bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aquatic microbial community is partially functionally redundant: insights from anin situreciprocal transplant experiment
Authors: Tandon Kshitij , Wan Min-Tao , Yang Chia-Chin , Yang Shan-Hua , Baatar Bayanmunkh , Chiu Chih-Yu , Tsai Jeng-Wei , Liu Wen-Cheng , Ng Chen Siang , Tang Sen-Lin 
Published: February 2020

AbstractMicrobial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed anin situreciprocal transplant experiment on the surface and bottom waters of two lakes with disparate trophic states and tracked changes in their microbial community and functional attributes for 6 weeks using high-throughput sequencing and functional approaches. The communities from both lakes were resistant to changes in composition after the reciprocal transplant, but their functions tended to become similar to the incubating lakes’ functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes, though with varying scales of similarity, suggesting partial functional redundancy. Furthermore, the entropy-basedL-divergence measure quantified the scale of partial functional redundancy in the lakes’ surface and bottom waters. This study establishes and quantifies the scale of partial functional redundancy in the freshwater ecosystem through empirical investigation.
LncRNA GAS5 attenuates fibroblast activation through inhibiting Smad3 signaling
Authors: Tang Rui , Wang Yung-Chun , Mei Xiaohan , Shi Ning , Sun Chengming , Ran Ran , Zhang Gui , Li Wenjing , Staveley-O’Carroll Kevin F. , Li Guangfu , Chen Shi-You 
Published: February 2020

AbstractTransforming Growth Factor β (TGF-β)-induced fibroblast activation is a key pathological event during tissue fibrosis. Long noncoding RNA (lncRNA) is a class of versatile gene regulators participating in various cellular and molecular processes. However, the function of lncRNA in fibroblast activation is still poorly understood. In this study, we identified growth arrest-specific transcript 5 (GAS5) as a novel regulator for TGF-β-induced fibroblast activation. GAS5 expression was downregulated in cultured fibroblasts by TGF-β and in resident fibroblasts from bleomycin-treated skin tissues. Overexpression of GAS5 suppressed TGF-β-induced fibroblast to myofibroblast differentiation. Mechanistically, GAS5 directly bound Smad3 and promoted Smad3 binding to PPM1A, a Smad3 dephosphatase, and thus accelerated Smad3 dephosphorylation in TGF-β-treated fibroblasts. In addition, GAS5 inhibited fibroblast proliferation. Importantly, local delivery of GAS5 via adenoviral vector suppressed bleomycin-induced skin fibrosis in mice. Collectively, our data revealed that GAS5 suppresses fibroblast activation and fibrogenesis through inhibiting TGF-β/Smad3 signaling, which provides a rationale for an lncRNA-based therapy to treat fibrotic diseases.
A screen forPlasmodium falciparumsporozoite surface protein binding to human hepatocyte surface receptors identifies novel host-pathogen interactions
Authors: Segireddy Rameswara Reddy , Dundas Kirsten , Knoeckel Julia , Galaway Francis , Wood Laura , Wright Gavin J , Douglas Alexander D 
Published: February 2020

AbstractSporozoite invasion of hepatocytes is a necessary step prior to development of malaria, with similarities, at the cellular level, to merozoite invasion of erythrocytes. In the case of the malaria blood-stage, efforts to identify host-pathogen protein-protein interactions have yielded important insights including vaccine candidates. In the case of sporozoite-hepatocyte invasion, the host-pathogen protein-protein interactions involved are poorly understood. Here, we performed a systematic screen to identify such interactions. We substantially extended previousPlasmodium falciparumand human surface protein ectodomain libraries, creating new libraries containing 88P. falciparumsporozoite protein coding sequences and 182 sequences encoding human hepatocyte surface proteins. Having expressed recombinant proteins from these sequences, we used a plate-based assay capable of detecting low affinity interactions between recombinant proteins, modified for enhanced throughput, to screen the proteins for interactions. We were able to test 7540 sporozoite-hepatocyte protein pairs under conditions likely to be sensitive for interaction. We report and characterise an interaction between human fibroblast growth factor receptor 4 (FGFR4) and theP. falciparumprotein Pf34, and describe an additional interaction between human low-density lipoprotein receptor (LDLR) and theP. falciparumprotein PIESP15. Strategies to inhibit these interactions may have value in malaria prevention, and the modified interaction screening assay and protein expression libraries we report may be of wider value to the community.
Non-canonical regulation of glycogenolysis and the Warburg phenotype by soluble adenylyl cyclase
Authors: Chang Jung-Chin , Go Simei , Gilglioni Eduardo H. , Li Hang Lam , Huang Hsu-Li , Levin Lonny R. , Buck Jochen , Verhoeven Arthur J. , Oude Elferink Ronald P.J. 
Published: February 2020

AbstractCyclic AMP is produced in cells by two very different types of adenylyl cyclases: the canonical transmembrane adenylyl cyclases (tmACs,ADCY1∼9) and the evolutionarily more conserved soluble adenylyl cyclase (sAC,ADCY10). While the role and regulation of tmACs is well documented, much less is known of sAC in cellular metabolism. We demonstrate here that sAC is an acute regulator of glycolysis, oxidative phosphorylation and glycogen metabolism, tuning their relative bioenergetic contributions. Suppression of sAC activity leads to aerobic glycolysis, enhanced glycogenolysis, decreased oxidative phosphorylation, and an elevated cytosolic NADH/NAD+ratio, resembling the Warburg phenotype. Importantly, we found that glycogen metabolism is regulated in opposite directions by cAMP depending on its location of synthesis and downstream effectors. While the canonical tmAC-cAMP-PKA axis promotes glycogenolysis, we identify a novel sAC-cAMP-Epac1 axis that suppresses glycogenolysis. These data suggest that sAC is an autonomous bioenergetic sensor that suppresses aerobic glycolysis and glycogenolysis when ATP levels suffice. When the ATP level falls, diminished sAC activity induces glycogenolysis and aerobic glycolysis to maintain energy homeostasis.
SICD6mA: Identifying 6mA Sites using Deep Memory Network
Authors: Liu Wenzhong , Li Hualan 
Published: February 2020

AbstractBackgroundDNA N6-methyladenine (6mA) is a kind of epigenetic modification in prokaryotes and eukaryotes, which involves multiple biological processes, such as gene regulation and tumorigenesis. Identifying 6mA contributes to understand its regulatory role. Therefore, to satisfy the needs of large-scale preliminary screening, it is necessary to develop the high-quality computational models for the rapid identification of 6mA sites. However, the existing calculation approaches are mostly specific to rice, and they have not been extensively applied to human genome.ResultsThis study proposed a classification method of deep learning based on the memory mechanism named SICD6mA. In addition, the large benchmark datasets were constructed for human and rice, respectively, which integrated the recently reported 6mA sites. According to the evaluation results, SICD6mA displayed favorable robustness during cross-validations, which achieved the area under the curve (AUC) values of 0.9824 and 0.9903 for Human and Rice’s genomes in independent test evaluations, separately.ConclusionsThe successful prediction rate of 6mA sites on cross-species genomes exhibited higher accuracy than that of the state-of-the-art methods. For the convenience of experimental scientists, the user-friendly tool SICD6mA was developed to predict the cross-species 6mA sites, thereby accelerating and facilitating future cross-species genome research.
Ancient MAPK ERK7 is regulated by an unusual inhibitory scaffold required for Toxoplasma apical complex biogenesis
Authors: Back Peter S. , O’Shaughnessy William J. , Moon Andy S. , Dewangan Pravin S. , Hu Xiaoyu , Sha Jihui , Wohlschlegel James A. , Bradley Peter J. , Reese Michael L. 
Published: February 2020

AbstractApicomplexan parasites use a specialized cilium structure called the apical complex to organize their secretory organelles and invasion machinery. The apical complex is integrally associated with both the parasite plasma membrane and an intermediate filament cytoskeleton called the inner membrane complex (IMC). While the apical complex is essential to the parasitic lifestyle, little is known about the regulation of apical complex biogenesis. Here, we identify AC9 (apical cap protein 9), a largely intrinsically disordered component of theToxoplasma gondiiIMC, as essential for apical complex development, and therefore for host cell invasion and egress. Parasites lacking AC9 fail to successfully assemble the tubulin-rich core of their apical complex, called the conoid. We use proximity biotinylation to identify the AC9 interaction network, which includes the kinase ERK7. Like AC9, ERK7 is required for apical complex biogenesis. We demonstrate that AC9 directly binds ERK7 through a conserved C-terminal motif and that this interaction is essential for ERK7 localization and function at the apical cap. The crystal structure of the ERK7:AC9 complex reveals that AC9 is not only a scaffold, but also inhibits ERK7 through an unusual set of contacts that displaces nucleotide from the kinase active site. ERK7 is an ancient and auto-activating member of the mitogen-activated kinase family and we have identified its first regulator in any organism. We propose that AC9 dually regulates ERK7 by scaffolding and concentrating it at its site of action while maintaining it in an “off” state until the specific binding of a true substrate.Significance StatementApicomplexan parasites include the organisms that cause widespread and devastating human diseases such as malaria, cryptosporidiosis, and toxoplasmosis. These parasites are named for a structure, called the “apical complex,” that organizes their invasion and secretory machinery. We found that two proteins, apical cap protein 9 (AC9) and an enzyme called ERK7 work together to facilitate apical complex assembly. Intriguingly, ERK7 is an ancient molecule that is found throughout Eukaryota, though its regulation and function are poorly understood. AC9 is a scaffold that concentrates ERK7 at the base of the developing apical complex. In addition, AC9 binding likely confers substrate selectivity upon ERK7. This simple competitive regulatory model may be a powerful but largely overlooked mechanism throughout biology.
Identity as career capital: enhancing employability in the creative industries and beyond
Authors: Mao Jina , Shen Yan 
Published: February 2020

PurposeThe purpose of this paper is to broaden the conversation about the link between identity and employability by investigating how identity can function as a type of career capital. Drawing on Bourdieu’s (1990) theory of practice and Côté’s (2016) identity capital model, the authors introduce the concept of identity capitalization and elaborate on the career practices people engage in to convert identity into career capital based on studies of careers in the creative industries.Design/methodology/approachThe conceptual development is based on an examination of studies of careers in the creative industries. The authors move beyond a single idiosyncratic occupational setting and offer insights about how individuals acquire, accumulate and deploy identity capital in response to varying occupational demands and institutional norms.FindingsThe authors identify three patterns of work – display work, authenticity work and personation work – that creative professionals use to harness identity as career capital to enhance their employability. The authors find that both the demand for authenticity and the existence of social inequalities in the creative industries present challenges for the acquisition, accumulation and deployment of identity capital.Originality/valueThe ability to harness one’s identity for career capital has become increasingly important for career actors in the face of a challenging labor market. This paper provides a conceptual understanding of the process of identity capitalization and presents concrete career practices in real-world settings. It also offers practical advice for individuals wishing to capitalize on their identity to maximize career opportunities.
Aspect-based sentiment analysis of reviews in the domain of higher education
Authors: Nikolić Nikola , Grljević Olivera , Kovačević Aleksandar 
Published: February 2020

Purpose
Student recruitment and retention are important issues for all higher education institutions. Constant monitoring of student satisfaction levels is therefore crucial. Traditionally, students voice their opinions through official surveys organized by the universities. In addition to that, nowadays, social media and review websites such as “Rate my professors” are rich sources of opinions that should not be ignored. Automated mining of students’ opinions can be realized via aspect-based sentiment analysis (ABSA). ABSA s is a sub-discipline of natural language processing (NLP) that focusses on the identification of sentiments (negative, neutral, positive) and aspects (sentiment targets) in a sentence. The purpose of this paper is to introduce a system for ABSA of free text reviews expressed in student opinion surveys in the Serbian language. Sentiment analysis was carried out at the finest level of text granularity – the level of sentence segment (phrase and clause).

Design/methodology/approach
The presented system relies on NLP techniques, machine learning models, rules and dictionaries. The corpora collected and annotated for system development and evaluation comprise students’ reviews of teaching staff at the Faculty of Technical Sciences, University of Novi Sad, Serbia, and a corpus of publicly available reviews from the Serbian equivalent of the “Rate my professors” website.

Findings
The research results indicate that positive sentiment can successfully be identified with the F-measure of 0.83, while negative sentiment can be detected with the F-measure of 0.94. While the F-measure for the aspect’s range is between 0.49 and 0.89, depending on their frequency in the corpus. Furthermore, the authors have concluded that the quality of ABSA depends on the source of the reviews (official students’ surveys vs review websites).

Practical implications
The system for ABSA presented in this paper could improve the quality of service provided by the Serbian higher education institutions through a more effective search and summary of students’ opinions. For example, a particular educational institution could very easily find out which aspects of their service the students are not satisfied with and to which aspects of their service more attention should be directed.

Originality/value
To the best of the authors’ knowledge, this is the first study of ABSA carried out at the level of sentence segment for the Serbian language. The methodology and findings presented in this paper provide a much-needed bases for further work on sentiment analysis for the Serbian language that is well under-resourced and under-researched in this area.
Facility managers’ responses to user post-occupancy feedback: a conceptual framework
Authors: Abisuga Abiodun Olatunji , Wang Cynthia Changxin , Sunindijo Riza Yosia 
Published: February 2020

PurposeThis study aims to explore the various approaches used in the general customer service industry to develop a conceptual framework for evaluating the responses of facility managers to user post-occupancy feedback.Design/methodology/approachThis study uses conceptual analysis based on a comprehensive review of relevant literature.FindingsThe results of the study established 24 propositions which are categorised under organisational response dimensions specific to facilities management (FM): timeliness, facilitation, redress, apology, credibility of explanation, attentiveness, effort and their relationships with overall satisfaction and post-feedback behaviour, such as word of mouth and acceptance to continue using the facilities.Research limitations/implicationsThe established propositions are derived from existing theories using a deductive approach. The framework can be further enhanced to suit various applications in FM services.Practical implicationsThis conceptual framework is a generic model, appropriate to many FM scenarios. The framework can be used to develop standard policies and procedures to foster and encourage collaborative relationships between users and facility managers. It reinforces transparency and trust between facility managers and users during the operation and management of the facilities, and improves FM effectiveness, facility performance and user post-occupancy experience.Originality/valueIn the FM area, no systematic approach has been previously established to evaluate and improve the response process to the users’ feedback. The proposed framework is a pioneer contribution in this area.
Students’ perceptions of librarians as teachers of information literacy at a large African university
Authors: Bangani Siviwe , Mashiyane Dina Mokgadi , Moyo Mathew , Masilo Boitumelo , Makate Glenda 
Published: February 2020

Purpose
The purpose of this study is to determine the students’ perceptions of librarians as teachers of information literacy at the North-West University in South Africa.

Design/methodology/approach
The study used a survey research method in which online questionnaires were used to gather data from students who would have attended information literacy classes.

Findings
Students found librarians to be effective teachers of information literacy, and they found the subject to be very useful. However, some of the surveyed students felt that a lot of the subject was presented in a short period, which could easily result in exhaustion and information overload. The use of local or vernacular languages was also indicated as an area requiring the librarians’ attention for the teachers to be more effective.

Practical implications
The results of this study support the assessment of librarians as teachers by students to assist them (librarians) to refine their teaching methods and to make the conduct of information literacy worthwhile for the students.

Social implications
The outcomes of this study may be used to advocate for more information literacy (IL) contact time with the students by librarians when negotiating with faculty. Further, these results may be used to showcase the value placed by students to IL.

Originality/value
This study is a welcome addition to the scant literature on the quality of teaching delivered by the librarians and the assessment mechanisms used to provide feedback on students’ learning of IL. This study is a first of its kind comparing the perceptions of librarians’ teaching abilities by postgraduate and undergraduate students.
Effects of interdisciplinary courses on future engineers' competency
Authors: Rhee Hyunjung , Han Jinyoung , Lee Minha , Choi Young-Wan 
Published: February 2020

PurposeThis study explores the effects of interdisciplinary education on engineering students by observing students' competencies before and after the programme.Design/methodology/approachThe effects of interdisciplinary education were studied over three years through the use of a survey to test the social competencies of organisational life and the interdisciplinary competencies of college students. A total of 5,185 responses were collected from engineering students who took part in interdisciplinary education programmes. The survey was conducted during weeks 3 and 14 of each semester, and a comparison test was used to reveal any changes.FindingsAmong the 12 competencies developed or adapted, leadership significantly improved during all six semesters. Analytical thinking, interpersonal competency, professional attitude, global-mindedness, and creative attitudes also improved in some of the semesters.Research limitations/implicationsIt was not possible to control for the effect of classes that students were attending in addition to the targeted interdisciplinary class. However, this study was able to examine empirically the improvement of competencies for future engineers, and its findings provide a basis for future researchers to elaborate on other competencies as well.Originality/valueThe study recommends competencies needed by engineers working in the Fourth Industrial Revolution, examining the effects of interdisciplinary education on competency development. It contributes to strengthening the current trend in universities that seek to reform interdisciplinary education by empirically verifying its effectiveness.
Cognitive needs and use of social media: a comparative study of gratifications sought and gratification obtained
Authors: Hussain Ashfaq , Shabir Ghulam , Taimoor-Ul-Hassan  
Published: February 2020

Purpose
The purpose of this study is to compare the gratification sought and gratification obtained for cognitive needs from social media among information professionals in the limelight of uses and gratification theory. Cognitive needs are related to knowledge, acquiring information, comprehension etc., and gratification sought and gratification obtained are two distinct components of the uses and gratification theory.

Design/methodology/approach
For this quantitative research study, a self-administered survey questionnaire was used to collect data from the participants of the study. Sample of this study was 700 information professionals who are necessarily users of social media.

Findings
Finding of this study depicted that gratification obtained and gratification sought from social media for cognitive needs are different from each other, and information professionals need to revisit their social media use for cognitive needs.

Research limitations/implications
The present study is limited to gratification sought and gratification obtained for cognitive needs among information professionals.

Practical implications
This study has determined that information professionals need to revisit their social media use for cognitive needs, as the obtained gratifications are different from gratification sought from social media.

Social implications
Social media provides versatility of information in different forms and large numbers of information professionals are the users of social media around globe. Perceived use of social media for cognitive needs has been resulted into destructed gratifications. This study has brought the actual outcome of the use of social media to the audience so that they may rectify their social media use.

Originality/value
This study is a significant contribution for information professionals to review the gratifications sought and obtained from social media for cognitive needs. It has been established in this study that gratifications sought are significantly different from gratifications obtained from social media among information professionals.