bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is there section deformation resulting in differential change of nuclear numerical densities along the z axis of thick methacrylate or paraffin sections?
Authors: Xu Wei , Guo Yang , Xiang Yu , Yang Zheng‐Wei 
Published: June 2019

AbstractThe optical disector, a three‐dimensional counting frame or probe in stereology, is often positioned in the middle (depth) of a thick section for unbiased nuclear counting. Using 30–40 μm thick methacrylate or paraffin sections for nuclear counting of neurons with the optical disector, however, some studies showed markedly higher nuclear densities at 10% of the section thickness near the top or bottom surface of the section, suggestive of deformation of section along its z axis and thus affecting the number estimation. To verify the findings, this study obtained two sets of 12–14 methacrylate sections (average thicknesses 21.7 and 29.4 μm) and two sets of 12 paraffin sections (average thicknesses 13.8 and 29.2 μm) from mature rat testes. Each section was used to count round spermatid nuclei in the seminiferous epithelium densely packed with the cells, using 3–4 consecutive disectors placed vertically (along the z axis of the section) from the top surface of the section, through the whole section thickness (two sets of methacrylate and paraffin sections) or in 80–83% of the thickness (other sections). The results demonstrated that, overall, there were no considerable nonuniform changes of the nuclear densities along the z axis of the sections.
The cephalic morphology of the troglobiontic cholevine species Troglocharinus ferreri (Coleoptera, Leiodidae)
Authors: Luo Xiao‐Zhu , Antunes‐Carvalho Caio , Wipfler Benjamin , Ribera Ignacio , Beutel Rolf G. 
Published: June 2019

AbstractLeiodidae are the second largest subterranean radiation of beetles at family rank. To explore morphological trends linked with troglobiontic habits and characters with potential phylogenetic significance, the head of the cave‐dwelling species Troglocharinus ferreri (Cholevinae, Leptodirini) was examined in detail. Overall, the general pattern is similar to what is found in Catops ventricosus (Cholevini). Shared apomorphic features include a fully exposed anterolateral concavity containing the antennal socket, a distinct bead above this depression, a bilobed lip‐like structure anterad the labrum, a flat elevated portion of the ventral mandibular surface, and a ventral process at the proximomesal edge of this mandibular area. The tentorial structures are well‐developed as in C. ventricosus, with a large laminatentorium and somewhat shortened dorsal arms. The mouthparts are largely unmodified, with the exception of unusually well‐developed extrinsic maxillary muscles. Features of T. ferreri obviously linked with subterranean habits are the complete lack of compound eyes, circumocular ridges, and optic lobes. A series of characters is similar to conditions found in other genera of Leptodirini: the head capsule completely lacks a protruding ocular region, a distinct neck is missing, the transverse occipital crest is indistinct, and the antennae are elongate and lack a distinct club. Two different trends of cephalic transformations occur in troglobiontic Leptodirini, with some genera like Troglocharinus and Leptodirus having elongated head capsules and antennae, and others having broadened, more transverse heads. In contrast, the modifications are more uniform in the closely related Ptomaphagini, with a pattern distinctly differing from Leptodirini: the head is transverse, with a distinctly protruding ocular region, a distinct transverse occipital crest, and a very narrow neck region.
Protist diversity and community assembly in surface sediments of the South China Sea
Authors: Wu Wenxue , Huang Bangqin 
Published: June 2019

AbstractProtists are pivotal components of marine ecosystems in terms of their high diversity, but protist communities have been poorly explored in benthic environments. Here, we investigated protist diversity and community assembly in surface sediments in the South China Sea (SCS) at a basin scale. Pyrosequencing of 18S rDNA was performed for a total of six samples taken from the surface seafloor at water depths ranging from 79 to 2,939 m. We found that Cercozoa was the dominant group, accounting for an average of 39.9% and 25.3% of the reads and operational taxonomic units (OTUs), respectively. The Cercozoa taxa were highly diverse, comprising 14 phylogenetic clades, six of which were affiliated with unknown groups belonging to Filosa and Endomyxa. Fungi were also an important group in both read‐ (18.1% on average) and OTU‐derived (9.3% on average) results. Moreover, the turnover patterns of the protist communities were differently explained by species sorting (53.3%), dispersal limitation (33.3%), mass effects (0%), and drift (13.3%). In summary, our findings show that the basin‐wide protist communities in the surface sediments of the SCS are primarily dominated by Cercozoa and are mainly assembled by species sorting and dispersal limitation.
Epigenetic polypharmacology: A new frontier for epi‐drug discovery
Authors: Tomaselli Daniela , Lucidi Alessia , Rotili Dante , Mai Antonello 
Published: June 2019

AbstractRecently, despite the great success achieved by the so‐called “magic bullets” in the treatment of different diseases through a marked and specific interaction with the target of interest, the pharmacological research is moving toward the development of “molecular network active compounds,” embracing the related polypharmacology approach. This strategy was born to overcome the main limitations of the single target therapy leading to a superior therapeutic effect, a decrease of adverse reactions, and a reduction of potential mechanism(s) of drug resistance caused by robustness and redundancy of biological pathways. It has become clear that multifactorial diseases such as cancer, neurological, and inflammatory disorders, may require more complex therapeutic approaches hitting a certain biological system as a whole. Concerning epigenetics, the goal of the multi‐epi‐target approach consists in the development of small molecules able to simultaneously and (often) reversibly bind different specific epi‐targets. To date, two dual histone deacetylase/kinase inhibitors (CUDC‐101 and CUDC‐907) are in an advanced stage of clinical trials. In the last years, the growing interest in polypharmacology encouraged the publication of high‐quality reviews on combination therapy and hybrid molecules. Hence, to update the state‐of‐the‐art of these therapeutic approaches avoiding redundancy, herein we focused only on multiple medication therapies and multitargeting compounds exploiting epigenetic plus nonepigenetic drugs reported in the literature in 2018. In addition, all the multi‐epi‐target inhibitors known in literature so far, hitting two or more epigenetic targets, have been included.
Identification of gene variants in 130 Han Chinese patients with hypospadias by targeted next‐generation sequencing
Authors: Zhang Wanyu , Shi Jinxiu , Zhang Chenhui , Jiang Xincheng , Wang Junqi , Wang Wei , Wang Defen , Ni Jihong , Chen Lifen , Lu Wenli , Xiao Yuan , Ye Weijing , Dong Zhiya 
Published: June 2019

AbstractBackgroundHypospadias is a common congenital malformation of male external genitalia, which mainly manifests as an abnormal urethral opening on the ventral side of the penis. The etiology and clinical phenotype of hypospadias is highly heterogeneous, and its clinical diagnosis is challenging. Currently, over 70% of patients have an unknown etiology. Here, we performed a targeted analysis of gene mutations in 130 patients with hypospadias of unknown etiology to find the precise genetic cause.MethodsWe developed a targeted next‐generation sequencing (NGS) panel, encompassing the exon coding regions of 105 genes involved in external genitalia and urogenital tract development and performed sequencing analysis on 130 children with hypospadias of unknown etiology.ResultsIn total, 25 patients with hypospadias (19.2%) were found to have 20 mutations among the nine genes involved in external genitalia and urogenital tract development, including 16 reported and four novel mutation sites. Twenty‐two patients (16.9%) had diagnostic variants. Multiple genetic mutations were identified in three of the 25 patients. Hypospadias combined with micropenis was the most common phenotype (68%) in 25 patients.ConclusionsHigher frequency mutations were identified in SRD5A2 (52%) and AR (24%) in our patient cohort. Middle or posterior hypospadias with micropenis may be significant indicators of genetic variations. Polygenic inheritance may be a rare genetic cause of hypospadias.
A convolutional neural network for ultra‐low‐dose CT denoising and emphysema screening
Authors: Zhao Tingting , McNitt‐Gray Michael , Ruan Dan 
Published: June 2019

PurposeReducing dose level to achieve ALARA is an important task in diagnostic and therapeutic applications of computed tomography (CT) imaging. Effective image quality enhancement strategies are crucial to compensate for the degradation caused by dose reduction. In the past few years, deep learning approaches have demonstrated promising denoising performance on natural/synthetic images. This study tailors a neural network model for (ultra‐)low‐dose CT denoising, and assesses its performance in enhancing CT image quality and emphysema quantification.MethodsThe noise statistics in low‐dose CT images has its unique characteristics and differs from that used in general denoising models. In this study, we first simulate the paired ultra‐low‐dose and targeted high‐quality image of reference, with a well‐validated pipeline. These paired images are used to train a denoising convolutional neural network (DnCNN) with residual mapping. The performance of the DnCNN tailored to CT denoising (DnCNN‐CT) is assessed over various dose reduction levels, with respect to both image quality and emphysema scoring quantification. The possible over‐smoothing behavior of DnCNN and its impact on different subcohort of patients are also investigated.ResultsPerformance evaluation results showed that DnCNN‐CT provided significant image quality enhancement, especially for very‐low‐dose level. With DnCNN‐CT denoising on 3%‐dose cases, the peak signal‐to‐noise ratio improved by 8 dB and the structure similarity index increased by 0.15. This outperformed the original DnCNN and the state‐of‐the‐art nonlocal‐mean‐type denoising scheme. Emphysema mask was also investigated, where lung voxels of abnormally low attenuation coefficient were marked as potential emphysema. Emphysema mask generated after DnCNN‐CT denoising on 3%‐dose image was demonstrated to agree well with that from the full‐dose reference. Despite over‐smoothing in DnCNN denoising, which contributed to slight underestimation of emphysema score compared to the reference, such minor overcorrection did not affect clinical conclusions. The proposed method provided effective detection for cases with appreciable emphysema while serving as a reasonable correction for normal cases without emphysema.ConclusionsThis work provides a tailored DnCNN for (ultra‐)low‐dose CT denoising, and demonstrates significant improvement on both the image quality and the clinical emphysema quantification accuracy over various dose levels. The clinical conclusion of emphysema obtained from the denoised low‐dose images agrees well with that from the full‐dose ones.
A thermally polarized 129Xe phantom for quality assurance in multi‐center hyperpolarized gas MRI studies
Authors: Bier Elianna A. , Nouls John C. , Wang Ziyi , He Mu , Schrank Geoff , Morales‐Medina Naomi , Hashoian Ralph , Svetlik Harvey , Mugler John P. , Driehuys Bastiaan 
Published: June 2019

PurposeHyperpolarized 129Xe MR is increasingly being adopted worldwide, but no standards exist for assessing or comparing performance at different 129Xe imaging centers. Therefore, we sought to develop a thermally polarized xenon phantom assembly, approximating the size of a human torso, along with an associated imaging protocol to enable rapid quality‐assurance imaging.MethodsMR‐compatible pressure vessels, with an internal volume of 5.85 L, were constructed from pressure‐rated, engineering grade PE4710 high‐density polyethylene. They were filled with a mixture of 61% natural xenon and 39% oxygen to approximately 11.6 bar and placed in a loader shell filled with a 0.56% saline solution to mimic the human chest. Imaging employed a 2D spoiled gradient‐echo sequence using non‐slice‐selective excitation (TR/TE = 750/6.13 ms, flip angle = 74°, FOV = 40 × 440 mm, matrix = 64 × 32, bandwidth = 30 Hz/pixel, averages = 4), resulting in a 1.6 min acquisition. System characterization and imaging were performed at 8 different MRI centers.ResultsAt 3 Telsa, 129Xe in the pressure vessels was characterized by T1 = 580.5 ± 8.3 ms, linewidth = 0.21 ppm, and chemical shift = +10.2 ppm. The phantom assembly was used to obtain transmit voltage calibrations and 2D and 3D images across multiple coil and scanner configurations at 8 sites. Across the 5 sites that employed a standard flexible chest coil, the SNR was 12.4 ± 1.8.ConclusionThe high‐density polyethylene pressure vessels filled with thermally polarized xenon and associated loader shell combine to form a phantom assembly that enables spectroscopic and imaging acquisitions that can be used for testing, quality assurance, and performance tracking—capabilities essential for standardizing hyperpolarized 129Xe MRI within and across institutions.
A randomized study comparing regular care with a nurse‐led clinic based on tight disease activity control and person‐centred care in patients with rheumatoid arthritis with moderate/high disease activity: A 6‐month evaluation
Authors: Bergsten Ulrika , Almehed Katarina , Baigi Amir , Jacobsson Lennart T.H. 
Published: June 2019

AbstractIntroductionA recent survey showed that 27% of rheumatoid arthritis (RA) patients had inadequately controlled disease activity. Hence, there is a need for new strategies aiming at improving patient outcomes. The aim of the present study was to evaluate the effect of a nurse‐led clinic with frequent visits, treat‐to‐target and person‐centred care of patients with established RA and moderate‐to‐high disease activity compared with patients receiving regular care.MethodsThe study was a randomized, controlled trial over 26 weeks, with a nonrandomized extension to week 50. Patients were randomized to an intervention group (IG; nurse‐led clinic) based on person‐centred care, frequent visits and “treat to target”, or to a control group (CG) which visited the clinic according to care as usual. The primary outcome was the difference in the DAS28 change between the IG and the CG groups.ResultsA total of 332 patients were screened for eligibility, of which 70 were randomly assigned to either the IG (n = 36) or the CG (n = 34) group. The primary outcome was not met, although patients in the IG group tended to improve more than those in the CG group (difference: 0.43 (95% confidence interval [CI] –0.27, 1.13). In both the IG and CG groups, delta‐DAS28 improved significantly. The European League Against Rheumatology moderate or good response was achieved by 76% (95% CI 58, 89) in the IG and 49% (95% CI 32, 65) in the CG group.ConclusionsDisease activity tended to improve more with the nurse‐led intervention compared with regular care, although the difference was not significant, probably partly due to the lack of statistical power.
Longitudinal Changes in Measures of Body Fat and Diet Among Adult Tsimane’ Forager‐Horticulturalists of Bolivia, 2002‐2010
Authors: Bethancourt Hilary J. , Leonard William R. , Tanner Susan , Schultz Alan F. , Rosinger Asher Y. 
Published: June 2019

ObjectiveThis study examined changes in body fat and diet among Tsimane’ forager‐horticulturalists and assessed how dietary shifts relate to increases in adiposity between 2002 and 2010.MethodsLongitudinal anthropometric and household‐level dietary recall data from 365 men and 339 women aged ≥20 years in the Tsimane’ Amazonian Panel Study were used. Multilevel mixed‐effects models estimated how BMI, body fat percentage, waist circumference, skinfolds, and fat‐free mass relate to household consumption of crops, hunted or fished foods, domesticated animal products, cooking oil, and refined grains and sugar.ResultsWomen’s prevalence of overweight and obesity increased from 22.6% and 2.4% in 2002 to 28.8% and 8.9% in 2010, respectively, and BMI increased by 0.60% ± 0.12% per year (P < 0.001). Increases in fat‐free mass accounted for some of this observed weight gain among women. Men’s prevalence of overweight and obesity increased from 16.2% and 0.7% to 25.0% and 2.2%, respectively, and BMI increased by 0.22% ± 0.09% per year (P = 0.009). Household use of cooking oil increased and was positively associated with female BMI. Consumption of domesticated animal products did not change significantly but was positively associated with female BMI and male waist circumference.ConclusionsEven small increases in energy‐dense market‐based foods can contribute to adiposity gains among a moderately active, subsistence‐based population.
Pregnancy loss after amniocentesis in monochorionic and dichorionic twin pregnancies: Results from a large population‐based dataset
Authors: Sperling Jeffrey D. , Zlatnik Marya G. , Norton Mary E. , Currier Robert J. 
Published: June 2019

AbstractObjectiveTo determine the loss rate after amniocentesis in twins.MethodsThis cohort study evaluated twin pregnancies with serum screening through the California Prenatal Screening Program. The primary outcome was loss of one or both twins at any gestational age. Exclusions were chromosomal/structural abnormalities, selective fetal reduction, terminations, neonatal deaths, ovum donation, and incomplete data. Loss rates were compared between three groups: (a) screen negative and no amniocentesis, (b) screen positive and accepted, or (c) declined amniocentesis. Multivariate logistic analysis generated adjusted odds ratios (aOR).ResultsThirty‐six thousand eight hundred twenty‐one twin pregnancies had screening: 2698 (7.3%) were screen positive for aneuploidy or neural tube defects (NTD). Among screen‐positive women, 861 (31.9%) were offered amniocentesis and 274 (31.8%) accepted. The post‐procedure loss rate among screen‐negative women was lower than among screen‐positive women (3.0% vs 7.4%; P < .001; aOR 2.62; 95% CI, 1.16‐2.99). Among screen‐positive women, the loss rate was similar for those who underwent amniocentesis and for those who declined (8.8% vs 6.8%; .32; aOR 1.32; 95% CI, 0.66‐1.91).ConclusionTwins that are screen positive for aneuploidy or NTD have an increased risk of pregnancy loss. Those who are screen positive and undergo amniocentesis do not have an increased loss rate.
A European multicentre drug utilisation study of the impact of regulatory measures on prescribing of codeine for pain in children
Authors: Hedenmalm Karin , Blake Kevin , Donegan Katherine , Macia Miguel‐Angel , Gil Miguel , Williams Julie , Montero Dolores , Candore Gianmario , Morales Daniel , Kurz Xavier , Arlett Peter 
Published: June 2019

AbstractPurposeIn June 2013, following recommendations from the World Health Organization (WHO) and Food and Drug Administration (FDA), the European Medicines Agency agreed updates to the codeine product information regarding use for pain in children younger than 12 years and children undergoing tonsillectomy or adenoidectomy (TA) for obstructive sleep apnoea. This study was conducted to (a) assess effectiveness of these measures on codeine prescribing in the “real‐world” setting and (b) test feasibility of a study using a common protocol by regulators with access to databases.MethodsThe study was performed using BIFAP (Spain), CPRD (UK), and IMS® Disease Analyzer (France and Germany) databases. Prescribers included general practitioners (GPs) (France and UK), GPs and paediatricians together (Spain), and GPs, paediatricians, and ear, nose, and throat (ENT) specialists separately (Germany). Between January 2010 and June 2015, prevalence of codeine prescribing was obtained every 6 months, and a time series analysis (joinpoint) was performed. Codeine prescribing within ±30 days of TA was also identified. Furthermore, doses, durations, and prior prescribing of other analgesics were investigated.ResultsOver the 5‐year period, codeine prescribing decreased in children younger than 12 years (by 84% in France and Spain, 44% in GP practices in Germany, and 33% in the United Kingdom). The temporal pattern was compatible with the regulatory intervention in France and the United Kingdom, whereas a decrease throughout the study period was seen in Germany and Spain. Decreased prescribing associated with TA was suggested in ENT practices in Germany.ConclusionsCodeine prescribing for children decreased in line with introduced regulatory measures. Multidatabase studies assessing impact of measures by EU regulators are feasible.
Measurement and mental health disparities: Psychopathology classification and identity assessment
Authors: Eaton Nicholas R. 
Published: June 2019

AbstractMental health disparities research compares groups of individuals with regard to their mental health status, and numerous studies have reported significant and burdensome disparities across populations. This literature is based almost entirely on traditional mental disorder constructs (e.g. major depressive disorder and borderline personality disorder) as defined by official nosologies, but these disorders are associated with numerous problems of reliability and validity. Advances in psychopathology classification research have converged on an alternative conceptualization of mental disorder structure, which comprises a set of transdiagnostic dimensions that cut across traditional diagnostic boundaries and overcome the limitations of traditional diagnoses. The application of these dimensions, particularly those of the hierarchical taxonomy of psychopathology model, holds great promise for mental health disparities research. Measurement considerations associated with these transdiagnostic dimensions, as well as participants' intersecting identities, are discussed. Incorporation of these measurement advances with statistical advances allows for the generation and testing of unique hypotheses related to minority stressors that may give rise to observed disparities. © 2019 John Wiley & Sons, Ltd.
Plant–Microbe Symbiosis: What Has Proteomics Taught Us?
Authors: Khatabi Behnam , Gharechahi Javad , Ghaffari Mohammad Reza , Liu Dilin , Haynes Paul A. , McKay Matthew J. , Mirzaei Mehdi , Salekdeh Ghasem Hosseini 
Published: June 2019

AbstractBeneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics‐based technologies has broadened our understanding of the molecular aspects of beneficial plant–microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis‐specific and symbiosis‐related proteins and post‐translational modifications that play a critical role in mediating symbiotic plant–microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other “omics” data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis‐based “omic” approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant‐associated microbial communities is also discussed.