bluuebunny/crossref_metadata_2025_split huggingface dataset:
“It doesn’t make sense, but it actually does”
Authors: Jung Hanbyul 
Published: March 2019

Abstract
The focus group is typically defined as a form of research interview involving a group of people, facilitated by a moderator with prepared questions (Puchta and Potter 2004). The purpose of focus groups is to elicit participants’ descriptions of feelings, opinions, perceptions, and attitudes concerning the topic. As in other interviews, focus groups lend findings that rely largely on the interactional contingencies and dynamics that occur within, and yet less work has focused on their interactional features. Using conversation analysis (CA), this chapter aims to respecify focus group interaction as a locus for participants’ locally, collaboratively and sometimes incongruently accomplished actions, specifically focusing on the contingency of participants’ discussion sequences. With data examples from focus groups that were conducted with Korean teachers of English (EFL) within a teacher development program evaluation context, this chapter outlines how participants make use of diverse interactional resources in collaboratively constructing responses. This analysis helps to illuminate the major findings of the focus groups.
Not Against Structure, but in Search of Better Structures
Authors: Levine Caroline 
Published: March 2019

Abstract
This brief essay responds to Winfried Fluck’s claim that Forms offers a theory of structures as “endless, all-pervasive domination.” It counters that forms are necessary to all collective life, and that the goal is therefore not to strive for a freedom from all structures, but to identify better, more just and capacitating forms than those we have now.
A City by the Sea: Uncovering Beirut's Media Waste
Authors: Atwood Blake 
Published: March 2019

AbstractWhat kinds of social, cultural, and political narratives emerge when we pay attention to how media are physically rendered as trash? By reducing media to their material forms and tracing their journey from use to disuse, the stories behind media activism start to appear. This article studies where Beirut’s media waste goes and who brings it there. A women-only beach, a refugee camp from the early 20th century, and some of the most vulnerable populations in Lebanon all exist alongside Beirut’s trash. They are part of the story of media in the Arab world because media are waste. While media activism in the Arab world is often marked by the visibility of bodies in protest, media waste in Lebanon is governed by a politics of invisibility that covers and hides the very social problems that media activism seeks to address.
Left ventricular concentric remodelling and functional impairment in women with ischaemia with no obstructive coronary artery disease and intermediate coronary flow reserve: a report from the WISE-CVD study
Authors: Park Seong-Mi , Wei Janet , Cook-Wiens Galen , Nelson Michael D , Thomson Louise , Berman Daniel , Handberg Eileen , Petersen John , Anderson David , Pepine Carl J , Merz C Noel Bairey 
Published: March 2019

Abstract

Aims
Women with evidence of ischaemia but no obstructive coronary artery disease (INOCA) often have coronary microvascular dysfunction (CMD). Although invasively measured coronary flow reserve (CFR) is useful for the diagnosis of CMD, intermediate CFR values are often found of uncertain significance. We investigated myocardial flow reserve and left ventricular (LV) structural and functional remodelling in women with suspected INOCA and intermediate CFR.

Methods and results
Women’s Ischemia Syndrome Evaluation-Coronary Vascular Dysfunction (WISE-CVD) study participants who had invasively measured intermediate CFR of 2.0≤ CFR ≤3.0 (n = 125) were included for this analysis. LV strain, peak filling rate (PFR) and myocardial perfusion reserve index (MPRI) were obtained by cardiac magnetic resonance imaging. Participants were divided: (i) Group 1 (n = 66) high MPRI ≥ 1.8, and (ii) Group 2 (n = 59) low MPRI < 1.8. The mean age was 54 ± 12 years and CFR was 2.46 ± 0.27. MPRI was significantly different but CFR did not differ between groups. LV relative wall thickness (RWT) trended higher in Group 2 and circumferential peak systolic strain and early diastolic strain rate were lower (P = 0.039 and P = 0.035, respectively), despite a similar LV ejection fraction and LV mass. PFR was higher in Group 1 and LV RWT was negatively related to PFR (r = −0.296, P = 0.001).

Conclusions
In women with suspected INOCA and intermediate CFR, those with lower MPRI had a trend towards more adverse remodelling and impaired diastolic LV function compared with those with higher MPRI. CFR was similar between the two groups. These findings provide evidence that both coronary microvessel vasomotion and structural and functional myocardial remodelling contribute to CMD.
Use of an expanded polytetrafluoroethylene valved patch with a sinus in right ventricular outflow tract reconstruction†
Authors: Miyazaki Takako , Yamagishi Masaaki , Yamamoto Yusuke , Itatani Keiichi , Asada Satoshi , Fujita Shuhei , Hongu Hisayuki , Maeda Yoshinobu , Yaku Hitoshi 
Published: March 2019

Abstract

OBJECTIVES:
The objective of this study was to evaluate our late outcomes using expanded polytetrafluoroethylene (ePTFE) valved patches with bulging sinuses and a fan-shaped valve for right ventricular outflow tract (RVOT) reconstruction.

METHODS:
Six hundred and ninety patients underwent RVOT reconstruction using fan-shaped ePTFE valves and ePTFE valved patches with a bulging sinus. The patients’ median age and weight were 1.3 years [range 4 days–64.2 years, interquartile range (IQR) 0.9–2.3 years] and 8.7 (range 2.8–83.1, IQR 7.4–10.5) kg, respectively. The patches were monocuspid in 634 patients, bicuspid in 49 patients and tricuspid in 7 patients. Preoperative and postoperative data were collected retrospectively from the patients’ medical records. The longest follow-up period was 17.5 (7.6 ± 3.9) years.

RESULTS:
There were no deaths related to the ePTFE patch. Pulmonary insufficiency was less than mild in 77.3%, and the peak RVOT gradient was <36 mmHg in 92.3% at the latest follow-up. Redo of RVOT reconstruction was performed in 40 patients, in no cases because of patch infection. Overall freedom from reoperation at 5, 10 and 15 years was 96.5%, 93.1% and 87.9%, respectively; by patient age, the rates at 5, 10 and 15 years for those younger than 1 year were 93.2%, 91.0% and 88.9%, respectively, while for those 1 year or older, they were 97.9%, 94.0% and 88.3%, respectively.

CONCLUSIONS:
Satisfactory long-term outcomes were achieved with ePTFE patches with a bulging sinus and a fan-shaped valve. This ePTFE valved patch could be the optimal choice for RVOT reconstruction.
Results for tricuspid valve surgery in adults with congenital heart disease other than Ebstein’s anomaly†
Authors: Lo Rito Mauro , Grandinetti Maria , Muzio Giulia , Varrica Alessandro , Frigiola Alessandro , Micheletti Angelo , Chessa Massimo , Giamberti Alessandro 
Published: March 2019

AbstractOBJECTIVES:Tricuspid valve (TV) surgery in the adult with congenital heart disease (ACHD) is a frequently performed procedure. The aim of this study was to analyse postoperative and medium-term outcomes.METHODS:We conducted a single-centre retrospective study of patients with ACHD who underwent TV surgery (January 2000–December 2016); patients with Ebstein’s anomalies were excluded. Operative and clinical records were reviewed. Outcomes considered were survival, grade of insufficiency/stenosis and TV reoperation at follow-up.RESULTS:A total of 128 patients with ACHD had TV surgery for functional regurgitation (n = 95), dysplasia (n = 23) and systemic TV (n = 10). Median age was 40.8 years [interquartile range (IQR) 25.3]; 55.5% were men. Preoperative regurgitation was classified as mild (n = 8), moderate (n = 47) and severe (n = 70). The TV was repaired in 109 as follows: ring annuloplasty (n = 43), de Vega annuloplasty (n = 29), Wooler annuloplasty (n = 13), commissural plasty (n = 9), Kay annuloplasty (n = 7) and others (n = 8). The TV was replaced in 19 patients with biological (n = 10) and mechanical (n = 9) prostheses. The median hospital stay was 12 days (IQR 10). The overall mortality rate was 8.6% (n = 11): 2 hospital deaths (1.6%) and 9 late deaths. Survival was 93% [95% confidence interval (CI) 85–97%] at 5 years and 83% (95% CI 70–91%) at 10 years. The median follow-up period was 4.95 years (IQR 7.7) with 1 TV reoperation. Echocardiographic assessment showed ≥moderate regurgitation in 34 (34.3%) patients. Suture plasty had a significantly higher incidence of TV regurgitation ≥moderate compared to ring annuloplasty (48.9% vs 26.3%; P = 0.033).CONCLUSIONS:TV surgery in the ACHD is frequently associated with other main procedures. Stabilizing the TV annulus with a prosthetic ring guarantees lower recurrence of moderate to severe regurgitation compared to suture plasty repair.
Modelling preference heterogeneity using a Bayesian finite mixture of Almost Ideal Demand Systems
Authors: Kehlbacher Ariane , Srinivasan Chittur , McCloy Rachel , Tiffin Richard 
Published: March 2019

AbstractDemand studies often use observable characteristics to proxy preference heterogeneity. It is likely, however, that some households with the same observable characteristics have quite different preferences. An alternative approach is to use a Gaussian mixture of Almost Ideal Demand Systems to capture the heterogeneity. We show how to estimate this with censored purchase data for 5 food categories using Bayesian inference. Using model outputs we infer four different preference classes; how distinct these classes are from one another and which food categories are driving the segmentation process.
Differential Effects of Rapamycin and Metformin in Combination With Rapamycin on Mechanisms of Proteostasis in Cultured Skeletal Myotubes
Authors: Wolff Christopher A , Reid Justin J , Musci Robert V , Bruns Danielle R , Linden Melissa A , Konopka Adam R , Peelor Frederick F , Miller Benjamin F , Hamilton Karyn L 
Published: March 2019

Abstract
mTOR inhibition extends life span in multiple organisms. In mice, when metformin treatment (Met) is added to the mTOR inhibitor rapamycin (Rap), median and maximal life span is extended to a greater degree than with Rap or Met alone. Treatments that extend life span often maintain proteostasis. However, it is less clear how individual tissues, such as skeletal muscle, maintain proteostasis with life span–extending treatments. In C2C12 myotubes, we used deuterium oxide (D2O) to directly measure two primary determinants of proteostasis, protein synthesis, and degradation rates, with Rap or Met+Rap treatments. We accounted for the independent effects of cell growth and loss, and isolated the contribution of autophagy and mitochondrial fission to obtain a comprehensive assessment of protein turnover. Compared with control, both Rap and Met+Rap treatments lowered mitochondrial protein synthesis rates (p &lt; .001) and slowed cellular proliferation (p &lt; .01). These changes resulted in greater activation of mechanisms promoting proteostasis for Rap, but not Met+Rap. Compared with control, both Rap and Met+Rap slowed protein breakdown. Autophagy and mitochondrial fission differentially influenced the proteostatic effects of Rap and Met+Rap in C2C12 myotubes. In conclusion, we demonstrate that Met+Rap did not increase protein turnover and that these treatments do not seem to promote proteostasis through increased autophagy.
Cutoff Value for Correcting White Blood Cell Count for Nucleated Red Blood Cells: What is it? Why is it Important?
Authors: Constantino Benie T , Rivera Gilbert Keith Q 
Published: March 2019

AbstractNucleated red blood cells (RBCs) are normally observed in the peripheral blood of neonates and during pregnancy. Under other conditions, the presence of nucleated RBCs in circulating blood indicates disorder in the blood-producing mechanism. The increased presence of nucleated RBCs, however, falsely elevates the leukocyte count, as measured by most automated hematology analyzers, warranting a manual correction of the leukocyte count. For a long time, cutoff values for correcting white blood cell (WBC) count for the presence of nucleated RBCs have been used regularly, particularly in developing countries. However, because those values are largely subjective, they can vary widely between laboratories worldwide. These varied cutoff values include 1, 5, 10, 20, and 50; it appears that the numbers 5 and 10 are the most common values used in corrections; the reasons require further elucidation. In this article, we discuss the merits of correcting the WBC count for nucleated RBCs at certain cutoff points.
Adverse perinatal outcomes for obese women are influenced by the presence of comorbid diabetes and hypertensive disorders
Authors: Aubry Evelyne M. , Oelhafen Stephan , Fankhauser Niklaus , Raio Luigi , Cignacco Eva L. 
Published: March 2019

AbstractMaternal obesity often occurs together with comorbid diabetes and hypertensive disorders. All three conditions are independently associated with negative perinatal outcomes. Our objective was to determine the risk and burden of adverse perinatal outcome that could attributed to maternal obesity in combination with a comorbid status.We analyzed data from 349’755 singleton deliveries in Switzerland between 2005 and 2016. For the association of maternal obesity in the presence or absence of comorbidities with various perinatal outcomes, we estimated adjusted relative risk (RR) using multivariate regression modeling and determined the multivariate-adjusted attributable fraction (AFp).Regardless of comorbidities, obesity was a main predictor for macrosomia, fracture of the clavicle, plexus paresis, failure to progress in labor and prolonged labor. However, we identified a second subset of outcomes, including neonatal hyperglycemia and preterm birth, that was only significantly linked to obesity in the presence of comorbidities. A third subset of outcomes was independently influenced by either obesity or comorbidities.We suggest that comorbidities such as diabetes and hypertensive disorders should be considered when relating maternal obesity to adverse perinatal outcomes.
A geometric representation unveils learning dynamics in primate neurons
Authors: Cohen Yarden , Schneidman Elad , Paz Rony 
Published: March 2019

AbstractPrimates can quickly and advantageously adopt new behaviors based on changing stimuli relationships. We studied acquisition of a classification task while recording single neurons in the dorsal-anterior-cingulate-cortex (dACC) and the Striatum. Monkeys performed trial-by-trial classification on a rich set of multi-cue patterns, allowing de-novo learning every few days. To examine neural dynamics during the learning itself, we represent each rule with a spanning set of the space formed by the stimuli features. Because neural preference can be expressed by feature combinations, we can track neural dynamics in geometrical terms in this space, allowing a compact description of neural trajectories by observing changes in either vector-magnitude and/or angle-to- rule. We find that a large fraction of cells in both regions follow the behavior during learning. Neurons in the dACC mainly rotate towards the policy, suggesting an increase in selectivity that approximates the rule; whereas in the Putamen we also find a prominent magnitude increase, suggesting strengthening of confidence. Additionally, magnitude increases in the striatum followed rotation in the dACC. Finally, the neural representation at the end of the session predicted next-day behavior. The use of this novel framework enables tracking of neural dynamics during learning and suggests differential yet complementing roles for these brain regions.
GCIB-SEM: A path to 10 nm isotropic imaging of cubic millimeter volumes
Authors: Hayworth K.J. , Peale D. , Januszewski M. , Knott G.W. , Lu Z. , Xu C.S. , Hess H.F. 
Published: March 2019

AbstractFocused Ion Beam Scanning Electron Microscopy (FIB-SEM) generates 3D datasets optimally suited for segmentation of cell ultrastructure and automated connectome tracing but is limited to small fields of view and is therefore incompatible with the new generation of ultrafast multibeam SEMs. In contrast, section-based techniques are multibeam-compatible but are limited in z-resolution making automatic segmentation of cellular ultrastructure difficult. Here we demonstrate a novel 3D electron microscopy technique, Gas Cluster Ion Beam SEM (GCIB-SEM), in which top-down, wide-area ion milling is performed on a series of thick sections, acquiring < 10 nm isotropic datasets of each which are then stitched together to span the full sectioned volume. Based on our results, incorporating GCIB-SEM into existing single beam and multibeam SEM workflows should be straightforward and should dramatically increase reliability while simultaneously improving z-resolution by a factor of 3 or more.
Development of a Comprehensive Antibody Staining Database using a Standardized Analytics Pipeline
Authors: Amir El-ad David , Lee Brian , Badoual Paul , Gordon Martin , Guo Xinzheng V. , Merad Miriam , Rahman Adeeb H. 
Published: March 2019

AbstractLarge-scale immune monitoring experiments (such as clinical trials) are a promising direction for biomarker discovery and responder stratification in immunotherapy. Mass cytometry is one of the tools in the immune monitoring arsenal. We propose a standardized workflow for the acquisition and analysis of large-scale mass cytometry experiments. The workflow includes two-tiered barcoding, a broad lyophilized panel, and the incorporation of a fully automated, cloud-based analysis platform. We applied the workflow to a large antibody staining screen using the LEGENDScreen kit, resulting in single-cell data for 350 antibodies over 71 profiling subsets. The screen recapitulates many known trends in the immune system and reveals potential markers for delineating MAIT cells. Additionally, we examine the effect of fixation on staining intensity and identify several markers where fixation leads to either gain or loss of signal. The standardized workflow can be seamlessly integrated into existing trials. Finally, the antibody staining data set is available as an online resource for researchers who are designing mass cytometry experiments in suspension and tissue.
High-throughput targeted gene deletion in the model mushroom Schizophyllum commune using pre-assembled Cas9 ribonucleoproteins
Authors: Vonk Peter Jan , Escobar Natalia , Wösten Han A. B. , Lugones Luis G. , Ohm Robin A. 
Published: March 2019

AbstractEfficient gene deletion methods are essential for the high-throughput study of gene function. Compared to most ascomycete model systems, gene deletion is more laborious in mushroom-forming basidiomycetes due to the relatively low incidence of homologous recombination (HR) and relatively high incidence of non-homologous end-joining (NHEJ). Here, we describe the use of pre-assembled Cas9-sgRNA ribonucleoproteins (RNPs) to efficiently delete the homeodomain transcription factor gene hom2 in the mushroom-forming basidiomycete Schizophyllum commune by replacing it with a selectable marker. All components (Cas9 protein, sgRNA, and repair template with selectable marker) were supplied to wild type protoplasts by PEG-mediated transformation, abolishing the need to optimize the expression of cas9 and sgRNAs. A Δku80 background further increased the efficiency of gene deletion. A repair template with homology arms of 250 bp was sufficient to induce homologous recombination, whereas 100 bp was not. This is the first report of the use of pre-assembled Cas9 RNPs in a mushroom-forming basidiomycete and this approach may also improve the genetic accessibility of non-model species.
Evaluating the within-host dynamics of Ranavirus infection with mechanistic disease models and experimental data
Authors: Mihaljevic Joseph R. , Greer Amy L. , Brunner Jesse L. 
Published: March 2019

AbstractMechanistic models are critical for our understanding of both within-host dynamics (i.e., pathogen population growth and immune system processes) and among-host dynamics (i.e., transmission). Rarely, however, have within-host models been synthesized with data to infer processes, validate hypotheses, or generate new theories. In this study we use mechanistic models and empirical, time-series data of viral titer to better understand the growth of ranaviruses within their amphibian hosts and the immune dynamics that limit viral replication. Specifically, we fit a suite of potential models to our data, where each model represents a hypothesis about the interactions between viral growth and immune defense. Through formal model comparison, we find a parsimonious model that captures key features of our time-series data: the viral titer rises and falls through time, likely due to an immune system response, and that the initial viral dosage affects both the peak viral titer and the timing of the peak. Importantly, our model makes several predictions, including the existence of long-term viral infections, that can be validated in future studies.
Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs
Authors: Wiemann Stefan , Weil Bernd , Wellenreuther Ruth , Gassenhuber Johannes , Glassl Sabine , Ansorge Wilhelm , Böcher Michael , Blöcker Helmut , Bauersachs Stefan , Blum Helmut , Lauber Jürgen , Düsterhöft Andreas , Beyer Andreas , Köhrer Karl , Strack Normann , Mewes Hans-Werner , Ottenwälder Birgit , Obermaier Brigitte , Tampe Jens , Heubner Dagmar , Wambutt Rolf , Korn Bernhard , Klein Michaela , Poustka Annemarie 
Published: March 2019

With the complete human genomic sequence being unraveled, the focus will shift to gene identification and to the functional analysis of gene products. The generation of a set of cDNAs, both sequences and physical clones, which contains the complete and noninterrupted protein coding regions of all human genes will provide the indispensable tools for the systematic and comprehensive analysis of protein function to eventually understand the molecular basis of man. Here we report the sequencing and analysis of 500 novel human cDNAs containing the complete protein coding frame. Assignment to functional categories was possible for 52% (259) of the encoded proteins, the remaining fraction having no similarities with known proteins. By aligning the cDNA sequences with the sequences of the finished chromosomes 21 and 22 we identified a number of genes that either had been completely missed in the analysis of the genomic sequences or had been wrongly predicted. Three of these genes appear to be present in several copies. We conclude that full-length cDNA sequencing continues to be crucial also for the accurate identification of genes. The set of 500 novel cDNAs, and another 1000 full-coding cDNAs of known transcripts we have identified, adds up to cDNA representations covering 2%–5 % of all human genes. We thus substantially contribute to the generation of a gene catalog, consisting of both full-coding cDNA sequences and clones, which should be made freely available and will become an invaluable tool for detailed functional studies.[The sequence data described in this paper have been submitted to the EMBL database under the accession nos. given in Table 2.]