bluuebunny/crossref_metadata_2025_split huggingface dataset:
A corpus-based analysis of the verb pleróo in Ancient Greek
Authors: Ioannou Georgios 
Published: August 2017

Abstract
This is a corpus-based study of the development of the verb pleróo in Ancient Greek, originally meaning fill, from the 6th c. bce in Classical Greek, up to the end of the 3rd c. bce in Hellenistic Koiné. It implements a hierarchical cluster analysis and a multiple correspondence analysis of the sum of the attested instances of pleróo of that period, divided by century. It explores the gains following a syncretism between two methodological strands: earlier introspective analyses postulating variant construals over intuitively grasped schematic configurations such as image schemas, and strictly inductive methods based on statistical analyses of correlations between co-occurring formal and semantic features. Thus, it examines the relevance of the container image-schema to the architecture of the schematic construction corresponding to the prototypical and historically preceding sense of pleróo, fill. Consequently, it observes how shifts in the featural configurations detected through statistical analysis, leading to the emergence of new senses, correspond to successive shifts on the perspectival salience of elements in the schematic construction of the verb.
Epidemiology, Clinical Features, and Outcome of Infective Endocarditis due to Abiotrophia Species and Granulicatella Species: Report of 76 Cases, 2000–2015
Authors: Téllez Adrián , Ambrosioni Juan , Llopis Jaume , Pericàs Juan M , Falces Carles , Almela Manel , Garcia de la Mària Cristina , Hernandez-Meneses Marta , Vidal Bàrbara , Sandoval Elena , Quintana Eduard , Fuster David , Tolosana José M , Marco Francesc , Moreno Asunción , Miro José M ,   Hospital Clínic Infective Endocarditis Investigators, Miró Jose M , Ambrosioni Juan , Pericàs Juan M , Téllez Adrian , Hernandez-Meneses Marta , Moreno Asunción , Garcia de la Mària Cristina , Garcia-Gonzalez Javier , Marco Francesc , Almela Manel , Vila Jordi , Quintana Eduard , Sandoval Elena , Paré Juan C , Falces Carlos , Pereda Daniel , Cartañá Ramon , Ninot Salvador , Azqueta Manel , Sitges Marta , Vidal Barbara , Pomar José L , Castella Manuel , Tolosana José M , Ortiz José , Fita Guillermina , Rovira Irene , Fuster David , Ramírez Jose , Brunet Mercè , Soy Dolors , Castro Pedro , Llopis Jaume 
Published: August 2017

AbstractBackgroundInfective endocarditis (IE) caused by Abiotrophia (ABI) and Granulicatella (GRA) species is poorly studied. This work aims to describe and compare the main features of ABI and GRA IE.MethodsWe performed a retrospective study of 12 IE institutional cases of GRA or ABI and of 64 cases published in the literature (overall, 38 ABI and 38 GRA IE cases).ResultsABI/GRA IE represented 1.51% of IE cases in our institution between 2000 and 2015, compared to 0.88% of HACEK (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella)–related IE and 16.62% of Viridans group streptococci (VGS) IE. Institutional ABI/GRA IE case characteristics were comparable to that of VGS, but periannular complications were more frequent (P = .008). Congenital heart disease was reported in 4 (10.5%) ABI and in 11 (28.9%) GRA cases (P = .04). Mitral valve was more frequently involved in ABI than in GRA (P < .001). Patient sex, prosthetic IE, aortic involvement, penicillin susceptibility, and surgical treatment were comparable between the genera. New-onset heart failure was the most frequent complication without genera differences (P = .21). Five (13.2%) ABI patients and 2 (5.3%) GRA patients died (P = .23). Factors associated with higher mortality were age (P = .02) and new-onset heart failure (P = .02). The genus (GRA vs ABI) was not associated with higher mortality (P = .23).ConclusionsGRA/ABI IE was more prevalent than HACEK IE and approximately one-tenth as prevalent as VGS; periannular complications were more frequent. GRA and ABI genera IE presented similar clinical features and outcomes. Overall mortality was low, and related to age and development of heart failure.
Radon inhalation induces manganese-superoxide dismutase in mouse brain via nuclear factor-κB activation
Authors: Kataoka Takahiro , Etani Reo , Kanzaki Norie , Kobashi Yusuke , Yunoki Yuto , Ishida Tsuyoshi , Sakoda Akihiro , Ishimori Yuu , Yamaoka Kiyonori 
Published: August 2017

Abstract
Although radon inhalation increases superoxide dismutase (SOD) activities in mouse organs, the mechanisms and pathways have not yet been fully clarified. The aim of this study was to determine the details of SOD activation in mouse brain tissue following the inhalation of radon at concentrations of 500 or 2000 Bq/m3 for 24 h. After inhalation, brains were removed quickly for analysis. Radon inhalation increased the manganese (Mn)-SOD level and mitochondrial SOD activity. However, the differences were not significant. There were no changes in the Cu/Zn-SOD level or cytosolic SOD activity. Radon inhalation increased the brain nuclear factor (NF)-κB content, which regulates the induction of Mn-SOD, in the nuclear and cytosolic compartments. The level of inhibitor of nuclear factor κB kinase subunit β (IKK-β), which activates NF-κB, was slightly increased by radon inhalation. The expression of cytoplasmic ataxia-telangiectasia mutated kinase in mice inhaling radon at 500 Bq/m3 was 50% higher than in control mice. In addition, NF-κB–inducing kinase was slightly increased after inhaling radon at 2000 Bq/m3. These findings suggest that radon inhalation might induce Mn-SOD protein via NF-κB activation that occurs in response to DNA damage and oxidative stress.
Thromboprophylaxis in Spinal Surgery
Authors: Mosenthal William P. , Landy David C. , Boyajian Haroutioun H. , Idowu Olumuyiwa A. , Shi Lewis L. , Ramos Edwin , Lee Michael J. 
Published: August 2017

Study Design.
Systematic review and meta-analysis.

Objective.
Determine the incidence of deep vein thrombosis (DVT) and pulmonary embolism (PE) in spinal surgery patients receiving no thromboprophylaxis, mechanoprophylaxis, and chemoprophylaxis.

Summary of Background Data.
The incidence of thromboembolic complications after spinal surgery is not well established. Although a variety of effective mechanical and chemical thromboprophylaxis interventions exist, their role in spinal surgery remains unclear. Spine surgeons are faced with the difficult decision of balancing the risk of death from a thromboembolic complication against the risk of permanent neurological damage from an epidural hematoma (EDH).

Methods.
The Medline database was queried using combinations of the terms related to the aforementioned subject matter. Articles meeting our predetermined inclusion criteria were reviewed and relevant data extracted. Meta-analyses were created using a random-effects model for incidence of DVT and PE by type of thromboprophylaxis, method of screening, and study type.

Results.
Twenty-eight articles were included in the final analyses. The higher mean incidence of DVT and PE in the mechanoprophylaxis group (DVT: 1%, PE: 0.81%) compared to the chemoprophylaxis group (DVT: 0.85%, PE: 0.58%) was not observed to be statistically significant. Six percent of PEs was fatal; the rate of EDHs was 0.3%. The incidence of DVT was higher in prospective studies (1.4%) compared to retrospective studies (0.61%); the incidence of DVT was not affected by whether the study screened only symptomatic patients.

Conclusion.
Although the incidence of DVT and PE was relatively low regardless of prophylaxis type, the true incidence is difficult to determine given the heterogeneous nature of the small number of studies available in the literature. Our findings suggest there may be a role for chemoprophylaxis given the relatively high rate of fatal PE. Future studies are needed to determine which patient population would benefit most from chemoprophylaxis.

Level of Evidence: 2
Noncontrast Magnetic Resonance Lymphography for Evaluation of Lymph Node Transfer for Secondary Upper Limb Lymphedema
Authors: Arrivé Lionel , Derhy Sarah , Dlimi Chrif , El Mouhadi Sanaa , Monnier-Cholley Laurence , Becker Corinne 
Published: August 2017

Background:
The authors’ purpose was to evaluate the results of axillary lymph node transplantation with noncontrast magnetic resonance lymphography in 15 patients with secondary upper limb lymphedema.

Methods:
Fifteen female patients with lymphedema following breast cancer treatment underwent lymph node transplantation. Noncontrast magnetic resonance lymphography was obtained with a free-breathing three-dimensional fast spin-echo sequence. Image analysis included criteria both before surgery (i.e., severity of lymphedema graded as absent, mild, moderate, or severe; involvement of the muscular compartment; and distal dilated lymphatic vessels) and after surgery (i.e., visualization of the site of transplantation; visualization of transplanted lymph nodes; and severity of lymphedema with regard to pretransplantation severity, namely, improvement, stability, or aggravation). Clinically, circumferential measures were performed at four different levels.

Results:
Follow-up magnetic resonance examinations were performed at least 6 months after lymph node transplantation, with a longest follow-up time of 42 months. In two patients, no lymphedema was visualized before lymph node transplantation with magnetic resonance lymphography. In the other 13 patients, lymphedema was mild in four patients, moderate in five patients, and severe in the other four patients. After lymph node transplantation, an improvement of upper limb lymphedema was observed in seven of nine patients with moderate or severe upper limb lymphedema. In the 11 patients in whom comparison of magnetic resonance lymphography with circumferential measurement was available, evaluations were concordant in 10 cases.

Conclusion:
Noncontrast magnetic resonance lymphography may be used as an objective technique to analyze the results of lymph node transplantation.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
The toxic nature of murine amylin and the immune responsivity of pancreatic islet to conformational antibody in mice
Authors: Erthal Luiza C. S. , Jotha-Mattos Luana , Lara Flávio Alves , dos Reis Sabrina Alves , Oliveira Pascarelli Bernardo Miguel de , Costa Cinthia Melo , Souza Kleber L. A. , Lima Luís Maurício T. R. 
Published: August 2017

ABSTRACTThe human amylin is a pancreatic peptide hormone cosecreted with amylin and found in hyperhormonemic state along with insulin in subclinical diabetes. Amylin has been associated with the pathology of type 2 diabetes, particularly due to its ability to assembly into toxic oligomers and amyloid speciments. On the other hand, some variants such as murine amylin has been described as non amyloidogenic, eitherin vitroorin vivo. Recent data have demonstrated the amyloid propensity of murine amylin and the therapeutic analogue pramlintide, suggesting a universality for amylin amyloidosis. Here we report the amyloidogenesis of murine amylin, which showed lower responsivity to the fluorescent probe thioflavin T compared to human amylin, but presented highly organized fibrilar amyloid material. The aggregation of murine amylin also resulted in the formation of cytotoxic specimens, as evaluatedin vitroin INS-1 cells. The aggregation product from murine amylin was responsive to a specific antibody raised against amyloid oligomers, the A11 oligomer antibody. Pancreatic islets of swiss mice have also shown responsivity for the anti-oligomer, indicating the natural abundance of such specimen in rodents. These data provide for the first time evidences for the toxic nature of oligomeric assemblies of murine amylin and its existence in non-transgenic mice.Highlights- Murine amylin forms oligomer species and amyloid fibrilsin vitro- The murine amylin aggregation product display cellular toxicity- A11 anti-oligomer antibody recognizes murine amylinin vitro- Non-transgenic mice display immunoresposivity to anti-oligomer in pancreatic islet
Computational correction of cross-contamination due to exclusion amplification barcode spreading
Authors: Larsson Anton JM , Stanley Geoff , Sinha Rahul , Weissman Irving L. , Sandberg Rickard 
Published: August 2017

AbstractRecent advances in sequencing technology have considerably increased the throughput and decreased the cost of short-read sequencing by using high-density patterned flow cells. However, high rates of cross-contamination between multiplexed libraries have been observed on data from these machines, likely due to index-switching during exclusion amplification1,2. Here, we demonstrate that a computational correction procedure based on the Sylvester equation removed 80-90% of the false positive expression signal and eliminated spurious clustering. The computational correction procedure can therefore be used to rescue aspects of affected sequence data so that researchers can take advantage of cost-effective sequencing on patterned flow cells.
Disruption of thyroid endocrine in zebrafish exposed to BDE-209
Authors: Li Dong , Wang Xin 
Published: August 2017

AbstractPolybrominated diphenyl ethers (PBDs) could adversely affect the thyroid endocrine system; previous studies report that BDE-209 has the potential effect on the fish thyroid endocrine system. In this study, we aimed to verify the bioconcentration and metabolism of BDE-209 in zebrafish. One day post-fertilization (dpf) zebrafish embryos were treated with different concentrations of BDE-209 (0, 0.01, 0.1 and 1 mg/L) until 10 dpf. BDE-209 was obviously accumulated in the zebrafish after 10 days exposure, and the metabolic products such as octa-BDE and nona-BDE were detected. After treated with BDE-209, the triiodthyronine (T3) and thyroxine (T4) levels were significantly decreased, suggesting that exposure to BDE-209 could disrupt the thyroid endocrine system in zebrafish. The transcriptional expression of genes involved in the hypothalamic-pituitary-thyroid (HPT) axis was altered. The mRNA expression levels of corticotrophin-releasing hormone (CRH) and thyroid-stimulating hormone (TSHβ) were significantly increased. The mRNA expression of pax8 and nkx2.1 which regulate thyroid development and synthesis were also increased. These data indicated that BDE-209 could disrupt the thyroid endocrine system in zebrafish, which could be assessed by hypothalamic-pituitary-thyroid axis.
Detection and removal of barcode swapping in single-cell RNA-seq data
Authors: Griffiths Jonathan A. , Richard Arianne C. , Bach Karsten , Lun Aaron T.L. , Marioni John C 
Published: August 2017

AbstractBarcode swapping results in the mislabeling of sequencing reads between multiplexed samples on the new patterned flow cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays, especially for single-cell studies where many samples are routinely multiplexed together. The severity and consequences of barcode swapping for single-cell transcriptomic studies remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in each of two plate-based single-cell RNA sequencing datasets. We found that approximately 2.5% of reads were mislabeled between samples on the HiSeq 4000 machine, which is lower than previous reports. We observed no correlation between the swapped fraction of reads and the concentration of free barcode across plates. Furthermore, we have demonstrated that barcode swapping may generate complex but artefactual cell libraries in droplet-based single-cell RNA sequencing studies. To eliminate these artefacts, we have developed an algorithm to exclude individual molecules that have swapped between samples in 10X Genomics experiments, exploiting the combinatorial complexity present in the data. This permits the continued use of cutting-edge sequencing machines for droplet-based experiments while avoiding the confounding effects of barcode swapping.
Landscape of human miRNA variation and conservation using Annotative Database of miRNA Elements, ADmiRE
Authors: Oak Ninad , Ghosh Rajarshi , Plon Sharon E. 
Published: August 2017

AbstractMicroRNAs (miRNAs) are the most abundant class of non-coding RNAs that regulate expression of >60% genes and are frequently deregulated in many human diseases. Sequence variants in miRNAs are expected to have a high impact on miRNA function. However, the lack of miRNA variant annotation and prioritization guidelines has hampered this analysis from whole genome/exome sequencing (WGS/WES) studies. Through the development of anAnnotativeDatabase ofmiRNAElements, ADmiRE workflow, we re-annotated the publicly available population dataset of gnomAD 15,596 WGS and 123,136 WES and describe 26,094 precursor-miRNA variants. AdmiRE annotates twice the miRNA variants predicted by existing tools which prioritize variation relative to protein coding regions. We provide the allele frequency distribution of miRNA variation which is comparable to variation in exonic regions. This distribution is similar for miRNAs located in the intragenic and intergenic genomic context. Moreover, ‘high confidence’ miRNAs (designated by miRBase) harbor less variation (the majority contributed by rare variants) compared with the remaining miRNAs. We identify 279 miRNAs highly constrained with little or no variation in gnomAD. We further describe the evolutionary conservation of miRNAs across 100 vertebrates and identify 434 highly conserved miRNAs. We demonstrate that these constraint and conservation metrics (now incorporated into the ADmiRE workflow) characterize miRNAs previously implicated in human diseases. In conclusion, through the development of ADmiRE, we comprehensively analyze the landscape of miRNA sequence variation in large human population datasets and provide miRNA vertebrate conservation scores to aid future studies of miRNA variation in human diseases.
A computational framework for detecting signatures of accelerated somatic evolution in cancer genomes
Authors: Smith Kyle S. , Ghosh Debashis , Pollard Katherine S. , De Subhajyoti 
Published: August 2017

ABSTRACTBy accumulation of somatic mutations, cancer genomes evolve, diverging away from the genome of the host. It remains unclear to what extent somatic evolutionary divergence is comparable across different regions of the cancer genome versus concentrated in specific genomic elements. We present a novel computational framework, SASE-mapper, to identify genomic regions that show signatures of accelerated somatic evolution (SASE) in a subset of samples in a cohort, marked by accumulation of an excess of somatic mutations compared to that expected based on local, context-aware background mutation rates in the cancer genomes. Analyzing tumor whole genome sequencing data for 365 samples from 5 cohorts we detect recurrent SASE at a genome-wide scale. The SASEs were enriched for genomic elements associated with active chromatin, and regulatory regions of several known cancer genes had SASE in multiple cohorts. Regions with SASE carried specific mutagenic signatures and often co-localized within the 3D nuclear space suggesting their common basis. A subset of SASEs was frequently associated with regulatory changes in key cancer pathways and also poor clinical outcome. While the SASE-associated mutations were not necessarily recurrent at base-pair resolution, the SASEs recurrently targeted same functional regions, with similar consequences. It is likely that regulatory redundancy and plasticity promote prevalence of SASE-like patterns in the cancer genomes.
A Deep Learning Model for Predicting Tumor Suppressor Genes and Oncogenes from PDB Structure
Authors: Tavanaei Amirhossein , Anandanadarajah Nishanth , Maida Anthony , Loganantharaj Rasiah 
Published: August 2017

AbstractWhile cancer is a heterogeneous complex of distinct diseases, the common underlying mechanism for uncontrolled tumor growth is due to mutations in proto-oncogenes and the loss of the regulatory function of tumor suppression genes. In this paper we propose a novel deep learning model for predicting tumor suppression genes (TSGs) and proto-oncogenes (OGs) from their Protein Data Bank (PDB) three dimensional structures. Specifically, we develop a convolutional neural network (CNN) to classify the feature map sets extracted from the tertiary protein structures. Each feature map set represents particular biological features associated with the atomic coordinates appearing on the outer surface of protein’s three dimensional structure. The experimental results on the collected dataset for classifying TSGs and OGs demonstrate promising performance with 82.57% accuracy and 0.89 area under ROC curve. The initial success of the proposed model warrants further study to develop a comprehensive model to identify the cancer driver genes or events using the principle cancer genes (TSG and OG).
Market reaction to open innovation announcements
Authors: Szutowski Dawid 
Published: August 2017

PurposeOpen innovation is of crucial importance for all companies operating in the economics of widely distributed knowledge. However, the effects of its disclosure remain largely uncharted in the case of service companies. Therefore, the purpose of this paper is to measure the impact of open innovation announcements on the market value (MV) of service enterprises.Design/methodology/approachThe research covered 398 open innovation announcements released by service companies. It was conducted in the whole of the European Union in the period February 2011-December 2016. The data were analysed in the short and long term with the use of event-study and buy-and-hold methods.FindingsThe results indicated the significant positive effect of open innovation disclosure in both short and long term. At the same time, the market was not able to immediately fully value the information in the short run and tended to overestimate the positive effect of the innovation announced. No significant leakage and dissemination effects were observed prior to the announcement. There was no significant difference in the magnitude of positive and negative reactions to the releases.Practical implicationsFrom the point of view of business practice the research proved the benefits of information disclosure and supported the long-term planning. From the investors’ viewpoint, it signalled the small risk of significant fluctuations resulting from aggressive trading prior to the announcement and unwinding part of the acquired position afterwards.Originality/valueThe paper attempts to fulfil the research gap on the impact of the announcements on open innovation on the MV of companies.