bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calibrating sample and hold stages with pruned Volterra kernels
Authors: Centurelli F. , Monsurrò P. , Rosato F. , Ruscio D. , Trifiletti A. 
Published: November 2015

Switched capacitor sample and hold (SHA) stages in deep submicron technologies can achieve hundreds of mega samples per second of sampling frequency, but are affected by several nonlinear effects which reduce their signal‐to‐noise‐and‐distortion ratio (SNDR): CMOS switch non‐idealities, amplifier nonlinearity, and incomplete settling. It is possible to model and correct distortions using Volterra kernels, which can be rather resource‐consuming as the number of parameters to estimate rapid increases with the order and length of the kernels. In this reported work, it is shown that a switched capacitor SHA, simulated using the 45 nm process by STMicroelectronics, can be calibrated to achieve a 10–24 dB improvement in SNDR. Computational costs are kept low using a different lag value for each kernel, and iteratively pruning the elements of the Volterra kernels which affect linearity the least. A technique for estimation and out‐of‐sample validation is presented and robustness checks are performed. A performance gain of 8.5 dB can be achieved with as few as 17 correction parameters, while 21 coefficients are enough to gain 12.2 dB, and 36 to gain 18.4 dB.
Design of dual‐bandpass filters using stepped‐impedance circular ring resonator
Authors: Wang Wensong , Cao Qunsheng , Yang Chenchen , Wang Yi , Chen Yinchao 
Published: November 2015

A stepped‐impedance circular ring resonator (SICRR) with two pairs of stubs is proposed for the design of a dual‐bandpass filter. This quad‐mode resonator is applied to produce two passbands. It is found that the centre frequencies and bandwidths of the two passbands can be tuned by varying the lengths of the stubs. Simulation results show that the defined impedance ratio K and the electrical length ratio α of between the SICRR segments can affect the frequency separation between the two passbands. A prototype filter centred at 3.4 and 5.56 GHz is designed and fabricated. Good agreement between the simulated and measured results was achieved for the SICRR filter.
The Effectiveness of Psychoeducational Intervention on Managing Symptom Clusters in Patients With Cancer
Authors: Xiao Wenli , Chow Ka Ming , So Winnie K. W. , Leung Doris Y. P. , Chan Carmen W. H. 
Published: November 2015

Background:
Managing symptom clusters instead of single symptoms could be more beneficial in cancer care. Psychoeducational intervention (PEI) has been highlighted as a promising symptom intervention, but the effect of PEI in the management of cancer symptom clusters remains unknown.

Objective:
The aim of this study was to evaluate the effectiveness of PEI on managing symptom clusters in patients with cancer.

Methods:
Six databases were searched, together with hand searching, to identify eligible randomized controlled trials from the year 2001 to July 2014. Data selection, quality appraisal of studies, and data extraction were conducted independently by 2 reviewers. Data were synthesized by use of a systematic narrative approach, and meta-analysis was conducted when this was possible.

Results:
Four eligible studies involving 343 cancer patients were included in the review. The methodological quality of the studies was generally fair. Symptom clusters seemed to improve with the provision of PEI. Meta-analysis shows significant improvement in functional performance.

Conclusions:
The evidence that PEI could alleviate cancer symptom clusters is encouraging but inconclusive in this review. Future well-designed investigations testing some commonly used PEI such as progressive muscle relaxation and patient education on various types of cancer symptom clusters are warranted.

Implications for Practice:
This review suggests a promising role of PEI in managing cancer symptom clusters. Healthcare providers should increase their awareness of managing symptom clusters using PEI to yield more effective and efficient cancer care.
Validation of Illumina’s Isaac variant calling workflow
Authors: Mainzer Liudmila S. , Chapman Brad A. , Hofmann Oliver , Rendon Gloria , Stephens Zachary D. , Jongeneel C. Victor 
Published: November 2015

AbstractAs the pace of implementing personalized medicine concepts increases, high-throughput variant calling on hundreds of individual genomes per day is a reality that will likely be faced by sequencing facilities across the country in the near future. While the scientific best practices for human variant calling workflows have been well defined, they also pose serious computational challenges at this high scale. Therefore, efforts in both academia and the private sector have focused on developing alternative workflows that may substantially reduce the computational cost per individual genome. Isaac is an “ultra-fast” variant calling workflow, designed by Illumina, Inc, and is claimed to be six times faster than BWA-GATK, with comparable sensitivity and specificity. This report is an independent review of Isaac, mainly focused on the accuracy of variant calls. We note that Isaac is indeed quite fast, and provide some benchmarks on a few hardware architectures. The overall conclusion from our analysis is that the Isaac workflow has undergone substantial improvement from version 01.14.11.27 to Isaac_2.0. The call accuracy is especially high on NA12878, however exomes tend to have a high fraction of false positive calls. We did not manage to reproduce the 99% sensitivity and specificity reported in the Illumina whitepaper, however that might be improved with further tweaking of the options. This report includes the information about some of the command-line parameters and documentation.
Modeling Small Non-canonical RNA Motifs with the Rosetta FARFAR Server
Authors: Yesselman Joseph D. , Das Rhiju 
Published: November 2015

AbstractNon-canonical RNA motifs help define the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only 10 nucleotides in size. Unfortunately, despite their small size, there is no reliable method to determine the ensemble of lowest energy structures of junctions and loops at atomic accuracy. This chapter outlines straightforward protocols using a webserver for Rosetta Fragment Assembly of RNA with Full Atom Refinement (FARFAR) (http://rosie.rosettacommons.org/rna_denovo/submit) to model the 3D structure of small non-canonical RNA motifs for use in visualizing motifs and for further refinement or filtering with experimental data such as NMR chemical shifts.
Micro-Pharmacodynamics: BridgingIn VitroandIn VivoExperimental Scales in Testing Drug Efficacy and Resistance
Authors: Rejniak Katarzyna A. 
Published: November 2015

AbstractSystemic chemotherapy is one of the main anticancer treatments used for most kinds of clinically diagnosed tumors. However, the efficacy of these drugs can be hampered by the physical attributes of the tumor tissue that can impede the transport of therapeutic agents to tumor cells in sufficient quantities. As a result, drugs that work wellin vitrooften fail at clinical trials when confronted with the complexities of interstitial transport within the tumor microenvironment. ThemicroPDmodel that we developed is used to investigate the penetration of drug molecules through the tumor tissue and influenced by the physical and metabolic properties of tumor microenvironment, and how it affects drug efficacy and the emergence of drug resistance.
Progressive lengthening of 3′ untranslated regions of mRNAs by alternative cleavage and polyadenylation in cellular senescence of mouse embryonic fibroblasts
Authors: Han Miao , Lv Guoliang , Nie Hongbo , Shen Ting , Niu Yichi , Li Xueping , Chen Meng , Zheng Xia , Li Wei , Ding Chen , Wei Gang , Gu Jun , Tian Xiao-Li , Zheng Yufang , Liu Xinhua , Hu Jinfeng , Tao Wei , Ni Ting 
Published: November 2015

ABSTRACTBackgroundCellular senescence has historically been viewed as an irreversible cell cycle arrest that acts to prevent cancer. Recent discoveries demonstrated that cellular senescence also played a vital role in normal embryonic development, tissue renewal and senescence-related diseases. Alternative cleavage and polyadenylation (APA) is an important layer of post-transcriptional regulation, which has been found playing an essential role in development, activation of immune cells and cancer progression. However, the role of APA in the process of cellular senescence remains unclear.Materials and MethodsWe applied high-throughput paired-end polyadenylation sequencing (PA-seq) and strand-specific RNA-seq sequencing technologies, combined systematic bioinformatics analyses and experimental validation to investigate APA regulation in different passages of mouse embryonic fibroblasts (MEFs) and in aortic vascular smooth muscle cells of rats (VSMCs) with different ages.ResultsBased on PA-seq, we found that genes in senescent cells tended to use distal pA sites and an independent bioinformatics analysis for RNA-seq drew the same conclusion. In consistent with these global results, both the number of genes significantly preferred to use distal pAs in senescent MEFs and VSMCs were significantly higher than genes tended to use proximal pAs. Interestingly, the expression levels of genes preferred to use distal pAs in senescent MFEs and VSMCs tended to decrease, while genes with single pAs did not show such trend. More importantly, genes preferred to use distal pAs in senescent MFEs and VSMCs were both enriched in common senescence-related pathways, including ubiqutin mediated proteolysis, regulation of actin cytoskeleton, cell cycle and wnt signaling pathway. By cis-elements analyses, we found that the longer 3′ UTRs of the genes tended to use distal pAs progressively can introduce more conserved binding sites of senescence-related miRNAs and RBPs. Furthermore, 375 genes with progressive 3′ UTR lengthening during MEF senescence tended to use more strong and conserved polyadenylation signal (PAS) around distal pA sites and this was accompanied the observation that expression level of core factors involved in cleavage and polyadenylation complex was decreased.ConclusionsOur finding that genes preferred distal pAs in senescent mouse and rat cells provide new insights for aging cells’ posttranscriptional gene regulation in the view of alternative polyadenylation given senescence response was thought to be a tumor suppression mechanism and more genes tended to use proximal pAs in cancer cells. In short, APA was a hidden layer of post-transcriptional gene expression regulation involved in cellular senescence.
Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs
Authors: Chen Jenny , Shishkin Alexander A. , Zhu Xiaopeng , Kadri Sabah , Maza Itay , Hanna Jacob H. , Regev Aviv , Garber Manuel 
Published: November 2015

AbstractBACKGROUNDRecent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across multitudes of species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: 1) identifying truly noncoding genes fromde novoreconstructed transcriptomes, and 2) prioritizing hundreds of resulting putative lncRNAs from each sample for downstream experimental interrogation.RESULTSWe presentslnckv, a computational lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-Sequencing data and further prioritizes lncRNAs by characterizing selective constraint as a proxy for function. Our filtering pipeline is comparable to manual curation efforts and more sensitive than previously published approaches. Further, we develop, for the first time, a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for both sequence and transcript evolution. Our analysis reveals that selection acts in several distinct patterns, and uncovers two notable classes of lncRNAs: one showing strong purifying selection at RNA sequence and another where constraint is restricted to the regulation but not the sequence of the transcript.CONCLUSIONOur novel comparative methods for lncRNAs reveals 233 constrained lncRNAs out of tens of thousands of currently annotated transcripts, which we believe should be prioritized for further interrogation. To aid in their analysis we provide theslncky Evolution Browseras a resource for experimentalists.
A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer
Authors: Mucaki Eliseos J. , Caminsky Natasha G. , Perri Ami M. , Lu Ruipeng , Laederach Alain , Halvorsen Matthew , Knoll Joan HM. , Rogan Peter K. 
Published: November 2015

ABSTRACTBackgroundSequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT).MethodsWe captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream ofATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2,andTP53were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk patients without identified mutations inBRCA1/2.Aside from protein coding changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented byin silicoand laboratory analysis of UTR structure.Results15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels).ConclusionsWe have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.
Does country-level governance enhance ethical behaviour of firms? An African perspective
Authors: Agyemang Otuo Serebour , Fantini Giulia , Frimpong Joyce 
Published: November 2015

Purpose
– The purpose of this paper is to examine the relationship between country-level governance and ethical behaviour of firms in African countries in the period 2009-2012.

Design/methodology/approach
– It uses a broad set of country-level governance ratings by the World Bank and data on ethical behaviour of firms by the World Economic Forum’s report on Global Competitiveness. Full data of a total of 39 African economies out of the 54 (including two disputed) economies over the sample period were obtained for this analysis.

Findings
– The authors find a statistically significant and positive relationship between country-level rule of law, regulatory quality, control of corruption and democracy, and firm ethical behaviour of firms in African economies. This implies that improvement in country-level rule of law, regulatory quality, control of corruption and democracy tends to be associated with sound ethical behaviour of firms in African economies. However, the authors did not find any statistically significant relationship between country-level accountability, political stability, outsider model of governance and ethical behaviour of firms.

Practical implications
– As a continent that is yet to fully discover its potential, the practice of good governance is particularly germane, as this may not only help ensure sound ethical standards of corporations, but may also aid the continent to attract foreign investors, which will beneficially impact economic growth and development of African economies. In this respect, efforts by governments across the continent to ensuring good governance are laudable. One possible way is to ensure an effective and transparent enforcement of laws to stimulate compliance in a specifically clear-cut manner by crafting costs for non-compliance (for instance, legal costs, investigation cost, imprisonment, dent to image and fines).

Originality/value
– This paper reinforces the belief that the existence of country-level good governance could provide and enhance cohesive and internally consistent ethical standards of companies.
Non-parametric decomposition and the choice of reference group
Authors: Anspal Sten 
Published: November 2015

Purpose
– The Ñopo (2008) method of non-parametric decomposition, a matching-based alternative to Oaxaca (1973) and Blinder’s (1973) method of wage gap decomposition, is subject to the so-called “index number problem” common to the Oaxaca-Blinder and many related methods: its results are sensitive to the (arbitrary) choice of either male or female sex as the reference category in decomposition. The purpose of this paper is to address this issue by proposing an extension to the method that is invariant to the choice of reference category.

Design/methodology/approach
– The Ñopo method is modified such that the wage structure of the average worker instead of either male or female worker’s is used as the reference, enabling one to distinguish the “male advantage” and “female advantage” portions of the gender wage gap. As an illustration, a decomposition of the gender wage gap is performed with the modified method, using data from 15 OECD countries.

Findings
– The empirical results using the Ñopo decomposition indicate substantial differences in estimates of the unexplained gap depending on which sex is used as the reference category. Moreover, this disparity varies significantly with the choice of covariates used in the decomposition. This confirms there is significant cross-country variation in the asymmetry between male advantage and female disadvantage and that a decomposition method making this explicit would be relevant in real world settings.

Originality/value
– The extension of the Ñopo method proposed in this paper offers a way of decomposing the wage gaps in a way that is not sensitive to the choice of the reference category.
Why choose a temporary employment?
Authors: Muzzolon Cristina , Spoto Andrea , Vidotto Giulio 
Published: November 2015

Purpose– The literature on volition indicates that the only dichotomous measure that differentiates voluntary from involuntary temporary workers is unable to fully explain temporary workers’ attitudes. There are more detailed explanations of why workers choose temporary work. The purpose of this paper is to develop and validate a scale of reasons for choosing temporary employment.Design/methodology/approach– The study is divided into two parts. In the first part, 32 items were selected based on the literature. They were administered to a sample of 337 Italian temporary agency workers. Then, an exploratory factor analysis was used. In the second part of the study, previous findings were subjected to a confirmatory factor analysis (CFA) considering a sample of 325 Italian temporary agency workers.Findings– A two-factor solution (i.e. integrated regulation and identified regulation) emerged from the CFA. The authors present the scale with means and standard deviations for the measurement of the constructs. The integrated regulation subscale appears sensitive enough to differentiate the contract preference.Research limitations/implications– The two samples were from a single temporary work agency, thus they did not represent the entire heterogeneous population of temporary workers.Originality/value– This study proposes a first attempt to construct a questionnaire about the reasons for choosing temporary employment in Italy that raises questions about how institutional factors within various labor markets influence issues of volition and employment contract choice.
A good or bad transition from school to work: who is responsible?
Authors: Defloor Bart , Van Ootegem Luc , Verhofstadt Elsy 
Published: November 2015

Purpose– The purpose of this paper is to analyse the determinants of the quality of the first job in Flanders (Belgium). The authors differentiate between circumstances on the one hand – individual characteristics beyond the control of the individuals such as gender or the unemployment rate at labour market entry – and efforts on the other hand – characteristics that are at least partly under the individuals’ control such as their educational attainment or labour motivation. The authors specifically take into account the fact that the former might influence the latter. A better understanding of the effects of these determinants can help to formulate (labour market) policy proposals (to ameliorate the school-to-work transition) that are responsibility-sensitive. The authors use the distance function to construct a one-dimensional measure of job quality – based on a list of job characteristics – and explain the variation in job quality in terms of circumstances and efforts. The empirical analysis is based on the 1978 birth cohort of the Flemish SONAR data. The results show that the quality of the first job is to a large extent depending on personal efforts and that circumstances have a considerable influence on the efforts. For this reason circumstances influence job quality twice. This is especially the case for gender and for the educational attainment of the individual’s mother. The labour market situation at labour market entry also plays a considerable role.Design/methodology/approach– The authors use the distance function to construct a one-dimensional measure of job quality – based on a list of job characteristics – and explain the variation in job quality in terms of circumstances and efforts. The empirical analysis is based on the 1978 birth cohort of the Flemish SONAR data.Findings– The results show that circumstances have a considerable influence on the efforts and for this reason circumstances influence job quality twice. This is especially the case for gender and for the educational attainment of the individual’s mother. The labour market situation at labour market entry also plays a considerable role.Originality/value– The paper contributes to the literature in several ways. First, it analyses the quality of the first job individuals get after leaving school and uses an equality of opportunity framework. This approach differs from an approach based on search duration or job satisfaction. Second, job quality is evaluated in a multidimensional way using the distance function. Third, the relation between job quality and circumstances – issues for which the individual is not responsible – and efforts – issues for which the individual is at least partly responsible – is investigated. The authors specifically take into account the fact that circumstances might influence efforts and investigate the consequences for labour market policy.