bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple jig for the anti-parallel alignment of linacs’ lasers
Authors: Okkalides Demetrios 
Published: January 2016

AbstractBackgroundDespite crossing at the isocentre, misaligned laser beams may cause significant positioning problems.PurposeThe jig proposed here is to be used in addition to the quality assurance procedures employed with linacs and deals with possible misalignments of transverse lasers.Materials and methodsIt is an inverted T construction with a two-sided rectangular, slightly transparent mirror set vertical on a piece of glass serving as its base. The device is carried by a horizontally set spirit-level surface and placed on the couch-top so that the sagittal laser passes through the vertical mirror’s plane. Then the therapy couch is translated along the Y direction until a laser beam shines on the corresponding side of the semi-transparent mirror. This spot is marked and is normally the linac’s isocentre set through an independent procedure employing a rotating plate. If the laser had been set properly, then its beam should be reflecting back on its source. If not, the alignment can be corrected by rotating and/or translating the laser holder until it does that. At the same time, it should be ensured that the beam does not wander away from the isocentre spot on the mirror. When both are achieved, the beam ends up perpendicular to the linac’s axis of rotation, while passing through the isocentre. The procedure can be repeated for the opposite laser.ConclusionThe jig was simple to construct and has been found quite useful in practice. The accuracy of patient positioning will be restricted only by the size of the laser beam’s cross-section.
Transparent superwetting nanofilms with enhanced durability at model physiological condition
Authors: Hwangbo Sunghee , Heo Jiwoong , Lin Xiangde , Choi Moonhyun , Hong Jinkee 
Published: January 2016

AbstractThere have been many studies on superwetting surfaces owing to the variety of their potential applications. There are some drawbacks to developing these films for biomedical applications, such as the fragility of the microscopic roughness feature that is vital to ensure superwettability. But, there are still only a few studies that have shown an enhanced durability of nanoscale superwetting films at certain extreme environment. In this study, we fabricated intrinsically stable superwetting films using the organosilicate based layer-by-layer (LbL) self-assembly method in order to control nano-sized roughness of the multilayer structures. In order to develop mechanically and chemically robust surfaces, we successfully introduced polymeric silsesquioxane as a building block for LbL assembly with desired fashion. Even in the case that the superhydrophobic outer layers were damaged, the films maintained their superhydrophobicity because of the hydrophobic nature of their inner layers. As a result, we successfully fabricated superwetting nano-films and evaluated their robustness and stability.
Architecture and Function of Mechanosensitive Membrane Protein Lattices
Authors: Kahraman Osman , Koch Peter D. , Klug William S. , Haselwandter Christoph A. 
Published: January 2016

AbstractExperiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms yielding supramolecular organization and collective function of membrane proteins remain largely unknown. Here we show that bilayer-mediated elastic interactions between membrane proteins can yield regular and distinctive lattice architectures of protein clusters and may provide a link between lattice architecture and lattice function. Using the mechanosensitive channel of large conductance (MscL) as a model system, we obtain relations between the shape of MscL and the supramolecular architecture of MscL lattices. We predict that the tetrameric and pentameric MscL symmetries observed in previous structural studies yield distinct lattice architectures of MscL clusters and that, in turn, these distinct MscL lattice architectures yield distinct lattice activation barriers. Our results suggest general physical mechanisms linking protein symmetry, the lattice architecture of membrane protein clusters and the collective function of membrane protein lattices.
Calcium-chelating alizarin and other anthraquinones inhibit biofilm formation and the hemolytic activity of Staphylococcus aureus
Authors: Lee Jin-Hyung , Kim Yong-Guy , Yong Ryu Shi , Lee Jintae 
Published: January 2016

AbstractStaphylococcal biofilms are problematic and play a critical role in the persistence of chronic infections because of their abilities to tolerate antimicrobial agents. Thus, the inhibitions of biofilm formation and/or toxin production are viewed as alternative means of controlling Staphylococcus aureus infections. Here, the antibiofilm activities of 560 purified phytochemicals were examined. Alizarin at 10 μg/ml was found to efficiently inhibit biofilm formation by three S. aureus strains and a Staphylococcus epidermidis strain. In addition, two other anthraquinones purpurin and quinalizarin were found to have antibiofilm activity. Binding of Ca2+ by alizarin decreased S. aureus biofilm formation and a calcium-specific chelating agent suppressed the effect of calcium. These three anthraquinones also markedly inhibited the hemolytic activity of S. aureus and in-line with their antibiofilm activities, increased cell aggregation. A chemical structure-activity relationship study revealed that two hydroxyl units at the C-1 and C-2 positions of anthraquinone play important roles in antibiofilm and anti-hemolytic activities. Transcriptional analyses showed that alizarin repressed the α-hemolysin hla gene, biofilm-related genes (psmα, rbf and spa) and modulated the expressions of cid/lrg genes (the holin/antiholin system). These findings suggest anthraquinones, especially alizarin, are potentially useful for controlling biofilm formation and the virulence of S. aureus.
Effect of spatial constraints on Hardy-Weinberg equilibrium
Authors: Chen Yi-Shin , Su Yi-Cheng , Pan Wei 
Published: January 2016

AbstractPanmixia is a key issue in maintaining genetic diversity, which facilitates evolutionary potential during environmental changes. Additionally, conservation biologists suggest the importance of avoiding small or subdivided populations, which are prone to losing genetic diversity. In this paper, computer simulations were performed to the genetic drift of neutral alleles in random mating populations with or without spatial constraints by randomly choosing a mate among the closest neighbours. The results demonstrated that the number of generations required for the neutral allele to become homozygous (Th) varied proportionally to the population size and also strongly correlated with spatial constraints. The average Thfor populations of the same size with spatial constraints was approximately one-and-a-half times longer than without constraints. With spatial constraints, homozygous population clusters formed, which reduced local diversity but preserved global diversity. Therefore, panmixia might be harmful in preserving the genetic diversity of an entire population. The results also suggested that the gene flow or gene exchange among the subdivided populations must be carefully processed to restrict diseases transmission or death during transportation and to monitor the genetic diversity. The application of this concept to similar systems, such as information transfer among peers, is also discussed.
Purification and Partial Characterization of a Novel Bacteriocin Synthesized by Lactobacillus paracasei HD1-7 Isolated from Chinese Sauerkraut Juice
Authors: Ge Jingping , Sun Yanyang , Xin Xing , Wang Ying , Ping Wenxiang 
Published: January 2016

AbstractBacteriocins have antimicrobial activities against food-spoiling bacteria and food-borne pathogens. Paracin 1.7, a bacteriocin synthesized by Lactobacillus paracasei HD1-7 isolated from Chinese sauerkraut juice, was studied. Following partial purification with ammonium sulfate precipitation, CM Sepharose Fast Flow and Sephadex G-10 chromatography, the molecular weight of Paracin 1.7 was about 10 kDa based on Tricine-SDS-PAGE results. A 2.87 fold purified bacteriocin was produced, reaching a final yield of 39.93% and the specific activity of 1.56 × 103 AU/mg. The N-terminal amino acid sequence of Paracin 1.7 was VSNTFFA and the LC/LTQ results revealed that the N-terminal amino acid sequence was similar to that of ABC-type oligopeptide transport system protein and N-acetylmuramoyl-L-alanine amidase. Paracin 1.7 was sensitive to protease K, had antimicrobial activities at a broad pH range (3.0–8.0) and was heat resistant (121 °C for 20 min). Paracin 1.7 from Lactobacillus paracasei HD1-7 is a novel bacteriocin that has potential applications in food preservation.
The LMO2 oncogene regulates DNA replication in hematopoietic cells
Authors: Sincennes Marie-Claude , Humbert Magali , Grondin Benoît , Lisi Véronique , Veiga Diogo F. T. , Haman André , Cazaux Christophe , Mashtalir Nazar , Affar EL Bachir , Verreault Alain , Hoang Trang 
Published: January 2016

Significance
Understanding how cell cycle and cell differentiation are coordinated during normal hematopoiesis will reveal molecular insights in leukemogenesis. LIM-only 2 (LMO2) is a transcriptional regulator that controls the erythroid lineage via activation of an erythroid-specific gene expression program. Here, we uncover an unexpected function for LMO2 in controlling DNA replication via protein–protein interactions with essential DNA replication enzymes. To our knowledge, this work provides the first evidence for a nontranscriptional function of LMO2 that drives the cell cycle at the expense of differentiation in the erythroid lineage and in thymocytes when misexpressed following genetic alterations. We propose that the nontranscriptional control of DNA replication uncovered here for LMO2 may be a more common function of oncogenic transcription factors than previously appreciated.
The Boston Children’s Hospital Academy: Development and Initial Assessment of a Hospital-Based Teaching Academy
Authors: Gooding Holly C. , McCarty Caitlin , Millson Rebecca , Jiang Hungyu , Armstrong Elizabeth , Leichtner Alan M. 
Published: January 2016

Problem
Medical education academies play an important role in the recognition and career advancement of educators. However, hospital-based clinical faculty have unique professional development needs that may not be met by medical-school-based academies.

Approach
The Boston Children’s Hospital Academy was founded in 2008 to serve the needs of its clinician–educators. It was open to junior faculty scholars and to senior faculty scholars and mentors, including interprofessional educators. To maintain membership, individuals must propose and work toward an education project or serve as a project mentor. In 2012, a survey was sent to all members, and annual project reports were reviewed to assess the academy’s impact.

Outcomes
Sixty-five members completed the survey. The majority agreed that the academy created a community of educators, provided opportunities for networking and scholarship, contributed to their personal identity as an educator, and led to recognition by their chief. Projects addressed curriculum development, faculty development, learner assessment, program assessment, and resource development. They largely focused on graduate medical education and on patient safety and quality. During their tenure in the academy (mean length of membership = 2.4 years), members produced an average of 4.4 education presentations and 1.9 education publications, and 11 members were promoted.

Next Steps
A hospital-based academy provides opportunities for interprofessional faculty development. Next steps include increasing interprofessional membership, wider dissemination of members’ successes, better integration with the hospital’s mission, specifically regarding graduate medical education and patient safety, and additional evaluation of the academy’s impact on project completion and members’ accomplishments.
The Cost of Ménière’s Disease: A Novel Multisource Approach
Authors: Tyrrell Jessica , Whinney David J. , Taylor Timothy 
Published: January 2016

Objectives:
To estimate the annual cost of Ménière’s disease and the cost per person in the UK population and to investigate the direct and indirect costs of the condition.

Design:
The authors utilized a multidata approach to provide the first estimate of the cost of Ménière’s. Data from the UK Biobank (a study of 500,000 individuals collected between 2007 and 2012), the Hospital Episode Statistics (data on all hospital admissions in England from 2008 to 2012) and the UK Ménière’s Society (2014) were used to estimate the cost of Ménière’s. Cases were self-reported in the UK Biobank and UK Ménière’s Society, within the Hospital Episode Statistics cases were clinician diagnosed. The authors estimated the direct and indirect costs of the condition, using count data to represent numbers of individuals reporting specific treatments, operations etc. and basic statistical analyses (χ2 tests, linear and logistic regression) to compare cases and controls in the UK Biobank.

Results:
Ménière’s was estimated to cost between £541.30 million and £608.70 million annually (equivalent to US $829.9 to $934.2 million), equating to £3,341 to £3,757 ($5112 to $5748) per person per annum. The indirect costs were substantial, with loss of earnings contributing to over £400 million per annum.

Conclusions:
For the first time, the authors were able to estimate the economic burden of Ménière’s disease. In the UK, the annual cost of this condition is substantial. Further research is required to develop cost–effective treatments and management strategies for Ménière’s to reduce the economic burden of the disease. These findings should be interpreted with caution due to the uncertainties inherent in the analysis.
Adjustment for Variable Adherence Under Hierarchical Structure
Authors: Holmes Tyson H. , Zulman Donna M. , Kushida Clete A. 
Published: January 2016

Background:
Variable adherence to assigned conditions is common in randomized clinical trials.

Objectives:
A generalized modeling framework under longitudinal data structures is proposed for regression estimation of the causal effect of variable adherence on outcome, with emphasis upon adjustment for unobserved confounders.

Research Design:
A nonlinear, nonparametric random-coefficients modeling approach is described. Estimates of local average treatment effects among compliers can be obtained simultaneously for all assigned conditions to which participants are randomly assigned within the trial. Two techniques are combined to address time-varying and time-invariant unobserved confounding—residual inclusion and nonparametric random-coefficients modeling. Together these yield a compound, 2-stage residual inclusion, instrumental variables model.

Subjects:
The proposed method is illustrated through a set of simulation studies to examine small-sample bias and in application to neurocognitive outcome data from a large, multicenter, randomized clinical trial in sleep medicine for continuous positive airway pressure treatment of obstructive sleep apnea.

Results:
Results of simulation studies indicate that, relative to a standard comparator, the proposed estimator reduces bias in estimates of the causal effect of variable adherence. Bias reductions were greatest at higher levels of residual variance and when confounders were time varying.

Conclusions:
The proposed modeling framework is flexible in the distributions of outcomes that can be modeled, applicable to repeated measures longitudinal structures, and provides effective reduction of bias due to unobserved confounders.
Winner’s curse correction and variable thresholding improve performance of polygenic risk modeling based on genome-wide association study summary-level data
Authors: Shi Jianxin , Park Ju-Hyun , Duan Jubao , Berndt Sonja , Moy Winton , Yu Kai , Song Lei , Wheeler William , Hua Xing , Silverman Debra , Garcia-Closas Montserrat , Hsiung Chao Agnes , Figueroa Jonine D , Cortessis Victoria K , Malats Núria , Karagas Margaret R , Vineis Paolo , Chang I-Shou , Lin Dongxin , Zhou Baosen , Seow Adeline , Matsuo Keitaro , Hong Yun-Chul , Caporaso Neil E. , Wolpin Brian , Jacobs Eric , Petersen Gloria , Klein Alison P. , Li Donghui , Risch Harvey , Sanders Alan R. , Hsu Li , Schoen Robert E. , Brenner Hermann , Stolzenberg-Solomon Rachael , Gejman Pablo , Lan Qing , Rothman Nathaniel , Amundadottir Laufey T. , Landi Maria Teresa , Levinson Douglas F. , Chanock Stephen J. , Chatterjee Nilanjan ,   MGS (Molecular Genetics of Schizophrenia) GWAS Consortium,   GECCO (The Genetics and Epidemiology of Colorectal Cancer Consortium),   The GAME-ON/TRICL (Transdisciplinary Research in Cancer of the Lung) GWAS Consortium,   PRACTICAL (PRostate cancer AssoCiation group To Investigate Cancer Associated aLterations) Consortium,   PanScan and PanC4 Consortium,   The GAMEON/ELLIPSE Consortium
Published: January 2016

AbstractRecent heritability analyses have indicated that genome-wide association studies (GWAS) have the potential to improve genetic risk prediction for complex diseases based on polygenic risk score (PRS), a simple modelling technique that can be implemented using summary-level data from the discovery samples. We herein propose modifications to improve the performance of PRS. We introduce threshold-dependent winner’s-curse adjustments for marginal association coefficients that are used to weight the SNPs in PRS. Further, as a way to incorporate external functional/annotation knowledge that could identify subsets of SNPs highly enriched for associations, we propose variable thresholds for SNPs selection. We applied our methods to GWAS summary-level data of 14 complex diseases. Across all diseases, a simple winner’s curse correction uniformly led to enhancement of performance of the models, whereas incorporation of functional SNPs was beneficial only for selected diseases. Compared to the standard PRS algorithm, the proposed methods in combination led to notable gain in efficiency (25-50% increase in the prediction R2) for 5 of 14 diseases. As an example, for GWAS of type 2 diabetes, winner’s curse correction improved prediction R2from 2.29% based on the standard PRS to 3.10% (P=0.0017) and incorporating functional annotation data further improved R2to 3.53% (P=2χ10-5). Our simulation studies illustrate why differential treatment of certain categories of functional SNPs, even when shown to be highly enriched for GWAS-heritability, does not lead to proportionate improvement in genetic risk-prediction because of non-uniform linkage disequilibrium structure.
Random recurrent networks near criticality capture the broadband power distribution of human ECoG dynamics
Authors: Chaudhuri Rishidev , He Biyu J. , Wang Xiao-Jing 
Published: January 2016

AbstractThe power spectrum of brain electric field potential recordings is dominated by an arrhythmic broadband signal but a mechanistic account of its underlying neural network dynamics is lacking. Here we show how the broadband power spectrum of field potential recordings can be explained by a simple random network of nodes near criticality. Such a recurrent network produces activity with a combination of a fast and a slow autocorrelation time constant, with the fast mode corresponding to local dynamics and the slow mode resulting from recurrent excitatory connections across the network. These modes are combined to produce a power spectrum similar to that observed in human intracranial EEG (i.e., electrocorticography, ECoG) recordings. Moreover, such a network naturally converts input correlations across nodes into temporal autocorrelation of the network activity. Consequently, increased independence between nodes results in a reduction in low-frequency power, which offers a possible explanation for observed changes in ECoG power spectra during task performance. Lastly, changes in network coupling produce changes in network activity power spectra reminiscent of those seen in human ECoG recordings across different arousal states. This model thus links macroscopic features of the empirical ECoG power spectrum to a parsimonious underlying network structure and proposes potential mechanisms for changes in ECoG power spectra observed across behavioral and arousal states. This provides a computational framework within which to generate and test hypotheses about the cellular and network mechanisms underlying whole brain electrical dynamics, their variations across behavioral states as well as abnormalities associated with brain diseases.
Analysis of Two-State Folding Using Parabolic Approximation I: Hypothesis
Authors: Sade Robert S. 
Published: January 2016

ABSTRACTA model which treats the denatured and native conformers of spontaneously-folding fixed two-state systems as being confined to harmonic Gibbs energy-wells has been developed. Within the assumptions of this model the Gibbs energy functions of the denatured (DSE) and the native state (NSE) ensembles are described by parabolas, with the mean length of the reaction coordinate (RC) being given by the temperature-invariant denaturantmvalue. Consequently, the ensemble-averaged position of the transition state ensemble (TSE) along the RC, and the ensemble-averaged Gibbs energy of the TSE are determined by the intersection of the DSE and the NSE-parabolas. The equations derived enable equilibrium stability and the rate constants to be rationalized in terms of the mean and the variance of the Gaussian distribution of the solvent accessible surface area of the conformers in the DSE and the NSE. The implications of this model for protein folding are discussed.
Incentive contract or tenure reform? Understanding the transition of forest resources management in China
Authors: Wei Jiegen , He Haoran 
Published: January 2016

Purpose
– China’s government has been facing a trade-off in choosing between tenure reform and forest concessions to manage forest resources. The purpose of this paper is to investigate how the government’s policy choices can be affected by environmental benefits and the economic value of forests.

Design/methodology/approach
– We build a simple theoretical model and employ province-level data.

Findings
– The results show that the government will allocate less forestland to local people if environmental concerns are more important and privatize less forest if the economic benefits from forest are higher.

Social implications
– Therefore, the transformation of forest management policies reflects not only the government’s own preferences but also its gradual adjustment to the changing market and institutional environment.

Originality/value
– The present paper provides a regulation approach that complements the growing literature on forest resource management.