bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal diagnosis of X‐linked myopathy associated with a VMA21 gene mutation afforded through a novel targeted exome sequencing strategy applied in fetuses with abnormal ultrasound findings
Authors: Konialis Christopher , Assimakopoulos Efstratios , Hagnefelt Birgitta , Karapanou Sophia , Sotiriadis Alexandros , Pangalos Constantinos 
Published: February 2017

Key Clinical MessageFetal malformations detected through routine prenatal ultrasound examination comprise a heterogeneous group potentially associated with genetic disorders where the underlying cause is difficult to establish. We present the prenatal diagnosis of a rare X‐linked myopathy involving a new VMA21 gene mutation, detected through a novel prenatal exome sequencing‐based approach.
Melanopsin expressing human retinal ganglion cells: Subtypes, distribution, and intraretinal connectivity
Authors: Hannibal Jens , Christiansen Anders Tolstrup , Heegaard Steffen , Fahrenkrug Jan , Kiilgaard Jens Folke 
Published: February 2017

AbstractIntrinsically photosensitive retinal ganglion cells (ipRGCs) expressing the photopigment melanopsin belong to a heterogenic population of RGCs which regulate the circadian clock, masking behavior, melatonin suppression, the pupillary light reflex, and sleep/wake cycles. The different functions seem to be associated to different subtypes of melanopsin cells. In rodents, subtype classification has associated subtypes to function. In primate and human retina such classification has so far, not been applied. In the present study using antibodies against N‐ and C‐terminal parts of human melanopsin, confocal microscopy and 3D reconstruction of melanopsin immunoreactive (‐ir) RGCs, we applied the criteria used in mouse on human melanopsin‐ir RGCs. We identified M1, displaced M1, M2, and M4 cells. We found two other subtypes of melanopsin‐ir RGCs, which were named “gigantic M1 (GM1)” and “gigantic displaced M1 (GDM1).” Few M3 cells and no M5 subtypes were labeled. Total cell counts from one male and one female retina revealed that the human retina contains 7283 ± 237 melanopsin‐ir (0.63–0.75% of the total number of RGCs). The melanopsin subtypes were unevenly distributed. Most significant was the highest density of M4 cells in the nasal retina. We identified input to the melanopsin‐ir RGCs from AII amacrine cells and directly from rod bipolar cells via ribbon synapses in the innermost ON layer of the inner plexiform layer (IPL) and from dopaminergic amacrine cells and GABAergic processes in the outermost OFF layer of the IPL. The study characterizes a heterogenic population of human melanopsin‐ir RGCs, which most likely are involved in different functions.
Stabilization Effect of Amino Acid Side Chains in Peptide Assemblies on Graphite Studied by Scanning Tunneling Microscopy
Authors: Guo Yuanyuan , Hou Jingfei , Zhang Xuemei , Yang Yanlian , Wang Chen 
Published: February 2017

AbstractAn analysis is presented of the effects of amino acid side chains on peptide assemblies in ambient conditions on a graphite surface. The molecularly resolved assemblies of binary peptides are examined with scanning tunneling microscopy. A comparative analysis of the assembly structures reveals that the lamellae width has an appreciable dependence on the peptide sequence, which could be considered as a manifestation of a stabilizing effect of side‐chain moieties of amino acids with high (phenylalanine) and low (alanine, asparagine, histidine and aspartic acid) propensities for aggregation. These amino acids are representative for the chemical structures involving the side chains of charged (histidine and aspartic acid), aromatic (phenylalanine), hydrophobic (alanine), and hydrophilic (asparagine) amino acids. These results might provide useful insight for understanding the effects of sequence on the assembly of surface‐bound peptides.
Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi‐level bead data
Authors: Parks David R. , El Khettabi Faysal , Chase Eric , Hoffman Robert A. , Perfetto Stephen P. , Spidlen Josef , Wood James C.S. , Moore Wayne A. , Brinkman Ryan R. 
Published: February 2017

AbstractWe developed a fully automated procedure for analyzing data from LED pulses and multilevel bead sets to evaluate backgrounds and photoelectron scales of cytometer fluorescence channels. The method improves on previous formulations by fitting a full quadratic model with appropriate weighting and by providing standard errors and peak residuals as well as the fitted parameters themselves. Here we describe the details of the methods and procedures involved and present a set of illustrations and test cases that demonstrate the consistency and reliability of the results. The automated analysis and fitting procedure is generally quite successful in providing good estimates of the Spe (statistical photoelectron) scales and backgrounds for all the fluorescence channels on instruments with good linearity. The precision of the results obtained from LED data is almost always better than that from multilevel bead data, but the bead procedure is easy to carry out and provides results good enough for most purposes. Including standard errors on the fitted parameters is important for understanding the uncertainty in the values of interest. The weighted residuals give information about how well the data fits the model, and particularly high residuals indicate bad data points. Known photoelectron scales and measurement channel backgrounds make it possible to estimate the precision of measurements at different signal levels and the effects of compensated spectral overlap on measurement quality. Combining this information with measurements of standard samples carrying dyes of biological interest, we can make accurate comparisons of dye sensitivity among different instruments. Our method is freely available through the R/Bioconductor package flowQB. © 2017 International Society for Advancement of Cytometry
Imaging Mass Cytometry
Authors: Chang Qing , Ornatsky Olga I. , Siddiqui Iram , Loboda Alexander , Baranov Vladimir I. , Hedley David W. 
Published: February 2017

AbstractImaging Mass Cytometry (IMC) is an expansion of mass cytometry, but rather than analyzing single cells in suspension, it uses laser ablation to generate plumes of particles that are carried to the mass cytometer by a stream of inert gas. Images reconstructed from tissue sections scanned by IMC have a resolution comparable to light microscopy, with the high content of mass cytometry enabled through the use of isotopically labeled probes and ICP‐MS detection. Importantly, IMC can be performed on paraffin‐embedded tissue sections, so can be applied to the retrospective analysis of patient cohorts whose outcome is known, and eventually to personalized medicine. Since the original description in 2014, IMC has evolved rapidly into a commercial instrument of unprecedented power for the analysis of histological sections. In this Review, we discuss the underlying principles of this new technology, and outline emerging applications of IMC in the analysis of normal and pathological tissues. © 2017 International Society for Advancement of Cytometry
The significance of parakeratosis alone in cervicovaginal cytology of turkish women
Authors: Kir Gozde , Sarbay Billur Cosan , Seneldir Hatice 
Published: February 2017

BackgroundWe aimed to analyze the significance of parakeratosis on an otherwise negative Papanicalaou (Pap) smear, in the absence of any characteristic human papilloma virus (HPV) findings.MethodsA total of 22,076 Papanicalaou smears that were diagnosed as negative for intraepithelial lesions or malignancy between 2013 and 2015 were included in this study. Samples were separated into two groups, according to the presence of parakeratosis. We investigated the association between parakeratosis in the cytology results and a high‐risk HPV status and high‐grade squamous intraepithelial lesion (HSIL) in the colposcopic biopsy specimens.ResultsA positive HPV result was more frequently identified in cases with parakeratosis than in cases without parakeratosis (P < 0.001). A histological diagnosis of HSIL was more frequently observed in HPV‐positive cases with a diagnosis of parakeratosis on cytology than in cases without parakeratosis (P = 0.8).ConclusionOur results demonstrate that a finding of parakeratosis on an otherwise negative Pap smear supports a follow‐up HPV DNA test. Also we should consider whether the presence of parakeratosis should be included in standard cytology reports. Additionally parakeratosis trended toward increased frequency of HSIL in follow‐up biopsy specimens. But it did not reach statistical significance. That is why larger studies are necessary to evaluate the association of parakeratosis and HSIL in colposcopic biopsy specimens. Diagn. Cytopathol. 2017;45:297–302. © 2016 Wiley Periodicals, Inc.
Analysis of transcriptional responses of normalizing genes on Crassostrea brasiliana under different experimental conditions
Authors: Müller Gabrielle do Amaral e Silva , de Lima Daína , Zacchi Flávia Lucena , Piazza Rômi Sharon , Lüchmann Karim Hahn , Mattos Jacó Joaquim , Schlenk Daniel , Bainy Afonso Celso Dias 
Published: February 2017

Abstract

Bivalves show remarkable plasticity to environmental changes and have been proposed as sentinel organisms in biomonitoring. Studies related to transcriptional analysis using quantitative real-time polymerase chain reaction (qRT-PCR) in these organisms have notably increased, imposing a need to identify and validate adequate reference genes for an accurate and reliable analysis. In the present study, 9 reference genes were selected from transcriptome data of Crassostrea brasiliana to identify their suitability as qRT-PCR normalizer genes. The transcriptional patterns were analyzed in gills of oysters under 3 different conditions: different temperatures (18, 24, or 32 °C) and phenanthrene (100 µg L−1) combined exposure; different salinities (10, 25, or 35‰) and phenanthrene combined exposure; and 10% of diesel fuel water-accommodated fraction (diesel-WAF) exposure. Reference gene stability was calculated using 5 algorithms (geNorm, NormFinder, BestKeeper, ΔCt, RefFinder). Transcripts of ankyrin-like (ANK), glyceraldehyde 3-phosphate dehydrogenase-like (GAPDH), and α-tubulin-like (TUBA) genes showed minor changes in different temperature/phenanthrene treatment. Transcripts of ANK, β-actin-like, and β-tubulin-like genes showed better stability at salinity/phenanthrene treatment, and ANK, TUBA, and 28S ribosomal protein-like genes showed the most stable transcription pattern in oysters exposed to diesel-WAF exposure. The present study constitutes the first systematic analysis of reference gene selection for qRT-PCR normalization in C. brasiliana. These genes could be employed in studies using qRT-PCR analysis under similar experimental conditions. Environ Toxicol Chem 2017;36:2190–2198. © 2017 SETAC
Venous Irritation Related to Intravenous Administration of Phenytoin versus Fosphenytoin
Authors: Jamerson Brenda D. , Dukes George E. , Brouwer Kim L.R. , Dorm Karl H. , Messenheimer John A. , Powell J. Robert 
Published: February 2017

Study Objective. To compare the frequency, severity, and time course of venous irritation after administration of a single intravenous dose of phenytoin with an equimolar dose of fosphenytoin, a water‐soluble phenytoin prodrug.Design. Randomized, double‐blind, two‐period, crossover study.Setting. University hospital clinical research unit.Patients. Twelve healthy volunteers within 15% of ideal body weight and with no clinically significant abnormalities on physical examination, medical history, or laboratory assessment.Interventions. Volunteers randomly received a 30‐minute infusion of phenytoin sodium 250 mg (250 mg/5 ml) or an equimolar dose of fosphenytoin 375 mg (375 mg/5 ml). Subjects returned for the crossover treatment 14–21 days later.Measurements and Main Results. Subjects assessed venous irritation (pain, burning, itching), and investigators evaluated phlebitis (erythema, swelling, tenderness), induration, exudation, and cording. Phenytoin was associated with a significantly higher degree of pain at the infusion site in all subjects and a significant degree of phlebitis in eight subjects (p<0.05); cording occurred in six subjects. The time course of phenytoin‐induced phlebitis was bimodal. Erythema and tenderness were prominent at the end of the infusion and again at 24 hours. Cording was first noted between 24 hours and 1 week after infusion. In contrast, fosphenytoin was associated with mild pain in two subjects, one incident of phlebitis, and no erythema or cording.Conclusions. Fosphenytoin administration resulted in significantly less venous irritation and phlebitis compared with an equimolar dose of phenytoin. The clinical use of this water‐soluble phenytoin prodrug should minimize the frequency and severity of infusion‐site reactions and should allow convenient, rapid, intravenous administration of drug, undiluted or admixed with intravenous solutions.
Quantification of neonatal lung parenchymal density via ultrashort echo time MRI with comparison to CT
Authors: Higano Nara S. , Fleck Robert J. , Spielberg David R. , Walkup Laura L. , Hahn Andrew D. , Thomen Robert P. , Merhar Stephanie L. , Kingma Paul S. , Tkach Jean A. , Fain Sean B. , Woods Jason C. 
Published: February 2017

PurposeTo demonstrate that ultrashort echo time (UTE) magnetic resonance imaging (MRI) can achieve computed tomography (CT)‐like quantification of lung parenchyma in free‐breathing, non‐sedated neonates. Because infant CTs are used sparingly, parenchymal disease evaluation via UTE MRI has potential for translational impact.Materials and MethodsTwo neonatal control cohorts without suspected pulmonary morbidities underwent either a research UTE MRI (n = 5; 1.5T) or a clinically‐ordered CT (n = 9). Whole‐lung means and anterior–posterior gradients of UTE‐measured image intensity (arbitrary units, au, normalized to muscle) and CT‐measured density (g/cm3) were compared (Mann–Whitney U‐test). Separately, a diseased neonatal cohort (n = 5) with various pulmonary morbidities underwent both UTE MRI and CT. UTE intensity and CT density were compared with Spearman correlations within ∼33 anatomically matched regions of interest (ROIs) in each diseased subject, spanning low‐ to high‐density tissues. Radiological classifications were evaluated in all ROIs, with mean UTE intensities and CT densities compared in each classification.ResultsIn control subjects, whole‐lung UTE intensities (0.51 ± 0.04 au) were similar to CT densities (0.44 ± 0.09 g/cm3) (P = 0.062), as were UTE (0.021 ± 0.020 au/cm) and CT (0.034 ± 0.024 [g/cm3]/cm) anterior–posterior gradients (P = 0.351). In diseased subjects' ROIs, significant correlations were observed between UTE and CT (P ≤0.007 in each case). Relative differences between UTE and CT were small in all classifications (4–25%).ConclusionThese results demonstrate a strong association between UTE image intensity and CT density, both between whole‐lung tissue in control patients and regional radiological pathologies in diseased patients. This indicates the potential for UTE MRI to longitudinally evaluate neonatal pulmonary disease and to provide visualization of pathologies similar to CT, without sedation/anesthesia or ionizing radiation.Level of Evidence: 3Technical Efficacy: Stage 2J. Magn. Reson. Imaging 2017;46:992–1000.
Changes to radiotherapy utilisation in Western NSW after the opening of a local service
Authors: Butler Sally M. 
Published: February 2017

AbstractIntroductionIn 2011, the first radiotherapy centre in Western NSW Local Health District (WNSWLHD) was opened in the city of Orange. Prior to this, patients travelled outside the health service, primarily to Sydney, to receive treatment. The aim of this study was to investigate if the establishment of the new rural radiotherapy service has changed the demographic profile, cancer type, treatment intent and number of patients treated.MethodsData were collected on WNSWLHD patients, 17 years of age and above, who received radiotherapy in either 2010 or 2012 in New South Wales (NSW) or Australian Capital Territory (ACT). The age, gender, treatment intent, cancer type and residential town were recorded.ResultsThe number of patients who accessed radiation increased from 573 to 667 between 2010 and 2012. The corresponding radiotherapy utilisation (RTU) rates were 29.3% in 2010 and 33.4% in 2012, an improvement of 4.1% (P = 0.01, 95% CI 1–7%). Patients travelled 128.5 km less for treatment in 2012 than in 2010 (338.7 km vs. 210.2 km, CI 111–145.5 km, P > 0.0001). All regions had an improvement in the RTU rates apart from the Remote region which decreased by 9% (31–20% in 2012). The number of palliative treatments increased significantly only within the Orange region. The number of male patients for treatments also significantly increased as there were 81 additional treatments (292 vs. 373) as did patients with a respiratory cancer (66 vs. 97).ConclusionsA new radiotherapy service in a sparsely populated health district significantly changed the pattern of radiotherapy use for those who lived only in the Orange region. Treatment capacity at the Orange radiotherapy centre has doubled with the opening of a second linear accelerator since this study was conducted. Thus, a follow‐up study is recommended to ascertain if radiotherapy rates remain low in the regions beyond Orange.
Prochlorococcus in the lab and in silico: The importance of representing exudation
Authors: Grossowicz Michal , Roth‐Rosenberg Dalit , Aharonovich Dikla , Silverman Jacob , Follows Michael J. , Sher Daniel 
Published: February 2017

AbstractIn this study, we test the applicability of the Droop/Caperon internal stores model to describe the growth and decline of the globally abundant marine cyanobacterium Prochlorococcus in batch culture as a function of internal and external inorganic and organic carbon and nitrogen. A rigorous parameter fitting exercise, constrained by the measured cell density, ammonium and inorganic carbon concentrations, revealed many different combinations of parameter values that provided equally good model‐data fit. Introducing data on C : N ratio from the published literature provided additional constraints which could only be satisfied with a structural change to the model. The simplest addition that satisfied these constraints and improved quantitative overall model‐data agreement was to explicitly represent excretion, which was predicted to account for 0.03–8.5% of the daily primary productivity; somewhat lower than previous estimates based on radiotracer incorporation. We argue that this significant and biologically meaningful process should not be neglected in models of marine phytoplankton.
A tale of pipes and reactors: Controls on the in‐stream dynamics of dissolved organic matter in rivers
Authors: Casas‐Ruiz Joan P. , Catalán Núria , Gómez‐Gener Lluís , von Schiller Daniel , Obrador Biel , Kothawala Dolly N. , López Pilar , Sabater Sergi , Marcé Rafael 
Published: February 2017

AbstractThe potential for rivers to alter the flux of dissolved organic matter (DOM) from land to ocean is widely accepted. Yet anticipating when and where rivers behave as active reactors vs. passive pipes of DOM stands as a major knowledge gap in river biogeochemistry, resulting in uncertainties for global carbon models. Here, we investigate the controls on in‐stream DOM dynamics by evaluating changes in DOM concentration and composition along several reaches of a medium‐sized river network over one full hydrological year. Roughly half of the observations over time and space showed active reactor conditions and, among these, similar proportion of gains and losses was measured. High water residence times promoted the active over passive behavior of the reaches, while DOM properties and nitrate availability determined whether they supplied or removed DOM from the river. Among different DOM fractions, protein‐like DOM both of terrestrial and aquatic origin seemed to drive bulk DOM patterns. Our study emphasizes the role of water residence time as a physical constraint for in‐stream processes, and provides new insights into the key factors governing the net balance between in‐stream gains and losses of DOM in rivers.
Distribution of trans‐resveratrol and its metabolites after acute or sustained administration in mouse heart, brain, and liver
Authors: Menet Marie‐Claude , Baron Stephanie , Taghi Meryam , Diestra Remi , Dargère Delphine , Laprévote Olivier , Nivet‐Antoine Valérie , Beaudeux Jean‐Louis , Bédarida Tatiana , Cottart Charles‐Henry 
Published: February 2017

ScopeTrans‐resveratrol is widely studied for its potentially beneficial effects on numerous disorders. It is rapidly metabolized and its metabolites can exhibit biological activity. The present study aimed to investigate whether acute or sustained trans‐resveratrol administration impacted on the distribution of trans‐resveratrol and its metabolites in brain, heart, and liver.Methods and resultsWe used ultra‐HPLC quadrupole‐TOF (UHPLC‐Q‐TOF) in a full‐scan mode to identify and assess large numbers of resveratrol metabolites. For acute intake, mice were overfed with a single dose of trans‐resveratrol (150 mg/kg) and organs were collected after 30 and 60 min. For sustained intake, trans‐resveratrol was given in the chow (0.04% w/w corresponding to 40 mg/kg/day), and plasma and the organs were collected after 3 months of this resveratrol diet. We found that trans‐resveratrol‐3‐O‐glucuronide and resveratrol‐3‐sulfate were the main metabolites found after acute intake, and free trans‐resveratrol (in the brain and heart) and dihydroresveratrol derivatives were found after sustained administrationConclusionsOur results show notable differences between acute and sustained administration of trans‐resveratrol and distribution of trans‐resveratrol and its metabolites in mouse heart, brain, and liver. The results suggest a strategy for development of galenic forms of resveratrol.
Metabolically healthy obesity and incident chronic kidney disease: The role of systemic inflammation in a prospective study
Authors: Lin Lin , Peng Kui , Du Rui , Huang Xiaolin , Lu Jieli , Xu Yu , Xu Min , Chen Yuhong , Bi Yufang , Wang Weiqing 
Published: February 2017

ObjectiveTo investigate the association between the metabolically healthy obesity (MHO) phenotype and incident chronic kidney disease (CKD) in a Chinese population and whether systemic inflammation affects this association.MethodsA cohort study was performed with 2,491 Chinese adults. Body mass index ≥ 25.0 kg/m2 was defined as obesity. CKD was defined as estimated glomerular filtration rate < 60 mL/min per 1.73 m2 or urinary albumin‐to‐creatinine ratio ≥ 30 mg/g. High‐sensitivity C‐reactive protein (hsCRP) was used as a surrogate marker of systemic inflammation.ResultsOver a median follow‐up period of 3.9 years, 243 of 2,491 participants developed incident CKD (9.8%). Compared with metabolically healthy nonobesity (MHNO), MHO was associated with incident CKD (odds ratio [OR] = 1.65, 95% confidence interval [CI] 1.01‐2.69), but not after adjustment for hsCRP. The MHO/hsCRP ≥ 0.20 mg/L group, but not the MHO/hsCRP < 0.20 mg/L group, had an increased OR for incident CKD (OR = 2.66, 95% CI 1.37‐5.14), with the MHNO/hsCRP < 0.20 mg/L group as the reference.ConclusionsMHO was significantly associated with incident CKD, and the level of systemic inflammation partially explained this association.