the left Ag supports the information buffering processes necessary for context-dependent semantic integration (narrative reading task). We applied online TMS to the left Ag to disrupt the buffering processes while female and male human participants integrated information between two paragraphs of text presented sequentially (i.e., context and target conditions). We assessed the effect of TMS on the left Ag by recording reading times for target conditions during the reading task and by asking participants to retrieve contextual information given the target condition as cue in a successive memory task. TMS applied over the left Ag during the reading task impaired the retrieval of contextual information in the memory task without affecting reading times. These results suggest that the Ag supports information buffering and context formation. This study provides the first evidence of a causal role of the left Ag in language tasks that require context-dependent semantic integration.Significance statementThe present study offers novel insights into the processes that are associated with the left angular gyrus (Ag) activation during context-dependent naturalistic language processing. We used TMS while human participants read written narratives to interfere with online language integration. We measured how TMS over the left Ag was affecting reading times and retrieval of integrated narrative representations. We were able to show that the left Ag is causally involved in information buffering and context formation.
Complex spikes encode reward expectation signals during visuomotor association learning
Authors: Sendhilnathan Naveen , Ipata Anna , Goldberg Michael E. 
Published: November 2019

AbstractClimbing fiber input to Purkinje cells has been thought to instruct learning related changes in simple spikes and cause behavioral changes through an error-based learning mechanism. Although, this framework explains simple motor learning, it cannot be extended to learning higher-order skills. Recently the cerebellum has been implicated in a variety of cognitive tasks and reward-based learning. Here we show that when a monkey learns a new visuomotor association, complex spikes predict the time of the beginning of the trial in a learning independent manner as well as encode a learning contingent reward expectation signal after the stimulus onset and reward delivery. These complex spike signals are unrelated to and were unlikely to instruct the reward based signal found in the simple spikes. Our results provide a more general role of complex spikes in learning and higher-order processing while gathering evidence for their participation in reward based learning.
Determining the content of vesicles captured by golgin tethers using LOPIT-DC
Authors: Shin John J.H. , Crook Oliver M. , Borgeaud Alicia , Cattin-Ortolá Jérôme , Peak-Chew Sew-Yeu , Chadwick Jessica , Lilley Kathryn S. , Munro Sean 
Published: November 2019

AbstractThe internal organisation of the cell depends on tethers at destination organelles to selectively capture incoming transport vesicles to facilitate SNARE-mediated fusion. The golgin long coiled-coil proteins function as tethers that contributes to this specificity at the Golgi (1). Golgin-97, golgin-245 and GCC88 golgins of the trans-Golgi capture vesicles derived from endosomes, which serve to recycle the critical Golgi machinery required to deliver lysosomal hydrolases and to maintain exocytosis. Retrograde trafficking from endosomes to the trans-Golgi network (TGN) is a complex process that involves the sorting of transmembrane cargo proteins into distinct transport vesicles by adaptors from multiple pathways. The content of these distinct vesicles, which golgin they target and the factors that mediate this targeting are not well understood. The major challenges that have limited advances in these areas is the transient nature of vesicle tethering, and the redundancies in their mechanisms that confound experimental dissection. To gain better insight into these problems, we performed organelle proteomics using the Localisation of Organelle Proteins by Isotope Tagging after Differential ultraCentrifugation (LOPIT-DC) method on a system in which an ectopic golgin causes vesicles to accumulate in a tethered state (2). By incorporating Bayesian statistical modelling into our analysis (3), we determined that over 45 transmembrane proteins and 51 peripheral membrane proteins of the endosomal network are on vesicles captured by golgin-97, including known cargo and components of the clathrin/AP-1, retromer-dependent and -independent transport pathways. We also determined a distinct class of vesicles shared by golgin-97, golgin-245 and GCC88 that is enriched in TMEM87A, a multi-pass transmembrane protein of unknown function that has previously been implicated in endosome-to-Golgi retrograde transport (4). Finally, we categorically demonstrate that the vesicles that these golgins capture are retrograde transport vesicles based on the lack of enrichment of lysosomal hydrolases in our LOPIT-DC data, and from correlative light electron tomography images of spherical vesicles captured by golgin-97. Together, our study demonstrates the power of combining LOPIT-DC with Bayesian statistical analysis in interrogating the dynamic spatial movement of proteins in transport vesicles.
C, N dual-doped ZnO nanofoams: a potential antimicrobial agent, an efficient visible light photocatalyst and SXAS studies
Authors: Kiran Kumar A. B. V. , Billa Sanjeev , Shankar Edugulla Girija , Subha M. C. S. 
Published: November 2019

It is crucial to develop an environmentally friendly and low-cost method to treat industrial effluent that contains soluble dyes and microbes. Most of the photocatalysts have been studied using an external light source that increases the cost of the purification process of effluent. This study focuses on developing efficient solar photocatalytic nanofoams. The controlled growth of ZnO nanofoams (CNZ nanofoams) in a simple method of thermal oxidation using a soft template is reported. Prepared nanofoams are characterized using X-ray diffraction, scanning electon microscopy and synchrotron soft X-ray absorption spectroscopy. By photocatalysis studies under direct sunlight it was found that within 120 min CNZ nanofoams degraded 99% of the dye. In addition, antimicrobial studies of multi-drug-resistant E. Fergusonii isolated from wastewater was carried out. These antimicrobial results showed a good inhibition zone, indicating that prepared nanofoams are both an effective solar photocatalyst and an antimicrobial agent.
Quality assurance in Afghan higher education: achievements and challenges
Authors: Welch Anthony , Wahidyar Attaullah 
Published: November 2019

PurposeThe purpose of this paper is to review the development of quality assurance (QA) processes in higher education in Afghanistan and chart and assess the current achievements and challenges. Drawing on fieldwork, documentary research and secondary sources, the analysis seeks to integrate these elements into an integrated overall analysis of the phenomenon of QA in Afghan higher education, including its evolution over time, with some attention given to the implications for future development.Design/methodology/approachThe methodology is based on field study, conducted by one of the authors, interviews with the Ministry of Higher Education officials by the second author, collection and analysis of policy documents and review of relevant literature.FindingsKey findings reveal some tensions between stated policies regarding QA in Afghan higher education: limited finance, growing levels of insecurity and limited capacity within the Ministry of Higher Education, including staff training. Some barriers within higher education institutions are also pointed out in both public and private higher educational institutions.Research limitations/implicationsImplications of the research are that although further funding is needed to institute QA in higher education institutions, both public and private, this is unlikely in the current circumstances, with donor funds limited and commitments not always fulfilled. Anti-corruption measures will continue to be important, and declining security, in some provinces more than others, will likely limit the effective implementation of QA measures.Practical implicationsGiven current conditions in Afghanistan, there are clear practical limits to what can be achieved in strengthening QA in higher education. The undoubted enthusiasm of the people, however, means that the situation must be addressed as far as possible. Greater engagement with regional QA networks, more training for QA assessors and greater regulation of the burgeoning private sector would go a long way to bring about improvement, as would ongoing efforts to rein in corruption.Social implicationsAn important move regarding direct social implications would be to maintain and strengthen moves to engage more women in higher education, including higher proportions of (senior) female administrative and academic staff. Although barriers to women’s empowerment are by no means restricted to the higher education sector, it should show the lead in both enrolment and employment.Originality/valueWhile QA in higher education is a major focus of higher education literature, there are less research studies on QA measures in developing country contexts and even less on fragile states such as Afghanistan. But for the country to prosper, good quality higher education is vital, and a study of the implementation of QA measures is an important contribution.
Market power, ownership and technical efficiency
Authors: Dai Jiawu , Li Xun 
Published: November 2019

Purpose
The purpose of this paper is to estimate oligopsony power in the upstream factor market and oligopoly power in the downstream product market. On this basis, the paper intends to examine the effects of both oligopsony and oligopoly power as well as ownership on technical efficiency which were rarely discussed in previous studies.

Design/methodology/approach
First, based on the stochastic frontier production function, the paper constructs a new model that is capable to estimate oligopsony power for each observation. Second, the paper employs the popular dual stochastic frontier cost function to estimate marginal cost as well as oligopoly power. Then, the system GMM method with different sets of instrumental variables is applied to test the effects of the two-sided market power and ownership on technical efficiency.

Findings
Using unbalanced panel data at the firm level, the paper demonstrates that oligopsony power is significantly variant across different sectors. The most notable point is that oligopsony power in China’s soya and peanut oil industries is negative, while that in pork and beef industries is much stronger than those in other industries. In addition, state-owned enterprises (SOEs) are found to be less technically efficient in most of the selected industries, while SOEs with higher oligopsony power tend to be more technically efficient than non-state-owned enterprises(NSOEs), which is consistent with the quiet life hypothesis.

Originality/value
This paper sheds light mainly on three aspects. First, it proposes a new model to estimate oligopsony power for each single firm. Second, it tests the effect of oligopsony power on technical efficiency. Third, it distinguishes the differential effect of oligopsony power on technical efficiency between SOEs and NSOEs.
Unveiling corporate values in a crisis-prone world: a cross-cultural study
Authors: Geysi Nilüfer , Türkel Selin , Uzunoğlu Ebru 
Published: November 2019

PurposeThe purpose of this paper is to compare corporate values of companies that exist in a volatile, uncertain, complex and ambiguous environment via semantic network analysis (SNA) approach. A secondary aim is to juxtapose these values with the expected values in turmoil from a cross-cultural perspective.Design/methodology/approachThe paper examines values statements of companies in Fortune 500 rankings of Turkey and the USA in 2016. The data regarding expected values in turmoil are obtained through expert appraisal from 20 public relations scholars from each country. SNA method is applied in both stages of the study.FindingsFindings show several common values for Turkish and American companies (e.g. customer focused and honest). However, Turkey reflects developing country values, such as “development oriented,” while American companies have post-materialist values, such as “respectful.” According to academicians’ perspectives, ideal corporate values should represent long-term orientation and relationship building.Practical implicationsTo the best of the authors’ knowledge, this is the first comparative study to take a network approach in the systematic examination corporate values in a business world that is threatened by crisis. Therefore, the results will generate implications for the corporate literature in addition to providing guidelines for corporate communication professionals.Originality/valueThis study is innovative in both context and methodology, comparing corporate values that exist in different sociocultural contexts via SNA, an approach which allows in-depth cultural analysis based on quantitative data.
Social media usage and activism by non-western budding PR professionals during crisis communication
Authors: Kutoglu Kuruç Ulfet , Opiyo Baruck 
Published: November 2019

PurposeA number of studies have documented the use and popularity of social networking sites among Millennials and late Millennials, especially in Western countries. However, the usage of these sites by non-Western young adults/late Millennials has just barely begun. Informed by literature and findings of recent research on audience information-seeking behavior and principles governing the usage of social media to obtain and disseminate crisis-related information, the purpose of this paper is to employ survey research to examine how senior PR-track non-Western late Millennial university students use social media to obtain and/or disseminate information on issues they perceived as “crises.”Design/methodology/approachA combination of survey research and critical communication methods were used to gather and analyze data from a sample of future non-Western budding PR professionals. Survey research was designed and used to investigate social media use among PR-major students studying at a large State University in the Mediterranean region to probe their perceptions of these media as forums for activism during moments of crisis. Questionnaire was designed to elicit responses on social media use and perceptions on a range of crisis-communication related issues, and their responses on the Likert scale that were later analyzed using the SPSS (version 21) program.FindingsThese future PR professionals appreciated the suitability of social media in disseminating crisis-communication messages. They also highlighted challenges that unethical use of such platforms pose to PR professionals. Social network sites were reported to be the most popular social media platforms used during crisis communication. Even though the respondents widely reported using social media to disseminate information during crisis situations – and answered in the affirmative that the use of social media at such times could positively contribute to social change, they did not consider themselves as activists who actively contribute to fostering of peace and justice.Originality/valueA number of studies have documented the use of social networking sites among Millennials especially in Western countries. However, the usage of these sites by non-Western late Millennials has just barely begun. This paper attempts to do this. The study explored social media usage by the non-Western late Millennial PR-track university students. Attempts were also made to elicit such PR professionals’ perceptions of whether social media contribute to activist movements and social change during crisis, and whether they physically acted as activist on social media to contribute to the improvement of societal ills, and to bring local/global peace or not.
Transferring family logic within a multinational corporation
Authors: Iwashita Hitoshi 
Published: November 2019

PurposeThe purpose of this paper is to extend the understandingof how family logic is transferred through mundane practices across the subsidiaries of a Japanese multinational corporation (MNC) in different national contexts.Design/methodology/approachIn order to fulfil this purpose, a comparative qualitative case study was adopted with emphasis on actors’ interpretations.FindingsThrough qualitative data analysis, three findings and their theoretical significances can be summarised. First, it was found that the constellations of family, market and religion logics were transferred differently. This is significant for Japanese management scholars since it illuminates the importance of actors who perceive the (non-) necessity of logics in a Japanese MNC facing institutional dualities. Second, it was found that the family logic is enacted at different levels and with different boundaries. This is significant for both institutionalists and international business scholars since it highlights the strong influence of language and religion in the transfer of logics from one country to another. Third, it was found that the enactment of the family logic greatly affects the acceptability of Japanese management practices. This is significant for business managers since it further proposes an intimate relationship between Japanese management practices and the meanings attached to the family logic.Originality/valueThe originality of this work stems from an updated comparative qualitative study of the management of a Japanese MNCs’ subsidiaries across different countries, providing in-depth insights for international business, Japanese subsidiary management and institutional logics perspectives.