bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model based normalization improves differential expression calling in low-depth RNA-seq
Authors: Zakharov Pavel N. , Sergushichev Alexey A. , Predeus Alexander V. , Artyomov Maxim N. 
Published: January 2015

AbstractRNA-seq is a powerful tool for gene expression profiling and differential expression analysis. Its power depends on sequencing depth which limits its high-throughput potential, with 10-15 million reads considered as optimal balance between quality of differential expression calling and cost per sample. We observed, however, that some statistical features of the data, e.g. gene count distribution, are preserved well below 10-15M reads, and found that they improve differential expression analysis at low sequencing depths when distribution statistics is estimated by pooling individual samples to a combined higher-depth library. Using a novel gene-by-gene scaling technique, based on the fact that gene counts obey Pareto-like distribution1, we re-normalize samples towards bigger sequencing depth and show that this leads to significant improvement in differential expression calling, with only a marginal increase in false positive calls. This makes differential expression calling from 3-4M reads comparable to 10-15M reads, improving high-throughput of RNA-sequencing 3-4 fold.
Characterization of Chloroplast Protein Import without Tic56, a Component of the 1-Megadalton Translocon at the Inner Envelope Membrane of Chloroplasts
Authors: Köhler Daniel , Montandon Cyril , Hause Gerd , Majovsky Petra , Kessler Felix , Baginsky Sacha , Agne Birgit 
Published: January 2015

Abstract
We report on the characterization of Tic56, a unique component of the recently identified 1-MD translocon at the inner envelope membrane of chloroplasts (TIC) in Arabidopsis (Arabidopsis thaliana) comprising Tic20, Tic100, and Tic214. We isolated Tic56 by copurification with Tandem Affinity Purification-tagged Toc159 in the absence of precursor protein, indicating spontaneous and translocation-independent formation of the translocon at the outer envelope membrane of chloroplasts (TOC) and TIC supercomplexes. Tic56 mutant plants have an albino phenotype and are unable to grow without an external carbon source. Using specific enrichment of protein amino termini, we analyzed the tic56-1 and plastid protein import2 (toc159) mutants to assess the in vivo import capacity of plastids in mutants of an outer and inner envelope component of the anticipated TOC-TIC supercomplex. In both mutants, we observed processing of several import substrates belonging to various pathways. Our results suggest that despite the severe developmental defects, protein import into Tic56-deficient plastids is functional to a considerable degree, indicating the existence of alternative translocases at the inner envelope membrane.
From community to public ownership: a tale of changing accountabilities
Authors: Fowler Carolyn J. , Cordery Carolyn J. 
Published: January 2015

Purpose
– The purpose of this paper is to examine changes in accountability as the provision and control of education moved from private nonprofit organisations to a public sector provider.

Design/methodology/approach
– Analysis of nineteenth century archival documents from significant primary educational providers in a major early New Zealand settlement.

Findings
– The nonprofit education provider utilised public meetings including public examinations, whose effect was to develop trust based on the education values it shared with its community of stakeholders. It also published financial reports which, along with inspections and statistical returns, were preferred once the government became the education provider. Such publications and inspections indicated bureaucracy and control. Nevertheless, government funding, rather than the nonprofit organisation’s dependence on its community, made education provision sustainable.

Research limitations/implications
– It has been suggested that the differences between public sector and private sector accounting and accountability are not always sharply defined (Carnegie and Napier, 2012). However, this case study shows that a change of education provider did lead to a marked difference in accountability. While theory suggests that public sector accountability should enhance democracy, the party best meeting this brief was the nonprofit provider, with the public sector provider preferring hierarchical accountability. It could be argued that funding dependence drove these different approaches as community accountability was traded for financial security.

Originality/value
– Distinctive study of accountability practices to external stakeholders, in a mid-nineteenth century education context.
(Dis)engaging with sustainability: evidence from an Australian business faculty
Authors: Dyball Maria Cadiz , Wang Andy F. , Wright Sue 
Published: January 2015

Purpose– The purpose of this paper is to explore how the lack of staff engagement with a university’s strategy on sustainability could be an enabling lever for organisational change. It examines the attitudes and views of employees of a business faculty at an Australian metropolitan university as it attempts to adopt a holistic approach to sustainability.Design/methodology/approach– The paper opted for a case study using data from an on-line survey, semi-directed interviews with key management personnel and archival material. Responses were analysed using Piderit’s (2000) notion of ambivalence.Findings– The paper provides empirical insights into why staff lacked engagement with the university’s strategy on sustainability. It suggests that staff were ambivalent, displaying dissonance in their personal beliefs on sustainability, the university’s strategy and the extent of their intentions to support the university. Staff were willing to offer ideas on how the university could, in the future, change towards sustainability. These ideas allow the possibility for the university to learn to adjust the scope of the implementation of its sustainability strategy.Research limitations/implications– The research results may lack generalisability. Therefore, researchers are encouraged to further examine staff attitudes on sustainability in higher education using Piderit’s notion of ambivalence. In-depth interviews and focus group discussions could allow a better understanding of harmony and dissonance in cognition of and intention for university sustainability strategies and initiatives by academic, professional and sessional staff.Practical implications– The paper includes implications for staff engagement with sustainability in higher education.Originality/value– This paper fulfils an identified need to study how staff engagement with sustainability in higher education can be enabled for organisational learning.
Institutional contradictions at and around the annual general meeting
Authors: Johed Gustav , Catasús Bino 
Published: January 2015

Purpose
– The purpose of this paper is to examine how a shareholder association prepares for and later act at the annual general meeting. It focusses on how the association evaluates corporate proposals to pay dividends and how they vote on equity distributions at the annual general meeting.

Design/methodology/approach
– This paper relies on observation of the shareholder association before the annual general meeting as well as at the meeting. The analysis is informed by institutional analysis as a way to make sense of how the association experience tension in the setting of the stock market and how it activates responses to these tensions.

Findings
– The shareholder association failed to target companies that comply with an institutionalized view of good ownership despite those companies distributing more equity than the association deems to be in line with sound governance. This the authors understand to result from institutional tensions between a traditional stewardship model of governance and the more recent financial investor logic that emphasizes equity distributions as mean to create shareholder wealth. As good ownership is often equated with long-term committed owners, which makes the association fail to target non-traditional companies that are similar to companies with traditional ownership in terms of dividend ratios.

Research limitations/implications
– The paper demonstrates how institutional logics influence micro-level action in offering guidance to individual members. There are two relevant aspects to this. First, it offers guidance in terms of how to identify whether a corporate proposal is in line with the associations’ policy. Second, institutional logics influence micro-level action because deviations from it require explanations.

Originality/value
– There are so far little qualitative research on how participants in governance mechanism use accounting to take decisions. In this way, the paper adds insight to both investor communities as well as behind the doors of the AGM.
The co-construction of NGO accountability
Authors: O'Dwyer Brendan , Boomsma Roel 
Published: January 2015

Purpose– The purpose of this paper is to deepen and advance the understanding of the construction of accountability within the relationship between government funders and development non-governmental organisations (NGOs).Design/methodology/approach– The paper presents a case study examining the process through which an influential Dutch development NGO, Oxfam Novib, constructed its own accountability while simultaneously seeking to influence shifts in government funder accountability requirements. It enrols a combination of comprehensive archival data on the Dutch government’s financing scheme for NGOs from 1965 to 2012 and in-depth interviews with Oxfam Novib managers and Dutch government officials. The co-evolution in accountability within Oxfam Novib and the government funding scheme is conceptualised using the notions of imposed, felt and adaptive accountabilityFindings– The case unveils the dynamics through which accountability within a major government funding scheme for NGOs was co-constructed by Oxfam Novib and the Dutch government’s development aid department. In particular, it reveals how this process was influenced by an internal evolution in Oxfam Novib’s organisational approach to accountability and an institutional context characterised by consensus-based economic and social policy making. The case also unveils the process through which Oxfam Novib’s influence declined as more demanding, narrowly focused government accountability requirements emerged in a setting that was increasingly critical of NGOs.Originality/value– The paper presents a rare example of a context where development NGOs have proactively sought and secured influence over the accountability demands of a key donor. It is unique in combining consideration of the internal evolution of accountability within an individual NGO (conceptualised as an evolution from felt to adaptive accountability) with a progression in the form of accountability required by governmental funders. The paper unveils the conditions under which NGO-preferred conceptions of accountability may gain (and lose) influence among key funders.
Electrical studies on biopolyurethane from cashew nut husk tannin
Authors: Sunija A.J. , Siva Ilango S. , Vinod Kumar K.P 
Published: January 2015

Purpose
– This paper aims to focus on the evaluation of the electrical properties of bio-based polyurethane material derived from cashew nut husk tannin and also the effect of temperature and frequency on the dielectric values and alternate current (AC) conductivity.

Design/methodology/approach
– Bio-based polyurethane is prepared from cashew nut husk tannin as polyol, their dielectric constant and dielectric loss factor are measured using an inductance capacitance resistance (LCR) metre, and the AC conductivity is determined using dielectric constant and loss values.

Findings
– The dielectric constant values are high, and the values decrease with an increase in frequency but increase with an increase in temperature. The AC conductivity values are low; hence, the material can be categorized as insulators or semi-conductors. Because the polyurethanes have a good dielectric value and are cost-effective, as they are derived from renewable biomaterial waste, they have promising applications for the future.

Research limitations/implications
– The experiment is carried out up to the frequency of 200 KHz because of the limitation in the instrument. But for the institute of printed circuits (IPC) and other specifications, the values of dielectric loss and dielectric constant will be generally coated for 1 MHz.

Practical implications
– The high dielectric constant and loss values show that the polyurethane can be opted for use as capacitors in electronic devices, and the values are comparable to the requirements of IPC4101A/24IPC; hence, they are suitable for the application as printed circuit board (PCB) laminate.

Social implications
– The use of biomaterial waste in the production of polyurethane will bring down the dependence of polyurethane industry on fossil fuel reserve, reduce carbon dioxide foot print and reduce the cost of production.

Originality/value
– The motivation of the work was its ecological aspect and also aims on the use of an alternative bio-based material in the PCB industry.
Multiphysics coupling simulation of RDE for PCB manufacturing
Authors: Ji Linxian , Wang Chong , Wang Shouxu , He Wei , Xiao Dingjun , Tan Ze 
Published: January 2015

Purpose– The purpose of this paper is to optimize experimental parameters and gain further insights into the plating process in the fabrication of high-density interconnections of printed circuit boards (PCBs) by the rotating disc electrode (RDE) model. Via metallization by copper electrodeposition for interconnection of PCBs has become increasingly important. In this metallization technique, copper is directly filled into the vias using special additives. To investigate electrochemical reaction mechanisms of electrodeposition in aqueous solutions, using experiments on an RDE is common practice.Design/methodology/approach– An electrochemical model is presented to describe the kinetics of copper electrodeposition on an RDE, which builds a bridge between the theoretical and experimental study for non-uniform copper electrodeposition in PCB manufacturing. Comsol Multiphysics, a multiphysics simulation platform, is invited to modeling flow field and potential distribution based on a two-dimensional (2D) axisymmetric physical modeling. The flow pattern in the electrolyte is determined by the 2D Navier–Stokes equations. Primary, secondary and tertiary current distributions are performed by the finite element method of multiphysics coupling.Findings– The ion concentration gradient near the cathode and the thickness of the diffusion layer under different rotating velocities are achieved by the finite element method of multiphysics coupling. The calculated concentration and boundary layer thicknesses agree well with those from the theoretical Levich equation. The effect of fluid flow on the current distribution over the electrode surface is also investigated in this model. The results reveal the impact of flow parameters on the current density distribution and thickness of plating layer, which are most concerned in the production of PCBs.Originality/value– By RDE electrochemical model, we build a bridge between the theoretical and experimental study for control of uniformity of plating layer by concentration boundary layer in PCB manufacturing. By means of a multiphysics coupling platform, we can accurately analyze and forecast the characteristic of the entire electrochemical system. These results reveal theoretical connections of current density distribution and plating thickness, with controlled parameters in the plating process to further help us comprehensively understand the mechanism of copper electrodeposition.
Computing method of thermal conductivity of heat dissipation vias in printed circuit board and its optimization
Authors: Xiao Shuo , Zhao Yang , Cao Yuan , Jiang Haifeng , Zhu Wenliang 
Published: January 2015

Purpose
– This paper aims to deduce a set of theory computational formula, and optimize and improve the heat conductivity of vias in printed circuit boards of electrical power apparatus.

Design/methodology/approach
– The authors adopted numerical simulation and experimental measurement to verify the reliability of this formula.

Findings
– Research result showed that 0.45 mm was the optimal bore diameter of vias; the conductivity had no obvious improvement when filling material was FR4 or Rogers, but if it was filled with texture of high thermal conductivity like soldering tine, the conductivity would improve a lot; the plating thickness of vias had a greater influence on thermal conductivity.

Originality/value
– Through the theory computational formula, this paper studied the influence of aperture of vias, filled materials and thickness of copper plated on vias on thermal conductivity.
Temperature simulation and its application in on-line temperature measurement of a micro drill bit
Authors: Shi Hongyan , Li Hui , Chen Shengzhi 
Published: January 2015

Purpose
– The purpose of this paper is to obtain the micro drill bit temperature field distribution in micro-drilling process and the temperature drop in retracting process with simulation software. Meanwhile, the key factors that affect the micro drill bit temperature will be obtained as well. The results can also be used to improve the accuracy in on-line drilling temperature measurement.

Design/methodology/approach
– The purpose of this paper is to obtain the micro drill bit temperature field distribution in micro-drilling process and the temperature drop in retracting process with simulation software. Meanwhile, the key factors that affect the micro drill bit temperature will be obtained as well. The results can also be used to improve the accuracy in on-line drilling temperature measurement.

Findings
– Micro drill bit high-temperature area mainly concentrates in the cutting edge and chisel edge. With the increase of spindle speed and feed speed, the micro drill bit highest temperature increased. The micro drill bit temperature drop rate reaches 20° in the micro-drilling retraction process with certain parameters. The micro drill bit highest temperature detected by an infrared camera is lower by 22° than that in real drilling. The simulation results can be used to guide the actual industrial production.

Originality/value
– The simulation results can be applied to revise the temperature measurement by an infrared camera in the drilling process. Drilling experiments show that the simulation method is correct and has certain practical significance. The current temperature measurement method can satisfy most of the requirements of temperature measurements.
Trust in school: a pathway to inhibit teacher burnout?
Authors: Van Maele Dimitri , Van Houtte Mieke 
Published: January 2015

Purpose– The purpose of this paper is to consider trust as an important relational source in schools by exploring whether trust lowers teacher burnout. The authors examine how trust relationships with different school parties such as the principal relate to distinct dimensions of teacher burnout. The authors further analyze whether school-level trust additionally influences burnout. In doing this, the authors account for other teacher and school characteristics.Design/methodology/approach– The authors use quantitative data gathered during the 2008-2009 school year from 673 teachers across 58 elementary schools in Flanders (i.e. the northern Dutch-speaking region of Belgium). Because teacher and school characteristics are simultaneously related to burnout, multilevel modeling is applied.Findings– Trust can act as a buffer against teacher burnout. Teachers’ trust in students demonstrates the strongest association with burnout compared to trust in principals or colleagues. Exploring relationships of trust in distinct school parties with different burnout dimensions yield interesting additional insights such as the specific importance of teacher-principal trust for teachers’ emotional exhaustion. Burnout is further an individual teacher matter to which school-level factors are mainly unrelated.Research limitations/implications– Principals fulfill an important role in inhibiting emotional exhaustion among teachers. They are advised to create a school atmosphere that is conducive for different kinds of trust relationships to develop. Actions to strengthen trust and inhibit teacher burnout are necessary, although further qualitative and longitudinal research is desirable.Originality/value– This paper offers a unique contribution by examining trust in different school parties as a relational buffer against teacher burnout. It indicates that principals can affect teacher burnout and prevent emotional exhaustion by nurturing trusting relationships in school.
Principals’ social interactions with teachers
Authors: Price Heather E. 
Published: January 2015

Purpose– The purpose of this paper is to link the social interactions between principals and their teachers to teachers’ perceptions of their students’ engagement with school, empirically testing the theoretical proposition that principals influence students through their teachers in the US charter school environment. The mediating influence of latent beliefs of trust and support are tested in this process.Design/methodology/approach– By analyzing pooled network and survey data collected in 15 Indianapolis charter schools using stepwise, fixed-effects regression techniques, this study tests the association between interactions of principals and teachers, on the one hand, and teachers’ perceptions of student engagement, on the other. The extent to which latent beliefs about teachers – in particular, trust in teachers and support of teachers by the administrators – mediate this relationship is also tested.Findings– Direct relationships between principal-teacher interactions and latent beliefs of trust and support are confirmed. Direct relationships between latent beliefs and perceptions of academic and school engagement are also confirmed. There is a relationship between principal-teacher interactions and teacher perceptions of student engagement, but the mediating effect of latent beliefs of trust and support accounts for much of the direct association. The reachability of the principal remains a significant and direct influence on teachers’ perceptions of academic engagement after accounting for trust and support.Research limitations/implications– Moving beyond principals’ personality dispositions in management and turning to the social relationships that they form with teachers adds to the understanding of how principal leadership affects student learning. Empirically distinguishing between the actual interactions and social dispositions of principals helps inform practical implications. Focussing on how principals’ social interactions with teachers influence teachers’ perceptions of students’ engagement provides a theoretical link as to how principals indirectly influence student achievement.Practical implications– The relationships that principals build with teachers have real implications on the beliefs of trust and support among teachers in a school and have a ripple effect on teachers’ perceptions of student engagement. These findings therefore suggest that frequently moving principals among schools is not an ideal policy.Originality/value– This study tests the theoretical boundaries of school organization research by using a within-schools design with charter schools. It also links leadership research to outcomes typically restricted to research on school culture and climate.