bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational methods using genome-wide association studies to predict radiotherapy complications and to identify correlative molecular processes
Authors: Oh Jung Hun , Kerns Sarah , Ostrer Harry , Powell Simon N. , Rosenstein Barry , Deasy Joseph O. 
Published: February 2017

AbstractThe biological cause of clinically observed variability of normal tissue damage following radiotherapy is poorly understood. We hypothesized that machine/statistical learning methods using single nucleotide polymorphism (SNP)-based genome-wide association studies (GWAS) would identify groups of patients of differing complication risk, and furthermore could be used to identify key biological sources of variability. We developed a novel learning algorithm, called pre-conditioned random forest regression (PRFR), to construct polygenic risk models using hundreds of SNPs, thereby capturing genomic features that confer small differential risk. Predictive models were trained and validated on a cohort of 368 prostate cancer patients for two post-radiotherapy clinical endpoints: late rectal bleeding and erectile dysfunction. The proposed method results in better predictive performance compared with existing computational methods. Gene ontology enrichment analysis and protein-protein interaction network analysis are used to identify key biological processes and proteins that were plausible based on other published studies. In conclusion, we confirm that novel machine learning methods can produce large predictive models (hundreds of SNPs), yielding clinically useful risk stratification models, as well as identifying important underlying biological processes in the radiation damage and tissue repair process. The methods are generally applicable to GWAS data and are not specific to radiotherapy endpoints.
Direct mapping of electrical noise sources in molecular wire-based devices
Authors: Cho Duckhyung , Lee Hyungwoo , Shekhar Shashank , Yang Myungjae , Park Jae Yeol , Hong Seunghun 
Published: February 2017

AbstractWe report a noise mapping strategy for the reliable identification and analysis of noise sources in molecular wire junctions. Here, different molecular wires were patterned on a gold substrate, and the current-noise map on the pattern was measured and analyzed, enabling the quantitative study of noise sources in the patterned molecular wires. The frequency spectra of the noise from the molecular wire junctions exhibited characteristic 1/f2 behavior, which was used to identify the electrical signals from molecular wires. This method was applied to analyze the molecular junctions comprising various thiol molecules on a gold substrate, revealing that the noise in the junctions mainly came from the fluctuation of the thiol bonds. Furthermore, we quantitatively compared the frequencies of such bond fluctuations in different molecular wire junctions and identified molecular wires with lower electrical noise, which can provide critical information for designing low-noise molecular electronic devices. Our method provides valuable insights regarding noise phenomena in molecular wires and can be a powerful tool for the development of molecular electronic devices.
Meta-analysis of optical low-coherence reflectometry versus partial coherence interferometry biometry
Authors: Huang Jinhai , McAlinden Colm , Huang Yingying , Wen Daizong , Savini Giacomo , Tu Ruixue , Wang Qinmei 
Published: February 2017

AbstractA meta-analysis to compare ocular biometry measured by optical low-coherence reflectometry (Lenstar LS900; Haag Streit) and partial coherence interferometry (the IOLMaster optical biometer; Carl Zeiss Meditec). A systematic literature search was conducted for articles published up to August 6th 2015 in the Cochrane Library, PubMed, Medline, Embase, China Knowledge Resource Integrated Database and Wanfang Data. A total of 18 studies involving 1921 eyes were included. There were no statistically significant differences in axial length (mean difference [MD] 0 mm; 95% confidence interval (CI) −0.08 to 0.08 mm; p = 0.92), anterior chamber depth (MD 0.02 mm; 95% CI −0.07 to 0.10 mm; p = 0.67), flat keratometry (MD −0.05 D; 95% CI −0.16 to 0.06 D; p = 0.39), steep keratometry (MD −0.09 D; 95% CI −0.20 to 0.03 D; p = 0.13), and mean keratometry (MD −0.15 D; 95% CI −0.30 to 0.00 D; p = 0.05). The white to white distance showed a statistically significant difference (MD −0.14 mm; 95% CI −0.25 to −0.02 mm; p = 0.02). In conclusion, there was no difference in the comparison of AL, ACD and keratometry readings between the Lenstar and IOLMaster. However the WTW distance indicated a statistically significant difference between the two devices. Apart from the WTW distance, measurements for AL, ACD and keratometry readings may be used interchangeability with both devices.
Reducing the Ideal Shear Strengths of ZrB2 by High Efficient Alloying Elements (Ag, Au, Pd and Pt)
Authors: Dai Fu-Zhi , Zhou Yanchun 
Published: February 2017

AbstractActivating the plasticity of ZrB2is a promising approach to improve its key properties for applications in hypersonic vehicles, including high temperature strength and thermal shock resistance. The present work demonstrates that ideal shear strength of ZrB2, which is a good indicator of the critical stress for dislocation nucleation, can be significantly reduced by dissolving of appropriate alloying elements. Analyzing on the bonding nature of ZrB2reveals that choosing alloying elements with low energy valence electrons will prevent electron transferring from alloying element to the electron deficient B-B π orbits, which will reduce the local stability of the region surrounding the alloying element. Under the criterion, elements withdelectrons tending to be full-filled (Ag, Au, Pd and Pt, the full-filled state is associated with low energy level) are selected as promising candidates with their prominent efficiency in reducing ideal shear strengths verified by first-principles calculations. The results provide useful guidelines for further designs of ZrB2based materials, especially for improving their mechanical properties.
An overall and dose-response meta-analysis of red blood cell distribution width and CVD outcomes
Authors: Hou Haifeng , Sun Tao , Li Cheng , Li Yuanmin , Guo Zheng , Wang Wei , Li Dong 
Published: February 2017

AbstractRed blood cell distribution width (RDW) is the coefficient of variation of red blood cell size, considered to be associated with cardiovascular disease (CVD). This study aimed to comprehensively synthesize previous studies on RDW and CVD outcomes through an overall and dose-response meta-analysis. PubMed, Embase and Web of Science were searched systematically for English and Chinese language publications up to November 30, 2015. We extracted data from publications matching our inclusion criteria for calculating pooled hazard ratio (HR), which was used to assess prognostic impact of RDW on CVD. Twenty-seven articles, consisting of 28 studies and 102,689 participants (mean age 63.9 years, 63,703 males/36,846 females, 2,140 gender-unmentioned subjects) were included in the present meta-analysis. The pooled HRs are 1.12 (95% CI = 1.09–1.15) for the association of all-cause mortality (ACM) per 1% increase of RDW, 1.12(95% CI = 1.08–1.17) for major adverse cardiac events (MACEs) per 1% increase of RDW. A dose-response curve relating RDW increase to its effect on CVD outcomes was established (pcurve < 0.001). For every 1-unit increase of RDW, there is an increased risk of occurrence of ACM (pooled HR = 1.03, 95% CI = 1.02–1.04) and MACEs (pooled HR = 1.04, 95% CI = 1.01–1.06). This study indicates RDW may be a prognostic indicator for CVD outcomes.
Comparison of nanoparticular hydroxyapatite pastes of different particle content and size in a novel scapula defect model
Authors: Hruschka Veronika , Tangl Stefan , Ryabenkova Yulia , Heimel Patrick , Barnewitz Dirk , Möbus Günter , Keibl Claudia , Ferguson James , Quadros Paulo , Miller Cheryl , Goodchild Rebecca , Austin Wayne , Redl Heinz , Nau Thomas 
Published: February 2017

AbstractNanocrystalline hydroxyapatite (HA) has good biocompatibility and the potential to support bone formation. It represents a promising alternative to autologous bone grafting, which is considered the current gold standard for the treatment of low weight bearing bone defects. The purpose of this study was to compare three bone substitute pastes of different HA content and particle size with autologous bone and empty defects, at two time points (6 and 12 months) in an ovine scapula drillhole model using micro-CT, histology and histomorphometry evaluation. The nHA-LC (38% HA content) paste supported bone formation with a high defect bridging-rate. Compared to nHA-LC, Ostim® (35% HA content) showed less and smaller particle agglomerates but also a reduced defect bridging-rate due to its fast degradation The highly concentrated nHA-HC paste (48% HA content) formed oversized particle agglomerates which supported the defect bridging but left little space for bone formation in the defect site. Interestingly, the gold standard treatment of the defect site with autologous bone tissue did not improve bone formation or defect bridging compared to the empty control. We concluded that the material resorption and bone formation was highly impacted by the particle-specific agglomeration behaviour in this study.
Encryption key distribution via chaos synchronization
Authors: Keuninckx Lars , Soriano Miguel C. , Fischer Ingo , Mirasso Claudio R. , Nguimdo Romain M. , Van der Sande Guy 
Published: February 2017

AbstractWe present a novel encryption scheme, wherein an encryption key is generated by two distant complex nonlinear units, forced into synchronization by a chaotic driver. The concept is sufficiently generic to be implemented on either photonic, optoelectronic or electronic platforms. The method for generating the key bitstream from the chaotic signals is reconfigurable. Although derived from a deterministic process, the obtained bit series fulfill the randomness conditions as defined by the National Institute of Standards test suite. We demonstrate the feasibility of our concept on an electronic delay oscillator circuit and test the robustness against attacks using a state-of-the-art system identification method.
Whole-Genome Sequencing of a Family with Hereditary Pulmonary Alveolar Proteinosis Identifies a Rare Structural Variant Involving CSF2RA/CRLF2/IL3RA Gene Disruption
Authors: Chiu Chih-Yung , Su Shih-Chi , Fan Wen-Lang , Lai Shen-Hao , Tsai Ming-Han , Chen Shih-Hsiang , Wong Kin-Sun , Chung Wen-Hung 
Published: February 2017

AbstractPulmonary alveolar proteinosis (PAP) is a rare pulmonary disease in which the abnormalities in alveolar surfactant accumulation are caused by impairments of GM-CSF pathway attributing to defects in a variety of genes. However, hereditary PAP is extremely uncommon and a detailed understanding in the genetic inheritance of PAP in a family may provide timely diagnosis, treatment and proper intervention including genetic consultation. Here, we described a comprehensive analysis of genome and gene expression for a family containing one affected child with a diagnosis of PAP and two other healthy siblings. Family-based whole-genome analysis revealed a homozygous deletion that disruptsCSF2RA, CRLF2, andIL3RAgene in the pseudoautosomal region of the X chromosome in the affected child and one of asymptomatic siblings. Further functional pathway analysis of differentially expressed genes in IL-1β-treated peripheral blood mononuclear cells highlighted the insufficiency of immune response in the child with PAP, especially the protection against bacterial infection. Collectively, our results reveal a novel allele as the genetic determinant of a family with PAP and provide insights into variable expressivity and incomplete penetrance of this rare disease, which will be helpful for proper genetic consultation and prompt treatment to avoid mortality and morbidity.
220 GHz high spatial resolution detector with above‐chip mounted dielectric lens
Authors: Shi Junyu , Cui Dasheng , Hao Haidong , Deng Changjiang , Lv Xin 
Published: February 2017

A novel and low‐cost solution to improve the radiation patterns of the on‐chip patch antenna at 220 GHz is proposed. The radiation performances are enhanced by mounting the lens on the patch. The air cavity in the lens not only reduces the focal length, but also provides space for chip integration. The imaging chip and antenna are fabricated and an experimental platform is built. The responsivity and radiation patterns are measured. The 3 dB beamwidths of the with‐lens detector in the E and H planes are 8° and 7°, respectively. Good agreement between the simulated and measured results is obtained.
Microstrip fed planar endfire circularly polarised antenna with enhanced bandwidth
Authors: Yao Yali , Zhang Fushun , Zhang Fan 
Published: February 2017

A wideband planar endfire circularly polarised loop antenna is proposed. The antenna is fed by a microstrip line with a novel ground plane instead of a coaxial probe. The microstrip line part and the loop part generate the vertical polarisation and the horizontal polarisation, respectively. Two stubs added on the loop contribute to the bandwidth improvement. The proposed antenna achieves wide impedance bandwidth (|S11| < −10 dB) and wide 3‐dB axial ratio bandwidth, both of which can cover the frequency range from 8.0 to 12.5 GHz (43.9%).
Photovoltaic performance of an alternating cold–hot method deposited CdSe thin films
Authors: Jiang Yaoyao , Li Yan , Wang Danyu , Mo Deqing , Zhong Fuxin , Gao Yunpeng , Zhu Yinian 
Published: February 2017

Cadmium selenide (CdSe) thin films were prepared on indium tin oxide substrate by an alternating cold–hot method, in which cadmium nitrate solution was used as a cold deposition solution, while sodium selenite and potassium borohydride mixed solution was used as a hot deposition solution. The influences of the preparation conditions such as the concentration of Cd(NO3)2, the number of deposition cycle and the cycle time, on the photoelectric performance of the sample under simulated sunlight were explored. The results show that the CdSe thin film prepared under the reaction conditions of 0.06 mol/l Cd(NO3)2 at the tenth deposition cycle (30 s per cycle) reaches the highest photovoltage of 0.285 V. Under the simulated solar illumination, the open‐circuit voltage and short‐circuit currents are 0.419 V and 5.57 mA/cm2, respectively. X‐ray diffraction indicates that the strongest diffraction peak at 42.215° of the (111) crystal plane is corresponding to 15.15 nm CdSe nanocrystals. Scanning electron microscopy observation shows that the thickness of the CdSe film is about 200 nm and the size of the spherical and uniformly dispersed nanocrystals is around 50 nm.
Should We Resect Hoffa's Fat Pad during Total Knee Replacement?
Authors: Yewlett Alun , Trickett Ryan , Forster Mark , Ghandour Adel , Sellars Hannah 
Published: February 2017

AbstractResection of Hoffa's fat pad during total knee arthroplasty is sometimes performed to improve access and view. Opponents of this technique argue that sacrificing the fat pad potentially compromises blood supply to the patellar tendon and it can subsequently shorten. Our objective was to identify any difference in the Insall-Salvati ratio of knees undergoing total knee arthroplasty between a cohort that had Hoffa's fat pad preserved and the one that had Hoffa's fat pad completely excised. The total knee arthroplasties by two surgeons at our institution were reviewed over a 3-year period. Surgeon A routinely preserves the fat pad and surgeon B routinely excises the fat pad. Radiographs preoperatively, immediately postoperatively, and at a minimum of 1-year follow up were analyzed for the Insall-Salvati ratio. A total of 161 knees were reviewed, 65 in the preserved group and 96 in the excised group with a mean age of 67 and 70 years, respectively. The mean preoperative Insall-Salvati ratio for the preserved group was 1.12 (±0.145) and excised group 1.16 (±0.168) (p = 0.094). The mean immediate postoperative Insall-Salvati ratio for the preserved group was 1.10 (±0.154) and for excised group 1.18 (±0.194). The difference in Insall-Salvati ratio from preoperative to the immediate postoperative period in the preserved group compared with the excised group demonstrated a significant difference (p = 0.010). However, the change of Insall-Salvati ratio at 1 year did not significantly differ between the groups (p = 0.059). There does not appear to be any difference in the Insall-Salvati ratios of both groups at 1 year's follow up; therefore, this study radiologically at least supports the use of either technique.
Clinical Efficacy and Safety of Negative-Pressure Wound Therapy on Flaps: A Systematic Review
Authors: Yu Panxi , Yu Nanze , Yang Xiaonan , Jin Xiaolei , Lu Haibin , Qi Zuoliang 
Published: February 2017

Background Although flap transfer is a popular reconstructive procedure with a high success rate, it is associated with a high complication rate and low salvage rate. During the past decade, negative-pressure wound therapy (NPWT) has been increasingly applied to facilitate flap transfer and salvage flaps threatened by complications. It has achieved some success, but its efficacy and safety remain controversial because of the limited number of reports and lack of systematic reviews.
Methods English-language articles describing the application of NPWT on flaps were screened using predetermined inclusion and exclusion criteria. The articles were summarized and divided into groups based on the purpose of NPWT application. The complication rate, success rate, and salvage rate were obtained.
Results Among the 3,395 articles searched, 16 articles describing 137 flaps were eligible. NPWT was applied on 105 (76.4%) newly transferred flaps to facilitate flap attachment and on 32 (23.4%) complication-threatened flaps to relieve flap infection and venous congestion. In total, complications developed in six flaps, three of which were lost; thus, the complication rate was 5.7% (6/105) and the success rate was 97.1% (102/105). Only 1 of the 32 threatened flaps was not successfully salvaged; thus, the salvage rate was 96.9% (31/32).
Conclusion NPWT may facilitate flap transfer with few side effects and help to rescue flaps threatened by infection and venous congestion with a high salvage rate. Further studies are needed to test the safety of NPWT application on flaps with arterial compromise.
Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations
Authors: Moraca Federica , Amato Jussara , Ortuso Francesco , Artese Anna , Pagano Bruno , Novellino Ettore , Alcaro Stefano , Parrinello Michele , Limongelli Vittorio 
Published: February 2017

Significance
A thorough characterization of the binding interaction between a drug and its molecular target is fundamental to successfully lead drug design. We demonstrate that this characterization is also possible using the recently developed method of funnel-metadynamics (FM), here applied to investigate the binding of berberine to DNA G-quadruplex. We computed a quantitatively well-characterized free-energy landscape that allows identifying two low-energy ligand binding modes and the presence of higher energy prebinding states. We validated the accuracy of our calculations by steady-state fluorescence experiments. The good agreement between the theoretical and experimental binding free-energy value demonstrates that FM is a most reliable method to study ligand/DNA interaction.
Inflammation and Arterial Stiffness in Chronic Kidney Disease: Findings From the CRIC Study
Authors: Peyster Eliot , Chen Jing , Feldman Harold I. , Go Alan S. , Gupta Jayanta , Mitra Nandita , Pan Qiang , Porter Anna , Rahman Mahboob , Raj Dominic , Reilly Muredach , Wing Maria R. , Yang Wei , Townsend Raymond R. ,   on behalf of the CRIC Study Investigators
Published: February 2017

Abstract

BACKGROUND
Chronic kidney disease (CKD) and arterial stiffness are associated with increased cardiovascular morbidity and mortality. Inflammation is proposed to have a role in the development of arterial stiffness, and CKD is recognized as a proinflammatory state. Arterial stiffness is increased in CKD, and cross-sectional data has suggested a link between increased inflammatory markers in CKD and higher measures of arterial stiffness. However, no large scale investigations have examined the impact of inflammation on the progression of arterial stiffness in CKD.

METHODS
We performed baseline assessments of 5 inflammatory markers in 3,939 participants from the chronic renal insufficiency cohort (CRIC), along with serial measurements of arterial stiffness at 0, 2, and 4 years of follow-up.

RESULTS
A total of 2,933 participants completed each of the follow-up stiffness measures. In cross-sectional analysis at enrollment, significant associations with at least 2 measures of stiffness were observed for fibrinogen, interleukin-6, high-sensitivity C-reactive protein, proteinuria, and composite inflammation score after adjustment for confounders. In longitudinal analyses, there were few meaningful correlations between baseline levels of inflammation and changes in metrics of arterial stiffness over time.

CONCLUSION
In a large cohort of CKD participants, we observed multiple significant correlations between initial markers of inflammation and metrics of arterial stiffness, but baseline inflammation did not predict changes in arterial stiffness over time. While well-described biologic mechanisms provide the basis for our understanding of the cross-sectional results, continued efforts to design longitudinal studies are necessary to fully elucidate the relationship between chronic inflammation and arterial stiffening.
Discriminating the reaction types of plant type III polyketide synthases
Authors: Shimizu Yugo , Ogata Hiroyuki , Goto Susumu 
Published: February 2017

Abstract

Motivation
Functional prediction of paralogs is challenging in bioinformatics because of rapid functional diversification after gene duplication events combined with parallel acquisitions of similar functions by different paralogs. Plant type III polyketide synthases (PKSs), producing various secondary metabolites, represent a paralogous family that has undergone gene duplication and functional alteration. Currently, there is no computational method available for the functional prediction of type III PKSs.

Results
We developed a plant type III PKS reaction predictor, pPAP, based on the recently proposed classification of type III PKSs. pPAP combines two kinds of similarity measures: one calculated by profile hidden Markov models (pHMMs) built from functionally and structurally important partial sequence regions, and the other based on mutual information between residue positions. pPAP targets PKSs acting on ring-type starter substrates, and classifies their functions into four reaction types. The pHMM approach discriminated two reaction types with high accuracy (97.5%, 39/40), but its accuracy decreased when discriminating three reaction types (87.8%, 43/49). When combined with a correlation-based approach, all 49 PKSs were correctly discriminated, and pPAP was still highly accurate (91.4%, 64/70) even after adding other reaction types. These results suggest pPAP, which is based on linear discriminant analyses of similarity measures, is effective for plant type III PKS function prediction.

Availability and Implementation
pPAP is freely available at ftp://ftp.genome.jp/pub/tools/ppap/

Supplementary information
Supplementary data are available at Bioinformatics online.