bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reporting Erectile Function Outcomes After Radiation Therapy for Prostate Cancer: Challenges in Data Interpretation
Authors: Wortel Ruud C. , Incrocci Luca , Mulhall John P. 
Published: September 2017

Abstract

Background
Choice of prostate cancer treatment is frequently influenced by the expected chance of treatment-induced side effects such as erectile dysfunction (ED). However, great discrepancy in cited ED rates exists in the contemporary radiation therapy literature.

Aim
To analyze the reported ED rates and cause of discrepancies and explore the strengths and limitations in the literature on radiation-induced ED.

Methods
We performed a PubMed literature search and reviewed the literature on ED rates associated with external-beam radiotherapy and brachytherapy from the past 10 years. Eighteen studies were eligible for inclusion and subsequently reviewed.

Outcomes
Variables required for interpretation of erectile function outcomes, including patient demographics, treatment characteristics, and sexual function outcomes.

Results
A large variety in the reported incidence of ED was found among studies. In part, these differences resulted from large variations in (i) study populations, (ii) patient characteristics, (iii) treatment characteristics, (iv) prescription of androgen deprivation therapy, (v) means of data acquisition, (vi) definitions of ED, (vii) temporal considerations, and (viii) erectile aid use. Relevant data required for adequate appraisal of sexual function outcomes were not always reported.

Clinical Implications
Based on the present findings, we present general recommendations for reporting of erectile function outcomes after radiotherapy for prostate cancer. These should improve future reports.

Strengths and Limitations
This is the first report that presents general requirements on reporting erectile function outcomes in the setting of radiotherapy for prostate cancer. We did not conduct a formal meta-analysis because we focused on concepts of research design; this might be considered a limitation.

Conclusion
In this review, we have highlighted the strengths and deficiencies of the current literature on ED after external-beam radiotherapy and brachytherapy for prostate cancer. We have made general recommendations to achieve some degree of standardization among reports and improve clinical interpretability.
International Islamic funds
Authors: Lesser Kathrin , Walkshäusl Christian 
Published: September 2017

AbstractInternationally‐investing Islamic equity funds from developed Islamic and non‐Islamic markets perform in general similar to the market. However, analyzing different market conditions, we provide evidence that funds domiciled in Islamic markets outperform their peers and funds from non‐Islamic markets during market turmoil, irrespective of the applied performance measurement model. We suggest that this outperformance is owed to the expertise of fund managers from developed Islamic markets who operate in a financial environment that is driven by Islamic principles. Our results are robust with respect to the standard Fama‐French three‐factor and four‐factor models as well as to the novel five‐factor model.
The relationship between chronic musculoskeletal pain, anxiety and mindfulness: Adjustments to the Fear-Avoidance Model of Chronic Pain
Authors: Curtin Katherine B. , Norris Deborah 
Published: September 2017

Abstract

Background and purpose
The Fear-Avoidance Model of Chronic Pain proposed by Vlaeyen and Linton states individuals enter a cycle of chronic pain due to predisposing psychological factors, such as negative affectivity, negative appraisal or anxiety sensitivity. They do not, however, address the closely related concept of anxious rumination. Although Vlaeyen and Linton suggest cognitive-behavioral treatment methods for chronic pain patients who exhibit pain-related fear, they do not consider mindfulness treatments. This cross-sectional study investigated the relationship between chronic musculoskeletal pain (CMP), ruminative anxiety and mindfulness to determine if (1) ruminative anxiety is a risk factor for developing chronic pain and (2) mindfulness is a potential treatment for breaking the cycle of chronic pain.

Methods
Middle-aged adults ages 35-50 years (N = 201) with self-reported CMP were recruited online. Participants completed standardized questionnaires assessing elements of chronic pain, anxiety, and mindfulness.

Results
Ruminative anxiety was positively correlated with pain catastrophizing, pain-related fear and avoidance, pain interference, and pain severity but negatively correlated with mindfulness. High ruminative anxiety level predicted significantly higher elements of chronic pain and significantly lower level of mindfulness. Mindfulness significantly predicted variance (R
2) in chronic pain and anxiety outcomes. Pain severity, ruminative anxiety, pain catastrophizing, pain-related fear and avoidance, and mindfulness significantly predicted 70.0% of the variance in pain interference, with pain severity, ruminative anxiety and mindfulness being unique predictors.

Conclusions
The present study provides insight into the strength and direction of the relationships between ruminative anxiety, mindfulness and chronic pain in a CMP population, demonstrating the unique associations between specific mindfulness factors and chronic pain elements.

Implications
It is possible that ruminative anxiety and mindfulness should be added into the Fear-Avoidance Model of Chronic Pain, with ruminative anxiety as a psychological vulnerability and mindfulness as an effective treatment strategy that breaks the cycle of chronic pain. This updated Fear-Avoidance Model should be explored further to determine the specific mechanism of mindfulness on chronic pain and anxiety and which of the five facets of mindfulness are most important to clinical improvements. This could help clinicians develop individualized mindfulness treatment plans for chronic pain patients.
Diffusion-driven nucleation from surface nuclei in hydrodynamic cavitation
Authors: Groß T. F. , Pelz P. F. 
Published: September 2017

Investigations about the role of nuclei and nucleation for the inception and formation of cavitation have been part of cavitation research since Harvey et al. (J. Cell. Physiol., vol. 24 (1), 1944, pp. 1–22) postulated the existence of gas filled crevices on surfaces and particles in liquids. In a supersaturated liquid, surface nuclei produce small gas bubbles due to mass transfer of gas or themselves work as weak spots in the liquid that are necessary for a phase change under technically relevant static pressures. Although various theories and models about nuclei and nucleation have found their way into standard literature, there is a lack of experimentally validated theories that describe the process of diffusion-driven nucleation in hydrodynamic cavitation. In order to close this gap we give new theoretical insights into the physics of this nucleation mechanism at technically relevant low supersaturations validated with extensive experimental results. The nucleation rate, the number of produced bubbles per second, is proportional to the supersaturation of the liquid and shows a nonlinear dependence on the shear rate at the surface nucleus. A model for the Strouhal number as dimensionless nucleation rate is derived allowing the estimation of nucleation rates from surface nuclei in hydrodynamic cavitation. The model provides three asymptotes, being a function of Péclet number, Weber number, the supersaturation of the liquid$\unicode[STIX]{x1D701}$and gas solubility$\unicode[STIX]{x1D6EC}$for three different detachment mechanisms,$Sr\propto \unicode[STIX]{x1D701}\unicode[STIX]{x1D6EC}We^{n}Pe^{1/3}$with$n=1/3,3/4,1$. The theoretical findings are in good agreement with experimental results, leading to a new assessment of the role of diffusion in cavitating flows.
Failed Legacies of Colonial Linguistics: Lessons from Tamil Books in French India and French Guiana
Authors: Das Sonia N. 
Published: September 2017

AbstractThe archives of French India and French Guiana, two colonies that were failing by the mid-nineteenth century, elucidate the legacy of colonial linguistics by drawing attention to the ideological and technological natures of colonial printing and the far-reaching and longstanding consequences of the European objectification of Indian vernaculars. Torn between religious, commercial, and imperialist agendas, the French in India both promoted Catholicism and advanced the scientific study of Tamil, the majority language spoken in the colonial headquarters of Pondicherry. There, a little known press operated by the Paris Foreign Missions shipped seventy-one dictionaries, grammars, and theological works printed in Tamil and French to Catholic schools undergoing secularization in French Guiana, a colony with several thousand Tamil indentured laborers. I analyze the books’ lexical, orthographic, and typographical forms, metalinguistic commentaries, publicity tactics, citational practices, and circulation histories by drawing on seldom-discussed materials from the Archives nationales d'outre-mer in Aix-en-Provence, France. I propose a theoretical framework to investigate how technology intersects with the historical relationship between language and colonialism, and argue that printing rivalries contributed to Orientalist knowledge production by institutionalizing semiotic and language ideologies about the nature of “perfectible” and “erroneous” signs. My comparative approach highlights the interdiscursive features of different genres and historical periods of Tamil documentation, and underscores how texts that emerged out of disparate religious and scientific movements questioned the veracity of knowledge and fidelity of sources. Such metalinguistic labor exposed the evolving stances of French Indologists toward Dravidian and Indo-Aryan linguistics and promoted religious and secular interests in educational and immigration policies.
Tyrosine dephosphorylated cortactin downregulates contractility at the epithelial zonula adherens through SRGAP1
Authors: Liang Xuan , Budnar Srikanth , Gupta Shafali , Verma Suzie , Han Siew-Ping , Hill Michelle M. , Daly Roger J. , Parton Robert G. , Hamilton Nicholas A. , Gomez Guillermo A. , Yap Alpha S. 
Published: September 2017

AbstractContractile adherens junctions support cell−cell adhesion, epithelial integrity, and morphogenesis. Much effort has been devoted to understanding how contractility is established; however, less is known about whether contractility can be actively downregulated at junctions nor what function this might serve. We now identify such an inhibitory pathway that is mediated by the cytoskeletal scaffold, cortactin. Mutations of cortactin that prevent its tyrosine phosphorylation downregulate RhoA signaling and compromise the ability of epithelial cells to generate a contractile zonula adherens. This is mediated by the RhoA antagonist, SRGAP1. We further demonstrate that this mechanism is co-opted by hepatocyte growth factor to promote junctional relaxation and motility in epithelial collectives. Together, our findings identify a novel function of cortactin as a regulator of RhoA signaling that can be utilized by morphogenetic regulators for the active downregulation of junctional contractility.
Unraveling the orientation of phosphors doped in organic semiconducting layers
Authors: Moon Chang-Ki , Kim Kwon-Hyeon , Kim Jang-Joo 
Published: September 2017

AbstractEmitting dipole orientation is an important issue of emitting materials in organic light-emitting diodes for an increase of outcoupling efficiency of light. The origin of preferred orientation of emitting dipole of iridium-based heteroleptic phosphorescent dyes doped in organic layers is revealed by simulation of vacuum deposition using molecular dynamics along with quantum mechanical characterization of the phosphors. Consideration of both the electronic transitions in a molecular frame and the orientation of the molecules at the vacuum/molecular film interface allows quantitative analyses of the emitting dipole orientation depending on host molecules and dopant structures. Interactions between the phosphor and nearest host molecules on the surface, minimizing the non-bonded van der Waals and electrostatic interaction energies determines the molecular alignment during the vacuum deposition. Parallel alignment of the main cyclometalating ligands in the molecular complex due to host interactions rather than the ancillary ligand orienting to vacuum leads to the horizontal emitting dipole orientation.
Precise engineering of quantum dot array coupling through their barrier widths
Authors: Piquero-Zulaica Ignacio , Lobo-Checa Jorge , Sadeghi Ali , El-Fattah Zakaria M. Abd , Mitsui Chikahiko , Okamoto Toshihiro , Pawlak Rémy , Meier Tobias , Arnau Andrés , Ortega J. Enrique , Takeya Jun , Goedecker Stefan , Meyer Ernst , Kawai Shigeki 
Published: September 2017

AbstractQuantum dots are known to confine electrons within their structure. Whenever they periodically aggregate into arrays and cooperative interactions arise, novel quantum properties suitable for technological applications show up. Control over the potential barriers existing between neighboring quantum dots is therefore essential to alter their mutual crosstalk. Here we show that precise engineering of the barrier width can be experimentally achieved on surfaces by a single atom substitution in a haloaromatic compound, which in turn tunes the confinement properties through the degree of quantum dot intercoupling. We achieved this by generating self-assembled molecular nanoporous networks that confine the two-dimensional electron gas present at the surface. Indeed, these extended arrays form up on bulk surface and thin silver films alike, maintaining their overall interdot coupling. These findings pave the way to reach full control over two-dimensional electron gases by means of self-assembled molecular networks.
Frequent miRNA-convergent fusion gene events in breast cancer
Authors: Persson Helena , Søkilde Rolf , Häkkinen Jari , Pirona Anna Chiara , Vallon-Christersson Johan , Kvist Anders , Mertens Fredrik , Borg Åke , Mitelman Felix , Höglund Mattias , Rovira Carlos 
Published: September 2017

AbstractStudies of fusion genes have mainly focused on the formation of fusions that result in the production of hybrid proteins or, alternatively, on promoter-switching events that put a gene under the control of aberrant signals. However, gene fusions may also disrupt the transcriptional control of genes that are encoded in introns downstream of the breakpoint. By ignoring structural constraints of the transcribed fusions, we highlight the importance of a largely unexplored function of fusion genes. Here, we show, using breast cancer as an example, that miRNA host genes are specifically enriched in fusion genes and that many different, low-frequency, 5ʹ partners may deregulate the same miRNA irrespective of the coding potential of the fusion transcript. These results indicate that the concept of recurrence, defined by the rate of functionally important aberrations, needs to be revised to encompass convergent fusions that affect a miRNA independently of transcript structure and protein-coding potential.
Predicting Causal Relationships from Biological Data: Applying Automated Causal Discovery on Mass Cytometry Data of Human Immune Cells
Authors: Triantafillou Sofia , Lagani Vincenzo , Heinze-Deml Christina , Schmidt Angelika , Tegner Jesper , Tsamardinos Ioannis 
Published: September 2017

AbstractLearning the causal relationships that define a molecular system allows us to predict how the system will respond to different interventions. Distinguishing causality from mere association typically requires randomized experiments. Methods for automated causal discovery from limited experiments exist, but have so far rarely been tested in systems biology applications. In this work, we apply state-of-the art causal discovery methods on a large collection of public mass cytometry data sets, measuring intra-cellular signaling proteins of the human immune system and their response to several perturbations. We show how different experimental conditions can be used to facilitate causal discovery, and apply two fundamental methods that produce context-specific causal predictions. Causal predictions were reproducible across independent data sets from two different studies, but often disagree with the KEGG pathway databases. Within this context, we discuss the caveats we need to overcome for automated causal discovery to become a part of the routine data analysis in systems biology.
Full hydrodynamic reversibility of the weak dimerization of vancomycin and elucidation of its interaction with VanS monomers at clinical concentration
Authors: Phillips-Jones Mary K. , Lithgo Ryan , Dinu Vlad , Gillis Richard B. , Harding John E. , Adams Gary G. , Harding Stephen E. 
Published: September 2017

AbstractThe reversibility and strength of the previously established dimerization of the important glycopeptide antibiotic vancomycin in four different aqueous solvents (including a medically-used formulation) have been studied using short-column sedimentation equilibrium in the analytical ultracentrifuge and model-independent SEDFIT-MSTAR analysis across a range of loading concentrations. The change in the weight average molar mass Mw with loading concentration was consistent with a monomer-dimer equilibrium. Overlap of data sets of point weight average molar masses Mw(r) versus local concentration c(r) for different loading concentrations demonstrated a completely reversible equilibrium process. At the clinical infusion concentration of 5 mg.mL−1 all glycopeptide is dimerized whilst at 19 µg.mL−1 (a clinical target trough serum concentration), vancomycin was mainly monomeric (<20% dimerized). Analysis of the variation of Mw with loading concentration revealed dissociation constants in the range 25-75 μM, commensurate with a relatively weak association. The effect of two-fold vancomycin (19 µg.mL−1) appears to have no effect on the monomeric enterococcal VanS kinase involved in glycopeptide resistance regulation. Therefore, the 30% increase in sedimentation coefficient of VanS on adding vancomycin observed previously is more likely to be due to a ligand-induced conformational change of VanS to a more compact form rather than a ligand-induced dimerization.
Transformation of ACC into aragonite and the origin of the nanogranular structure of nacre
Authors: Macías-Sánchez Elena , Willinger Marc G. , Pina Carlos M. , Checa Antonio G. 
Published: September 2017

AbstractCurrently a basic tenet in biomineralization is that biominerals grow by accretion of amorphous particles, which are later transformed into the corresponding mineral phase. The globular nanostructure of most biominerals is taken as evidence of this. Nevertheless, little is known as to how the amorphous-to-crystalline transformation takes place. To gain insight into this process, we have made a high-resolution study (by means of transmission electron microscopy and other associated techniques) of immature tablets of nacre of the gastropod Phorcus turbinatus, where the proportion of amorphous calcium carbonate is high. Tablets displayed a characteristic nanoglobular structure, with the nanoglobules consisting of an aragonite core surrounded by amorphous calcium carbonate together with organic macromolecules. The changes in composition from the amorphous to the crystalline phase indicate that there was a higher content of organic molecules within the former phase. Within single tablets, the crystalline cores were largely co-oriented. According to their outlines, the internal transformation front of the tablets took on a complex digitiform shape, with the individual fingers constituting the crystalline cores of nanogranules. We propose that the final nanogranular structure observed is produced during the transformation of ACC into aragonite.
SHP2 Regulates the Osteogenic Fate of Growth Plate Hypertrophic Chondrocytes
Authors: Wang Lijun , Huang Jiahui , Moore Douglas C. , Zuo Chunlin , Wu Qian , Xie Liqin , von der Mark Klaus , Yuan Xin , Chen Di , Warman Matthew L. , Ehrlich Michael G. , Yang Wentian 
Published: September 2017

AbstractTransdifferentiation of hypertrophic chondrocytes into bone-forming osteoblasts has been reported, yet the underlying molecular mechanism remains incompletely understood. SHP2 is an ubiquitously expressed cytoplasmic protein tyrosine phosphatase. SHP2 loss-of-function mutations in chondroid cells are linked to metachondromatosis in humans and mice, suggesting a crucial role for SHP2 in the skeleton. However, the specific role of SHP2 in skeletal cells has not been elucidated. To approach this question, we ablated SHP2 in collagen 2α1(Col2α1)-Cre- and collagen 10α1(Col10α1)-Cre-expressing cells, predominantly proliferating and hypertrophic chondrocytes, using “Cre-loxP”-mediated gene excision. Mice lacking SHP2 in Col2α1-Cre-expressing cells die at mid-gestation. Postnatal SHP2 ablation in the same cell population caused dwarfism, chondrodysplasia and exostoses. In contrast, mice in which SHP2 was ablated in the Col10α1-Cre-expressing cells appeared normal but were osteopenic. Further mechanistic studies revealed that SHP2 exerted its influence partly by regulating the abundance of SOX9 in chondrocytes. Elevated and sustained SOX9 in SHP2-deficient hypertrophic chondrocytes impaired their differentiation to osteoblasts and impaired endochondral ossification. Our study uncovered an important role of SHP2 in bone development and cartilage homeostasis by influencing the osteogenic differentiation of hypertrophic chondrocytes and provided insight into the pathogenesis and potential treatment of skeletal diseases, such as osteopenia and osteoporosis.
Enhanced unbiased sampling of protein dynamics using evolutionary coupling information
Authors: Shamsi Zahra , Moffett Alexander S. , Shukla Diwakar 
Published: September 2017

ABSTRACTOne of the major challenges in atomistic simulations of proteins is efficient sampling of pathways associated with rare conformational transitions. Recent developments in statistical methods for computation of direct evolutionary couplings between amino acids within and across polypeptide chains have allowed for inference of native residue contacts, informing accurate prediction of protein folds and multimeric structures. In this study, we assess the use of distances between evolutionarily coupled residues as natural choices for reaction coordinates which can be incorporated into Markov state model-based adaptive sampling schemes and potentially used to predict not only functional conformations but also pathways of conformational change, protein folding, and protein-protein association. We demonstrate the utility of evolutionary couplings in sampling and predicting activation pathways of the β2-adrenergic receptor (β2-AR), folding of the FiP35 WW domain, and dimerization of the E. coli molybdopterin synthase subunits. We find that the time required for β2-AR activation and folding of the WW domain are greatly diminished using evolutionary couplings-guided adaptive sampling. Additionally, we were able to identify putative molybdopterin synthase association pathways and near-crystal structure complexes from protein-protein association simulations.