bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated replication of cone beam CT‐guided treatments in the Pinnacle3 treatment planning system for adaptive radiotherapy
Authors: Hargrave Catriona , Mason Nicole , Guidi Robyn , Miller Julie‐Anne , Becker Jillian , Moores Matthew , Mengersen Kerrie , Poulsen Michael , Harden Fiona 
Published: October 2015

AbstractIntroductionTime‐consuming manual methods have been required to register cone‐beam computed tomography (CBCT) images with plans in the Pinnacle3 treatment planning system in order to replicate delivered treatments for adaptive radiotherapy. These methods rely on fiducial marker (FM) placement during CBCT acquisition or the image mid‐point to localise the image isocentre. A quality assurance study was conducted to validate an automated CBCT‐plan registration method utilising the Digital Imaging and Communications in Medicine (DICOM) Structure Set (RS) and Spatial Registration (RE) files created during online image‐guided radiotherapy (IGRT).MethodsCBCTs of a phantom were acquired with FMs and predetermined setup errors using various online IGRT workflows. The CBCTs, DICOM RS and RE files were imported into Pinnacle3 plans of the phantom and the resulting automated CBCT‐plan registrations were compared to existing manual methods. A clinical protocol for the automated method was subsequently developed and tested retrospectively using CBCTs and plans for six bladder patients.ResultsThe automated CBCT‐plan registration method was successfully applied to thirty‐four phantom CBCT images acquired with an online 0 mm action level workflow. Ten CBCTs acquired with other IGRT workflows required manual workarounds. This was addressed during the development and testing of the clinical protocol using twenty‐eight patient CBCTs. The automated CBCT‐plan registrations were instantaneous, replicating delivered treatments in Pinnacle3 with errors of ±0.5 mm. These errors were comparable to mid‐point‐dependant manual registrations but superior to FM‐dependant manual registrations.ConclusionThe automated CBCT‐plan registration method quickly and reliably replicates delivered treatments in Pinnacle3 for adaptive radiotherapy.
Numerical modeling of magneto‐hydrodynamics flows using reproducing kernel particle method
Authors: Tatari Mehdi , Shahriari Mostafa , Raoofi Mohammadreza 
Published: October 2015

SummaryIn this paper, we develop some mesh‐free particle methods for magneto‐hydrodynamics equations. Our focus is on the problems with high Hartmann numbers, which generate unstable solutions in most numerical methods. Several numerical tests validate the efficiency of our methods. Copyright © 2015 John Wiley & Sons, Ltd.
Interaction and visual performance in stereoscopic displays: A review
Authors: Lin Chiuhsiang Joe , Woldegiorgis Bereket Haile 
Published: October 2015

AbstractIn this paper, authors systematically selected and reviewed articles related to stereoscopic displays and their advances, with a special focus on perception, interaction, and corresponding challenges. The aim was to understand interaction‐related problems, provide possible explanations, and identify factors that limit their applications. Despite promising advancements, there are still issues that researchers in the field fail to explain precisely. The two major problems in stereoscopic viewing are, compared with the real world, objects are perceived to be smaller than they actually are and there are discomfort and visual syndromes. Furthermore, there is general agreement that humans underestimate their egocentric distance in a virtual environment (VE). Our analysis revealed that in the real world, distance estimation is about 94% accurate, but in VE, it is only about 80% accurate. This problem could reduce the efficacy of different sensory motor‐based applications where interaction is important. Experts from human factors, computing, psychology, and others have studied contributing factors such as types of perception/response method, quality of graphics, associated stereoscopic conditions, experience in virtual reality (VR), and distance signals. This paper discusses the factors requiring further investigation if the VR interaction is to be seamlessly realized. In addition, engineering research directions aiming at improving current interaction performances are recommended.
Preoperative neutrophil to lymphocyte ratio predicts survival in patients with T1‐2N0 colorectal cancer
Authors: Shin Jun Sang , Suh Kwang Wook , Oh Seung Yeop 
Published: October 2015

PurposeNeutrophil to lymphocyte ratio (NLR) is reported to be associated with prognosis of colorectal cancer. The aim of this study is to determine whether the NLR is a predictor of oncological outcomes in patients with stage I colorectal cancer who underwent curative surgery.MethodsTwo hundred sixty‐nine patients with stage I colorectal cancer who underwent surgical resection between December 2003 and December 2011 were retrospectively reviewed. The cutoff for NLR was defined as three by maximizing log‐rank test statistics. We compared patients with a low NLR and those with a high NLR in terms of survival.ResultsThe 5‐year disease‐free survival (DFS) and cancer‐specific survival (CSS) rates were lower in patients with a high NLR compared to those with a low NLR in stage I colorectal cancer (89.5% vs. 97.4%, P = 0.006; 94.0% vs. 98.9%, P = 0.022). Cox multivariate analysis demonstrated that preoperative NLR was independently associated with DFS (HR, 5.216; 95%CI, 1.400–19.431; P = 0.014) and CSS (HR, 6.190; 95%CI, 1.034–37.047; P = 0.046) in patients with stage I colorectal cancer.ConclusionThe preoperative NLR is a prognostic factor predicting DFS and CSS in patients with stage I colorectal cancer who underwent curative surgery. J. Surg. Oncol. 2015;112:654–657. © 2015 Wiley Periodicals, Inc.
Correlation of single‐breath count test and neck flexor muscle strength with spirometry in myasthenia gravis
Authors: Elsheikh Bakri , Arnold W. David , Gharibshahi Shahram , Reynolds Jerold , Freimer Miriam , Kissel John T. 
Published: October 2015

ABSTRACTIntroduction: Although formal spirometry is the gold standard for monitoring respiratory function in patients with myasthenia gravis (MG), such testing is often delayed or unavailable. There is a need for a simple bedside test that can accurately measure respiratory function. Methods: We conducted a prospective, cross‐sectional, single‐blind study in adults with acetylcholine receptor antibody positive MG. Participants performed the single breath count test (SBCT) and underwent manual muscle strength testing, and a respiratory therapist performed spirometry blinded to SBCT and strength results. Results : Thirty‐one patients, aged 57 ± 19 years participated. SBCT showed significant correlations with forced vital capacity (FVC), negative inspiratory force, and neck flexor strength (P < 0.01). FVC showed significant correlation with neck flexor strength (P = 0.02) but no correlation with shoulder abductor strength. Conclusions: These data suggest that the SBCT and neck flexor strength testing are valuable tools for bedside assessment of respiratory function in MG patients. Muscle Nerve 53: 134–136, 2016
Crystal structure of quinone‐dependent alcohol dehydrogenase from Pseudogluconobacter saccharoketogenes. A versatile dehydrogenase oxidizing alcohols and carbohydrates
Authors: Rozeboom Henriëtte J. , Yu Shukun , Mikkelsen Rene , Nikolaev Igor , Mulder Harm J. , Dijkstra Bauke W. 
Published: October 2015

AbstractThe quinone‐dependent alcohol dehydrogenase (PQQ‐ADH, E.C. 1.1.5.2) from the Gram‐negative bacterium Pseudogluconobacter saccharoketogenes IFO 14464 oxidizes primary alcohols (e.g. ethanol, butanol), secondary alcohols (monosaccharides), as well as aldehydes, polysaccharides, and cyclodextrins. The recombinant protein, expressed in Pichia pastoris, was crystallized, and three‐dimensional (3D) structures of the native form, with PQQ and a Ca2+ ion, and of the enzyme in complex with a Zn2+ ion and a bound substrate mimic were determined at 1.72 Å and 1.84 Å resolution, respectively. PQQ‐ADH displays an eight‐bladed β‐propeller fold, characteristic of Type I quinone‐dependent methanol dehydrogenases. However, three of the four ligands of the Ca2+ ion differ from those of related dehydrogenases and they come from different parts of the polypeptide chain. These differences result in a more open, easily accessible active site, which explains why PQQ‐ADH can oxidize a broad range of substrates. The bound substrate mimic suggests Asp333 as the catalytic base. Remarkably, no vicinal disulfide bridge is present near the PQQ, which in other PQQ‐dependent alcohol dehydrogenases has been proposed to be necessary for electron transfer. Instead an associated cytochrome c can approach the PQQ for direct electron transfer.
Software‐aided structural elucidation in drug discovery
Authors: Ahlqvist Marie , Leandersson Carina , Hayes Martin A. , Zamora Ismael , Thompson Richard A. 
Published: October 2015

RationaleStructural information on metabolites obtained in relevant biological systems can have considerable impact on the design of new drug candidates. However, with demanding turnaround times, the amount of available structural information may become rate limiting.MethodsThe workflow for metabolite identification used in our laboratory was compared to a workflow using a software tool built for computer‐assisted metabolite identification. The present study covered the in vitro metabolism of a diverse set of 65 in‐house compounds. The compounds were profiled across three liver‐based systems, 17 compounds were tested in human liver microsomes (HLM), 12 in rat hepatocytes (RHEP), and 36 in human hepatocytes (HHEP).ResultsFor 92% of the metabolites reported, the exact match or Markush representations were in agreement between the two workflows. The major specific biotransformations in hepatocytes which formed the metabolites were aromatic or aliphatic hydroxylations (33%), N‐dealkylations (15%) and glucuronidations (12%).ConclusionsThe software was shown to perform well for structural elucidation of metabolites from both phase I and phase II metabolism where the focus was on quickly understanding the rate‐limiting metabolic step(s). Copyright © 2015 John Wiley & Sons, Ltd.
Identification and activation of novel biosynthetic gene clusters by genome mining in the kirromycin producer Streptomyces collinus Tü 365
Authors: Iftime Dumitrita , Kulik Andreas , Härtner Thomas , Rohrer Sabrina , Niedermeyer Timo Horst Johannes , Stegmann Evi , Weber Tilmann , Wohlleben Wolfgang 
Published: October 2015

Abstract
Streptomycetes are prolific sources of novel biologically active secondary metabolites with pharmaceutical potential. S. collinus Tü 365 is a Streptomyces strain, isolated 1972 from Kouroussa (Guinea). It is best known as producer of the antibiotic kirromycin, an inhibitor of the protein biosynthesis interacting with elongation factor EF-Tu. Genome Mining revealed 32 gene clusters encoding the biosynthesis of diverse secondary metabolites in the genome of Streptomyces collinus Tü 365, indicating an enormous biosynthetic potential of this strain. The structural diversity of secondary metabolisms predicted for S. collinus Tü 365 includes PKS, NRPS, PKS-NRPS hybrids, a lanthipeptide, terpenes and siderophores. While some of these gene clusters were found to contain genes related to known secondary metabolites, which also could be detected in HPLC–MS analyses, most of the uncharacterized gene clusters are not expressed under standard laboratory conditions. With this study we aimed to characterize the genome information of S. collinus Tü 365 to make use of gene clusters, which previously have not been described for this strain. We were able to connect the gene clusters of a lanthipeptide, a carotenoid, five terpenoid compounds, an ectoine, a siderophore and a spore pigment-associated gene cluster to their respective biosynthesis products.
David and Goliath: chemical perturbation of eukaryotes by bacteria
Authors: Ho Louis K , Nodwell Justin R 
Published: October 2015

AbstractEnvironmental microbes produce biologically active small molecules that have been mined extensively as antibiotics and a smaller number of drugs that act on eukaryotic cells. It is known that there are additional bioactives to be discovered from this source. While the discovery of new antibiotics is challenged by the frequent discovery of known compounds, we contend that the eukaryote-active compounds may be less saturated. Indeed, despite there being far fewer eukaryotic-active natural products these molecules interact with a far richer diversity of molecular and cellular targets.
Mixed Systems Based on Erucyl Amidopropyl Betaine and Nanoparticles: Self‐Organization and Rheology
Authors: Gaynanova Gulnara A. , Valiakhmetova Alsu R. , Kuryashov Dmitry A. , Bashkirtseva Natalia Yu. , Zakharova Lucia Ya. 
Published: October 2015

AbstractThe aggregation behavior and flow characteristics of systems based on zwitterionic surfactant, erucyl amidopropyl betaine, silica and alumina nanoparticles in a wide range of surfactant concentrations from molecular to micellar solutions were studied using surface tensiometry, conductometry, dynamic and electrophoretic light scattering, and rheology techniques. The adsorption of zwitterionic surfactant molecules occurs on both positively and negatively charged surfaces via an electrostatic interaction mechanism. As a result, addition of a small amount silica nanoparticles (0.5–0.8 wt%) increases the surfactant solution's viscosity by more than two times.
The effects of pubertal timing on externalizing behaviors in adolescence and early adulthood: A meta‐analytic review
Authors: Dimler Laura M. , Natsuaki Misaki N. 
Published: October 2015

ABSTRACTUsing a meta‐analytic approach, this investigation examines the association between early pubertal timing and externalizing behaviors in adolescence and early adulthood. The findings showed that the effect size of early pubertal maturation on externalizing behaviors was r = 0.180. This small, yet significant effect size is consistent with the models of early pubertal maturation in that early maturation is associated with higher levels of externalizing behaviors. Using contrast analyses, we examined three potential moderators of this association: sex, the concurrent versus long‐term effect of early puberty, and types of puberty assessments. Neither sex nor type of pubertal timing assessment moderated the effect significantly. However, results indicated that the effect was stronger for studies that measured pubertal timing and externalizing behaviors concurrently rather than longitudinally (i.e., examining prospective effect of pubertal timing on later externalizing behaviors). The findings are discussed in terms of implications for future research.
School‐related social support and subjective well‐being in school among adolescents: The role of self‐system factors
Authors: Tian Lili , Zhao Jie , Huebner E. Scott 
Published: October 2015

ABSTRACTThis 6‐week longitudinal study aimed to examine a moderated mediation model that may explain the link between school‐related social support (i.e., teacher support and classmate support) and optimal subjective well‐being in school among adolescents (n = 1316). Analyses confirmed the hypothesized model that scholastic competence partially mediated the relations between school‐related social support and subjective well‐being in school, and social acceptance moderated the mediation process in the school‐related social support‐‐> subjective well‐being in school path and in the scholastic competence‐‐> subjective well‐being in school path. The findings suggested that both social contextual factors (e.g., school‐related social support) and self‐system factors (e.g., scholastic competence and social acceptance) are crucial for adolescents' optimal subjective well‐being in school. Limitations and practical applications of the study were discussed.
International Federation of Gynecology and Obstetrics opinion on reproductive health impacts of exposure to toxic environmental chemicals
Authors: Di Renzo Gian Carlo , Conry Jeanne A. , Blake Jennifer , DeFrancesco Mark S. , DeNicola Nathaniel , Martin James N. , McCue Kelly A. , Richmond David , Shah Abid , Sutton Patrice , Woodruff Tracey J. , van der Poel Sheryl Ziemin , Giudice Linda C. 
Published: October 2015

AbstractExposure to toxic environmental chemicals during pregnancy and breastfeeding is ubiquitous and is a threat to healthy human reproduction. There are tens of thousands of chemicals in global commerce, and even small exposures to toxic chemicals during pregnancy can trigger adverse health consequences. Exposure to toxic environmental chemicals and related health outcomes are inequitably distributed within and between countries; universally, the consequences of exposure are disproportionately borne by people with low incomes. Discrimination, other social factors, economic factors, and occupation impact risk of exposure and harm. Documented links between prenatal exposure to environmental chemicals and adverse health outcomes span the life course and include impacts on fertility and pregnancy, neurodevelopment, and cancer. The global health and economic burden related to toxic environmental chemicals is in excess of millions of deaths and billions of dollars every year. On the basis of accumulating robust evidence of exposures and adverse health impacts related to toxic environmental chemicals, the International Federation of Gynecology and Obstetrics (FIGO) joins other leading reproductive health professional societies in calling for timely action to prevent harm. FIGO recommends that reproductive and other health professionals advocate for policies to prevent exposure to toxic environmental chemicals, work to ensure a healthy food system for all, make environmental health part of health care, and champion environmental justice.
5‐Hydroxytryptamine promotes hepatocellular carcinoma proliferation by influencing β‐catenin
Authors: Fatima Sarwat , Shi Xiaoke , Lin Zesi , Chen Guo-qing , Pan Xiao-hua , Wu Justin Che-Yuen , Ho John W. , Lee Nikki P. , Gao Hengjun , Zhang Ge , Lu Aiping , Bian Zhao Xiang 
Published: October 2015

5‐Hydroxytryptamine (5‐HT), a neurotransmitter and vasoactive factor, has been reported to promote proliferation of serum‐deprived hepatocellular carcinoma (HCC) cells but the detailed intracellular mechanism is unknown. As Wnt/β‐catenin signalling is highly dysregulated in a majority of HCC, this study explored the regulation of Wnt/β‐catenin signalling by 5‐HT. The expression of various 5‐HT receptors was studied by quantitative real‐time polymerase chain reaction (qPCR) in HCC cell lines as well as in 33 pairs of HCC tumours and corresponding adjacent non‐tumour tissues. Receptors 5‐HT1D (21/33, 63.6%), 5‐HT2B (12/33, 36.4%) and 5‐HT7 (15/33, 45.4%) were overexpressed whereas receptors 5‐HT2A (17/33, 51.5%) and 5‐HT5 (30/33, 90.1%) were reduced in HCC tumour tissues. In vitro data suggests 5‐HT increased total β‐catenin, active β‐catenin and decreased phosphorylated β‐catenin protein levels in serum deprived HuH‐7 and HepG2 cells compared to control cells under serum free medium without 5‐HT. Activation of Wnt/β‐catenin signalling was evidenced by increased expression of β‐catenin downstream target genes, Axin2, cyclin D1, dickoppf‐1 (DKK1) and glutamine synthetase (GS) by qPCR in serum‐deprived HCC cell lines treated with 5‐HT. Additionally, biochemical analysis revealed 5‐HT disrupted Axin1/β‐catenin interaction, a critical step in β‐catenin phosphorylation. Increased Wnt/β‐catenin activity was attenuated by antagonist of receptor 5‐HT7 (SB‐258719) in HCC cell lines and patient‐derived primary tumour tissues in the presence of 5‐HT. SB‐258719 also reduced tumour growth in vivo. This study provides evidence of Wnt/β‐catenin signalling activation by 5‐HT and may represent a potential therapeutic target for hepatocarcinogenesis.
Ultrasound‐Based Detection of Low Muscle Mass for Diagnosis of Sarcopenia in Older Adults
Authors: Minetto Marco A. , Caresio Cristina , Menapace Tommaso , Hajdarevic Arnel , Marchini Andrea , Molinari Filippo , Maffiuletti Nicola A. 
Published: October 2015

AbstractObjectiveTo establish muscle‐specific cut‐off values for ultrasound‐based detection of low muscle mass, and to assess its prevalence in a population of frail older subjects when applying the cut‐points of different muscles and those of different sarcopenic indices.DesignCross‐sectional study.SettingGeriatric outpatient clinic and clinical research laboratory.MethodsA total of 44 older adults (30 women and 14 men, mean age 82 years, range 67‐93 years) and 60 younger individuals (30 women and 30 men, mean age 26 years, range 20‐36 years) participated. Body composition and thickness of 4 lower limb muscles (rectus femoris, vastus lateralis, tibialis anterior, medial gastrocnemius) were respectively assessed by bioelectrical impedance analysis (BIA) and ultrasonography.Main Outcome MeasurementsSite‐specific cut‐points for ultrasound‐based assessment of low muscle mass (muscle thickness values 2 standard deviations below the gender‐specific means of our sample of younger subjects) and comparative prevalence rates of low muscle mass.ResultsThe following site‐specific cut‐points for muscle thickness were identified: rectus femoris: 20 mm in men and 16 mm in women; vastus lateralis: 17 mm in men and 15 mm in women; tibialis anterior: 23 mm in men and 22 mm in women; and medial gastrocnemius: 13 mm in both men and women. The prevalence of low muscle mass in older adults was highly dependent on the muscle being investigated; it varied from 86% for thigh muscles to 30% for leg muscles. Moreover, the prevalence of low muscle mass was highly dependent on the applied diagnostic criterion and on the adopted cut‐off value; it ranged from 2% to 75% for different BIA‐derived criteria.ConclusionsWe suggest that muscle ultrasonography provides physiatrists with a practical and accurate tool for identifying individuals with low muscle mass. However, the usability of cut‐off values established in our group of healthy younger subjects of white ethnicity to identify low muscle mass in older individuals of different ethnic groups remains to be demonstrated in future studies.
Reliability of Ultrasound Imaging Measures of Transverse Abdominis and Lumbar Multifidus in Various Positions
Authors: Mangum L. Colby , Sutherlin Mark A. , Saliba Susan A. , Hart Joseph M. 
Published: October 2015

AbstractObjectiveTo determine the reliability of measurement of muscle activation via ultrasound imaging measures of the transverse abdominis (TrA) and lumbar multifidus (LM) in tabletop, seated, standing, and walking conditions.DesignDescriptive laboratory study.SettingUniversity research laboratory.ParticipantsSixteen healthy participants (age, 20.4 ± 1.8 years; height, 167.7 ± 9.0 cm; mass, 65.1 ± 10.8 kg).InterventionsNone.Main Outcome MeasurementsThe activation ratio (AR) of TrA and LM and preferential activation ratio of TrA in tabletop, seated, standing, and walking positions were assessed by the same examiner during 2 ultrasound imaging sessions 24‐72 hours apart. Statistical analysis included determination of intraclass correlation coefficients (ICCs) using analysis of variance for each muscle and position between sessions.ResultsExcellent reliability was found in TrA AR between sessions for healthy participants in the tabletop position (ICC3,k = 0.903), and acceptable to excellent reliability was found in seated (ICC3,k = 0.613), standing (ICC3,k = 0.553), and walking (ICC3,k = 0.737) positions. LM AR was fair in the tabletop position for these participants (ICC3,k = 0.264). The preferential activation ratio for healthy participants was substantially reliable in tabletop and seated positions (ICC3,k = 0.668, 0.684) and showed fair reliability for walking (ICC3,k = 0.455).ConclusionsUltrasound imaging is a reliable method of measuring muscle thickness across multiple positions in healthy persons. This measure may be used to compare abdominal muscle thickness across populations or after interventions. LM AR was only found to be reliable in the tabletop position.