bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian inference of transcriptional branching identifies regulators of early germ cell development in humans
Authors: Penfold Christopher A. , Sybirna Anastasiya , Reid John , Venzor Aracely Castillo , Drousioti Elena , Huang Yun , Grant Murray , Wernisch Lorenz , Ghahramani Zoubin , Surani M. Azim 
Published: July 2017

AbstractDuring embryonic development, cells undertake a series of fate decisions to form a complete organism comprised of various cell types, epitomising a branching process. A striking example of branching occurs in humans around the time of implantation, when primordial germ cells (PGCs), precursors of sperm and eggs, and somatic lineages are specified. Due to inaccessibility of human embryos at this stage of development, understanding the mechanisms of PGC specification remains difficult. The integrative modelling of single cell transcriptomics data from embryos and appropriatein vitromodels should prove to be a useful resource for investigating this system, provided that the cells can be suitably ordered over a developmental axis. Unfortunately, most methods for inferring cell ordering were not designed with structured (time series) data in mind. Although some probabilistic approaches address these limitations by incorporating prior information about the developmental stage (capture time) of the cell, they do not allow the ordering of cells over processes with more than one terminal cell fate. To investigate the mechanisms of PGC specification, we develop a probabilistic pseudotime approach, branch-recombinant Gaussian process latent variable models (B-RGPLVMs), that use an explicit model of transcriptional branching in individual marker genes, allowing the ordering of cells over developmental trajectories with arbitrary numbers of branches. We use first demonstrate the advantage of our approach over existing pseudotime algorithms and subsequently use it to investigate early human development, as primordial germ cells (PGCs) and somatic cells diverge. We identify known master regulators of human PGCs, and predict roles for a variety of signalling pathways, transcription factors, and epigenetic modifiers. By concentrating on the earliest branched signalling events, we identified an antagonistic role for FGF receptor (FGFR) signalling pathway in the acquisition of competence for human PGC fate, and identify putative roles for PRC1 and PRC2 in PGC specification. We experimentally validate our predictions using pharmacological blocking of FGFR or its downstream effectors (MEK, PI3K and JAK), and demonstrate enhanced competency for PGC fatein vitro, whilst small molecule inhibition of the enzymatic component of PRC1/PRC2 reveals reduced capacity of cells to form PGCsin vitro. Thus, B-RGPLVMs represent a powerful and flexible data-driven approach for dissecting the temporal dynamics of cell fate decisions, providing unique insights into the mechanisms of early embryogenesis. Scripts relating to this analysis are available from:https://github.com/cap76/PGCPseudotime
Patient-derived xenografts undergo murine-specific tumor evolution
Authors: Ben-David Uri , Ha Gavin , Tseng Yuen-Yi , Greenwald Noah F. , Oh Coyin , Shih Juliann , McFarland James M. , Wong Bang , Boehm Jesse S. , Beroukhim Rameen , Golub Todd R. 
Published: July 2017

AbstractPatient-derived xenografts (PDXs) have become a prominent model for studying human cancerin vivo. The underlying assumption is that PDXs faithfully represent the genomic features of primary tumors, retaining their molecular characteristics throughout propagation. However, the genomic stability of PDXs during passaging has not yet been evaluated systematically. Here we monitored the dynamics of copy number alterations (CNAs) in 1,110 PDX samples across 24 cancer types. We found that new CNAs accumulated quickly, such that within four passages an average of 12% of the genome was affected by newly acquired CNAs. Selection for preexisting minor clones was a major contributor to these changes, leading to both gains and losses of CNAs. The rate of CNA acquisition in PDX models was correlated with the extent of both aneuploidy and genetic heterogeneity observed in primary tumors of the same tissue. However, the specific CNAs acquired during PDX passaging differed from those acquired during tumor evolution in patients, suggesting that PDX tumors are subjected to distinct selection pressures compared to those that exist in human hosts. Specifically, several recurrent CNAs observed in primary tumors gradually disappeared in PDXs, indicating that events undergoing positive selection in humans can become dispensable during propagation in mice. Finally, we found that the genomic stability of PDX models also affected their responses to chemotherapy and targeted drugs. Our findings thus highlight the need to couple the timing of PDX molecular characterization to that of drug testing experiments. These results suggest that while PDX models are powerful tools, they should be used with caution.
Insights into global planktonic diatom diversity: Comparisons between phylogenetically meaningful units that account for time
Authors: Nakov Teofil , Beaulieu Jeremy M. , Alverson Andrew J. 
Published: July 2017

AbstractMetabarcoding has offered unprecedented insights into microbial diversity. In many studies, short DNA sequences are binned into consecutively higher Linnaean ranks, and ranked groups (e.g., genera) are the units of biodiversity analyses. These analyses assume that Linnaean ranks are biologically meaningful and that identically ranked groups are comparable. We used a meta-barcode dataset for marine planktonic diatoms to illustrate the limits of this approach. We found that the 20 most abundant marine planktonic diatom genera ranged in age from 4 to 134 million years, indicating the non-equivalence of genera because some had more time to diversify than others. Still, species richness was only weakly correlated with genus age, highlighting variation in rates of speciation and/or extinction. Taxonomic classifications often do not reflect phylogeny, so genus-level analyses can include phylogenetically nested genera, further confounding rank-based analyses. These results underscore the indispensable role of phylogeny in understanding patterns of microbial diversity.
Auditor switching and audit fee discounting: the Iranian experience
Authors: MohammadRezaei Fakhroddin , Mohd-Saleh Norman 
Published: July 2017

Purpose
The purpose of this paper is to examine the impact of auditor switching on audit fee discounting in Iran. The increased competition in the Iranian audit market following audit market liberalization in 2001 has resulted in a rapid increase in auditor switching and reduces the relative bargaining power of auditors compared to the clients. It is expected that auditor switching results in fee discounting because the relative bargaining power of an auditor (client) is likely to be at the minimum (maximum) point during the initial period of engagement. Since the increased bargaining power of a client in initial year seems to be different in the case of different type of auditor switching (from a state auditor to a private and from a private auditor to another), the magnitude of fee discounting is expected to be different.

Design/methodology/approach
The objective is tested using a sample of 1,022 firm-year observations between 2001 and 2010. This study applies the multivariate regression model using the first difference specification of audit fee as a dependent variable.

Findings
Multivariate analysis reveals that auditor switching results in 14 percent of fee discounting. In addition, the results show that 18 and 13 percent of fees discounting during the initial year of engagement arise from cases of auditor switching involving a change from state auditors to private auditors, and a change from one private auditor to another, respectively. The findings support bargaining power view explanation in relation to audit fees discounting in initial year engagement.

Originality/value
This study is the first to examine the impact of auditor switching (and analyzed different types of auditor switching) on audit fee discounting using the bargaining power view.
A sizing improvement methodology based on adjustment of interior accommodation rates across measurement categories within a size chart
Authors: Pei Jie , Park Huiju , Ashdown Susan P. , Vuruskan Arzu 
Published: July 2017

Purpose
The purpose of this paper is to identify common issues among commercial body size charts, and to propose a sizing improvement methodology without changing the number of sizes in the range. One goal is to equalize the number of people accommodated by each size within the range, and to propose a way to evaluate the effectiveness of the improvement.

Design/methodology/approach
The proposed method consists of three phases: (Phase I) identify target population; (Phase II) analysis of existing size charts; and (Phase III) improvement of the initial size chart. Phase III is the key process, which includes repeated manipulation of intersize intervals of the three primary measurements (chest, waist and hip) for improved consistency of overall and interior accommodate rates among the three measurement categories. A program was developed in RStudio® to generate trials and side-by-side bar plots for visualization of the differences in accommodate rates.

Findings
The main issue in commercial body size charts observed is the inconsistency of the interior accommodation rates among measurement categories. Some other issues include: lack of important measurements, failure to provide ranges and gaps between measurement ranges of adjacent sizes.

Originality/value
This paper proposed a complete work flow to improve body size charts to fix the common issues. The method integrates historic size information and new anthropometric information extracted from a national-scale sizing database (e.g. SizeUSA). The study also brought association of the secondary body measurements with primary measurements without using linear regression. Hence, information from body size charts can be more efficiently used in acquiring other size information.
A project perspective on doctoral studies – a student point of view
Authors: Backlund Fredrik 
Published: July 2017

Purpose
Many doctoral students never obtain a doctoral degree, and many do not finish their studies in time. To promote aspects of effectiveness and efficiency in doctoral studies, the purpose of this paper is to explore a project perspective, more specifically how doctoral students experience their studies in terms of key dimensions of projects.

Design/methodology/approach
Written reflections concerning a project perspective in doctoral studies, based on 18 students at a Swedish university, have been categorised and analysed by the means of the qualitative research software NVivo.

Findings
Main findings are reflections on the project manager role including both the supervisor and the doctoral student, and different views on project control parameters and the concepts goal-seeking and goal-orientation. A more comprehensive picture of project planning is presented, compared with the Individual Study Plan, including different project methods and tools that can be suitable in a doctoral project.

Research limitations/implications
The study is based on a limited number of doctoral students; however, the aim has been to give examples of project perspectives. The findings could be valuable for increased understanding of doctoral studies and of the project management field in general.

Practical implications
The study can induce awareness among doctoral students and supervisors of a project perspective in doctoral studies, promoting aspects of efficiency and effectiveness.

Originality/value
Compared to previous research, this study explicitly tries to understand how doctoral students make sense of their doctoral studies from a project perspective.
Temporal withdrawal behaviors in an educational policy context
Authors: Rosenblatt Zehava , Shapira-Lishchinsky Orly 
Published: July 2017

Purpose
The purpose of this paper is to investigate the differential relations between two teacher withdrawal behaviors: work absence and lateness, and two types of school ethics: organizational justice (distributive, procedural) and ethical climate (formal, caring), all in the context of school turbulent environment.

Design/methodology/approach
Data were collected from 1,016 teachers in 35 Israeli high schools. The GLIMMIX procedure was used to consider simultaneously the hierarchical structure of the data, as well as the two dependent variables (absence and lateness).

Findings
The results showed that lateness was negatively related to two relatively short-term aspects of school ethics: distributive justice, in particular for women, and formal ethical climate. Absence was negatively related to a relatively long-term aspect of school ethics: caring climate, in particular for low- to medium-level seniority teachers.

Research limitations/implications
The paper’s theoretical contribution is to explicate the unique relation of each temporal withdrawal behavior to specific dimensions of the school ethical constructs studied.

Practical implications
In order to reduce teachers’ temporal withdrawal behaviors, school management may need to attenuate policy that taps into organizational ethics, while considering the effects of school culture and turbulent environment.

Originality/value
This study offers a time perspective, which fine-tunes understanding of teachers’ lateness and absence behaviors, while pointing out the unique relations of lateness and absence to school ethical within educational policy context.
Marketing research on mergers and acquisitions: a systematic review and future directions
Authors: Christofi Michael , Leonidou Erasmia , Vrontis Demetris 
Published: July 2017

PurposeThe purpose of this paper is to systematically review and critically examine marketing research on mergers and acquisitions (M&As), and articulates its importance and relevance in consideration of the growing influence of the M&A phenomenon in the global economy.Design/methodology/approachA two-stage systematic review of the extant literature was conducted focusing on peer-reviewed journal articles published during a 28 year period – from 1987 to 2014.FindingsA systematic analysis of 32 journal articles reveals that M&A research is a vibrant and rapidly growing stream of the broader marketing domain, and that it is contextually, methodologically and thematically diverse. The findings also highlight several literature trends and shortcomings, as well as the complex nature of the relationship between marketing and M&As.Originality/valueOn the basis of the critique, we develop an ambitious research agenda that raises exciting new research questions for the scholar community and helps promote future theory development in marketing, strategy, and other related disciplines.
An interactive system framework to enable design for disassembly
Authors: Desai Anoop , Mital Anil 
Published: July 2017

Purpose
The purpose of this paper is to present an interactive system to enable product design for disassembly and to offer robust and quick design solutions based on designers’ input.

Design/methodology/approach
The system utilizes an interactive questionnaire to communicate with the designer. The questionnaire is in the form of binary questions (Yes/No) and design questions that would enable the system to learn the objectives of the design. Solutions are based on a CAD supported design platform. The efficiency of each design is calculated using disassembly time as the metric of measurement using motion-time measurement (MTM). The designer would be able to make an informed decision with respect to component functionality, ease of disassembly and disassembly time. The paper presents a detailed framework and structure of this system.

Findings
The value of the system is corroborated by means of a case study of an actual product design. The system is structured to offer multiple solutions to a design problem so as to enable the designer to choose the option that best serves their needs.

Originality/value
This novel interactive system would accept customers’ design preferences as input and offer multiple solutions in order to solve the design problem. Process time is directly calculated using the MTM system of measurement by converting design features into time measurement units. Disassembly time can then be easily converted into disassembly cost by using standard conversion rates. The value to designers is obvious.
Countervailing the liability of newness by bringing in active initial investors: the case of Facebook
Authors: Cristofaro Matteo 
Published: July 2017

Purpose
This paper aims to present how Facebook overcame its liability of newness period, helping the interpretation of the same initial financial and organizational troubles faced by current unicorns.

Design/methodology/approach
In this study, the case study method has been used.

Findings
This story shows how the inclusion of active initial investors in the strategic team is pivotal for a firm’s survival. This case study depicts in depth the first years of life of the social network Facebook, focusing on the initial investors’ role for the survival of the firm.

Originality/value
This paper shows how an initial strategic team (especially the inexperienced) may benefit from the inclusion of active initial investors in terms of financed capital, and of further financing and refocusing of the strategic direction.
Does Whey Protein Supplementation Improve the Nutritional Status in Hypoalbuminemic Peritoneal Dialysis Patients?
Authors: Hassan Kamal 
Published: July 2017

AbstractLimited data are available regarding the effects of whey protein on the nutritional status of the peritoneal dialysis population. This study evaluated the effects of whey protein supplementation for 12 weeks on the nutritional status in hypoalbuminemic peritoneal dialysis patients. Thirty‐six stable adult patients on maintenance peritoneal dialysis with serum albumin levels <3.5 g/dL were enrolled in the study and were divided into two groups similar in their serum albumin and normalized protein equivalent of total nitrogen appearance (nPNA). Nineteen patients were instructed to receive 1.2 g/kg per day of protein diet and additional whey protein supplement at a dose of 25% of the instructed daily protein diet (whey protein group), and 17 patients were instructed to receive 1.2 g/kg per day protein diet without additional whey protein supplementation (control group). Nutritional status was assessed using two measures: nPNA and lean tissue mass index (LTI) obtained by whole‐body bioimpedance spectroscopy technique. In the whey protein group serum albumin and nPNA significantly increased from baseline to week 6 (P < 0.001, P = 0.034; respectively) and from week 6 to week 12 (P < 0.001, P = 0.001; respectively); LTI significantly increased from week 6 to week 12 (P = 0.022). Compared to the control group at week 12, serum albumin, nPNA and LTI values were significantly higher in the whey protein group (P < 0.001, P = 0.002, P = 0.001; respectively). This study demonstrated for the first time that oral supplementation with whey protein improves nutritional status and is well tolerated in hypoalbuminemic PD patients.
What does it cost to feed aged care residents in Australia?
Authors: Hugo Cherie , Isenring Elisabeth , Sinclair David , Agarwal Ekta 
Published: July 2017

AimFunding cuts to the aged care industry impact catering budgets and aged care staffing levels, which may in turn affect the nutritional status of aged care residents. This paper reports average food expenditure and trends in Australian residential aged care facilities (RACFs).MethodsThis is a retrospective study collecting RACFs’ economic outlay data through a quarterly online survey conducted over the 2015 and 2016 financial years.ResultsData were compiled from 817 RACFs, representing 64 256 residential beds and 23 million bed‐days Australia‐wide. The average total spend in Australian Dollars (AUD) on catering consumables (including cutlery/crockery, supplements, paper goods) was $8.00 per resident per day (prpd) and $6.08 prpd when looking at the raw food and ingredients budget alone. Additional data from over half the RACFs (n = 456, 56%) indicate a 5% decrease in food cost ($0.31 prpd) in the last year, particularly in fresh produce, with a simultaneous 128% ($0.50 prpd) increase in cost for supplements and food replacements. Current figures are comparatively less than aged care food budgets internationally (US, UK and Canada), less than community‐dwelling older adults ($17.25 prpd) and 136% less than Australian corrective services ($8.25 prpd).ConclusionsThe current spend on food in RACFs has decreased compared with previous years, reflecting an increasing reliance on supplements, and is significantly less than current community food spend.
Feasibility of spacers to facilitate postoperative radiotherapy for retroperitoneal sarcomas
Authors: Reid Jessica , Smith Richard , Borg Martin , Dobbins Christopher , Gowda Raghu , Chryssidis Steve , Borg Matthew , Neuhaus Susan 
Published: July 2017

AbstractIntroductionThe role and timing of postoperative radiotherapy (PORT) in the management of retroperitoneal sarcoma (RPS) remains controversial.MethodThis is a retrospective cohort review of patients undergoing curative resection for RPS at a single institution between January 2011 and July 2016. Patient selection was through the South Australian Soft Tissue Tumour Multidisciplinary Group (MDT) based at Royal Adelaide Hospital. An individualised approach, including assessment of resectability, histopathological grade and subtype, and radiotherapy considerations, was taken for each patient. Patients offered preoperative radiotherapy or palliation were excluded. A saline‐filled spacer was inserted following operative resection. Radiotherapy commenced postoperatively. Patients underwent laparotomy to remove the device approximately 6 weeks post completion of PORT. Primary endpoints were technical feasibility, perioperative morbidity and radiation toxicity. Secondary endpoints were local recurrence (LR), distant recurrence (DR) and death.ResultsDuring the study period, 40 patients with RPS were managed through the MDT. Twelve patients (ages 33–78) underwent PORT utilising spacers. Radiotherapy toxicity was reported in four patients and extensive adhesions observed in another four patients during spacer removal. Median follow‐up was 35 months (range 4–60). Seven patients remain alive and disease free. Four patients developed LR, three developed DR. Three patients died; two with DR and one with LR. Two patients with recurrent/progressive disease are alive; one with DR and one with LR.ConclusionUse of intraoperative spacers to facilitate PORT is feasible, with acceptable toxicity following resection of RPS. Patient selection for this approach remains to be determined.