bluuebunny/crossref_metadata_2025_split huggingface dataset:
A finite mixture model for X‐chromosome association with an emphasis on microbiome data analysis
Authors: Espin‐Garcia Osvaldo , Croitoru Kenneth , Xu Wei 
Published: January 2019

AbstractAnalysis of the X chromosome has been largely neglected in genetic studies mainly because of complex underlying biological mechanisms. On the other hand, the study of human microbiome data (typically over‐dispersed counts with an excess of zeros) has generated great interest recently because of advancements in next‐generation sequencing technologies. We propose a novel approach to infer the association between host genetic variants in the X‐chromosome and microbiome data. The method accounts for random X‐chromosome inactivation (XCI), skewed (or nonrandom) XCI (XCI‐S), and escape of XCI (XCI‐E). The inference is performed through a finite mixture model (FMM), in which an indicator variable denoting the “true” biological mechanism is treated as missing data. An expectation‐maximization algorithm on zero‐inflated and two‐part models is implemented to estimate genetic effects. We investigate the performance of the FMM along with strategies that assume XCI and XCI‐E mechanisms for all subjects compared with alternative approaches. Briefly, an XCI mechanism codes males’ genotypes as homozygous females, whereas under XCI‐E, males are treated as heterozygous females. By comprehensive simulations, we evaluate tests of the hypothesis under a computationally efficient score statistic. In summary, the FMM renders reduced bias and commensurate power compared to XCI, XCI‐E, and alternative strategies while maintaining adequate Type 1 error control. The proposed method has far‐reaching applications. In particular, we illustrate its usage on a large‐scale human microbiome study, the Genetic, Environmental and Microbial (GEM) project, to test for the genetic association on the X chromosome.
Identification of a novel biomarker for pyridoxine‐dependent epilepsy: Implications for newborn screening
Authors: Wempe Michael F. , Kumar Amit , Kumar Vijay , Choi Yu J. , Swanson Michael A. , Friederich Marisa W. , Hyland Keith , Yue Wyatt W. , Van Hove Johan L. K. , Coughlin Curtis R. 
Published: January 2019

AbstractPyridoxine‐dependent epilepsy (PDE) is often characterized as an early onset epileptic encephalopathy with dramatic clinical improvement following pyridoxine supplementation. Unfortunately, not all patients present with classic neonatal seizures or respond to an initial pyridoxine trial, which can result in the under diagnosis of this treatable disorder. Restriction of lysine intake and transport is associated with improved neurologic outcomes, although treatment should be started in the first year of life to be effective. Because of the documented diagnostic delay and benefit of early treatment, we aimed to develop a newborn screening method for PDE. Previous studies have demonstrated the accumulation of Δ1‐piperideine‐6‐carboxylate and α‐aminoadipic semialdehyde in individuals with PDE, although these metabolites are unstable at room temperature (RT) limiting their utility for newborn screening. As a result, we sought to identify a biomarker that could be applied to current newborn screening paradigms. We identified a novel metabolite, 6‐oxo‐pipecolate (6‐oxo‐PIP), which accumulates in substantial amounts in blood, plasma, urine, and cerebral spinal fluid of individuals with PDE. Using a stable isotope‐labeled internal standard, we developed a nonderivatized liquid chromatography tandem mass spectrometry‐based method to quantify 6‐oxo‐PIP. This method replicates the analytical techniques used in many laboratories and could be used with few modifications in newborn screening programs. Furthermore, 6‐oxo‐PIP was measurable in urine for 4 months even when stored at RT. Herein, we report a novel biomarker for PDE that is stable at RT and can be quantified using current newborn screening techniques.
Predictive value of the induction test with atrial burst pacing with regard to long‐term recurrence after ablation in persistent atrial fibrillation
Authors: Kawai Shunsuke , Mukai Yasushi , Inoue Shujiro , Yakabe Daisuke , Nagaoka Kazuhiro , Sakamoto Kazuo , Takase Susumu , Chishaki Akiko , Tsutsui Hiroyuki 
Published: January 2019

AbstractBackgroundInduction test of atrial fibrillation (AF) is one of endpoint measures in catheter ablation (CA). However, its predictive value in long‐term outcome remains controversial.MethodsNinety‐eight patients (61 years, 77 males) with persistent AF who underwent pulmonary vein antrum isolation‐based CA were retrospectively analyzed. We determined whether inducibility of AF/atrial tachyarrhythmias (AT) by atrial burst pacing at the end of CA and other characteristics were associated with the recurrence of AF/AT. Atrial burst pacing was performed with 30‐beat from the coronary sinus; increasing from 240 to 320 ppm. Inducibility was defined as AF/AT lasting ≥5 minutes following atrial burst pacing.ResultsAF/AT was induced in 50 patients (51%). During 1 year of follow‐up, 71 patients (72.4%) had no recurrence of AF/AT. A logistic regression analysis showed that female gender (OR 3.8; P = 0.02), multiple sessions (OR 3.5; P = 0.02), and early recurrence of AF/AT (OR 5.3; P = 0.004) were associated with clinical recurrence. AF/AT Inducibility was not associated with clinical recurrence (P = 0.65). A subanalysis in patients with enlarged LA (LA diameter ≥45 mm, n = 40) showed that AF/AT inducibility was associated with recurrence (OR 8.1; P = 0.04). The positive and negative predictive values of AF/AT inducibility for AF/AT recurrence were 41 and 89%, respectively. Negative predictive value was increased to 92.3% when the inducibility was defined as AF/AT of ≥30 seconds following atrial burst pacing.ConclusionsAF/AT inducibility cannot predict long‐term clinical recurrence in patients with persistent AF. However, it may have a prognostic value especially in patients with enlarged LA.
Counterion‐Mediated Self‐Assembly of Ion‐Containing Block Copolymers on the Basis of the Hofmeister Series
Authors: Zhong Jiaxing , Luo Haipeng , Tang Qiuju , Lei Zhentao , Tong Zaizai 
Published: January 2019

AbstractA Cl− and I− ion‐containing amphiphilic diblock copolymer [PEO‐b‐P(qVBC‐co‐St)], IBCP, which comprises the poly(ethylene oxide) block and poly(quaternized 4‐vinylbenzyl chloride‐co‐styrene) is prepared by sequence reactions. Then the counterion‐mediated self‐assembly behavior in aqueous solution is investigated in detail. The hydrophilicity of anion containing units (qVBC) is controlled by the nature of the different counterions after ion exchange, which is crucial in regulating the self‐assembly process. The addition of Br−, I−, and SCN− counterions (based on the Hofmeister series) results in the formation of tighter ion‐pairs with cations (i.e., more hydrophobic as the qVBC units), which triggers spheres to vesicles, micro‐meter long cylinders and “branched wormlike” aggregates, respectively. Moreover, addition of different amounts of Cl− also causes morphological transition from spheres to long cylinders. And this morphological transition is totally reversible after removing additional Cl−. The adhesive collisions of spherical particles may contribute to the observed sphere‐to‐cylinder morphological transition.
ETA‐m‐PAN and its Composite Membrane with High Performance Prepared by In Situ Modification/NIPS Principle
Authors: Qin Yang , Wang Yi‐Xing , Yang Hu , Xu Zhen‐liang 
Published: January 2019

AbstractEthanolamine‐modified polyacrylonitrile (ETA‐m‐PAN) membrane is prepared by in situ modification integrated with a nonsolvent‐induced phase separation method for the first time. The results reveal that both the morphology and the separation performance of the modified membrane change greatly with condition parameters. The membrane formation mechanism is carefully investigated, which is related to the change in the molecular structure and hydrophilic property of ETA‐m‐PAN. The cross‐linked structure leads to the formation of ETA‐m‐PAN spongy membrane. The optimized condition parameters are determined by permeability‐selectivity analysis. Furthermore, the composite membrane with ETA‐m‐PAN as the selective layer is prepared by a dual‐casting method. The obtained membrane shows a good property, flux of 650L m−2 h−1 bar−1, 82% BSA rejection, and 84% water flux recovery ratio. This work demonstrates the great potential of this integrated method for new membrane preparation.
Campylobacter spp. and bacteriophages from broiler chickens: Characterization of antibiotic susceptibility profiles and lytic bacteriophages
Authors: Nowaczek Anna , Urban‐Chmiel Renata , Dec Marta , Puchalski Andrzej , Stępień‐Pyśniak Dagmara , Marek Agnieszka , Pyzik Ewelina 
Published: January 2019

AbstractBacteria of the genus Campylobacter are the most common pathogens causing zoonotic diseases in humans. Therefore, the aim of the study was to isolate Campylobacter bacteria from broiler chickens and evaluate their susceptibility to selected antibiotics by determining minimum inhibitory concentrations (MIC), followed by isolation and characterization of bacteriophages specific for Campylobacter spp. The material for the study consisted of field isolates of Campylobacter spp. obtained from the gut (cecum) of broiler chickens directly after slaughter in slaughterhouses, and bacteriophages specific for these strains. We isolated 48 strains from poultry (140 broiler chickens): 31 strains of Campylobacter jejuni and 17 of Campylobacter coli. Identification of the strains was confirmed by multiplex PCR and MALDI‐TOF mass spectrometry. Over 83% of Campylobacter strains were resistant to ciprofloxacin, and over half the isolates were resistant to erythromycin, gentamicin, and tetracycline. Resistance to three or more antibiotics was observed in 91.6% of all strains. Four bacteriophages were obtained, and on the basis of their morphological structure, they were assigned to two families of the order Caudovirales: Myoviridae and Siphoviridae. A high percentage of the Campylobacter strains were resistant to at least three of the antibiotic groups tested. All of the phages exhibited lytic activity against the Campylobacter spp. isolates, but the antibacterial effect of the phages was not observed for all strains.
Ancrocorticia populi gen. nov., sp. nov, isolated from the symptomatic bark of Populus × euramericana canker
Authors: Xu Guan‐tang , Xue Han , Piao Chun‐gen , Guo Min‐wei , Li Yong 
Published: January 2019

AbstractA Gram‐staining positive facultative anaerobic, non‐motile strain, sk1b4T, was isolated from canker of symptomatic bark tissue of a Populus × euramericana. 16S rRNA gene sequence analyses showed that strain sk1b4T shared the highest similarity with Arcanobacterium phocisimile (94.1%). Within the phylogenetic tree, the novel isolate formed a distinct branch from Actinobaculum, Arcanobacterium, and Trueperella. The percentage of conserved proteins calculated from genomic sequence indicated a low level of relatedness between the novel strain and its phylogenetic neighbors. Growth of the novel strain occurred at temperatures between 10 and 41°C, and within a pH range of 6.0–9.0; optimal growth occurred at 30°C and at pH 6.0–9.0. Growth also occurred within a NaCl concentration of 1%–5% (w/v). The major fatty acids of the strain were C14:0, C16:0, and C18:1 ω9c, and major polar lipids were glycolipid, phosphatidylinositol mannoside, phospholipid, diphosphatidylglycerol, and phosphatidylglycerol. Respiratory quinone was absent. On the basis of phenotypic and genotypic characteristics, we propose that the novel isolate should be classified as a novel species in a new genus: Ancrocorticia populi gen. nov., sp. nov. The type strain is sk1b4T (=CFCC 14564T= KCTC 39919T).
Full 1H and 13C NMR spectral assignment of conjugated valerolactone metabolites isolated from urine of black tea consumers by means of SPE‐prepLC–MS–LC–MS‐NMR
Authors: de Roo Niels , Wilmsen Sanne M. J. , Mihaleva Velitchka V. , Jacobs Doris M. , van Duynhoven John P. M. 
Published: January 2019

AbstractThe health benefits of black tea have been linked to polyphenol metabolites that target specific modes of action in the human body. A major bottleneck in unravelling the underlying mechanisms is the preparative isolation of these metabolites, which hampers their structural elucidation and assessment of in vitro bioactivity. A solid phase extraction (SPE)‐preparative liquid chromatography (prepLC)–MS–LC–MS‐NMR workflow was implemented for preparative isolation of conjugated valerolactone metabolites of catechin‐based polyphenols from urine of black tea consumers. First, the urine was cleaned and preconcentrated using an SPE method. Subsequently, the clean urine concentrate was injected on a preparative LC column, and conjugated valerolactones were obtained by MS‐guided collection. Reconstituted fractions were further separated on an analytical LC column, and valerolactone fractions were collected in an MS‐guided manner. These were reconstituted in methanol‐d4 and identified and quantified using 1D and 2D homo‐ and hetereonuclear NMR experiments (at a field strength of 14.1 T), in combination with mass spectrometry. This resulted in the full spectral 1H and 13C NMR assignments of five conjugated valerolactones. These metabolites were collected in quantities of 8–160 μg and purities of 70–91%. The SPE‐prepLC–MS–LC–MS‐NMR workflow is suitable for isolating metabolites that occur at sub‐μM concentrations in a complex biofluid such as urine. The workflow also provides an alternative for cumbersome and expensive de novo synthesis of tea metabolites for testing in bioactivity assays or for use as authentic analytical standards for quantification by mass spectrometry.
SUPER: A blockwise curve‐fitting method for accelerating MR parametric mapping with fast reconstruction
Authors: Hu Chenxi , Peters Dana C. 
Published: January 2019

PurposeTo investigate Shift Undersampling improves Parametric mapping Efficiency and Resolution (SUPER), a novel blockwise curve‐fitting method for accelerating parametric mapping with very fast reconstruction.MethodsSUPER uses interleaved k‐space undersampling, which enables a blockwise decomposition of the otherwise large‐scale cost function to improve the reconstruction efficiency. SUPER can be readily combined with SENSE to achieve at least 4‐fold acceleration. D‐factor, a parametric‐mapping counterpart of g‐factor, was proposed and formulated to compare spatially heterogeneous noise amplification because of different acceleration methods. As a proof‐of‐concept, SUPER/SUPER‐SENSE was validated using T1 mapping, by comparing them to alternative model‐based methods, including MARTINI and GRAPPATINI, via simulations, phantom imaging, and in vivo brain imaging (N = 5), over criteria of normalized root‐mean‐squares error (NRMSE), average d‐factor, and computational time per voxel (TPV). A novel SUPER‐SENSE MOLLI cardiac T1‐mapping sequence with improved resolution (1.4 mm × 1.4 mm) was compared to standard MOLLI (1.9 mm × 2.5 mm) in 8 healthy subjects.ResultsIn brain imaging, 2‐fold SUPER achieved lower NRMSE (0.04 ± 0.02 vs. 0.11 ± 0.02, P < 0.01), lower average d‐factor (1.01 ± 0.002 vs. 1.12 ± 0.004, P < 0.001), and lower TPV (4.6 ms ± 0.2 ms vs. 79 ms ± 3 ms, P < 0.001) than 2‐fold MARTINI. Similarly, 4‐fold SUPER‐SENSE achieved lower NRMSE (0.07 ± 0.01 vs. 0.13 ± 0.03, P = 0.02), lower average d‐factor (1.15 ± 0.01 vs. 1.20 ± 0.01, P < 0.001), and lower TPV (4.0 ms ± 0.1 ms vs. 72 ms ± 3 ms, P < 0.001) than 4‐fold GRAPPATINI. In cardiac T1 mapping, SUPER‐SENSE MOLLI yielded similar myocardial T1 (1151 ms ± 63 ms vs. 1159 ms ± 32 ms, P = 0.6), slightly lower blood T1 (1643 ms ± 86 ms vs. 1680 ms ± 79 ms, P = 0.004), but improved spatial resolution compared with standard MOLLI in the same imaging time.ConclusionSUPER and SUPER‐SENSE provide fast model‐based reconstruction methods for accelerating parametric mapping and improving its clinical appeal.
Ultrasound appears to be a reliable technique for the diagnosis of piriformis syndrome
Authors: Zhang Wenhua , Luo Fangqiong , Sun Hongjun , Ding Hongyu 
Published: January 2019

ABSTRACTIntroduction: Piriformis muscle syndrome (PS) is a disorder encompassing a constellation of symptoms, including buttock and hip pain. In this study we aimed to assess the value of ultrasound (US) in the diagnosis of PS. Methods: Thirty‐three clinically diagnosed PS patients and 26 healthy volunteers underwent a clinical PS scoring examination and US and MRI assessment of the bilateral piriformis muscles. The areas under the receiver operating characteristic curves (AUROCs) of the US parameters (i.e., increased thickness [iTh] and increased cross‐sectional area [iCSA]) for piriformis muscle were evaluated. Results: On US and MRI, the thickness and CSA were increased in PS patients. The AUROCs for the iTh and iCSA for discriminating stage 0 (healthy volunteers) from stage 1 through stage 3 (PS patients) were 0.88 and 0.95, respectively. Discussion: US may be a reliable technique for the clinical diagnosis of PS. Muscle Nerve 59:411–416, 2019
Improving piezoelectric and pyroelectric properties of electrospun PVDF nanofibers using nanofillers for energy harvesting application
Authors: Abbasipour Mina , Khajavi Ramin , Yousefi Ali Akbar , Yazdanshenas Mohammad Esmail , Razaghian Farhad , Akbarzadeh Abdolhamid 
Published: January 2019

In this study, it was aimed to increase the piezoelectric and pyroelectric properties of electrospun polyvinylidene fluoride (PVDF) nanofibers simultaneously by using specific nanofillers. Graphene oxide (GO), graphene, and halloysite nanotubes with different concentrations (0, 0.05, 0.4, and 1.6% wt/wt) were combined with PVDF solution and were fabricated in the form of nanofibers through electrospinning. Pyroelectric properties of samples were measured by submerging sealed samples in hot water (360°K) and ice (270°K). The piezoelectric properties of the samples were evaluated through bending tests. The microstructural, mechanical, and thermal properties of the electrospun PVDF nanocomposite were investigated using scanning electron microscope, Instron instrument, and thermogravimetric analysis, respectively. To further support the experimental observations for generating electric voltage in the bended nanogenerator, the PVDF nanogenerator (PNG) was also modeled by a finite element analysis based on the theory of linear piezoelectricity using COMSOL Multiphysics simulation software. Experimental results showed that adding nanofillers could improve the piezoelectric and pyroelectric properties of all samples, associated with the increment of β‐phase in the nanofibers. It was concluded that adding nanofillers could increase pyroelectricity about 50% more than piezoelectricity in pristine PVDF nanofiber web. The PNG containing 1.6 wt% GO showed the highest efficiency in terms of piezoelectricity and pyroelectricity. In addition, the results showed that the ratio of piezoelectric to pyroelectric coefficients was constant (~1.5) and it was independent of the nanofiller type and content. The effect of external force and vibration frequency on the output voltage was also investigated. Increasing the compressive force and vibration frequency caused a greater output voltage. Finally, the fabricated nanogenerator was integrated on insole and elbow to investigate its energy harvesting capabilities from body movement.
Barriers and facilitators to participating in physical activity for adults with breast cancer receiving adjuvant treatment: A qualitative metasynthesis
Authors: Lavallée Jacqueline F. , Abdin Shanara , Faulkner James , Husted Margaret 
Published: January 2019

AbstractObjectivePhysical activity can improve the health and well‐being of individuals receiving adjuvant treatment for breast cancer, but engagement in physical activity can be low. This review synthesises the barriers and facilitators to engaging with and participating in physical activity whilst receiving treatment.MethodsThe metasynthesis of qualitative studies is reported in line with the PRISMA statement. We systematically searched eight databases (MEDLINE, EMBASE, CENTRAL, PsycINFO, CINAHL, British Library, OpenGrey, and Conference Proceedings Citation Index) from inception to November 30, 2017. A total of 1276 abstracts were retrieved and screened by two reviewers independently. Data from eligible studies were extracted and critically appraised. As this review concerns qualitative studies only, a CER‐QUAL GRADE assessment was completed.ResultsA total of 13 studies were included. Four clear themes emerged (side effects of treatment, beliefs about physical activity, focus on health not illness, and social factors) each containing both barriers and facilitators. Key facilitators to participating in physical activity during adjuvant treatment included positive physical benefits, improvements in psychological well‐being, and increased self‐esteem and empowerment. Further, having a knowledgeable instructor, tailored information, and a supportive environment were important to women undergoing treatment. Main barriers included fatigue and pain, as well as work and caring responsibilities.ConclusionsIncorporating physical activity into treatment regimens is important. Focusing on being less sedentary and providing accurate, tailored information should be prioritised within future interventions. Having a supportive environment and accounting for the particular barriers or facilitators to engagement identified here should aid the success of future interventions.
Scaling up sustainability: Concepts and practices of the ecovillage approach
Authors: Singh Bijay , Keitsch Martina M. , Shrestha Mahesh 
Published: January 2019

AbstractSince the Brundtland definition, practitioners and theoreticians have strived to deal with incoherencies in the concept of sustainability or sustainable development, partly because the concept is defined on a global level and applied through local level initiatives. Explanatorily, describing the three sustainability dimensions (social, economic and ecological), the pillar model of sustainability has become popular. However, several authors indicate that a comprehensive understanding, methods and tools on how the dimensions relate to each other in the pillar model of sustainability, are absent. Further, sustainable interventions must express their relations through visible spatial terms and interpret them with the help of values and beliefs that can be handed over to future generations (temporal aspect). Many interventions that are expressed in sustainability dimensions often lack these spatial and temporal considerations. As a result, interventions lack case‐ and context‐specific concerns, objectives, priorities and possibilities, and often seem short‐term goal‐oriented. Within tensions between global and local, and spatial–temporal necessity, ecovillage is an emerging approach for shaping a sustainable future at grass roots level, and an opportunity to deal with the challenge of managing nature conservation in a community with culturally, socially and economically diverse actors. Hence, the overall objective of this article is to identify concepts and practices of ecovillage as sustainable way of living connected to a context. The attempt is to construe integrative understanding to sustainability and to express spatial and temporal aspects analytically. This understanding can be scaled up to strategies and policies. The article uses a literature review of various secondary sources, journals, narratives, and conference papers on sustainability and ecovillage. The article assumes that it is important to develop the framework analytically prior to empirical research. Findings indicate that to yield sustainable, inclusive and equitable outcomes, it is important to focus on the cultural and regional aspects. This focus can also provide a transition from local to national and global interventions and thereby become a mediator between different levels of sustainability, global and local.