bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of histological features to predict MUC2 expression in colon cancer tissues
Authors: Periyakoil Preethi , Clarke Michael F. , Sahoo Debashis 
Published: March 2019

AbstractColorectal cancer (CRC) is the third-most common form of cancer among Americans. Like normal colon tissue, CRC cells are sustained by a subpopulation of “stem cells” that possess the ability to self-renew and differentiate into more specialized cancer cell types. In normal colon tissue, the enterocytes, goblet cells and other epithelial cells in the mucosa region have distinct morphologies that distinguish them from the other cells in the lamina propria, muscularis mucosa, and submucosa. However, in a tumor, the morphology of the cancer cells varies dramatically. Cancer cells that express genes specific to goblet cells significantly differ in shape and size compared to their normal counterparts. Even though a large number of hematoxylin and eosin (H&E)-stained sections and the corresponding RNA sequencing (RNASeq) data from CRC are available from The Cancer Genome Atlas (TCGA), prediction of gene expression patterns from tissue histological features has not been attempted yet. In this manuscript, we identified histological features that are strongly associated with MUC2 expression patterns in a tumor. Specifically, we show that large nuclear area is associated with MUC2-high tumors (p < 0.001). This discovery provides insight into cancer biology and tumor histology and demonstrates that it may be possible to predict certain gene expressions from histological features.
Auditory cortex shapes sound responses in the inferior colliculus
Authors: Blackwell Jennifer M. , Lesicko Alexandria , Rao Winnie , De Biasi Mariella , Geffen Maria N. 
Published: March 2019

AbstractThe extensive feedback from the auditory cortex (AC) to the inferior colliculus (IC) supports critical aspects of auditory behavior but has not been extensively characterized. Previous studies demonstrated that activity in IC is altered by focal electrical stimulation and pharmacological inactivation of AC, but these methods lack the ability to selectively manipulate projection neurons. We measured the effects of selective optogenetic modulation of cortico-collicular feedback projections on IC sound responses in mice. Activation of feedback increased spontaneous activity and decreased stimulus selectivity in IC, whereas suppression had no effect. To further understand how microcircuits in AC may control collicular activity, we optogenetically modulated different cortical neuronal subtypes, specifically parvalbumin-positive (PV) and somatostatin-positive (SST) inhibitory interneurons. We found that modulating either type of interneuron did not affect IC sound-evoked activity. Combined, our results identify that activation of excitatory projections, but not inhibition-driven changes in cortical activity, affects collicular sound responses.
An Exon Skipping Screen Identifies Antitumor Drugs That Are Potent Modulators of Pre-mRNA Splicing, Suggesting New Therapeutic Applications
Authors: Shi Yihui , Bray Walter , Smith Alexander J. , Zhou Wei , Calaoagan Joy , Lagisetti Chandraiah , Sambucetti Lidia , Crews Phillip , Lokey R. Scott , Webb Thomas R. 
Published: March 2019

ABSTRACTAgents that modulate pre-mRNA splicing are of interest in multiple therapeutic areas, including cancer. We report our recent screening results with the application of a cell-based Triple Exon Skipping Luciferase Reporter (TESLR) using a library that is composed of FDA approved drugs, clinical compounds, and mechanistically characterized tool compounds. Confirmatory assays showed that three clinical antitumor therapeutic candidates (milciclib, PF-3758309 and PF-030871) are potent splicing modulators and that these drugs are, in fact, nanomolar inhibitors of multiple kinases involved in the regulation the spliceosome. We also report the identification of new SF3B1 antagonists (sudemycinol C and E) and show that these antagonists can be used to develop a displacement assay for SF3B1 small molecule ligands. These results further supports the broad potential for the development of agents that target the spliceosome for the treatment of cancer and other diseases, as well as new avenues for chemotherapeutic discovery.
Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage
Authors: Cuscó Anna , Salas Anna , Torre Celina , Francino Olga 
Published: March 2019

AbstractLong-read metagenomics –using single-molecule sequencers– has the potential to assembly entire genomes, even from complex metagenomics datasets. Using long-read metagenomics with Nanopore sequencing in pooled samples, we aim to improve the individual taxonomic profiles obtained with V4 16S rRNA massive sequencing and to assemble the fecal metagenome of healthy dogs.Fecal samples from healthy dogs were sequenced individually using V4 16S rRNA gene and in pools using a shallow metagenomics approach with Nanopore sequencing. Long-read metagenomics allowed us refining the V4 16S rRNA results up to the species level and determining the main bacterial species inhabiting on fecal microbiota of our cohort of healthy dogs. Among them, the most abundant were Fusobacterium varium; Megamonas hypermegale; Bacteroides vulgatus; Blautia hansenii; Clostridium perfringens; and Clostridoides difficile. Once performed the metagenome assembly, one contig was suggested to be circular and hit to an uncultured crAssphage.To conclude, shallow long-read metagenomics with pooled samples using MinION allowed characterizing the dog fecal microbiota at lower taxonomic level, such as bacterial species. The assembly of the reads retrieved a contig that represents a circular draft genome of an uncultured CrAssphage from dog fecal samples that is one of the most abundant bacteriophages in the human gut.
Method to generate growth and degrowth models obtained from combinations of existing models applied to agrarian sciences
Authors: Santos André Luiz Pinto dos , Moreira Guilherme Rocha , Gomes-Silva Frank , Brito Cícero Carlos Ramos de , Costa Maria Lindomárcia Leonardo da , Pereira Luiz Gustavo Ribeiro , Maurício Rogério Martins , Azevêdo José Augusto Gomes , Pereira José Marques , Ferreira Alexandre Lima , Filho Moacyr Cunha 
Published: March 2019

AbstractMathematical models that describe gas production are widely used to estimate the rumen degradation digestibility and kinetics. The present study presents a method to generate models by combining existing models and to propose the von Bertalanffy-Gompertz two-compartment model based on this method. The proposed model was compared with the logistic two-compartment one to indicate which best describes the kinetic curve of gas production through the semi-automatedin vitrotechnique from different pinto peanut cultivars. The data came from an experiment grown and harvested at the Far South Animal Sciences station (Essul) in Itabela, BA, Brazil and gas production was read at 2, 4, 6, 8, 10, 12, 14, 17, 20, 24, 28, 32, 48, 72, and 96 h after the start of thein vitrofermentation process. The parameters were estimated by the least squares method using the iterative Gauss-Newton process in the software R version 3.4.1. The best model to describe gas accumulation was based on the adjusted coefficient of determination, residual mean squares, mean absolute deviation, Akaike information criterion, and Bayesian information criterion. The von Bertalanffy-Gompertz two-compartment model had the best fit to describe the cumulative gas production over time according to the methodology and conditions of the present study.
Three-dimensional genome reorganization during mouse spermatogenesis
Authors: Luo Zhengyu , Wang Xiaorong , Wang Ruoyu , Chen Jian , Chen Yusheng , Xu Qianlan , Cao Jun , Gong Xiaowen , Wu Ji , Yang Yungui , Li Wenbo , Han Chunsheng , Sun Fei , Song Xiaoyuan 
Published: March 2019

AbstractThree-dimensional genome organization plays an important role in many biological processes. Yet, how the genome is packaged at the molecular level during mammalian spermatogenesis remains unclear. Here, we performed Hi-C in seven sequential stages during mouse spermatogenesis. We found that topological associating domains (TADs) and chromatin loops underwent highly dynamic reorganization. They displayed clear existence in primitive type A spermatogonia, disappearance at pachytene stage, and reestablishment in spermatozoa. Surprisingly, even in the absence of TADs and chromatin loops at pachytene stage, CTCF remained bound at TAD boundary regions (identified in primitive type A spermatogonia). Additionally, many enhancers and promoters exhibited features of open chromatin and transcription remained active at pachytene stage. A/B compartmentalization and segmentation ratio were conserved in different stages of spermatogenesis in autosomes, although there were A/B compartment switching events correlated with gene activity changes. Intriguingly, A/B compartment structure on the X chromosome disappeared during pacSC, rST and eST stages. Together, our work uncovered a dynamic three-dimensional chromatin organization during mouse spermatogenesis and suggested that transcriptional regulation could be independent of TADs and chromatin loops at specific developmental stages.
Inter-organizational relationships: toward a reconceptualization of constructs
Authors: Agostini Lara , Nosella Anna , Teshome Mehari Beyene 
Published: March 2019

PurposeThe purpose of this paper is to provide a reconceptualization of existing constructs within the inter-organizational relationship (IOR) domain to face two main issues: the proliferation of constructs emerged because of a fast-growing body of literature, and the interchangeable and ambiguous use of constructs.Design/methodology/approachFirst, the authors surveyed the literature regarding IORs using a structured process supported by the use of bibliometric technique, and then the authors organized an expert panel process that contributes to refine the reconceptualization of the constructs.FindingsThe results of the analyses allow a further confirmation of the inconsistency in the definition of IOR constructs and provide a clear reconceptualization of the inter-organizational network and alliance constructs, recognized as the most relevant in this domain.Originality/valueBeing the first attempt to deal with the issue of construct reconceptualization in the IOR domain practically, and considering that clear construct definitions serve as a necessary basis for theory building, this paper has relevant implications for the development of theory related to the different types of IORs.
The role of supporter engagement in enhancing crowdfunding success
Authors: Efrat Kalanit , Gilboa Shaked , Sherman Arie 
Published: March 2019

Purpose
Recent research has addressed the marketing aspects incorporated in crowdfunding activity, establishing their relevance to campaign success. In line with this, research has begun to explore the behavioral aspects of crowdfunding participants, drawing on the buyer–seller interaction. The purpose of this paper is to expand on this trend by investigating the role of supporter engagement and its link to campaign success.

Design/methodology/approach
The proposed model was tested using structural equation modeling analysis. Data collection was based on a survey of 116 supporters, combined with outcome data of 530 crowdfunding campaigns.

Findings
The study’s findings revealed that supporters distinguish between their engagement to the campaign and to the campaign’s creator. However, both aspects of engagement affect community establishment and supporters’ promotion efforts. The authors also found that these indicators of engagement are associated with campaign success.

Originality/value
Research on crowdfunding supporters have focused to date on criteria contributing to campaigns success, exploring the motivational aspects associated with such activity. The current study expands this perspective by examining supporters’ engagement, differentiating between engaging with the creator and engaging with the campaign. Recommendations for creators include making efforts to establish supporter engagement to facilitate active promotion and shape future support intentions, thus facilitating enhanced outcomes for both current and future campaigns.
Evolving talent management patterns and challenges in Russia and Kazakhstan
Authors: Khoreva Violetta , Kostanek Edyta 
Published: March 2019

Purpose
The purpose of this paper is to investigate the evolving patterns and challenges of talent management (TM) in the emerging markets of Russia and Kazakhstan from the employer perspective. Increasing the understanding of how TM is recognized from the employer perspective may better equip us to address how to effectively manage and lead the available talents in these and other emerging markets.

Design/methodology/approach
The authors conducted a qualitative study comprising 50 semi-structured interviews, with 37 business leaders from Russian subsidiaries, and 13 from Kazakh subsidiaries, in all cases of Nordic Multinational enterprises (MNEs).

Findings
The study supports the object approach to TM in the emerging markets of Russia and Kazakhstan. The authors reveal that the exclusive and developable talent philosophy is predominant in these emerging markets, where TM faces the challenges of fierce competition for talents and an insufficient supply, so business leaders tend to be reluctant to inform employees of their talent pool membership. The results demonstrate that MNEs do not act independently of context, thus supporting calls for consideration of the local institutional context.

Originality/value
TM is still a somewhat novel idea in many emerging economies, and challenges related to managing talents are believed to be far more complex in such settings. Furthermore, to the best of authors’ knowledge, no studies have investigated the notion of talent and TM conceptualization in the emerging markets from an employer perspective.
Learning environment and primary school efficiency
Authors: Lee Boon L. , Worthington Andrew , Wilson Clevo 
Published: March 2019

Purpose
Existing studies of school efficiency primarily specify teacher inputs as the number of teachers and perhaps the student-teacher ratio. As a result, there is no direct qualitative recognition of the learning environment. The purpose of this paper is to incorporate the learning environment directly into the assessment of school efficiency.

Design/methodology/approach
The authors employ data envelopment analysis to derive efficiency scores and the double-bootstrap truncated regression approach in Simar and Wilson’s (2007) Journal of Econometrics to quantify the sources of efficiency in 430 Queensland state primary schools. In the first stage, the outputs of student National Assessment Program-Literacy and Numeracy scores and the inputs of full-time equivalent teaching staff and cumulative capital expenditure per student are used to measure efficiency. In the second stage, the authors specify an index of community socio-educational advantage, class size, the share of teachers with postgraduate qualifications, funds spent on professional development, and surveyed opinions from parents/caregivers, students, staff and principals on the learning environment to explain these measures of efficiency.

Findings
Socio-economic background and the teaching environment affect school efficiency. Although not all variables related to teacher contribution are significant, there is evidence to suggest that teachers have a positive influence on student performance hence school efficiency. Teachers ability to clearly explain the requirements of schoolwork tasks and listening to student opinions sets an ideal student engagement environment which can have a profound impact on student learning.

Practical implications
From a policy perspective, policy makers should target resources at inefficient schools aimed at enhancing student learning through teacher development and, at the same time, providing financial and non-financial educational assistance to students and their families from a low socio-educational background.

Originality/value
This is the first large-scale primary school efficiency analysis to incorporate the Simar and Wilson (2007) approach to explaining the determinants of efficiency, including teaching environment from the perspective of students, teachers and other stakeholders.
Teaching activities in higher medical school: innovations and management features
Authors: Коlomiets Olga Mikhailovna , Litvinova Tatijana Mikhailovna 
Published: March 2019

PurposeThe purpose of this paper is to reveal the essence of innovations and their application in teaching in connection with the student’s educational outcomes.Design/methodology/approachThe sample of the study consists of 588 third-year students of the I.M. Sechenov First Moscow State Medical University. The paper describes the use of innovations in teaching in the context of the competence-activity approach, which implements the psychological process of learning of social experience in the practice of education.FindingsThis paper reflects the content of a scientific research on a relevant topic in the field of modern education – the implementation of four innovations in teaching, the guarantee that each student masters the educational outcomes that meet the requirements of the Bologna Declaration to the quality of training of graduates and the development of competence-based education ideas. The paper presents the learning and professional activities that focus on constructing a mental image of educational outcomes in the student’s mind and independent training that focus on automating the student’s activity, with a view to solving the practical tasks of modeling socio-professional situations on the basis of the mental image in the mind.Research limitations/implicationsThere are some limitations with this research. The sample is small and this makes broad generalization difficult. In total, 588 participants (both Russian and foreign) from 611 upper-year medical students of State Medical University were involved in research work. This may have functioned as a measurement ceiling. With that, all the proposed tools are universal. The authors tried to describe their specific in as much detail as possible. The findings are also consistent with the urgent publications of researchers in the field. Thus, the authors believe there will be no problems with their implementation in other medical universities.Practical implicationsThe practical value of the study is that it shows medical university professors a model of teaching activities, which guarantees that each student achieves educational outcomes of the planned quality.Originality/valueThe authors propose new didactic means, which help to manage each student’s activities according to individual educational trajectory.
Promoting math teacher active learning with the lesson study approach
Authors: Obara Samuel , Bikai Nie 
Published: March 2019

PurposeRecent years have seen a movement toward using active learning to ground professional development in classroom practice. The paper aims to discuss this issue.Design/methodology/approachThe present case study describes how a group of middle school mathematics teachers improved classroom instruction through the use of lesson study.FindingsThis case study suggests the success of the lesson study in supporting teachers’ active learning.Originality/valueFor the lesson study, teachers’ active learning is assessed across four dimensions.
Embracing ambiguity
Authors: Towey Dave , Walker James , Ng Ricky 
Published: March 2019

Purpose
Embracing reflective practice and retrospection, with a goal of identifying commonalities, this paper aims to examine delivery of engineering subjects in both traditional higher education (THE) and technical and vocational education and training (TVET).

Design/methodology/approach
Reflections on actions and autoethnography were used to examine the teaching and learning experiences of three educators across two higher education (HE) institutions (HEIs) in the greater Chinese context. Literature reviews and historical contexts are outlined to support the approaches and insights identified.

Findings
This paper presents a number of common characteristics and challenges identified across both THE and TVET. Drawing on the successful embrace of ambiguity and change in recent software engineering (SE) development paradigms, recommendations are made for how the agile SE themes can be applied in a larger sense to address the wider challenges facing both THE and TVET.

Originality/value
To the best of the authors’ knowledge, this is the first time that engineering education has been examined and contrasted in the contexts of THE and TVET. The similarities and common challenges may represent a new focus for related work, and the presented insights, from agile methodologies in SE, represent a new perspective for viewing future HE and TVET sustainability.
Facility decision making process with modified value engineering approach
Authors: Zhao Cencheng , Yang Eunhwa , Nie Yiqian , Russo Justin D. 
Published: March 2019

PurposeThis paper aims to provide organizations with a new tool to make decisions related to a facility (building) selection process. Traditionally, value engineering (VE) applies the Value = Function/Cost formula to evaluate the worth of a product. In this paper, the VE-based facility-selection approach is proposed, where the cost of a facility is expressed in net present value (NPV) as it contains the net expense of purchasing or leasing a building as well as the time value of money. Also, a method of quantifying functions and involved risks of different facility choices is proposed.Design/methodology/approachThe framework of the VE-based facility-selection process is broken down into three steps: preparation, calculation/analysis and assessment. In the latter part of this paper, the authors share a sample analysis by illustrating the analysis and decision-making process when three hypothetical facility-selection options are available.FindingsThe sample analysis indicates that companies can get the lowest cost and risk while improving their functions to achieve the highest value by using the modified VE formula to drive an optimal option for company’s business expansion and facility-selection process.Originality/valueThis paper provides organizations with a strategic system and process to select proper facilities or buildings for business expansion. The VE approach suggested in this study can allow facility/real estate portfolio decision-makers to analyze financial and functional aspects of the facility at the same time and obtain the value coefficient when they choose a new facility from different options. Finally, they can select the best option, which has the highest value coefficient, given financial and functional considerations.