bluuebunny/crossref_metadata_2025 huggingface dataset:
Comment: Butler and Randall’s “Emotional Coregulation in Close Relationships”
Authors: Troxel Wendy M.
Published: March 2013

The study of dyadic coregulation has emerged as a compelling and innovative approach to understanding the links between close relationships and health and functioning. However, the study of dyadic coregulation has been hampered, in part, by the lack of a precise operational definition of the construct and a lack of a framework for systematically evaluating and statistically modeling coregulatory processes. Butler and Randall (2013) present a cogent framework that clearly defines what coregulation is and what it is not, which is critical for advancing this important area of study. Nevertheless, several important questions still remain unaddressed, including the role of individual differences in coregulatory processes; the feasibility of distinguishing between coregulation and related constructs, such as stress-buffering; and potential clinical implications of coregulation.
Comment: The Appraising Brain: Towards a Neuro-Cognitive Model of Appraisal Processes in Emotion
Authors: Brosch Tobias , Sander David
Published: March 2013

Appraisal theories have described elaborate mechanisms underlying the elicitation of emotion at the psychological-cognitive level, but typically do not integrate neuroscientific concepts and findings. At the same time, theoretical developments in appraisal theory have been pretty much ignored by researchers studying the neuroscience of emotion. We feel that a stronger integration of these two literatures would be highly profitable for both sides. Here we outline a blueprint of the “appraising brain.” To this end, we review neuroimaging research investigating the processing of major appraisal variables, and sketch a neuro-cognitive process model of appraisal with a special emphasis on the chronometry and the recursive aspect of emotional evaluation. We hope that this contribution will stimulate more hypothesis-driven research on the neuroscience of appraisal.
Author Reply: On the Frontiers of Appraisal Theory
Authors: Roseman Ira J.
Published: March 2013

The special section commentators take us to the frontiers of appraisal theory. Following their lead, I discuss cross-cultural commonalities, domain-specific appraisals, individual differences, nonappraisal determinants, and a blueprint for the appraising brain.
Organizational sciences’ obsession with “that’s interesting!”
Authors: Pillutla Madan M. , Thau Stefan
Published: March 2013

We suggest that the organizational science’s increasing preoccupation with “interesting” theories and “counterintuitive” facts can lead to nonreplicable findings, fragmented theory, and irrelevance. The focus on the interesting and novel reveals a profound misunderstanding of the scientific enterprise. Organizational scholarship will be better off if it reverts to according primacy to the problem being solved over novel theory development.
Tetralogy of Fallot
Authors: Barron David J.
Published: March 2013

Management of the cyanotic neonate with tetralogy of Fallot (ToF) remains a challenging condition. Outcomes for single-stage repair of ToF have steadily improved over the past 30 years and the best results have been achieved with repair between 3 and 9 months of age. The traditional management of cyanotic neonates and small infants has been palliation with a Blalock–Taussig shunt, but this continues to carry a significant mortality that has remained relatively constant even in the contemporary series. This has led to the promotion of neonatal complete repair, but analysis of published outcomes would suggest that this also carries significant risk compared to repair at an older age. Low birth weight and small pulmonary arteries (PAs) remain the greatest independent risk factors. Right ventricular outflow tract (RVOT) stenting may offer an alternative approach to neonatal repair in high-risk neonates and allow for PA growth and delay of repair until the child reaches a safer age. A stratified approach to early management utilizing RVOT stenting in high-risk cases may lead to better overall outcomes.
Isolated Left Common Carotid Artery Connected to the Pulmonary Artery
Authors: Fouilloux Virginie , Gran Célia , Kreitmann Bernard
Published: March 2013

A three-year-old boy was referred for persistent arterial duct. Transthoracic echocardiography showed a right aortic arch and an unusual Doppler flow in the arch vessels and the pulmonary artery. The tomodensitometry showed a right-sided aortic arch, with successive origin of the right common carotid, the right subclavian artery, and an aberrant (lusoria) left subclavian artery. The left common carotid took origin from the pulmonary trunk. During surgery, a fibrous cord independent from the anomaly was identified. An end-to-side anastomosis between the left carotid and the ascending aorta was done and the fibrous cord was divided. Was this fibrous cord a ductal ligament?
Bilateral Branch Pulmonary Artery Banding as a Bridge to Decision/Preoperative Optimization of High-Risk Neonates With Hypoplastic Left Heart Syndrome
Authors: Kurkluoglu Mustafa , Jonas Richard A. , Sinha Pranava
Published: March 2013

We present our experience with bilateral branch pulmonary artery banding as a bridge to decision/optimization of hemodynamics, followed by standard Norwood stage I palliation in very high-risk infants with hypoplastic left heart syndrome.
A Coevolutionary Model as a Collaborative Mechanism for the Business Exchange in the High-technology Industrial Value Chain
Authors: Kabiraj Sajal , Uniyal Dwarika Prasad
Published: March 2013

The High-technology industries are highly capital-intensive enterprises dealing with short life cycle products, offering potential to simultaneously examine different perspectives of collaborative relationships. Although the extant literature on collaborative activities in business enterprises has progressed along the different stages in the industrial value chain, there is lack of cohesion in the current state of the art. Conceptual clarity and contextual description in particular are dispersed and disintegrated in the current state. In order to integrate the literature and highlight its contributions, it is essential to provide a more technical description and a discussion on supply chain collaboration from various perspectives of the High-technology industry. In this article, the issues pertaining to responsiveness, collaborative development practices, strategic procurement and information technology (IT), and control-oriented approaches are presented. By effectively doing so, we provide a comprehensive literature review to determine the scope for future research in the High-technology industries and other similar manufacturing environments.
Single nucleotide variation in the TP53 3′ untranslated region in diffuse large B-cell lymphoma treated with rituximab-CHOP: a report from the International DLBCL Rituximab-CHOP Consortium Program
Authors: Li Yong , Gordon Michael W. , Xu-Monette Zijun Y. , Visco Carlo , Tzankov Alexander , Zou Dehui , Qiu Lugui , Montes-Moreno Santiago , Dybkaer Karen , Orazi Attilio , Zu Youli , Bhagat Govind , Richards Kristy L. , Hsi Eric D. , Choi William W. L. , Han van Krieken J. , Huang Qin , Ai Weiyun , Ponzoni Maurilio , Ferreri Andrés J. M. , Winter Jane N. , Go Ronald S. , Piris Miguel A. , Møller Michael B. , Wu Lin , Wang Michael , Ramos Kenneth S. , Medeiros L. Jeffrey , Young Ken H.
Published: March 2013

Key Points

TP53 3′UTR variations demonstrate prognostic value in DLBCL.
Strong convergence theorems for equilibrium problems and weak Bregman relatively nonexpansive mappings in Banach spaces
Authors: Agarwal Ravi P , Chen Jia-Wei , Cho Yeol Je
Published: March 2013

In this paper, a shrinking projection algorithm based on the prediction correction method for equilibrium problems and weak Bregman relatively nonexpansive mappings is introduced and investigated in Banach spaces, and then the strong convergence of the sequence generated by the proposed algorithm is derived under some suitable assumptions. These results are new and develop some recent results in this field.

MSC:26B25, 47H09, 47J05, 47J25.
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics
Authors: de Matos Paula , Cham Jennifer A , Cao Hong , Alcántara Rafael , Rowland Francis , Lopez Rodrigo , Steinbeck Christoph
Published: March 2013

User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users’ requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.

For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.

We employed several UCD techniques, including: persona development, interviews, ‘canvas sort’ card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.
Overexpression of the transcription factor RAP2.6 leads to enhanced callose deposition in syncytia and enhanced resistance against the beet cyst nematode Heterodera schachtiiin Arabidopsis roots
Authors: Ali Muhammad Amjad , Abbas Amjad , Kreil David P , Bohlmann Holger
Published: March 2013

Background

Cyst nematodes invade the roots of their host plants as second stage juveniles and induce a syncytium which is their source of nutrients throughout their life. A transcriptome analysis of syncytia induced by the beet cyst nematode Heterodera schachtii in Arabidopsis roots has shown that gene expression in the syncytium is different from that of the root with thousands of genes upregulated or downregulated. Among the downregulated genes are many which code for defense-related proteins. One gene which is strongly downregulated codes for the ethylene response transcription factor RAP2.6. The genome of Arabidopsis contains 122 ERF transcription factor genes which are involved in a variety of developmental and stress responses.

Results

Expression of RAP2.6 was studied with RT-PCR and a promoter::GUS line. During normal growth conditions the gene was expressed especially in roots and stems. It was inducible by Pseudomonas syringae but downregulated in syncytia from a very early time point on. Overexpression of the gene enhanced the resistance against H. schachtii which was seen by a lower number of nematodes developing on these plants as well as smaller syncytia and smaller female nematodes. A T-DNA mutant had a reduced RAP2.6 transcript level but this did not further increase the susceptibility against H. schachtii. Neither overexpression lines nor mutants had an effect on P. syringae. Overexpression of RAP2.6 led to an elevated expression of JA-responsive genes during early time points after infection by H. schachtii. Syncytia developing on overexpression lines showed enhanced deposition of callose.

Conclusions

Our results showed that H. schachtii infection is accompanied by a downregulation of RAP2.6. It seems likely that the nematodes use effectors to actively downregulate the expression of this and other defense-related genes to avoid resistance responses of the host plant. Enhanced resistance of RAP2.6 overexpression lines seemed to be due to enhanced callose deposition at syncytia which might interfere with nutrient import into syncytia.
Effects of Δ40p53, an isoform of p53 lacking the N-terminus, on transactivation capacity of the tumor suppressor protein p53
Authors: Hafsi Hind , Santos-Silva Daniela , Courtois-Cox Stéphanie , Hainaut Pierre
Published: March 2013

Background

The p53 protein is expressed as multiple isoforms that differ in their N- and C-terminus due to alternative splicing, promoter or codon initiation usage. Δ40p53 lacks the first 39 residues containing the main transcriptional activation domain, resulting from initiation of translation at AUG +40 in fully spliced p53 mRNA or in a specific variant mRNA retaining intron 2. Overexpression of Δ40p53 antagonizes wild-type p53 in vitro. However, animal models of Δ40p53 in mouse or Zebrafish have shown complex phenotypes suggestive of p53-dependent growth suppressive effects.

Methods

We have co-transfected expression vectors for p53 and Δ40p53 in p53-null cell lines Saos-2 and H1299 to show that Δ40p53 forms mixed oligomers with p53 that bind to DNA and modulate the transcription of a generic p53-dependent reporter gene.

Results

In H1299 cells, co-expression of the two proteins induced a decrease in transcription with amplitude that depended upon the predicted composition of the hetero-tetramer. In Saos-2, a paradoxical effect was observed, with a small increase in activity for hetero-tetramers predicted to contain 1 or 2 monomers of Δ40p53 and a decrease at higher Δ40p53/p53 ratios. In this cell line, co-transfection of Δ40p53 prevented Hdm2-mediated degradation of p53.

Conclusion

Δ40p53 modulates transcriptional activity by interfering with the binding of Hdm2 to hetero-tetramers containing both Δ40p53 and p53. These results provide a basis for growth suppressive effects in animal models co-expressing roughly similar levels of p53 and Δ40p53.
Monitoring post mortem changes in porcine muscle through 2-D DIGE proteome analysis of Longissimus muscle exudate
Authors: Di Luca Alessio , Elia Giuliano , Mullen Anne Maria , Hamill Ruth M
Published: March 2013

Background

Meat quality is a complex trait influenced by a range of factors with post mortem biochemical processes highly influential in defining ultimate quality. High resolution two-dimensional DIfference Gel Electrophoresis (2-D DIGE) and Western blot were applied to study the influence of post mortem meat ageing on the proteome of pork muscle. Exudate collected from the muscle following centrifugation was analysed at three timepoints representing a seven day meat ageing period.

Results

The intensity of 136 spots varied significantly (p < 0.05) across this post mortem period and 40 spots were identified using mass spectrometry. The main functional categories represented were metabolic proteins, stress-related proteins, transport and structural proteins. Metabolic and structural proteins were generally observed to increase in abundance post mortem and many likely represent the accumulation of the degradation products of proteolytic enzyme activity. In contrast, stress-related proteins broadly decreased in abundance across the ageing period. Stress response proteins have protective roles in maintaining cellular integrity and a decline in their abundance over time may correlate with a reduction in cellular integrity and the onset of meat ageing. Since cellular conditions alter with muscle ageing, changes in solubility may also contribute to observed abundance profiles.

Conclusions

Muscle exudate provided valuable information about the pathways and processes underlying the post mortem ageing period, highlighting the importance of post mortem modification of proteins and their interaction for the development of meat quality traits.
Au/Pd core-shell nanoparticles with varied hollow Au cores for enhanced formic acid oxidation
Authors: Hsu Chiajen , Huang Chienwen , Hao Yaowu , Liu Fuqiang
Published: March 2013

A facile method has been developed to synthesize Au/Pd core-shell nanoparticles via galvanic replacement of Cu by Pd on hollow Au nanospheres. The unique nanoparticles were characterized by X-ray diffraction, X-ray photoelectron spectroscopy, transmission electron microscopy, ultraviolet–visible spectroscopy, and electrochemical measurements. When the concentration of the Au solution was decreased, grain size of the polycrystalline hollow Au nanospheres was reduced, and the structures became highly porous. After the Pd shell formed on these Au nanospheres, the morphology and structure of the Au/Pd nanoparticles varied and hence significantly affected the catalytic properties. The Au/Pd nanoparticles synthesized with reduced Au concentrations showed higher formic acid oxidation activity (0.93 mA cm-2 at 0.3 V) than the commercial Pd black (0.85 mA cm-2 at 0.3 V), suggesting a promising candidate as fuel cell catalysts. In addition, the Au/Pd nanoparticles displayed lower CO-stripping potential, improved stability, and higher durability compared to the Pd black due to their unique core-shell structures tuned by Au core morphologies.
The transmembrane domain of HIV-1 Vpu is sufficient to confer anti-tetherin activity to SIVcpz and SIVgor Vpu proteins: cytoplasmic determinants of Vpu function
Authors: Kluge Silvia F , Sauter Daniel , Vogl Michael , Peeters Martine , Li Yingying , Bibollet-Ruche Frederic , Hahn Beatrice H , Kirchhoff Frank
Published: March 2013

Background

The acquisition of effective Vpu-mediated anti-tetherin activity to promote virion release following transmission of SIVcpzPtt from central chimpanzees (Pan troglodytes troglodytes) to humans distinguishes pandemic HIV-1 group M strains from non-pandemic group N, O and P viruses and may have been a prerequisite for their global spread. Some functional motifs in the cytoplasmic region of HIV-1 M Vpus proposed to be important for anti-tetherin activity are more frequently found in the Vpu proteins of SIVcpzPtt than in those of SIVcpzPts infecting eastern chimpanzees (P. t. schweinfurthii), that have not been detected in humans, and SIVgor from gorillas, which is closely related to HIV-1 O and P. Thus, SIVcpzPtt strains may require fewer adaptive changes in Vpu than SIVcpzPts or SIVgor strains to counteract human tetherin.

Results

To examine whether SIVcpzPtt may only need changes in the transmembrane domain (TMD) of Vpu to acquire anti-tetherin activity, whereas SIVcpzPts and SIVgor may also require changes in the cytoplasmic region, we analyzed chimeras between the TMD of an HIV-1 M Vpu and the cytoplasmic domains of SIVcpzPtt (n = 2), SIVcpzPts (n = 2) and SIVgor (n = 2) Vpu proteins. Unexpectedly, all of these chimeras were capable of counteracting human tetherin to enhance virion release, irrespective of the presence or absence of the putative adaptor protein binding sites and the DSGxxS β-TrCP binding motif reported to be critical for effective anti-tetherin activity of M Vpus. It was also surprising that in three of the six chimeras the gain of anti-tetherin function was associated with a loss of the CD4 degradation activity since this function was conserved among all parental HIV-1, SIVcpz and SIVgor Vpu proteins.

Conclusions

Our results show that changes in the TMD of SIVcpzPtt, SIVcpzPts and SIVgor Vpus are sufficient to render them active against human tetherin. Thus, several previously described domains in the extracellular region of Vpu are not absolutely essential for tetherin antagonism but may be required for other Vpu functions.
BDNF Regulates Atypical PKC at Spinal Synapses to Initiate and Maintain a Centralized Chronic Pain State
Authors: Melemedjian Ohannes K , Tillu Dipti V , Asiedu Marina N , Mandell Edward K , Moy Jamie K , Blute Victoria M , Taylor Caleb J , Ghosh Sourav , Price Theodore J
Published: March 2013

Background

Chronic pain is an important medical problem affecting hundreds of millions of people worldwide. Mechanisms underlying the maintenance of chronic pain states are poorly understood but the elucidation of such mechanisms have the potential to reveal novel therapeutics capable of reversing a chronic pain state. We have recently shown that the maintenance of a chronic pain state is dependent on an atypical PKC, PKMζ, but the mechanisms involved in controlling PKMζ in chronic pain are completely unknown. Here we have tested the hypothesis that brain derived neurotrophic factor (BDNF) regulates PKMζ, and possibly other aPKCs, to maintain a centralized chronic pain state.

Results

We first demonstrate that although other kinases play a role in the initiation of persistent nociceptive sensitization, they are not involved in the maintenance of this chronic pain state indicating that a ZIP-reversible process is responsible for the maintenance of persistent sensitization. We further show that BDNF plays a critical role in initiating and maintaining persistent nociceptive sensitization and that this occurs via a ZIP-reversible process. Moreover, at spinal synapses, BDNF controls PKMζ and PKCΛ nascent synthesis via mTORC1 and BDNF enhances PKMζ phosphorylaton. Finally, we show that BDNF signaling to PKMζ and PKCΛ is conserved across CNS synapses demonstrating molecular links between pain and memory mechanisms.

Conclusions

Hence, BDNF is a key regulator of aPKC synthesis and phosphorylation and an essential mediator of the maintenance of a centralized chronic pain state. These findings point to BDNF regulation of aPKC as a potential therapeutic target for the permanent reversal of a chronic pain state.
Clinical balance assessment: perceptions of commonly-used standardized measures and current practices among physiotherapists in Ontario, Canada
Authors: Sibley Kathryn M , Straus Sharon E , Inness Elizabeth L , Salbach Nancy M , Jaglal Susan B
Published: March 2013

Background

Balance impairment is common in multiple clinical populations, and comprehensive assessment is important for identifying impairments, planning individualized treatment programs, and evaluating change over time. However, little information is available regarding whether clinicians who treat balance are satisfied with existing assessment tools. In 2010 we conducted a cross-sectional survey of balance assessment practices among physiotherapists in Ontario, Canada, and reported on the use of standardized balance measures (Sibley et al. 2011 Physical Therapy; 91: 1583-91). The purpose of this study was to analyse additional survey data and i) evaluate satisfaction with current balance assessment practices and standardized measures among physiotherapists who treat adult or geriatric populations with balance impairment, and ii) identify factors associated with satisfaction.

Methods

The questionnaire was distributed to 1000 practicing physiotherapists. This analysis focuses on questions in which respondents were asked to rate their general perceptions about balance assessment, the perceived utility of individual standardized balance measures, whether they wanted to improve balance assessment practices, and why. Data were summarized with descriptive statistics and utility of individual measures was compared across clinical practice areas (orthopaedic, neurological, geriatric or general rehabilitation).

Results

The questionnaire was completed by 369 respondents, of which 43.4% of respondents agreed that existing standardized measures of balance meet their needs. In ratings of individual measures, the Single Leg Stance test and Berg Balance Scale were perceived as useful for clinical decision-making and evaluating change over time by over 70% of respondents, and the Timed Up-and-Go test was perceived as useful for decision-making by 56.9% of respondents and useful for evaluating change over time by 62.9% of respondents, but there were significant differences across practice groups. Seventy-nine percent of respondents wanted to improve their assessments, identifying individual, environmental and measure-specific barriers. The most common barriers were lack of time and knowledge.

Conclusions

This study offers new information on issues affecting the evaluation of balance in clinical settings from a broad sample of physiotherapists. Continued work to address barriers by specific practice area will be critical for the success of any intervention attempting to implement optimal balance assessment practices in the clinical setting.
Prospective evaluation of quality of life 54 months after high-dose intensity-modulated radiotherapy for localized prostate cancer
Authors: Goineau Aurore , Marchand Virginie , Rigaud Jérome , Bourdin Sylvain , Rio Emmanuel , Campion Loic , Bonnaud-Antignac Angélique , Mahé Marc-André , Supiot Stéphane
Published: March 2013

Objective

To determine late toxicity and quality of life (QoL) in patients with localized prostate cancer after high-dose intensity-modulated radiotherapy (IMRT).

Patient and methods

This was a prospective study in patients with localized prostate adenocarcinoma who had been treated by IMRT (76 Gy) between February and November 2006. Physicians scored acute and late toxicity using the Common Terminology Criteria for Adverse Events (version 3.0). Patients completed cancer and prostate-specific QoL questionnaires (EORTC QLQ-C30 and QLQ-PR25) before IMRT (baseline) and at 2, 6, 18 and 54 months.

Result

Data were available for 38 patients (median age, 73 years) (18% low risk; 60% intermediate risk; 32% high risk). The incidence of urinary and gastrointestinal toxicity was respectively: immediately post IMRT: 36.8% and 23.7% (grade 1), 5.3% and 5.3% (grade 2), 2.6% and 0% (grade 3); at 18 months: 23.7% and 10.3% (grade 1), 26.3% and 13.2% (grade 2), 0% and 2.6% (grade 3); at 54 months: 34.2% and 23.7% (grade 1), 5.3% and 15.8% (grade 2), 5.3% and 0% (grade 3). At 54 months, significant worsening was reported by patients for 11/19 QoL items but the worsening was clinically relevant (>10 points) for 7 items only: physical, role as well as social functioning, fatigue, pain, dyspnoea and constipation. There was no significant difference between 54-month and baseline QoL scores for global health, gastrointestinal symptoms, treatment-related symptoms and sexual function. However, there was significant - but clinically non-relevant (<10 points) - worsening of urinary symptom.

Conclusion

High-dose IMRT to the prostate with accurate patient positioning did not induce any clinically relevant worsening in late urinary and gastrointestinal QoL at 54 months. Impaired physical and role functioning may be related to age and comorbidities.
In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae
Authors: Amara Flavio , Colombo Riccardo , Cazzaniga Paolo , Pescini Dario , Csikász-Nagy Attila , Falconi Marco Muzi , Besozzi Daniela , Plevani Paolo
Published: March 2013

Background

The genome of living organisms is constantly exposed to several damaging agents that induce different types of DNA lesions, leading to cellular malfunctioning and onset of many diseases. To maintain genome stability, cells developed various repair and tolerance systems to counteract the effects of DNA damage. Here we focus on Post Replication Repair (PRR), the pathway involved in the bypass of DNA lesions induced by sunlight exposure and UV radiation. PRR acts through two different mechanisms, activated by mono- and poly-ubiquitylation of the DNA sliding clamp, called Proliferating Cell Nuclear Antigen (PCNA).

Results

We developed a novel protocol to measure the time-course ratios between mono-, di- and tri-ubiquitylated PCNA isoforms on a single western blot, which were used as the wet readout for PRR events in wild type and mutant S. cerevisiae cells exposed to acute UV radiation doses. Stochastic simulations of PCNA ubiquitylation dynamics, performed by exploiting a novel mechanistic model of PRR, well fitted the experimental data at low UV doses, but evidenced divergent behaviors at high UV doses, thus driving the design of further experiments to verify new hypothesis on the functioning of PRR. The model predicted the existence of a UV dose threshold for the proper functioning of the PRR model, and highlighted an overlapping effect of Nucleotide Excision Repair (the pathway effectively responsible to clean the genome from UV lesions) on the dynamics of PCNA ubiquitylation in different phases of the cell cycle. In addition, we showed that ubiquitin concentration can affect the rate of PCNA ubiquitylation in PRR, offering a possible explanation to the DNA damage sensitivity of yeast strains lacking deubiquitylating enzymes.

Conclusions

We exploited an in vivo and in silico combinational approach to analyze for the first time in a Systems Biology context the events of PCNA ubiquitylation occurring in PRR in budding yeast cells. Our findings highlighted an intricate functional crosstalk between PRR and other events controlling genome stability, and evidenced that PRR is more complicated and still far less characterized than previously thought.
Broadband seismic data — The importance of low frequencies
Authors: ten Kroode Fons , Bergler Steffen , Corsten Cees , de Maag Jan Willem , Strijbos Floris , Tijhof Henk
Published: March 2013

We considered the importance of low frequencies in seismic reflection data for enhanced resolution, better penetration, and waveform and impedance inversion. We reviewed various theoretical arguments underlining why adding low frequencies may be beneficial and provided experimental evidence for the improvements by several case studies with recently acquired broadband data. We discussed where research and development efforts in the industry with respect to low frequencies should be focusing.
Wavefield-separation methods for dual-sensor towed-streamer data
Authors: Day Anthony , Klüver Tilman , Söllner Walter , Tabti Hocine , Carlson David
Published: March 2013

A dual-sensor towed streamer records the pressure and vertical component of particle motion associated with the incident wavefield that may be used to separate the wavefield into its up- and downgoing parts. This procedure requires information about the water properties (wave-propagation velocity and density) and is robust in the presence of errors in the estimation of these quantities of the magnitude likely to be encountered. In practice, the particle motion data recorded by current towed marine streamers encounter very strong mechanical noise such that, for the lowest frequencies, the wavefield separation must be approximated by deconvolving the ghost function from the pressure data. This procedure requires information about the streamer depth and is robust to small depth errors over the frequency range for which it is required for dual-sensor streamer processing, but it is much more sensitive if applied over the bandwidth necessary to deghost pressure data acquired at a conventional streamer depth. The signal-to-noise ratio can be further enhanced by recombining the up- and downgoing pressure fields at the sea surface, which has the effect of applying a ghostlike filter to noise that is recorded by only one of the two sensors. In practical marine acquisition scenarios, spatial sampling is often insufficient to yield an accurate result, especially in the crossline direction. If each streamer is processed independently assuming that the wavefield propagation is purely inline, significant errors can be introduced. For arrivals with high emergent angles, errors may also be introduced even if the wavefield propagation actually is purely inline due to incorrect treatment of spatially aliased energy. However, these effects are almost entirely confined to very shallow events. They can be mitigated by using independently derived information about the crossline propagation angle and, for data comprising predominantly forward scattered energy, appropriate application of linear moveout.
Directional wavefield decomposition
Authors: Yarman Evren , Ramírez Adriana C.
Published: March 2013

We bring an alternative view to the computation of the upgoing wavefield and generalize it to directional wavefield decomposition. We start by comparing the integral representation of the upgoing wavefield to the dispersion relation of the wave equation. Developing the relationship between the two, we write a Fourier transform representation that allows to generalize wavefield decomposition to an arbitrary direction. Decomposing the wavefield for arbitrary incoming and outgoing directions at the source and the receiver allows a complete decomposition of the data that can be used for many purposes, such as selecting or enhancing illumination directions for imaging and inversion.
Optimal Scaling of the Random Walk Metropolis: General Criteria for the 0.234 Acceptance Rule
Authors: Sherlock Chris
Published: March 2013

Scaling of proposals for Metropolis algorithms is an important practical problem in Markov chain Monte Carlo implementation. Analyses of the random walk Metropolis for high-dimensional targets with specific functional forms have shown that in many cases the optimal scaling is achieved when the acceptance rate is approximately 0.234, but that there are exceptions. We present a general set of sufficient conditions which are invariant to orthonormal transformation of the coordinate axes and which ensure that the limiting optimal acceptance rate is 0.234. The criteria are shown to hold for the joint distribution of successive elements of a stationarypth-order multivariate Markov process.
On the Generalized Drift Skorokhod Problem in One Dimension
Authors: Reed Josh , Ward Amy , Zhan Dongyuan
Published: March 2013

We show how to write the solution to the generalized drift Skorokhod problem in one-dimension in terms of the supremum of the solution of a tractable unrestricted integral equation (that is, an integral equation with no boundaries). As an application of our result, we equate the transient distribution of a reflected Ornstein–Uhlenbeck (OU) process to the first hitting time distribution of an OU process (that is not reflected). Then, we use this relationship to approximate the transient distribution of the GI/GI/1 + GI queue in conventional heavy traffic and the M/M/N/N queue in a many-server heavy traffic regime.
Sharp Bounds for Sums of Dependent Risks
Authors: Puccetti Giovanni , Rüschendorf Ludger
Published: March 2013

Sharp tail bounds for the sum of d random variables with given marginal distributions and arbitrary dependence structure have been known since Makarov (1981) and Rüschendorf (1982) for d=2 and, in some examples, for d≥3. Based on a duality result, dual bounds have been introduced in Embrechts and Puccetti (2006b). In the homogeneous case, F1=···=Fn, with monotone density, sharp tail bounds were recently found in Wang and Wang (2011). In this paper we establish the sharpness of the dual bounds in the homogeneous case under general conditions which include, in particular, the case of monotone densities and concave densities. We derive the corresponding optimal couplings and also give an effective method to calculate the sharp bounds.
Asymptotics of Hybrid Fluid Queues with Lévy Input
Authors: Dębicki Krzysztof , Sierpińska Iwona , Zwart Bert
Published: March 2013

Let {X(t):t∈ℝ} be the integrated on–off process with regularly varying on-periods, and let {Y(t):t∈ℝ} be a centered Lévy process with regularly varying positive jumps (independent of X(·)). We study the exact asymptotics of ℙ(supt≥0{X(t)+Y(t)-ct}>u) as u→∞, with special attention to the case r=c, where r is the increase rate of the on–off process during the on-periods.
Asymptotic Analysis of Hoppe Trees
Authors: Leckey Kevin , Neininger Ralph
Published: March 2013

We introduce and analyze a random tree model associated to Hoppe's urn. The tree is built successively by adding nodes to the existing tree when starting with the single root node. In each step a node is added to the tree as a child of an existing node, where these parent nodes are chosen randomly with probabilities proportional to their weights. The root node has weight ϑ>0, a given fixed parameter, all other nodes have weight 1. This resembles the stochastic dynamic of Hoppe's urn. For ϑ=1, the resulting tree is the well-studied random recursive tree. We analyze the height, internal path length, and number of leaves of the Hoppe tree withnnodes as well as the depth of the last inserted node asymptotically asn→∞. Mainly expectations, variances, and asymptotic distributions of these parameters are derived.
Dynamic Signatures of Coherent Systems Based on Sequential Order Statistics
Authors: Burkschat M. , Navarro J.
Published: March 2013

Sequential order statistics can be used to describe the ordered lifetimes of components in a system, where the failure of a component may affect the performance of remaining components. In this paper mixture representations of the residual lifetime and the inactivity time of systems with such failure-dependent components are considered. Stochastic comparisons of differently structured systems are obtained and properties of the weights in the mixture representations are examined. Furthermore, corresponding representations of the residual lifetime and the inactivity time of a system given the additional information about a previous failure time are derived.
The Laplace Transform of Hitting Times of Integrated Geometric Brownian Motion
Authors: Metzler Adam
Published: March 2013

In this note we compute the Laplace transform of hitting times, to fixed levels, of integrated geometric Brownian motion. The transform is expressed in terms of the gamma and confluent hypergeometric functions. Using a simple Itô transformation and standard results on hitting times of diffusion processes, the transform is characterized as the solution to a linear second-order ordinary differential equation which, modulo a change of variables, is equivalent to Kummer's equation.
Cohesin codes – interpreting chromatin architecture and the many facets of cohesin function
Authors: Rudra Soumya , Skibbens Robert V.
Published: March 2013

Sister chromatid tethering is maintained by cohesin complexes that minimally contain Smc1, Smc3, Mcd1 and Scc3. During S-phase, chromatin-associated cohesins are modified by the Eco1/Ctf7 family of acetyltransferases. Eco1 proteins function during S phase in the context of replicated sister chromatids to convert chromatin-bound cohesins to a tethering-competent state, but also during G2 and M phases in response to double-stranded breaks to promote error-free DNA repair. Cohesins regulate transcription and are essential for ribosome biogenesis and complete chromosome condensation. Little is known, however, regarding the mechanisms through which cohesin functions are directed. Recent findings reveal that Eco1-mediated acetylation of different lysine residues in Smc3 during S phase promote either cohesion or condensation. Phosphorylation and SUMOylation additionally impact cohesin functions. Here, we posit the existence of a cohesin code, analogous to the histone code introduced over a decade ago, and speculate that there is a symphony of post-translational modifications that direct cohesins to function across a myriad of cellular processes. We also discuss evidence that outdate the notion that cohesion defects are singularly responsible for cohesion-mutant-cell inviability. We conclude by proposing that cohesion establishment is linked to chromatin formation.
A Review of Wind Turbine Noise Perception, Annoyance and Low Frequency Emission
Authors: Doolan Con
Published: March 2013

Current literature concerning the perception, annoyance and emission of low-frequency noise from wind turbines are reviewed. Wind turbine noise has been shown to be annoying to people with annoyance related to noise load. Other factors, such as those related to visual, economic and psychological effects, were also shown to affect a person's annoyance of wind turbine noise. Published infrasound (noise at frequencies less than 20 Hz) measurements show that levels at typical residential set-back distances are too low to be directly audible, but may be perceived via window rattling. On the other hand, low-frequency noise levels, in the frequency range of 20–200 Hz may exceed audibility thresholds and it is postulated they may be correlated with annoyance. A review of general low-frequency noise annoyance studies is presented and highlights the similarities of many wind turbine noise complaints with those due to low-frequency noise. The paper concludes with a suggestion to develop a new methodology that can simultaneously acquire annoyance and noise data at the time a person believes they are annoyed by wind turbine noise.
Substructural Method for Vibration Analysis of the Elastically Connected Double-Beam System
Authors: Huang M. , Liu J. K.
Published: March 2013

Free and forced vibration analyses of the two parallel beams connected to each other by the uniformly distributed vertical springs have been conducted in this contribution. The coupled motion equations were derived by using the free interface substructural method, and both of the free vibration characteristics and the forced vibration responses of the complex double-beam system were obtained. The mode localization and frequency loci veering phenomena would take place in such weakly coupled double beam system when there is a disorder in the system. By comparing with the available data in the literature, our numerical results were verified, and the well agreements were observed. These investigations showed that the proposed method is general and can be extended easily for vibration analysis of coupled double plate system or other complex systems.
Numerical Simulation of Flows about a Stationary and a Free-Falling Cylinder Using Immersed Boundary-Finite Difference Lattice Boltzmann Method
Authors: Rojas Roberto , Hayashi Kosuke , Seta Takeshi , Tomiyama Akio
Published: March 2013

The applicability of the immersed boundary-finite difference lattice Boltzmann method (IB-FDLBM) to high Reynolds number flows about a circular cylinder is examined. Two-dimensional simulations of flows past a stationary circular cylinder are carried out for a wide range of the Reynolds number, Re, i.e., 1 ≤ Re ≤ 1×105. An immersed boundary-lattice Boltzmann method (IB-LBM) is also used for comparison. Then free-falling circular cylinders are simulated to demonstrate the feasibility of predicting moving particles at high Reynolds numbers. The main conclusions obtained are as follows: (1) steady and unsteady flows about a stationary cylinder are well predicted with IB-LBM and IB-FDLBM, provided that the spatial resolution is high enough to satisfy the conditions of numerical stability, (2) high spatial resolution is required for stable IB-LBM simulation of high Reynolds number flows, (3) IB-FDLBM can stably simulate flows at very high Reynolds numbers without increasing the spatial resolution, (4) IB-FDLBM gives reasonable predictions of the drag coefficient for 1 ≤ Re ≤ 1×105, and (5) IB-FDLBM gives accurate predictions for the motion of free-falling cylinders at intermediate Reynolds numbers.
A Linear Programming Approach to Nonstationary Infinite-Horizon Markov Decision Processes
Authors: Ghate Archis , Smith Robert L.
Published: March 2013

Nonstationary infinite-horizon Markov decision processes (MDPs) generalize the most well-studied class of sequential decision models in operations research, namely, that of stationary MDPs, by relaxing the restrictive assumption that problem data do not change over time. Linear programming (LP) has been very successful in obtaining structural insights and devising solution methods for stationary MDPs. However, an LP approach for nonstationary MDPs is currently missing. This is because the LP formulation of a nonstationary infinite-horizon MDP includes countably infinite variables and constraints, and research on such infinite-dimensional LPs has traditionally faced several hurdles. For instance, duality results may not hold; an extreme point may not be a basic feasible solution; and in the context of a simplex algorithm, a pivot operation may require infinite data and computations, and a sequence of improving extreme points need not converge in value to optimal. In this paper, we tackle these challenges and establish (1) weak and strong duality, (2) complementary slackness, (3) a basic feasible solution characterization of extreme points, (4) a one-to-one correspondence between extreme points and deterministic Markovian policies, and (5) we devise a simplex algorithm for an infinite-dimensional LP formulation of nonstationary infinite-horizon MDPs. Pivots in this simplex algorithm use finite data, perform finite computations, and generate a sequence of improving extreme points that converges in value to optimal. Moreover, this sequence of extreme points gets arbitrarily close to the set of optimal extreme points. We also prove that decisions prescribed by these extreme points are eventually exactly optimal in all states of the nonstationary infinite-horizon MDP in early periods.
Corporate citizens and the UN Global Compact: explaining cross-national variations in turnout
Authors: Bernhagen Patrick , Mitchell Neil J. , Thissen-Smits Marianne
Published: March 2013

Business and public partnerships in socially responsible behavior have become a central pillar of global governance, but one that is unevenly developed in different countries. Despite the transnational character of business operations, national context is of theoretical as well as policy significance. To explain cross-country variation in corporate commitment to social responsibility we investigate the political conditions that encourage firms to participate in the United Nations Global Compact. Drawing on a theory of corporate social responsibility as motivated by self-interest and external pressure, we examine the influence of external actors and the locally specific mobilization of bias. Analyzing participation levels in 145 countries, we find that a democratic regime and Global Compact participation by countervailing groups are associated with higher levels of business participation in the program. Contrary to earlier studies relying on smaller numbers of countries, we find no evidence that a country's relationship with the UN or the domestic political strength of environmental interests account for cross-national variation in corporate engagement with the Global Compact.
Price Shopping in Consumer-Directed Health Plans
Authors: Sood Neeraj , Wagner Zachary , Huckfeldt Peter , Haviland Amelia M.
Published: March 2013

We use health insurance claims data from 63 large employers to estimate the extent of price shopping for nine common outpatient services in consumer-directed health plans (CDHPs) compared to traditional health plans. The main measures of price shopping include (1) the total price paid on the claim, (2) the share of claims from low- and high-cost providers, and (3) the savings from price shopping relative to choosing prices randomly. All analyses control for individual and zip code level demographics and plan characteristics. We also estimate differences in price shopping within CDHPs depending on expected health care costs and whether the service was bought before or after reaching the deductible. For eight out of nine services analyzed, prices paid by CDHP and traditional plan enrollees did not differ significantly; CDHP enrollees paid 2.3% less for office visits. Similarly, office visits was the only service where CDHP enrollment resulted in a significantly larger share of claims from low-cost providers and greater savings from price shopping relative to traditional plans. There was also no evidence that, within CDHP plans, consumers with lower expected medical expenses exhibited more price shopping or that consumers exhibited more price shopping before reaching the deductible.