bluuebunny/crossref_metadata_2025_split huggingface dataset:
Motion planning for a rapid mobile manipulator using model-based ZMP stabilization
Authors: Choi Dongil , Oh Jun-ho 
Published: November 2014

SUMMARYThis paper introduces a novel approach to motion planning for a rapid mobile manipulator using inverted pendulum models. Our aim was to realize an actual rapid mobile manipulator with high acceleration and speed performance for an object's delivery. In our research, we developed an actual rapid mobile manipulator called KDMR-1. We proposed simple motion planning methods using a single inverted pendulum model (SIPM) and a double inverted pendulum model (DIPM), which are easily adaptable to a real-time system with only a small computational burden. The SIPM was useful for basic movement but did not provide object carrying capability. For that, a DIPM was proposed. In both models, we designed linear quadratic optimal controllers to stabilize the Zero Moment Point (ZMP). Two kinds of ZMP stabilization strategies were proposed, fixed ZMP and relaxed ZMP. Using these strategies, we realized optimal ZMP stabilizations for a real-time rapid mobile manipulator. For decoupled forward and rotational linear DIPM, we designed a centrifugal acceleration compensation model in the manner of feedback linearization. The experimental results showed high acceleration and speed performances during rapid object delivery.
Controlled trials of vitamin D, causality and type 2 statistical error
Authors: Gillie OIiver 
Published: November 2014

AbstractTwo recent studies published in The Lancet (Autier et al. (2013) Lancet Diabetes Endocrinol2, 76–89 and Bolland et al. (2014) Lancet Diabetes Endocrinol2, 307–320) have concluded that low levels of vitamin D are not a cause but a consequence of ill health brought about by reduced exposure to the sun, an association known as ‘reverse causality’. The scientific evidence and reasoning for these conclusions are examined here and found to be faulty. A null result in a clinical trial of vitamin D in adults need not lead to a conclusion of reverse causation when low vitamin D is found in observational studies of the same disease earlier in life. To assume an explanation of reverse causality has close similarities with type 2 statistical error.For example, a null result in providing vitamin D for treatment of adult bones that are deformed in the pattern of the rachitic rosary would not alter the observation that lack of vitamin D can cause rickets in childhood and may have lasting consequences if not cured with vitamin D. Other examples of diseases considered on a lifetime basis from conception to adulthood are used to further illustrate the issue, which is evidently not obvious and is far from trivial.It is concluded that deficiency of vitamin D in cohort studies, especially at critical times such as pregnancy and early life, can be the cause of a number of important diseases. Denial of the possible benefits of vitamin D, as suggested by insistent interpretation of studies with reverse causation, may lead to serious harms, some of which are listed.
Innovations of Candidate Selection Methods: Polling Primary and Kobo under the New Electoral Rules in Taiwan and Japan
Authors: YU CHING-HSIN , CHEN-HUA YU ERIC , SHOJI KAORI 
Published: November 2014

AbstractThis paper explores the linkage between electoral systems and candidate selection methods (CSMs) by analyzing two innovations of CSMs in Taiwan and Japan: polling primary and kobo, respectively. With an assumption that parties’ CSMs reflect their strategies to win elections, this article offers the rationale behind why and how major parties in Taiwan and Japan adjusted their CSMs to meet the challenges posed by the transition of electoral rules in each country from single non-transferable vote (SNTV) systems to mixed-member majoritarian (MMM) systems. We argue that a party's choice of CSMs reflects its rationale for maximizing the prospects of winning under the given electoral rule, which counters the ‘no-finding’ conclusion in some previous large-N studies on the linkage between electoral systems and choices of CSMs. Additionally, our findings highlight the importance of institutional factors, such as electoral systems, in explaining CSM reforms in a comparative perspective.
Ionic electroactive polymer artificial muscles in space applications
Authors: Punning Andres , Kim Kwang J. , Palmre Viljar , Vidal Frédéric , Plesse Cédric , Festin Nicolas , Maziz Ali , Asaka Kinji , Sugino Takushi , Alici Gursel , Spinks Geoff , Wallace Gordon , Must Indrek , Põldsalu Inga , Vunder Veiko , Temmer Rauno , Kruusamäe Karl , Torop Janno , Kaasik Friedrich , Rinne Pille , Johanson Urmas , Peikolainen Anna-Liisa , Tamm Tarmo , Aabloo Alvo 
Published: November 2014

AbstractA large-scale effort was carried out to test the performance of seven types of ionic electroactive polymer (IEAP) actuators in space-hazardous environmental factors in laboratory conditions. The results substantiate that the IEAP materials are tolerant to long-term freezing and vacuum environments as well as ionizing Gamma-, X-ray and UV radiation at the levels corresponding to low Earth orbit (LEO) conditions. The main aim of this material behaviour investigation is to understand and predict device service time for prolonged exposure to space environment.
Splitting, linking, knotting, and solitonic escape of topological defects in nematic drops with handles
Authors: Tasinkevych Mykola , Campbell Michael G. , Smalyukh Ivan I. 
Published: November 2014

SignificanceThere are few theoretical predictions of knotted, linked, solitonic, and other topologically nontrivial field configurations, which can be tested by experiments, due to the lack of experimentally accessible systems and techniques. This work presents an experimental realization and thorough theoretical analysis of interplay between topologies of the nematic field and closed confining surfaces with systematically varied genus. Handlebody-shaped nematic drops with normal boundary conditions reveal a large diversity of controlled field configurations, including ones with linked and knotted half-integer defect lines that are topologically distinct from predictions of mathematical theorems and that can exist only in nonpolar media. Our model system may become a testbed for probing a scale-invariant interplay of topologies of confining surfaces, fields, and defects.
Signaling pathways activated by a protease allergen in basophils
Authors: Rosenstein Rachel K. , Bezbradica Jelena S. , Yu Shuang , Medzhitov Ruslan 
Published: November 2014

SignificanceHelminths and allergens stimulate type 2 immune responses by largely unknown mechanisms. Proteolytic activity is a common feature of many helminths and allergens and can promote activation of the immune system. Signaling pathways activated by these proteases remain poorly characterized and are the focus of this study. Using basophils as model type 2 immune cells, we identified roles for the immunoreceptor tyrosine-based activation motif (ITAM)-containing adaptor Fc receptor γ-chain and calcium signaling in protease-stimulated basophil activation. We suggest models to explain how protease sensing, ITAM signaling, and nuclear factor of activated T cells pathways contribute to produce allergic type 2 responses. Elucidation of these signaling pathways and ultimately the identity of protease allergen sensors will be important for the development of pharmacologic strategies to target the initiation of allergic responses.
Liat1, an arginyltransferase-binding protein whose evolution among primates involved changes in the numbers of its 10-residue repeats
Authors: Brower Christopher S. , Rosen Connor E. , Jones Richard H. , Wadas Brandon C. , Piatkov Konstantin I. , Varshavsky Alexander 
Published: November 2014

Significance
We describe the discovery and analyses of a previously uncharacterized protein, termed Liat1 (ligand of Ate1), which has been identified because of its interactions with the Ate1 arginyltransferase, a component of the N-end rule pathway of protein degradation. All vertebrates contain proteins similar to mouse Liat1. Remarkably, Liat1 proteins of some primates contain tandem repeats of a 10-residue sequence, whereas Liat1 proteins of other mammals contain a single copy of this motif. Quantities of these repeats are, in general, different in Liat1 of different primates. For example, there are 4, 13, 13, and 17 repeats in the gorilla, orangutan, bonobo, and human Liat1, respectively, suggesting that repeat number changes in this previously uncharacterized protein may contribute to evolution of primates.
Methicillin-ResistantStaphylococcus aureus:Site of Acquisition and Strain Variation in High-Risk Nursing Home Residents with Indwelling Devices
Authors: Gibson Kristen E. , McNamara Sara E. , Cassone Marco , Perri Mary Beth , Zervos Marcus , Mody Lona ,   on behalf of the Targeted Infection Prevention (TIP) Study Team, Ann Arbor, Michigan
Published: November 2014

Objective.Characterize the clinical and molecular epidemiology of new methicillin-resistantStaphylococcus aureus(MRSA) acquisitions at nasal and extranasal sites among high-risk nursing home (NH) residents.Design.Multicenter prospective observational study.Setting.Six NHs in southeast Michigan.Participants.A total of 120 NH residents with an indwelling device (feeding tube and/or urinary catheter).Methods.Active surveillance cultures from the nares, oropharynx, groin, perianal area, wounds (if present), and device insertion site(s) were collected upon enrollment, at day 14, and monthly thereafter. Pulsed-field gel electrophoresis and polymerase chain reaction for SCCmec, agr, and Panton-Valentine leukocidin were performed.Results.Of 120 participants observed for 16,290 device-days, 50 acquired MRSA (78% transiently, 22% persistently). New MRSA acquisitions were common in extranasal sites, particularly at device insertion, groin, and perianal areas (27%, 23%, and 17.6% of all acquisitions, respectively). Screening extranasal sites greatly increases the detection of MRSA colonization (100% of persistent carriers and 97.4% of transient carriers detected with nares, groin, perianal, and device site sampling vs 54.5% and 25.6%, respectively, for nares samples alone). Colonization at suprapubic urinary catheter sites generally persisted. Healthcare-associated MRSA (USA100 and USA100 variants) were the dominant strains (79.3% of all new acquisition isolates). Strain diversity was more common in transient carriers, including acquisition of USA500 and USA300 strains.Conclusion.Indwelling device insertion sites as well as the groin and perianal area are important sites of new MRSA acquisitions in NH residents and play a role in the persistency of MRSA carriage. Clonal types differ among persistent and transient colonizers.
Impact of Vaginal-Rectal Ultrasound Examinations with Covered and Low-Level Disinfected Transducers on Infectious Transmissions in France
Authors: Leroy Sandrine , M’Zali Fatima , Kann Michael , Weber David J. , Smith David D. 
Published: November 2014

Background.The risk of cross-infection from shared ultrasound probes in endorectal and vaginal ultrasonography due to low-level disinfection (LLD) is difficult to estimate because potential infections are also sexually transmitted diseases, and route of contamination is often difficult to establish. In France, the widely used standard for prevention of infections is through the use of probe covers and LLD of the ultrasound transducer by disinfectant wipes. We performed an in silico simulation based on a systematic review to estimate the number of patients infected after endorectal or vaginal ultrasonography examination using LLD for probes.Study design.We performed a stochastic Monte Carlo computer simulation to produce hypothetical cohorts for a population of 4 million annual ultrasound examinations performed in France, and we estimated the number of infected patients for human immunodeficiency virus (HIV), herpes simplex virus, hepatitis B virus, hepatitis C virus, human papilloma virus, cytomegalovirus, and Chlamydia trachomatis. Modeling parameters were estimated by meta-analysis when possible.Results.The probability of infection from a contaminated probe ranged from 1% to 6%, depending on the pathogen. For cases of HIV infection, this would result in approximately 60 infected patients per year. For other common viral infections, the number of new cases ranged from 1,600 to 15,000 per year that could be attributable directly to ultrasound and LLD procedures.Conclusions.Our simulation results showed that, despite cumulative use of probe cover and LLD, there were still some cases of de novo infection that may be attributable to ultrasound procedures. These cases are preventable by reviewing the currently used LLD and/or upgrading LLD to high-level disinfection, as recommended by the US Centers for Disease Control and Prevention.
Detecting differential peaks in ChIP-seq signals with ODIN
Authors: Allhoff Manuel , Seré Kristin , Chauvistré Heike , Lin Qiong , Zenke Martin , Costa Ivan G. 
Published: November 2014

Abstract
Motivation: Detection of changes in deoxyribonucleic acid (DNA)–protein interactions from ChIP-seq data is a crucial step in unraveling the regulatory networks behind biological processes. The simplest variation of this problem is the differential peak calling (DPC) problem. Here, one has to find genomic regions with ChIP-seq signal changes between two cellular conditions in the interaction of a protein with DNA. The great majority of peak calling methods can only analyze one ChIP-seq signal at a time and are unable to perform DPC. Recently, a few approaches based on the combination of these peak callers with statistical tests for detecting differential digital expression have been proposed. However, these methods fail to detect detailed changes of protein–DNA interactions.
Results: We propose an One-stage DIffereNtial peak caller (ODIN); an Hidden Markov Model-based approach to detect and analyze differential peaks (DPs) in pairs of ChIP-seq data. ODIN performs genomic signal processing, peak calling and p-value calculation in an integrated framework. We also propose an evaluation methodology to compare ODIN with competing methods. The evaluation method is based on the association of DPs with expression changes in the same cellular conditions. Our empirical study based on several ChIP-seq experiments from transcription factors, histone modifications and simulated data shows that ODIN outperforms considered competing methods in most scenarios.
Availability and implementation: http://costalab.org/wp/odin .
Contact: ivan.costa@rwth-aachen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
The great escape? The contribution of the empire to Portugal's economic growth, 1500–1800
Authors: Costa Leonor Freire , Palma Nuno , Reis Jaime 
Published: November 2014

Abstract
Newly assembled macroeconomic statistics for early modern Portugal reveal one of Europe's most vigorous colonial traders but one of its least successful growth records. Was the empire a blessing or a drag to the economy? Using an estimated dynamic model, we conclude that intercontinental trade had a substantial and increasingly positive impact on economic growth. In the heyday of colonial expansion, eliminating the economic links to empire would have reduced Portugal's per capita income by at least a fifth. While the empire helped the domestic economy, it was not sufficient to annul the tendency of the latter toward decline in relation to Europe's advanced core, which began to set in from the seventeenth century onward, but only became definite after 1800. We conclude that the explanation for Portugal's long-term backwardness must be sought primarily in domestic conditions.
How well do Radiologic Assessments of Truncal and Shoulder Balance Correlate With Cosmetic Assessment Indices in Lenke 1C Adolescent Idiopathic Scoliosis?
Authors: Sharma Shallu , Andersen Thomas , Wu Chunsen , Sun Haolin , Wang Yu , Hansen Ebbe S. , Bünger Cody E. 
Published: November 2014

Study Design:
A correlation study.

Objective:
The primary objective was to determine the correlation between radiologic and cosmetic indices of trunk and shoulder balance before and after scoliosis surgery in Lenke 1C adolescent idiopathic scoliosis and to determine whether postoperative trunk shift is affiliated with worsening of the patients’ cosmesis.

Summary of Background Data:
Achieving a symmetrical appearance with truncal and shoulder balance is of prime importance to adolescent idiopathic scoliosis patients and their surgeons. However, surgeons prefer radiographic indices rather than measures of patients’ clinical appearance. If radiographic indices are to be considered accurate depictions of the patient’s cosmesis, radiologic and cosmetic indices must necessarily exhibit high association.

Methods:
Radiographic and cosmetic indices of trunk and shoulder balance, along with posterior trunk symmetry index, were measured preoperatively and 3 months postoperatively in 33 Lenke 1C scoliosis patients. Pearson correlation analysis was performed. Paired t test was used to determine significant changes in radiographic and cosmetic indices after surgery. Independent-sample t test was used for all intergroup analyses in trunk shift and no-trunk-shift groups.

Results:
Correlation coefficients between radiologic and cosmetic indices ranged between −0.63 and 0.70 with thoracic apical vertebra-central sacral vertical line (AV-CSVL) distance and first rib angle showing consistent correlations with cosmetic trunk and cosmetic shoulder balance indices. Trunk shift, a postoperative iatrogenic phenomenon, was seen in 19 (58%) patients. These patients had higher preoperative thoracic AV-CSVL translation, thoracic apical vertebra-first thoracic vertebra (AV-T1) translation, thoracic deformity correction rate, AV-T1 correction rates, and shorter fusions compared with the no-trunk-shift group. Posterior trunk symmetry index worsened in trunk shift group and improved significantly (−7.94 vs. 16.53) in no-trunk-shift group. Significant association (P=0.004) was seen between radiographic and cosmetic trunk shift.

Conclusions:
Radiographic indices can only minisculely (r≤0.7) reflect cosmetic deformity in Lenke 1C scoliosis, which emphasizes not only the vulnerability of overreliance on radiographic indices but also the vital importance of clinical cosmetic evaluations. In particular, cosmetic shoulder height and angle are not represented by radiographic indices. However, radiograph trunk shift was significantly associated with cosmetic trunk shift in cosmetic pictures.
High-Resolution Transcript Profiling of the Atypical Biotrophic Interaction betweenTheobroma cacaoand the Fungal PathogenMoniliophthora perniciosa
Authors: Teixeira Paulo José Pereira Lima , Thomazella Daniela Paula de Toledo , Reis Osvaldo , do Prado Paula Favoretti Vital , do Rio Maria Carolina Scatolin , Fiorin Gabriel Lorencini , José Juliana , Costa Gustavo Gilson Lacerda , Negri Victor Augusti , Mondego Jorge Maurício Costa , Mieczkowski Piotr , Pereira Gonçalo Amarante Guimarães 
Published: November 2014

AbstractWitches’ broom disease (WBD), caused by the hemibiotrophic fungus Moniliophthora perniciosa, is one of the most devastating diseases of Theobroma cacao, the chocolate tree. In contrast to other hemibiotrophic interactions, the WBD biotrophic stage lasts for months and is responsible for the most distinctive symptoms of the disease, which comprise drastic morphological changes in the infected shoots. Here, we used the dual RNA-seq approach to simultaneously assess the transcriptomes of cacao and M. perniciosa during their peculiar biotrophic interaction. Infection with M. perniciosa triggers massive metabolic reprogramming in the diseased tissues. Although apparently vigorous, the infected shoots are energetically expensive structures characterized by the induction of ineffective defense responses and by a clear carbon deprivation signature. Remarkably, the infection culminates in the establishment of a senescence process in the host, which signals the end of the WBD biotrophic stage. We analyzed the pathogen's transcriptome in unprecedented detail and thereby characterized the fungal nutritional and infection strategies during WBD and identified putative virulence effectors. Interestingly, M. perniciosa biotrophic mycelia develop as long-term parasites that orchestrate changes in plant metabolism to increase the availability of soluble nutrients before plant death. Collectively, our results provide unique insight into an intriguing tropical disease and advance our understanding of the development of (hemi)biotrophic plant-pathogen interactions.
The effects of ERP systems implementation on management accounting in Iranian organizations
Authors: Abbasi Solmaz , Zamani Mahmoud , Valmohammadi Changiz 
Published: November 2014

Purpose
– The aim of this paper is to study the effects of enterprise resource planning (ERP) on management accounting in Iranian organizations. Preparing and offering different reports and budgets remain important activities for accountants, and directly implementing ERP systems improves the quality of these reports through real-time data transfer.

Design/methodology/approach
– The research methods used in this paper are descriptive surveys with questionnaires and interviews as the main data collection tools. Statistical population comprises every organization which has implemented an ERP system with financial/accounting modules. The participating 12 organizations were selected based on consultation with experts, and a seven-item Likert questionnaire was prepared and its validity approved and used to collect data. The t-test and Friedman test were applied to assess the hypotheses and rank parameters.

Findings
– Results revealed that the highest effects of implementing an ERP in surveyed Iranian organizations are improving standard levels and the quality of reports, creating more organizational integration and empowering personnel.

Research limitations/implications
– As the implementation of ERP in Iran is still in its initial phases and the sample is restricted to only four organizations, when considering the generalizability of the obtained results, caution should be taken.

Originality/value
– This research is among the few studies on the effects of ERP implementation on accounting management departments, particularly in the context of Iran.