bluuebunny/crossref_metadata_2025_split huggingface dataset:
Psychometric properties of the PHQ-9 depression scale in people with multiple sclerosis: a systematic review
Authors: Patrick Sarah , Connick Peter 
Published: May 2018

AbstractBackgroundDepression affects approximately 25% of people with MS (pwMS) at any given time. It is however under recognised in clinical practice, in part due to a lack of uptake for brief assessment tools and uncertainty about their psychometric properties. The 9-item Patient Health Questionnaire (PHQ-9) is an attractive candidate for this role.ObjectiveTo synthesise published findings on the psychometric properties of the 9-item Patient Health Questionnaire (PHQ-9) when applied to people with multiple sclerosis (pwMS).Data sourcesPubMed, Medline and ISI Web of Science databases, supplemented by hand-searching of references from all eligible sources.Study eligibility criteriaPrimary literature written in English and published following peer-review with a primary aim to evaluate the performance of the PHQ-9 in pwMS.Outcome measuresPsychometric performance with respect to appropriateness, reliability, validity, responsiveness, precision, interpretability, acceptability, and feasibility.ResultsSeven relevant studies were identified, these were of high quality and included 5080 participants from all MS disease-course groups. Strong evidence was found supporting the validity of the PHQ-9 as a unidimensional measure of depression. Used as a screening tool for major depressive disorder (MDD) with a cut-point of 11, sensitivity was 95% sensitivity and specificity 88.3% (PPV 51.4%, NPV 48.6%). Alternative scoring systems that may address the issue of overlap between somatic features of depression and features of MS per se are being developed, although their utility remains unclear. However data on reliability was limited, and no specific evidence was available on test-retest reliability, responsiveness, acceptability, or feasibility.ConclusionsThe PHQ-9 represents a suitable tool to screen for MDD in pwMS. However use as a diagnostic tool cannot currently be recommended, and the potential value for monitoring depressive symptoms cannot be established without further evidence on test-retest reliability, responsiveness, acceptability, and feasibility.PROSPERO register ID: CRD42017067814
Gelatinase B/matrix metalloproteinase-9 is a phase-specific effector molecule, independent from Fas, in experimental autoimmune encephalomyelitis
Authors: Ugarte-Berzal Estefania , Berghmans Nele , Boon Lise , Martens Erik , Vandooren Jennifer , Cauwe Bénédicte , Thijs Greet , Proost Paul , Damme Jo Van , Opdenakker Ghislain 
Published: May 2018

AbstractGelatinase B/matrix metalloproteinase-9 (MMP-9) triggers multiple sclerosis (MS) and the animal model of experimental autoimmune encephalomyelitis (EAE) by the breakdown of the blood-brain barrier. Interestingly, MMP-9 is beneficial in systemic autoimmunity caused by Fas-deficiency. Fas-deficient (faslpr)and Fas-ligand-deficient mice are protected against EAE. We here investigated the interaction between Fas and MMP-9 in the setting of induction of EAE and compared short- and long-term effects. We provoked EAE with myelin oligodendrocyte glycoprotein (MOG) peptide and compared EAE development in four genotypes (wild-type (WT), single knockoutmmp-9−/−,faslpr, andmmp-9−/−/faslpr) and monitored leukocytes, cytokines and chemokines as immunological parameters. As expected,faslprmice were resistant against EAE induction, whereas MMP-9 single knockout mice were not. In the doublemmp-9−/−/faslprmice the effects on disease scores pointed to independent rather than interrelated disease mechanisms. On a short term, leukocytes infiltrated into the brain and cytokines and chemokines after EAE induction were significantly higher in all the four genotypes studied, even in thefaslprandmmp9-/-/faslpr, which did not develop clinical disease. The levels of MMP-9 but not of MMP-2 were increased in the brain and in the peripheral organs after EAE induction. After 40 days all the animals recovered and did not show signs of EAE. However, the absence of MMP-9 in the remission phase suggested a protective role of MMP-9 in the late phase of the disease, thus singlemmp-9−/−mice presented a delayed onset and remission in comparison with WT animals suggesting a phase-dependent role of MMP-9 in the disease. Nevertheless, the levels of some cytokines and chemokines were remained higher than in control animals even 100 days after EAE induction, attesting to a prolonged state of immune activation. We thus yielded new insights and useful markers to monitor this activated immune status. Furthermore, MMP-9 but not MMP-2 levels remained increased in the brains and, to a higher extend, in the spleens of the WT mice even during the remission phase, which is in line with the role of MMP-9 as a useful marker and a protective factor for EAE in the remission phase.
GraphSeq: Accelerating String Graph Construction for De Novo Assembly on Spark
Authors: Su Chung-Tsai , Chang Ming-Tai , Cheng Yun-Chian , Li Yun-Lung , Wang Yao-Ting 
Published: May 2018

AbstractSummary: De novo genome assembly is an important application on both uncharacterized genome assembly and variant identification in a reference-unbiased way. In comparison with de Brujin graph, string graph is a lossless data representation for de novo assembly. However, string graph construction is computational intensive. We propose GraphSeq to accelerate string graph construction by leveraging the distributed computing framework.Availability and Implementation: GraphSeq is implemented with Scala on Spark and freely available at https://www.atgenomix.com/blog/graphseq.Supplementary information: Supplementary data are available at Bioinformatics online.
Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA
Authors: Anwer Muhammad Usman , Davis Amanda , Davis Seth Jon , Quint Marcel 
Published: May 2018

SummaryELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well-studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential Zeitnehmers that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development is completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.One sentence summaryELF3 and GI are essential for circadian clock mediated photoperiod sensing.
Prenatal growth map of the mouse knee joint by mean of deformable registration technique
Authors: Giorgi Mario , Sotiriou Vivien , Fanchini Niccolo’ , Conigliaro Simone , Bignardi Cristina , Nowlan Niamh C. , Dall’Ara Enrico 
Published: May 2018

AbstractJoint morphogenesis is the process during which distinct and functional joint shapes emerge during pre- and post-natal joint development. In this study, a repeatable semi-automatic protocol capable of providing a 3D realistic developmental map of the prenatal mouse knee joint was designed by combining Optical Projection Tomography imaging (OPT) and a deformable registration algorithm (Sheffield Image Registration toolkit, ShIRT). Eleven left limbs of healthy murine embryos were scanned with OPT (voxel size: 14.63¼m) at two different stages of development: Theiler stage (TS) 23 (approximately 14.5 embryonic days) and 24 (approximately 15.5 embryonic days). One TS23 limb was used to evaluate the precision of the displacement predictions for this specific case. The remaining limbs were then used to estimate Developmental Tibia and Femur Maps. Acceptable uncertainties of the displacement predictions were found for both epiphyses (between 0.7 and 1.4 μm, along all directions and anatomical sites) for nodal spacing of 1 voxel. The protocol was found to be reproducible with maximum Modified Housdorff Distance differences equal to 1.9 μm and 1.5 μm for the tibial and femoral epiphyses respectively. The effect of the initial shape of the rudiment affected the developmental maps by 21.7 μm and 21.9 μm for the tibial and femoral epiphyses respectively, which correspond to 1.4 and 1.5 times the voxel size. To conclude, this study proposes a repeatable semi-automatic protocol capable of providing mean 3D realistic developmental map of a developing rudiment allowing researchers to study how growth and adaptation are directed by biological and mechanobiological factors.
On the importance of accounting for intraspecific genomic relatedness in multi-species studies
Authors: Joly Simon , Flynn Dan F. B. , Wolkovich Elizabeth 
Published: May 2018

AbstractAnalyses in many fields of ecology are increasingly considering multiple species and multiple individuals per species. Premises of statistical tests are often violated with such datasets because of the non-independence of residuals due to phylogenetic relationships or intraspecific population structure. If comparative approaches that account for the phylogenetic relationships of species are well developed and their benefits demonstrated, the importance of considering the intraspecific genetic structure, especially in combination with the phylogenetic structure, has rarely been addressed.We investigated whether it is beneficial to account for intraspecific genomic relatedness in multi-species studies. For this, we used a Phylogenetic Mixed Model to analyze first a suite of simulated data and then results from one example ecological study—a budburst experiment where clippings of 10 tree and shrub species were subjected to different temperatures and photoperiods.We found that accounting for intraspecific genetic structure yields more accurate and precise fixed effects as well as increased statistical power, but more so when the relative importance of the intraspecific to the phylogenetic genetic structure is greater. Analysis of the budburst experiment further showed that accounting for intraspecific and phylogenetic structures yields improved estimates of warming and photoperiod effects and their interaction in explaining the time to budburst.Our results show that statistical gains can be made by incorporating information on the intraspecific genomic relatedness of individuals in multi-species studies. This is relevant for investigations that are interested in intraspecific variation and that plan to include such observations in statistical tests.
Somatic Mutations Render Human Exome and Pathogen DNA more Similar
Authors: Ebrahimzadeh Ehsan , Engler Maggie , Tse David , Cristescu Razvan , Tchamkerten Aslan 
Published: May 2018

AbstractImmunotherapy has recently shown important clinical successes in a substantial number of oncology indications. Additionally, the tumor somatic mutation load has been shown to associate with response to these therapeutic agents, and specific mutational signatures are hypothesized to improve this association, including signatures related to pathogen insults. We sought to study in silico the validity of these observations and addressed three questions. First, we investigated whether somatic mutations typically involved in cancer may increase, in a statistically meaningful manner, the similarity between common pathogens and the human exome. Our study shows that specific common mutagenic processes like those resulting from exposure to ultraviolet light (in melanoma) or smoking (in lung cancer) induce, in the upper range of biologically plausible frequencies, peptides in the cancer exome that are statistically more similar to pathogen peptides than the normal exome. Second, we investigated whether this increased similarity is due to the specificities of the mutagenic process or uniformly random mutations at equal rate would trigger the same effect. For certain pathogens the increased similarity is more pronounced for specific mutagenic processes than for uniformly random mutations and for other pathogens the effects cannot be distinguished. Finally, we investigated whether specific mutational processes result in amino-acid changes with functional relevance that are more likely to be immunogenic. We showed that functional tolerance to mutagenic processes across species generally suggests more resilience to natural processes than to denovo mutagenesis. These results support the idea that recognition of pathogen sequences as well as differential functional tolerance to mutagenic processes may play an important role in the immune recognition process involved in tumor infiltration by lymphocytes.
DeepEM: Deep 3D ConvNets With EM For Weakly Supervised Pulmonary Nodule Detection
Authors: Zhu Wentao , Vang Yeeleng S. , Huang Yufang , Xie Xiaohui 
Published: May 2018

AbstractRecently deep learning has been witnessing widespread adoption in various medical image applications. However, training complex deep neural nets requires large-scale datasets labeled with ground truth, which are often unavailable in many medical image domains. For instance, to train a deep neural net to detect pulmonary nodules in lung computed tomography (CT) images, current practice is to manually label nodule locations and sizes in many CT images to construct a sufficiently large training dataset, which is costly and difficult to scale. On the other hand, electronic medical records (EMR) contain plenty of partial information on the content of each medical image. In this work, we explore how to tap this vast, but currently unexplored data source to improve pulmonary nodule detection. We propose DeepEM, a novel deep 3D ConvNet framework augmented with expectation-maximization (EM), to mine weakly supervised labels in EMRs for pulmonary nodule detection. Experimental results show that DeepEM can lead to 1.5% and 3.9% average improvement in free-response receiver operating characteristic (FROC) scores on LUNA16 and Tianchi datasets, respectively, demonstrating the utility of incomplete information in EMRs for improving deep learning algorithms.1
Risk implications from the selection of rainfall index insurance intervals
Authors: Westerhold Ashlee , Walters Cory , Brooks Kathleen , Vandeveer Monte , Volesky Jerry , Schacht Walter 
Published: May 2018

Purpose
The purpose of this paper is to empirically examine the financial outcomes from forage production and RI-PRF insurance interval for two locations in Nebraska. Both locations provide historical forage production and precipitation data, allowing the authors to examine the relation between RI-PRF net income and forage production.

Design/methodology/approach
The authors focus on evaluating the producer net income and risk (measured as variance of net income) by examining the relation between farm precipitation and production and comparing multiple insurance intervals to no insurance. Each insurance interval will likely have a different relation (basis risk) between observed production and return from insurance and, therefore, a different impact on the variance of net incomes. The impact on variance of net incomes identifies the risk-reducing aspects of RI-PRF insurance intervals. The authors then rank each scenario into four mutually exclusive zones that describe the risk-reducing effectiveness and whether the subsidy is working correctly.

Findings
The authors found both risk increasing and decreasing insurance intervals exist at both locations. One insurance scenario (low in BBR) provided the highest net income while increasing risk, suggesting a profit maximizing opportunity. RI-PRF reduces net income risk with intervals insuring during high expected precipitation (growing season); while net income risk increases with intervals insuring low expected precipitation (non-growing season, winter months). The farmer would want to insure during the high expected precipitation months, which coincides with the growing season, since RI-PRF lowers the net income risk. For the government, removing net income risk increasing intervals improves the allocation of government resources.

Originality/value
In this paper, the authors modeled the relation between RI-PRF interval selection using the historical forage production data at two locations in Nebraska. The use of historical forage production data allowed the authors to precisely identify the risk-reducing effectiveness of RI-PRF interval selection.
Building firm capability through imitative innovation: Chinese manufacturing SME cases
Authors: Si Steven , Wang Song , Welch Steven M. 
Published: May 2018

PurposeThis study aims to investigate how firm capability can be accumulated with the inputs of learning efforts targeted at resolving barriers existing in the imitative innovation process. This paper takes imitative innovation as a process involving a few stages during which learning efforts are targeted at overcoming barriers existing within each process.Design/methodology/approachThe multiple case study approach has been adopted to explore how Chinese manufacturing small and medium enterprises (SMEs) learn and increase their technological capabilities through a continuous process of product refinement and improvement based on imitative innovation. In particular, the authors accentuate the learning efforts that firms must make to cope with various technological barriersFindingsIt is revealed that during the initial stages of imitative innovation, the organizational learning of Chinese manufacturing SMEs is highly constrained by the limitations of their technological resources and capabilities. It is also found that original equipment manufacturers can play an important role in providing Chinese learners with both explicit and tacit technological knowledge.Originality/valueThis study investigates how firm capability can be accumulated with the inputs of learning efforts targeted at resolving barriers existing in the imitative innovation process. The multiple case study approach has been adopted to explore how Chinese manufacturing SMEs learn and increase their technological capabilities through a continuous process of product refinement and improvement based on imitative innovation that could add new and great value to this research area.
Brokers or platforms? A longitudinal study of how hybrid interorganizational partnerships for regional innovation deal with VUCA environments
Authors: Ungureanu Paula , Bertolotti Fabiola , Macri Diego 
Published: May 2018

PurposeThe purpose of this paper is to investigate the role played by turbulent environments in the evolution of hybrid (i.e. multi-party, cross-sector) partnerships for regional innovation. Although extant research suggests that organizations decide to participate in such partnerships to cope with their turbulent environments, little is known about how actual perceptions of turbulent environments influence the setup and evolution of a partnership.Design/methodology/approachThe qualitative study adopts a longitudinal design to investigate the evolution of a cross-sector regional innovation partnership between ten very different organizations. With the help of the VUCA (volatility, uncertainty, complexity and ambiguity) model proposed by Bennett and Lemoine (2014a), the authors study the relation between partners’ initial perceptions of environmental turbulence and the models adopted for the partnership throughout its lifecycle (emergent, brokering and platform).FindingsThe authors show that partners’ intentions to solve perceived environmental turbulence through collaboration can have the unexpected consequence of triggering perceived turbulence inside the collaboration itself. Specifically, the authors show that perceived partnership VUCA at each stage is a result of partners’ attempts to cope with the perceived VUCA in the previous stage.Practical implicationsThe study highlights a set of common traps that both public and private organizations engaged in hybrid partnerships might fall into precisely as they try to lower VUCA threats in their environments.Originality/valueThe work accounts for the relationship between external and internal perceptions of VUCA in hybrid partnerships for regional innovation, and, in particular, provides a better understanding of what happens when organizations choose to enter hybrid partnerships in order to deal with perceived threats in their environments.
Factors affecting student use of Web-based services
Authors: Arif Muhammad , Ameen Kanwal , Rafiq Muhammad 
Published: May 2018

Purpose
The delivery of information services in higher education is increasingly relying on Web-based systems. The low adoption and underutilization of information systems have been major problems for developing countries such as Pakistan in terms of realizing their full benefits. This study aims to investigate factors affecting student use of Allama Iqbal Open University’s (AIOU) Web-based services by using the Unified Theory of Acceptance and Use of Technology (UTAUT) from the perspective of Pakistani distance education.

Design/methodology/approach
This study has adopted quantitative research design with the UTAUT model as a theoretical framework. A self-completion structured questionnaire-based survey has been administered to 388 master’s level students, selected through systematic sampling from the target population. The response rate was 82 per cent (318). All statistical tests have been performed using IBM SPSS (version 20.0) and Process macro for SPSS.

Findings
Findings of the model’s hypotheses reveal that performance expectancy, effort expectancy and social influence are significant predictors of student behavioural intention to use AIOU Web-based services, whereas actual student use is dependent on facilitating conditions and student behavioural intention to use. The impact of moderating variables with respect to age, gender and experience did not influence the actual use of the Web services. However, the research model significantly measured (62.1 per cent) the actual use of AIOU Web-based services by the students.

Research limitations/implications
This study is delimited to the UTAUT model to investigate the phenomena. Besides this, the context of the study is the voluntary instead of mandatory usage of Web services. A study conducted in mandatory settings, in which students are bound to use Web services, may have different results.

Originality/value
This is the first attempt to apply the UTAUT model to investigate the factors affecting student use of Web-based services from the perspective of distance education and the findings prove strong support for the model.