bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic generation of design structure matrices through the evolution of product models
Authors: Gopsill James A. , Snider Chris , McMahon Chris , Hicks Ben 
Published: October 2016

AbstractDealing with component interactions and dependencies remains a core and fundamental aspect of engineering, where conflicts and constraints are solved on an almost daily basis. Failure to consider these interactions and dependencies can lead to costly overruns, failure to meet requirements, and lengthy redesigns. Thus, the management and monitoring of these dependencies remains a crucial activity in engineering projects and is becoming ever more challenging with the increase in the number of components, component interactions, and component dependencies, in both a structural and a functional sense. For these reasons, tools and methods to support the identification and monitoring of component interactions and dependencies continues to be an active area of research. In particular, design structure matrices (DSMs) have been extensively applied to identify and visualize product and organizational architectures across a number of engineering disciplines. However, the process of generating these DSMs has primarily used surveys, structured interviews, and/or meetings with engineers. As a consequence, there is a high cost associated with engineers' time alongside the requirement to continually update the DSM structure as a product develops. It follows that the proposition of this paper is to investigate whether an automated and continuously evolving DSM can be generated by monitoring the changes in the digital models that represent the product. This includes models that are generated from computer-aided design, finite element analysis, and computational fluid dynamics systems. The paper shows that a DSM generated from the changes in the product models corroborates with the product architecture as defined by the engineers and results from previous DSM studies. In addition, further levels of product architecture dependency were also identified. A particular affordance of automatically generating DSMs is the ability to continually generate DSMs throughout the project. This paper demonstrates the opportunity for project managers to monitor emerging product dependencies alongside changes in modes of working between the engineers. The application of this technique could be used to support existing product life cycle change management solutions, cross-company product development, and small to medium enterprises who do not have a product life cycle management solution.
A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways
Authors: Huang Tianzhi , Alvarez Angel A. , Pangeni Rajendra P. , M. Horbinski Craig , Lu Songjian , Kim Sung-Hak , James C. David , J. Raizer Jeffery , A. Kessler John , Brenann Cameron W. , Sulman Erik P. , Finocchiaro Gaetano , Tan Ming , Nishikawa Ryo , Lu Xinghua , Nakano Ichiro , Hu Bo , Cheng Shi-Yuan 
Published: October 2016

AbstractMolecularly defined subclassification is associated with phenotypic malignancy of glioblastoma (GBM). However, current understanding of the molecular basis of subclass conversion that is often involved in GBM recurrence remain rudimentary at best. Here we report that canonical Wnt signalling that is active in proneural (PN) but inactive in mesenchymal (MES) GBM, along with miR-125b and miR-20b that are expressed at high levels in PN compared with MES GBM, comprise a regulatory circuit involving TCF4-miR-125b/miR-20b-FZD6. FZD6 acts as a negative regulator of this circuit by activating CaMKII–TAK1–NLK signalling, which, in turn, attenuates Wnt pathway activity while promoting STAT3 and NF-κB signalling that are important regulators of the MES-associated phenotype. These findings are confirmed by targeting differentially enriched pathways in PN versus MES GBM that results in inhibition of distinct GBM subtypes. Correlative expressions of the components of this circuit are prognostic relevant for clinical GBM. Our findings provide insights for understanding GBM pathogenesis and for improving treatment of GBM.
Insights into cancer severity from biomolecular interaction mechanisms
Authors: Raimondi Francesco , Singh Gurdeep , Betts Matthew J. , Apic Gordana , Vukotic Ranka , Andreone Pietro , Stein Lincoln , Russell Robert B. 
Published: October 2016

AbstractTo attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or –nucleic acid) most often perturbed in cancer, highlighting several potentially novel cancer genes. Over half of these interfaces involve protein-small-molecule interactions highlighting their overall importance in cancer. We found distinct differences in the predominance of perturbed interfaces between cancers and histological subtypes and presence or absence of certain interfaces appears to correlate with cancer severity.
CO2 Capture in the Sustainable Wheat-Derived Activated Microporous Carbon Compartments
Authors: Hong Seok-Min , Jang Eunji , Dysart Arthur D. , Pol Vilas G. , Lee Ki Bong 
Published: October 2016

AbstractMicroporous carbon compartments (MCCs) were developed via controlled carbonization of wheat flour producing large cavities that allow CO2 gas molecules to access micropores and adsorb effectively. KOH activation of MCCs was conducted at 700 °C with varying mass ratios of KOH/C ranging from 1 to 5, and the effects of activation conditions on the prepared carbon materials in terms of the characteristics and behavior of CO2 adsorption were investigated. Textural properties, such as specific surface area and total pore volume, linearly increased with the KOH/C ratio, attributed to the development of pores and enlargement of pores within carbon. The highest CO2 adsorption capacities of 5.70 mol kg−1 at 0 °C and 3.48 mol kg−1 at 25 °C were obtained for MCC activated with a KOH/C ratio of 3 (MCC-K3). In addition, CO2 adsorption uptake was significantly dependent on the volume of narrow micropores with a pore size of less than 0.8 nm rather than the volume of larger pores or surface area. MCC-K3 also exhibited excellent cyclic stability, facile regeneration, and rapid adsorption kinetics. As compared to the pseudo-first-order model, the pseudo-second-order kinetic model described the experimental adsorption data methodically.
Possible neural mechanisms of psychotherapy for trauma-related symptoms: cerebral responses to the neuropsychological treatment of post-traumatic stress disorder model individuals
Authors: Amano Tamaki , Toichi Motomi 
Published: October 2016

AbstractPsychotherapy is often effective for treating psychogenic disorders, but the changes that occur in the brain during such treatments remain unknown. To investigate this, we monitored cerebral activity throughout an entire session using a psychotherapeutic technique in healthy subjects. Since post-traumatic stress disorder (PTSD) is a typical psychogenic psychiatric disorder, we used PTSD-model volunteers who had experienced a moderately traumatic event. The technique used as psychotherapy was eye movement desensitisation and reprocessing (EMDR), a standard method for treating PTSD. The oxygenated haemoglobin concentration ([oxy-Hb]), a sensitive index of brain activation, measured using multi-channel near-infrared spectroscopy, revealed changes in [oxy-Hb] in the superior temporal sulcus (STS) and orbitofrontal cortex (OFC). During a vital therapeutic stage, a significant reduction in the activation by forced eye movements was observed in the right STS, and a trend toward a reduction in the left OFC. The hyperactivation of the right STS on the recall of unpleasant memories, and its normalisation by eye movements, seem to reflect an important neural mechanism of the psychotherapy. These findings suggest that psychotherapy for traumatic symptoms involves brain regions related to memory representation and emotion, and possibly those that link memory and emotion, such as the amygdala.
High expression of new genes in trochophore enlightening the ontogeny and evolution of trochozoans
Authors: Xu Fei , Domazet-Lošo Tomislav , Fan Dingding , Dunwell Thomas L. , Li Li , Fang Xiaodong , Zhang Guofan 
Published: October 2016

AbstractAnimals with trochophore larvae belong to Trochozoa, one of the main branches of Bilateria. In addition to exhibiting spiral cleavage and early cell fate determination, trochozoans typically undergo indirect development, which contributes to the most unique characteristics of their ontogeny. The indirect development of trochozoans has provoked discussion regarding the origin and evolution of marine larvae and is interesting from the perspective of phylogeny-ontogeny correspondence. While these phylo-onto correlations have an hourglass shape in Deuterostomia, Ecdysozoa, plants and even fungi, they have seldom been studied in Trochozoa, and even Lophotrochozoa. Here, we compared the ontogenetic transcriptomes of the Pacific oyster,Crassostrea gigas(Bivalvia, Mollusca), the Pacific abalone,Haliotis discus hannai(Gastropoda, Mollusca), and the sand wormPerinereis aibuhitensis(Polychaeta, Annelida) using several complementary phylotranscriptomic methods to examine their evolutionary trajectories. The results revealed the late trochophore stage as the phylotypic phase. However, this basic pattern is accompanied with increased use of new genes in the trochophore stages which marks specific adaptations of the larval body plans.
Kupffer cells induce Notch-mediated hepatocyte conversion in a common mouse model of intrahepatic cholangiocarcinoma
Authors: Terada Maiko , Horisawa Kenichi , Miura Shizuka , Takashima Yasuo , Ohkawa Yasuyuki , Sekiya Sayaka , Matsuda-Ito Kanae , Suzuki Atsushi 
Published: October 2016

AbstractIntrahepatic cholangiocarcinoma (ICC) is a malignant epithelial neoplasm composed of cells resembling cholangiocytes that line the intrahepatic bile ducts in portal areas of the hepatic lobule. Although ICC has been defined as a tumor arising from cholangiocyte transformation, recent evidence from genetic lineage-tracing experiments has indicated that hepatocytes can be a cellular origin of ICC by directly changing their fate to that of biliary lineage cells. Notch signaling has been identified as an essential factor for hepatocyte conversion into biliary lineage cells at the onset of ICC. However, the mechanisms underlying Notch signal activation in hepatocytes remain unclear. Here, using a mouse model of ICC, we found that hepatic macrophages called Kupffer cells transiently congregate around the central veins in the liver and express the Notch ligand Jagged-1 coincident with Notch activation in pericentral hepatocytes. Depletion of Kupffer cells prevents the Notch-mediated cell-fate conversion of hepatocytes to biliary lineage cells, inducing hepatocyte apoptosis and increasing mortality in mice. These findings will be useful for uncovering the pathogenic mechanism of ICC and developing prevenient and therapeutic strategies for this refractory disease.
Lifespan adversity and later adulthood telomere length in the nationally representative US Health and Retirement Study
Authors: Puterman Eli , Gemmill Alison , Karasek Deborah , Weir David , Adler Nancy E. , Prather Aric A. , Epel Elissa S. 
Published: October 2016

SignificanceThe gradual aging of the immune system is partly marked by shortened telomeres, the DNA–protein caps at the ends of chromosomes that protect genes from degradation. This study undertakes a lifespan approach to stress and leukocyte telomere length in a nationally representative sample of US residents. By using data from 16 y of the Health and Retirement Study, childhood and adulthood life stressors were examined for their individual and combined associations with increased odds of having short telomeres. Accumulated adverse experiences in childhood significantly predicted an increased likelihood of having short telomeres later in life, suggesting a potential pathway through which childhood experiences have been previously shown to predict adulthood morbidity and mortality.
Gate fidelity and coherence of an electron spin in an Si/SiGe quantum dot with micromagnet
Authors: Kawakami Erika , Jullien Thibaut , Scarlino Pasquale , Ward Daniel R. , Savage Donald E. , Lagally Max G. , Dobrovitski Viatcheslav V. , Friesen Mark , Coppersmith Susan N. , Eriksson Mark A. , Vandersypen Lieven M. K. 
Published: October 2016

Significance
A quantum computer is able to solve certain problems that cannot be solved by a classical computer within a reasonable time. The building block of a quantum computer is called a quantum bit (qubit), the counterpart of the conventional binary digit (bit). A qubit unavoidably interacts with its environment, leading to errors in the qubit state. This article reports on the qubit performance of an electron spin in a silicon/silicon-germanium (Si/SiGe) quantum dot, and examines the dominant error mechanisms. We demonstrate that this qubit can be electrically controlled with sufficient accuracy so that remaining errors could, in principle, be corrected using known protocols, even without isotopically purified silicon. This qubit also offers a quantum memory that lasts for almost 0.5 ms.
Democratic and Republican physicians provide different care on politicized health issues
Authors: Hersh Eitan D. , Goldenberg Matthew N. 
Published: October 2016

Significance
Political beliefs have been shown to spill over into nonpolitical domains, such as consumer spending, choice of romantic partner, and job hiring. Our evidence suggests that political beliefs predict the professional decisions of primary care physicians. On politicized health issues, like marijuana and abortion, physicians' partisan identity is highly correlated with their treatment decisions. Because physicians regularly interact with patients on politically sensitive health issues and because the medical profession is increasingly politicized (e.g., state governments are regulating politicized aspects of medicine), it is necessary to understand how doctors’ own political worldviews may impact their actions in the medical examination room.
Wnt/β-catenin signaling promotes self-renewal and inhibits the primed state transition in naïve human embryonic stem cells
Authors: Xu Zhuojin , Robitaille Aaron M. , Berndt Jason D. , Davidson Kathryn C. , Fischer Karin A. , Mathieu Julie , Potter Jennifer C. , Ruohola-Baker Hannele , Moon Randall T. 
Published: October 2016

Significance
Pluripotent stem cells (PSCs) can exist in a naïve or primed pluripotency state. Naïve PSCs correspond to an earlier developmental state more closely related to cells from the preimplantation embryo and may have more robust developmental potential than primed PSCs. However, understanding the molecular mechanisms that regulate naïve PSC behaviors such as self-renewal, differentiation, or preservation of the naïve state is incomplete. Here, we report that Wnt/β-catenin signaling promotes the self-renewal of naïve human embryonic stem cells (hESCs). When grown in conditions that inhibit Wnt/β-catenin signaling, naïve hESCs remain undifferentiated but have a more primed-like protein expression profile. Our results suggest that Wnt/β-catenin signaling plays a critical role in regulating human naïve pluripotency.
Effect of resonant magnetic perturbations on microturbulence in DIII-D pedestal
Authors: Holod I. , Lin Z. , Taimourzadeh S. , Nazikian R. , Spong D. , Wingen A. 
Published: October 2016

Abstract
Vacuum resonant magnetic perturbations (RMP) applied to otherwise axisymmetric tokamak plasmas produce in general a combination of non-resonant effects that preserve closed flux surfaces (kink response) and resonant effects that introduce magnetic islands and/or stochasticity (tearing response). The effect of the plasma kink response on the linear stability and nonlinear transport of edge turbulence is studied using the gyrokinetic toroidal code GTC for a DIII-D plasma with applied n  =  2 vacuum RMP. GTC simulations use the 3D equilibrium of DIII-D discharge 158103 (Nazikian et al 2015 Phys. Rev. Lett. 114 105002), which is provided by nonlinear ideal MHD VMEC equilibrium solver in order to include the effect of the plasma kink response to the external field but to exclude island formation at rational surfaces. Analysis using the GTC simulation results reveal no increase of growth rates for the electrostatic drift wave instability and for the electromagnetic kinetic-ballooning mode in the presence of the plasma kink response to the RMP. Furthermore, nonlinear electrostatic simulations show that the effect of the 3D equilibrium on zonal flow damping is very weak and found to be insufficient to modify turbulent transport in the electrostatic turbulence.
Identifying the source of super-high energetic electrons in the presence of pre-plasma in laser–matter interaction at relativistic intensities
Authors: Wu D. , Krasheninnikov S.I. , Luan S.X. , Yu W. 
Published: October 2016

Abstract
The generation of super-high energetic electrons influenced by pre-plasma in relativistic intensity laser–matter interaction is studied in a one-dimensional slab approximation with particle-in-cell simulations. Different pre-plasma scale lengths and laser intensities are considered, showing an increase in both particle number and cut-off kinetic energy of electrons with the increase of pre-plasma scale length and laser intensity, the cut-off kinetic energy greatly exceeding the corresponding laser ponderomotive energy. A two-stage electron acceleration model is proposed to explain the underlying physics. The first stage is attributed to the synergetic acceleration by longitudinal electric field and counter-propagating laser pulses, and a scaling law is obtained with efficiency depending on the pre-plasma scale length and laser intensity. These electrons pre-accelerated in the first stage could build up an intense electrostatic potential barrier with maximal value several times as large as the initial electron kinetic energy. Some of the energetic electrons could be further accelerated by reflection off the electrostatic potential barrier, with their finial kinetic energies significantly higher than the values pre-accelerated in the first stage.
A constant intrinsic thickness for dwarf irregular galaxies?
Authors: Johnson Megan C. , Hunter Deidre A. , Kamphuis Peter , Wang Jing 
Published: October 2016

Abstract
We assess the intrinsic thickness parameter, qo, for a sample of dwarf irregular galaxies and compare to larger, more massive spiral galaxy systems. We use optical photometry to determine b/a (minor-to-major axial ratio), and we use the H i kinematic inclination angle to derive qo. We find that qo ranges from 0.1 to 0.8 for the dwarfs. We find a trend in qo with luminosity, indicating that fainter dwarfs are thicker than brighter ones, similar to previous studies. However, we also find a trend in qo with H i kinematic inclination, which indicates that either the radius at which we measure b/a may be too small, or, that the stellar and gas discs have different inclinations. Because we selected only those objects that have nearly identical morphological and kinematic position angles, we find the latter reason unlikely. We find a weak trend in qo with hz/RD (ratio of stellar scaleheight to scalelength), which points to b/a not fully representing the stellar disc distribution. We conclude that a constant qo may not be appropriate for dwarf irregulars.
The effect of whole-body vibration training on lean mass in postmenopausal women: a systematic review and meta-analysis
Authors: Rubio-Arias Jacobo Á. , Marín-Cascales Elena , Ramos-Campo Domingo J. , Martínez-Rodríguez Alejandro , Chung Linda H. , Alcaraz Pedro E. 
Published: October 2016

Abstract

Objective:
The purpose of the present systematic review and meta-analysis was to evaluate published, randomized controlled trials that investigated the effects of whole-body vibration training (WBVT) on lean mass in postmenopausal women.

Methods:
The following electronic databases were searched from September to October 2015: PubMed, Web of Science, and Cochrane. Two different authors tabulated, independently, the selected indices in identical predetermined forms. The methodological quality of all randomized trial studies was evaluated according to the modified PEDro scale. In each trial, the effect size of the intervention was calculated by the difference between pre- and postintervention lean mass in WBVT postmenopausal women. For controlled trials, the effect size of the WBVT was also calculated by the difference in lean mass after the WBVT and in control participants.

Results:
Of the 189 articles found from the database search and all duplicates removed, 5 articles were analyzed. The lean mass of 112 postmenopausal women who performed either WBVT or a control protocol was evaluated. The methodological quality of the trials was high, where the mean score was 8 out of a possible 10 points. No significant improvements in lean mass with WBVT were found in postmenopausal women. In addition, there was no significant difference in lean mass between WBVT and control postmenopausal women.

Conclusions:
This meta-analysis demonstrated that WBVT alone may not be a sufficient stimulus to increase lean mass in postmenopausal women. Thus, additional complimentary training methods with WBVT are needed to increase muscle size in women with lower hormonal responses.
Employment conditions and work-related stressors are associated with menopausal symptom reporting among perimenopausal and postmenopausal women
Authors: Bariola Emily , Jack Gavin , Pitts Marian , Riach Kathleen , Sarrel Philip 
Published: October 2016

Abstract

Objective:
While many women undergo menopausal transition while they are in paid employment, the effect of poor working conditions on women's experience of the menopause has received scant empirical attention. We examined associations between employment conditions, work-related stressors, and menopausal symptom reporting among perimenopausal and postmenopausal working women.

Methods:
Data were drawn from an online survey conducted between 2013 and 2014 involving 476 perimenopausal and postmenopausal women working in the higher education sector in Australia. Survey questions assessed demographics; health-related variables; menopausal symptom reporting; employment status; presence of flexible working hours; presence of temperature control; job autonomy; and supervisor support.

Results:
A forced entry multivariable regression analysis revealed that high supervisor support (β = −0.10, P = 0.04), being employed on a full-time basis (β = −0.11, P = 0.02), and having control over workplace temperature (β = −0.11, P = 0.02) were independently associated with lower menopausal symptom reporting.

Conclusions:
These findings may help inform the development of tailored occupational health policies and programs that cater for the needs of older women as they transition through menopause in the workplace.