bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning for the modeling of interfaces in energy storage and conversion materials
Authors: Artrith Nongnuch
Published: May 2019

The properties and atomic-scale dynamics of interfaces play an important role for the performance of energy storage and conversion devices such as batteries and fuel cells. In this topical review, we consider recent progress in machine-learning (ML) approaches for the computational modeling of materials interfaces. ML models are computationally much more efficient than first principles methods and thus allow to model larger systems and extended timescales, a necessary prerequisites for the accurate description of many interface properties. Here we review the recent major developments of ML-based interatomic potentials for atomistic modeling and ML approaches for the direct prediction of materials properties. This is followed by a discussion of ML applications to solid–gas, solid–liquid, and solid–solid interfaces as well as to nanostructured and amorphous phases that commonly form in interface regions. We then highlight how ML has been used to obtain important insights into the structure and stability of interfaces, interfacial reactions, and mass transport at interfaces. Finally, we offer a perspective on the current state of ML potential development and identify future directions and opportunities for this exciting research field.
Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata
Authors: Klaas Manfred , Haiminen Niina , Grant Jim , Cormican Paul , Finnan John , Arojju Sai Krishna , Utro Filippo , Vellani Tia , Parida Laxmi , Barth Susanne
Published: May 2019

Background and Aims

Perennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging.

Methods

In this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths.

Key Results

This allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered.

Conclusions

Reed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.
ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra
Authors: Nguyen Dai Hai , Nguyen Canh Hao , Mamitsuka Hiroshi
Published: May 2019

Motivation

Metabolite identification is an important task in metabolomics to enhance the knowledge of biological systems. There have been a number of machine learning-based methods proposed for this task, which predict a chemical structure of a given spectrum through an intermediate (chemical structure) representation called molecular fingerprints. They usually have two steps: (i) predicting fingerprints from spectra; (ii) searching chemical compounds (in database) corresponding to the predicted fingerprints. Fingerprints are feature vectors, which are usually very large to cover all possible substructures and chemical properties, and therefore heavily redundant, in the sense of having many molecular (sub)structures irrelevant to the task, causing limited predictive performance and slow prediction.

Results

We propose ADAPTIVE, which has two parts: learning two mappings (i) from structures to molecular vectors and (ii) from spectra to molecular vectors. The first part learns molecular vectors for metabolites from given data, to be consistent with both spectra and chemical structures of metabolites. In more detail, molecular vectors are generated by a model, being parameterized by a message passing neural network, and parameters are estimated by maximizing the correlation between molecular vectors and the corresponding spectra in terms of Hilbert-Schmidt Independence Criterion. Molecular vectors generated by this model are compact and importantly adaptive (specific) to both given data and task of metabolite identification. The second part uses input output kernel regression (IOKR), the current cutting-edge method of metabolite identification. We empirically confirmed the effectiveness of ADAPTIVE by using a benchmark data, where ADAPTIVE outperformed the original IOKR in both predictive performance and computational efficiency.

Availability and implementation

The code will be accessed through http://www.bic.kyoto-u.ac.jp/pathway/tools/ADAPTIVE after the acceptance of this article.
Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level
Authors: Sarkar Hirak , Srivastava Avi , Patro Rob
Published: May 2019

With the advancements of high-throughput single-cell RNA-sequencing protocols, there has been a rapid increase in the tools available to perform an array of analyses on the gene expression data that results from such studies. For example, there exist methods for pseudo-time series analysis, differential cell usage, cell-type detection RNA-velocity in single cells, etc. Most analysis pipelines validate their results using known marker genes (which are not widely available for all types of analysis) and by using simulated data from gene-count-level simulators. Typically, the impact of using different read-alignment or unique molecular identifier (UMI) deduplication methods has not been widely explored. Assessments based on simulation tend to start at the level of assuming a simulated count matrix, ignoring the effect that different approaches for resolving UMI counts from the raw read data may produce. Here, we present minnow, a comprehensive sequence-level droplet-based single-cell RNA-sequencing (dscRNA-seq) experiment simulation framework. Minnow accounts for important sequence-level characteristics of experimental scRNA-seq datasets and models effects such as polymerase chain reaction amplification, cellular barcodes (CB) and UMI selection and sequence fragmentation and sequencing. It also closely matches the gene-level ambiguity characteristics that are observed in real scRNA-seq experiments. Using minnow, we explore the performance of some common processing pipelines to produce gene-by-cell count matrices from droplet-bases scRNA-seq data, demonstrate the effect that realistic levels of gene-level sequence ambiguity can have on accurate quantification and show a typical use-case of minnow in assessing the output generated by different quantification pipelines on the simulated experiment.

Supplementary information

Supplementary data are available at Bioinformatics online.
Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms
Authors: Lin Ruogu , Zeng Xiangrui , Kitani Kris , Xu Min
Published: May 2019

Motivation

Since 2017, an increasing amount of attention has been paid to the supervised deep learning-based macromolecule in situ structural classification (i.e. subtomogram classification) in cellular electron cryo-tomography (CECT) due to the substantially higher scalability of deep learning. However, the success of such supervised approach relies heavily on the availability of large amounts of labeled training data. For CECT, creating valid training data from the same data source as prediction data is usually laborious and computationally intensive. It would be beneficial to have training data from a separate data source where the annotation is readily available or can be performed in a high-throughput fashion. However, the cross data source prediction is often biased due to the different image intensity distributions (a.k.a. domain shift).

Results

We adapt a deep learning-based adversarial domain adaptation (3D-ADA) method to timely address the domain shift problem in CECT data analysis. 3D-ADA first uses a source domain feature extractor to extract discriminative features from the training data as the input to a classifier. Then it adversarially trains a target domain feature extractor to reduce the distribution differences of the extracted features between training and prediction data. As a result, the same classifier can be directly applied to the prediction data. We tested 3D-ADA on both experimental and realistically simulated subtomogram datasets under different imaging conditions. 3D-ADA stably improved the cross data source prediction, as well as outperformed two popular domain adaptation methods. Furthermore, we demonstrate that 3D-ADA can improve cross data source recovery of novel macromolecular structures.

Availability and implementation

https://github.com/xulabs/projects

Supplementary information

Supplementary data are available at Bioinformatics online.
TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain
Authors: Gao Yan , Liu Bo , Wang Yadong , Xing Yi
Published: May 2019

Motivation

Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) sequencing technologies can produce long-reads up to tens of kilobases, but with high error rates. In order to reduce sequencing error, Rolling Circle Amplification (RCA) has been used to improve library preparation by amplifying circularized template molecules. Linear products of the RCA contain multiple tandem copies of the template molecule. By integrating additional in silico processing steps, these tandem sequences can be collapsed into a consensus sequence with a higher accuracy than the original raw reads. Existing pipelines using alignment-based methods to discover the tandem repeat patterns from the long-reads are either inefficient or lack sensitivity.

Results

We present a novel tandem repeat detection and consensus calling tool, TideHunter, to efficiently discover tandem repeat patterns and generate high-quality consensus sequences from amplified tandemly repeated long-read sequencing data. TideHunter works with noisy long-reads (PacBio and ONT) at error rates of up to 20% and does not have any limitation of the maximal repeat pattern size. We benchmarked TideHunter using simulated and real datasets with varying error rates and repeat pattern sizes. TideHunter is tens of times faster than state-of-the-art methods and has a higher sensitivity and accuracy.

Availability and implementation

TideHunter is written in C, it is open source and is available at https://github.com/yangao07/TideHunter
epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology
Authors: Creed Jordan H , Aden-Buie Garrick , Monteiro Alvaro N , Gerke Travis A
Published: May 2019

Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery.

Availability and implementation

epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/ where we have additionally made publicly available the source code and a Docker containerized version of the application.
Fatal Yellow Fever in a Kidney Transplant Patient
Authors: Pierrotti Lígia C , Duarte-Neto Amaro N , Song Alice T W , Ventura Carlucci G , David-Neto Elias , Azevedo Luiz S
Published: May 2019

A kidney-transplanted patient, unvaccinated against yellow fever (YF), developed high fever, progressed rapidly to hepatic insufficiency and coma, and died 8 days later. Real-time polymarase chain reaction for YF virus collected on the seventh day of symptoms was positive. Autopsy showed disseminated infection and midzonal hepatitis with apoptotic hepatocytes and minimal inflammatory reaction.
Laparoscopic magnetic sphincter augmentation versus fundoplication for gastroesophageal reflux disease: systematic review and pooled analysis
Authors: Guidozzi Nadia , Wiggins Tom , Ahmed Ahmed R , Hanna George B , Markar Sheraz R
Published: May 2019

Magnetic sphincter augmentation (MSA) has been proposed as a less invasive, more appealing alternative intervention to fundoplication for the treatment of gastroesophageal reflux disease (GERD). The aim of this study was to evaluate clinical outcomes following MSA for GERD control in comparison with laparoscopic fundoplication. A systematic electronic search for articles was performed in Medline, Embase, Web of Science, and Cochrane Library for single-arm cohort studies or comparative studies (with fundoplication) evaluating the use of MSA. A random-effects meta-analysis for postoperative proton pump inhibitor (PPI) use, GERD-health-related quality of life (GERD-HRQOL), gas bloating, ability to belch, dysphagia, and reoperation was performed. The systematic review identified 6 comparative studies of MSA versus fundoplication and 13 single-cohort studies. Following MSA, only 13.2% required postoperative PPI therapy, 7.8% dilatation, 3.3% device removal or reoperation, and esophageal erosion was seen in 0.3%. There was no significant difference between the groups in requirement for postoperative PPI therapy (pooled odds ratio, POR = 1.08; 95%CI 0.40–2.95), GERD-HRQOL score (weighted mean difference, WMD = 0.34; 95%CI −0.70–1.37), dysphagia (POR = 0.94; 95%CI 0.57–1.55), and reoperation (POR = 1.23; 95%CI 0.26–5.8). However, when compared to fundoplication MSA was associated with significantly less gas bloating (POR = 0.34; 95%CI 0.16–0.71) and a greater ability to belch (POR = 12.34; 95%CI 6.43–23.7). In conclusion, magnetic sphincter augmentation achieves good GERD symptomatic control similar to that of fundoplication, with the benefit of less gas bloating. The safety of MSA also appears acceptable with only 3.3% of patients requiring device removal. There is an urgent need for randomized data directly comparing fundoplication with MSA for the treatment of GERD to truly evaluate the efficacy of this treatment approach.
Prognostic implications of global, left ventricular myocardial work efficiency before cardiac resynchronization therapy
Authors: van der Bijl Pieter , Vo Ngoc Mai , Kostyukevich Marina V , Mertens Bart , Ajmone Marsan Nina , Delgado Victoria , Bax Jeroen J
Published: May 2019

Aims

Cardiac resynchronization therapy (CRT) restores mechanical efficiency to the failing left ventricular (LV) by resynchronization of contraction. Global, LV myocardial work efficiency (GLVMWE) can be quantified non-invasively with echocardiography. The prognostic implication of GLVMWE remains unexplored, and we therefore related GLVMWE before CRT to long-term prognosis.

Methods and results

Data were analysed from an ongoing registry of patients with Class I indications for CRT. GLVMWE was defined as the ratio of constructive work in all LV segments, divided by the sum of constructive and wasted work in all LV segments, as a percentage. It was derived from speckle tracking strain echocardiography and non-invasive blood pressure measurements, taken pre-CRT. Patients were dichotomized according to baseline, median GLVMWE [75%; interquartile range (IQR) 66–81%]. A total of 153 patients (66 ± 10 years, 72% male, 48% ischaemic heart disease) were analysed. After a median follow-up of 57 months (IQR 28–76 months), 31% of patients died. CRT recipients with less efficient baseline energetics (GLVMWE <75%) demonstrated lower event rates than patients with more efficient baseline energetics (GLVMWE ≥75%) (log-rank test, P = 0.029). On multivariable analysis, global LV wasted work ratio <75% pre-CRT was independently associated with a decreased risk of all-cause mortality (hazard ratio 0.48, 95% confidence interval 0.25–0.92; P = 0.027), suggesting that the potential for improvement in LV efficiency is important for CRT benefit.

Conclusion

GLVMWE can be derived non-invasively from speckle tracking strain echocardiography and non-invasive blood pressure recordings. A lower GLVMWE before CRT is independently associated with improved long-term outcome.
Effects of mesenchymal stem cell transfer on orthodontically induced root resorption and orthodontic tooth movement during orthodontic arch expansion protocols: an experimental study in rats
Authors: Gul Amuk Nisa , Kurt Gokmen , Karsli Erol , Ozcan Servet , Acar Mustafa Burak , Amuk Mehmet , Lekesizcan Ayca , Gurgan Cem Abdulkadir
Published: May 2019

Objectives

The aim was to evaluate the effects of mesenchymal stem cell (MSC) transfer to periodontal ligament (PDL) on the inhibition and/or repair of orthodontically induced root resorption (OIRR) during and after arch expansion and on the orthodontic tooth movement (OTM) rate of the maxillary first molar teeth of rats.

Material and methods

Sixty Wistar rats were divided into three groups as the untreated group, MSC and control injections during the expansion period group (EMSC-EC), and MSC and control injections at the retention period group (RMSC-RC). Fifty grams of orthodontic force was applied to the maxillary first molar teeth of the rats for 14 days in the vestibular direction, and then, 20 days of retention was carried out. MSCs and control injections were performed every 3 days in the EC, RC, EMSC, and RMSC groups. At the end of the experiment, samples were prepared for OTM evaluation, mRNA expression analysis, micro-computed tomography measurements, cementum thickness calculations, and structural examinations.

Results

The amount of OTM in EMSC group was significantly higher than in EC group (P < 0.001). MSC transfer during the expansion and retention periods reduced the number of resorption lacunae, volumetric and linear resorptive measurements, and cyclooxygenase-2 and receptor activator of nuclear factor kappa B ligand (RANKL) mRNA expression levels, and increased the osteoprotegerin (OPG) expression levels, OPG/RANKL ratio, and cementum thickness in the EMSC and RMSC groups.

Conclusions

MSC transfer to PDL during expansion increased the amount of OTM. Injection of MSC during the retention period was found to be slightly more effective in prevention and/or repair of OIRR than MSC transfer during the expansion period.
Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei
Authors: Jiang Boyun , Sun Jingfeng , Lv Aijun , Hu Xiucai , Shi Hongyue , Sung YeongYik , Wang Qingkui , Wang Yang
Published: May 2019

Two DNA extraction methods, the Zirmil-beating cell disruption method (ZBC) and the QIAamp fast DNA stool mini kit (QIA), were used to extract DNA from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, and their microbial communities were analyzed using 16S rDNA high-throughput sequencing. Results were obtained in terms of the number of reads, alpha diversity indexes, beta diversity indexes and taxonomic composition. The alpha diversity indexes of the community, according to the ZBC method, were higher than those according to the QIA method. Furthermore, results from the three samples using the ZBC method were less consistent than those where the QIA method was used. Further, using the latter method led to substantive clustering. It is suggested that the QIA method is more stable and repeatable than the ZBC method. Although the two extraction methods shared the major abundant microflora based on 16S rDNA high-throughput sequencing, bias associated with diversity analysis indexes and certain species was observed.
Social Integration and Terminal Decline in Life Satisfaction Among Older Japanese
Authors: Nakagawa Takeshi , Hülür Gizem
Published: May 2019

Objectives

Well-being typically exhibits pronounced deteriorations with approaching death, with sizeable interindividual variations in levels and changes. It is less well understood how psychosocial factors contribute to these individual differences. We examined whether and how social integration is associated with terminal trajectories of well-being, indexed as life satisfaction.

Method

Data were drawn from 1,119 deceased Japanese participants of a 15-year longitudinal study (age at death: M = 79.2 years; SD = 7.7 years; 43.1% women). Life satisfaction, structural and functional features of social integration (e.g., frequency of contact with family and nonfamily, and perceived overall support, respectively), sociodemographic characteristics, and physical function were assessed.

Results

Social integration predicted individual differences in terminal decline in life satisfaction, after controlling for age at death, gender, education, and physical function: More diverse social relationships were associated with higher levels of life satisfaction at 1 year before death. In addition, individuals who exhibited more decline in social participation and perceived less support showed more pronounced decline with increasing proximity of death.

Discussion

This study suggests that social integration plays a protective role in late-life well-being and that sustaining an active social life and supportive social interactions may help mitigate terminal decline in well-being.
Perceptual Inhibition Is Not a Specific Component of the Sensory Integration Process Necessary for a Rapid Voluntary Step Initiation in Healthy Older Adults
Authors: Magnard Justine , Berrut Gilles , Couturier Catherine , Cattagni Thomas , Cornu Christophe , Deschamps Thibault
Published: May 2019

Objectives

We investigated whether performing step initiation during a proprioceptive perturbation would require greater perceptual or motor inhibitory control in older adults.

Method

Fifty-two healthy adults (young: n = 26, mean age 22.5 years vs. older: n = 26, mean age 70.1 years) performed a stepping reaction time task, with different inhibition requirements (i.e., perceptual vs. motor inhibitory conflict), with two proprioceptive configurations: with and without application of Achilles tendon vibrations.

Results

Beyond a systematically greater stepping reaction time in older adults (p < .01), no difference was found between the perceptual versus motor inhibitory conflict resolution, regardless of age and proprioceptive configuration. Furthermore, slower reaction time was observed for young participants in the presence of Achilles tendon vibrations unlike older adults, who showed the same reactive stepping performance with or without vibrations (p < .05).

Discussion

These findings show that perceptual inhibition cannot be considered as specifically involved in the central processing of proprioceptive signals, at least not in active older adults. Rather than motor system malfunctioning or a reduced amount of proprioceptive afference, we propose that cortical-proprioceptive processing in older adults remains as effective as in young adults, regardless of the high attentional requirements for step responses.
Valve-sparing root reimplantation in anomalous right coronary origin
Authors: Ram Duvuru , Lund Jens Teglgaard
Published: May 2019

Anomalous origin of coronary artery is a rare anomaly. Performing valve-sparing root reimplantation for aortic root pathology in these patients is challenging. There are modified techniques for performing valve-sparing procedures in this rare subset of patients. Herein, we present a case of anomalous right coronary origin from left ostium managed by conventional valve-sparing root reimplantation.
Effects of super-dosing phytase and inositol on growth performance and blood metabolites of weaned pigs housed under commercial conditions1
Authors: Moran Kory , Wilcock Pete , Elsbernd Amanda , Zier-Rush Cate , Boyd R Dean , van Heugten Eric
Published: May 2019

A total of 2,156 weaned pigs (6.75 ± 0.11 kg BW) were used in a 42-d study to evaluate whether improvements in growth performance associated with super-dosing phytase can be explained by the complete dephosphorylation of phytate and liberation of inositol. Two phytase doses (0 and 2,500 FTU/kg) and 3 inositol concentrations (0%, 0.15%, and 0.30%) were combined to create 6 dietary treatments in a 2 × 3 factorial arrangement. Pigs were fed a 3-phase feeding program, with periods being 10, 10, and 22 d, respectively. Blood samples were collected on days 0, 21, and 42 from a subset of 48 pigs to analyze mineral and myo-inositol concentrations. During Phase 1, super-dosing phytase tended to improve ADG compared with pigs fed diets without phytase (P = 0.09). Increasing concentrations of inositol improved the efficiency of gain in pigs fed diets without phytase (1,022.1, 1,040.9, and 1,089.2 g/kg), but not diets with phytase (1,102.2, 1,087.2, and 1,076.2 g/kg), and this improvement was equivalent to that observed with super-dosing phytase in the absence of inositol (interaction, P = 0.015). During Phase 2, super-dosing phytase improved ADG (P = 0.001), resulting in heavier BW (P = 0.007). During Phase 3 and overall, inositol supplementation increased ADG and ADFI in a quadratic manner (P < 0.10), with the highest ADG and ADFI observed for pigs fed 0.15% of inositol. Super-dosing phytase increased serum Zn on day 21, but not on day 42 (interaction, P = 0.008), increased serum Cu (P = 0.01), but decreased serum Fe (P = 0.02). Plasma myo-inositol increased linearly from 66.9 to 97.1 and 113.2 nmol/mL with increasing inositol (P < 0.001). When plasma myo-inositol was analyzed within the subgroup of pigs fed diets without added inositol, super-dosing phytase increased plasma myo-inositol from 57.81 to 76.05 nmol/mL (0 and 2,500 FTU/kg, respectively; P = 0.05). Results demonstrate that exogenous inositol improved efficiency of gain in weaned pigs to the same level as that observed with super-dosing phytase, but this occurred only during the first 10 d of the nursery period. This suggests that the improvement in efficiency of growth when applying super-dosing phytase could be linked, in part, to complete dephosphorylation of phytate and liberation of myo-inositol, and that myo-inositol had a greater metabolic impact in piglets immediately after weaning. Consequently, myo-inositol may be a conditionally essential nutrient for young pigs during weaning stress, but further research is needed to prove this hypothesis.
Proposed BoNT/A and /B Peptide Substrates Cannot Detect Multiple Subtypes in the Endopep-MS Assay
Authors: Kalb Suzanne R , Baudys Jakub , Kiernan Kaitlyn , Wang Dongxia , Becher François , Barr John R
Published: May 2019

Botulinum neurotoxins (BoNTs) are a family of protein toxins consisting of seven known serotypes (BoNT/A—BoNT/G) and multiple subtypes within the serotypes, and all of which cause the disease botulism—a disease of great public health concern. Accurate detection of BoNTs in human clinical samples is therefore an important public health goal. To achieve this goal, our laboratory developed a mass spectrometry-based assay detecting the presence of BoNT via its enzymatic activity on a peptide substrate. Recently, publications reported the use of new peptide substrates to detect BoNT/A and /B with improved results over other peptide substrates. However, the authors did not provide results of their peptide substrate on multiple subtypes of BoNT. In this work, we describe the results of testing the new substrates with multiple BoNT/A and /B subtypes and find that the substrates cannot detect many subtypes of BoNT/A and /B.
Rodent population density and survival respond to disturbance induced by timber harvest
Authors: Nelson Dana L , Kellner Kenneth F , Swihart Robert K
Published: May 2019

Many small mammal populations respond quickly to timber harvest aimed at oak (Quercus) regeneration, which alters microhabitat. We used mark-release–recapture data collected 6–8 years postharvest from the Hardwood Ecosystem Experiment in southern Indiana, United States, to model density and apparent survival of eastern chipmunks (Tamias striatus) and white-footed mice (Peromyscus leucopus) as a function of timber harvest treatments (shelterwood, clearcut, patch cut, and unharvested control). Density, estimated using spatial capture–recapture, increased for chipmunks in all types of harvest openings, but survival was unaffected by harvest. Chipmunk densities in unharvested forest matrix habitat averaged 58% and 71% lower relative to harvest openings and opening edges, respectively. White-footed mouse density was less responsive to timber harvest, but monthly survival rates were reduced by 13% in shelterwoods and 17% in patch cuts relative to control sites. Both rodent species tended to exhibit distance-dependent responses, with higher density of home-range centers near harvest boundaries relative to forest matrix. Structural complexity created at the edges of timber harvest openings can benefit rodents associated with edge habitat 6–8 years after harvest, presumably due to improved foraging efficiency and resource diversity. Cascading effects of rodent demographic responses are likely to affect predation and seed dispersal, which are critical trophic interactions in oak forest ecosystems.
Diagnostic accuracy and added value of qualitative radiological review of 1H-magnetic resonance spectroscopy in evaluation of childhood brain tumors
Authors: Manias Karen A , Gill Simrandip K , MacPherson Lesley , Oates Adam , Pinkey Benjamin , Davies Paul , Zarinabad Niloufar , Davies Nigel P , Babourina-Brooks Ben , Wilson Martin , Peet Andrew C
Published: May 2019

Background

1H-magnetic resonance spectroscopy (MRS) facilitates noninvasive diagnosis of pediatric brain tumors by providing metabolite profiles. Prospective studies of diagnostic accuracy and comparisons with conventional MRI are lacking. We aimed to evaluate diagnostic accuracy of MRS for childhood brain tumors and determine added clinical value compared with conventional MRI.

Methods

Children presenting to a tertiary pediatric center with brain lesions from December 2015 through 2017 were included. MRI and single-voxel MRS were acquired on 52 tumors and sequentially interpreted by 3 radiologists, blinded to histopathology. Proportions of correct diagnoses and interrater agreement at each stage were compared. Cases were reviewed to determine added value of qualitative radiological review of MRS through increased certainty of correct diagnosis, reduced number of differentials, or diagnosis following spectroscopist evaluation. Final diagnosis was agreed by the tumor board at study end.

Results

Radiologists’ principal MRI diagnosis was correct in 69%, increasing to 77% with MRS. MRI + MRS resulted in significantly more additional correct diagnoses than MRI alone (P = .035). There was a significant increase in interrater agreement when correct with MRS (P = .046). Added value following radiologist interpretation of MRS occurred in 73% of cases, increasing to 83% with additional spectroscopist review. First histopathological diagnosis was available a median of 9.5 days following imaging, with 25% of all patients managed without conclusive histopathology.

Conclusions

MRS can improve the accuracy of noninvasive diagnosis of pediatric brain tumors and add value in the diagnostic pathway. Incorporation into practice has the potential to facilitate early diagnosis, guide treatment planning, and improve patient care.
Queer Performativity
Authors: Milani Tommaso M.
Published: May 2019

The aim of this chapter is to present and re-read Judith Butler’s well-known performativity theory. The main argument advanced here is that, even though Butler’s work is widely viewed as instigating the field of queer studies, it is perhaps time to revisit performativity in order to queer it. The act of queering should be understood in the context of this chapter in two ways. First, it entails going against the sociolinguistic grain and troubling the linguistic core of performativity in a way that engages with “aspects of experience and reality that do not present themselves in propositional or even in verbal form” (Sedgwick 2003: 6), such as affect, embodiment, and the materiality of the built environment. The embodied and affective aspects of performativity are illustrated with the help of examples from gender and sexual activism in Israel, which show how multi-semiotic and sensory meanings are performatively brought into being in order to stake political claims. Second, queering performativity entails questioning the antinormative mantra encoded in the very notion of queer. This requires going back to a performative utterance par excellence—“I do” in wedding ceremonies—in order open up an uneasy self-reflection about (anti)normativity in queer scholarship.
Introduction
Authors: Paulus Paul B. , Nijstad Bernard A.
Published: May 2019

Group creativity research has a relatively short history. Although there is a long tradition of research on individual creativity, for many years there was little acknowledgment of the creative potential of groups. In recent years this has changed, and this book provides a comprehensive overview of this work on group creativity. This chapter provides a brief history of the research on group creativity. It also summarizes the key contributions of each chapter, dealing with the impact of individual characteristics or behavior, basic processes or theoretical approaches, various contexts in which group creative occurs, and various applications of group creativity. Finally, we highlight common themes, and suggest directions for future research.
PIECE Together
Authors: Goncalo Jack A. , Katz Joshua H. , Ellis Lillien M.
Published: May 2019

Norms regulate and direct behavior in groups, but the role that norms play in the creative process has been controversial. This chapter develops a theoretical perspective in which norms are tools that can be leveraged to facilitate creativity in teams. It begins by identifying a set of five key behaviors that support creative collaboration—the PIECE(s) of team creativity—Participation, Independence, Elaboration, Communication, and Exploration. It then identifies specific norms that can encourage the emergence of each of the five critical behaviors, the conditions that make these norms salient, and the underlying psychological and behavioral mechanisms through which norms impact creativity. It also reviews recent and growing evidence suggesting that strengthening creativity-relevant norms with the threat of overt social sanctions can encourage the emergence of behavior appropriate to the task of being creative and thus facilitate, rather than thwart, creative collaboration. Finally, it concludes with suggestions for future research on norms in creative work groups.
Effective Brainstorming
Authors: Paulus Paul B. , Kenworthy Jared B.
Published: May 2019

This chapter reviews the extensive literature on brainstorming to determine potential best practices. It presents the major theoretical perspectives and highlights their relationship to the various factors that influence the effectiveness of brainstorming. It examines the utility of verbal brainstorming, electronic brainstorming, and brainwriting for generation of creative ideas. It evaluates the effects of instructions, breaks, facilitators, training, tapping semantic categories, turnover, and group size. It also notes the gaps that exist in the literature and future research directions. It is clear that there is now considerable evidence to guide effective brainstorming and produce performances in groups that exceed those of comparable sets of solitary brainstormers.
Newcomer Influence and Creativity in Work Groups
Authors: Levine John M. , Choi Hoon-Seok , Moreland Richard
Published: May 2019

The major premise of this chapter is that newcomers in task groups have the potential to produce unintentional or intentional influence that facilitates group creativity. In the former case, newcomers’ mere presence elicits changes in the group. In the latter case, newcomers introduce ideas with the goal of improving group processes or outcomes. This chapter argues that intentional influence is based on newcomers’ motivation to generate and suggest ideas and current members’ willingness to consider and accept these ideas. In analyzing such influence, the chapter discusses factors associated with newcomers, current members, and the group as a whole that can affect the perceived opportunity/threat value of newcomers’ ideas and thereby current members’ receptivity to these ideas. It concludes by identifying outstanding questions regarding the mechanisms underlying intentional newcomer influence.
When Does a Right to Life Arise?
Authors: Wardle Lynn D.
Published: May 2019

The question of when a legal right to life first arises in the course of a human being’s development is pertinent to a variety of contexts, including protection of prenatal life from injury by persons other than the gestational mother, what to do with frozen embryos when the couple who created them divorces, and how to treat children born with severe disabilities, as well as the more familiar context of state regulation, restriction, or prohibition of abortion. This chapter first summarizes social and biological science findings relevant to this question, then details development of legal rules and constitutional doctrine pertaining to abortion regulation before contrasting that with protections for prenatal life in other contexts. It concludes that the most coherent answer to the question when a right to life arises is that the right to life is coextensive with the biological life of the human being, and that a legal right to remain alive arises when a human being comes into existence and continues until it ceases to be a human being—that is, when its life has ended. This might provide justification for greater restrictions on abortion, but that could depend on additional considerations.
Latinx Folklore and Folklife
Authors: Cantú Norma E.
Published: May 2019

This article, which focuses on the traditional cultural expressions of the Latinx community in the United States, first traces the history and development of Chicanx and Latinx folklore studies. Second, it presents the ways that the study and engagement with these expressions serve as tools for addressing social justice issues faced by Latinxs in the United States in the twenty-first century. To guide future work in the field, it concludes with an assessment of Latinx folklore studies and its role in reconfiguring and reimagining folklore and folklife studies in general. Within this discussion, the essay presents two key aspects of Latinx folklore and folklife that have defined the field—the academic study of folklore and the public-sector engagement by community scholars. Both have affected the ways that Latinx folkloristics have changed the field during the last hundred years and are shaping it as we leave behind outmoded and limited ways of seeing the cultural production of the second-largest ethnic minority in the United States.
Publishing and Technology
Authors: Maxwell John
Published: May 2019

This chapter provides a very broad picture of publishing technology as it has evolved over time, making the case that publishing has always been a technological endeavour. Publishing technology in the earliest sense was marshalled to transcend space and time and, with industrialization, to acheive economies of scale in labour and material in the service of audiences. The evolution of publishing technology can be understood as a pursuit of ‘scaling up’ both in the sense of industrial economics and of the ability to gather and reach audiences. Digital technologies have destabilized industrial economies of scale, but enabled far greater and more nuanced audience reach; we live today suspended in a kind of tension between traditional industrial thinking and a newer post-industrial model of society and communications. A comparison of the ebook—manifestly of concern to most traditional publishers today—with the larger development of the open Web platform makes these tensions particularly instructive.
Networks
Authors: Scolari Carlos A.
Published: May 2019

Digital networks shape traditional actors (authors, readers, librarians, publishers, and other intermediaries), institutions (libraries, bookstores), processes (collaborative writing, translation, correction), and texts (hypertext, open access, wiki technology). The article deals with the main transformations in these fields from a media ecology perspective. Media Ecology is a discipline first outlined in the early 1960s by researchers like Marshall McLuhan, Neil Postman, and Walter Ong. From this perspective, the emergence of the World Wide Web in the 1990s and social media in the 2000s radically changed the conditions of the media ecosystem. In this new context the old media and actors must adapt to the new environment if they want to survive. The chapter deals with these mutations and adaptations in the specific field of book publishing.
Nominals and Event Structure
Authors: Moltmann Friederike
Published: May 2019

This chapter discusses three semantic approaches to event nominalizations: The Davidsonian, the Kimian, and the truthmaker-based approach. It argues that a combination of the three approaches is required for the semantics of the full range of event and state nominalizations as well as the related phenomenon of adverbial modification. The chapter also presents data regarding a distinction between two sorts of nominalizations of psychological and illocutionary verbs that challenge the received view of the identity of the events described by verbs and by (non-gerundive) deverbal nominalizations. These data bear on a distinction between ‘actions’ and ‘products’ introduced by the Polish philosopher Twardowski.
Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment
Authors: Sprecher Kate E , Ritchie Hannah K , Burke Tina M , Depner Christopher M , Smits Alexandra N , Dorrestein Pieter C , Fleshner Monika , Knight Rob , Lowry Christopher A , Turek Fred W , Vitaterna Martha H , Wright Kenneth P
Published: May 2019

Study Objectives

Determine stability of individual differences in executive function, cognitive processing speed, selective visual attention, and maintenance of wakefulness during simulated sustained operations with combined sleep restriction and circadian misalignment.

Methods

Twenty healthy adults (eight female), aged 25.7 (±4.2 SD), body mass index (BMI) 22.3 (±2.1) kg/m2 completed an 18-day protocol twice. Participants maintained habitual self-selected 8-hour sleep schedules for 2 weeks at home prior to a 4-day laboratory visit that included one sleep opportunity per day: 8 hours on night 1, 3 hours on night 2, and 3 hours on mornings 3 and 4. After 3 days of unscheduled sleep at home, participants repeated the entire protocol. Stability and task dependency of individual differences in performance were quantified by intra-class correlation coefficients (ICC) and Kendall’s Tau, respectively.

Results

Performance on Stroop, Visual Search, and the Maintenance of Wakefulness Test were highly consistent within individuals during combined sleep restriction and circadian misalignment. Individual differences were trait-like as indicated by ICCs (0.54–0.96) classified according to standard criteria as moderate to almost perfect. Individual differences on other performance tasks commonly reported in sleep studies showed fair to almost perfect ICCs (0.22–0.94). Kendall’s rank correlations showed that individual vulnerability to sleep restriction and circadian misalignment varied by task and by metric within a task.

Conclusions

Consistent vulnerability of higher-order cognition and maintenance of wakefulness to combined sleep restriction and circadian misalignment has implications for the development of precision countermeasure strategies for workers performing safety-critical tasks, e.g. military, police, health care workers and emergency responders.
Environmental correlates of tardigrade community structure in mosses and lichens in the Great Smoky Mountains National Park (Tennessee and North Carolina, USA)
Authors: Nelson Diane R , Bartels Paul J , Fegley Stephen R
Published: May 2019

A major inventory of tardigrades in the Great Smoky Mountains National Park was conducted and we compared tardigrade species composition in moss and lichen samples and analysed environmental correlates of tardigrade community structure. We also compared these tardigrades with those collected from soil. The basic dataset from tree mosses and lichens consisted of 336 samples, 9200 individuals and 43 species. The supplemental dataset from rock mosses and lichens consisted of 29 samples, 811 individuals, and 41 species. Collectively, there were 57 species present in mosses and lichens. Eleven species were found uniquely on rock habitats. Two-way ANOVAs for various community metrics showed no significant differences between substrate (moss versus lichen) or height (ground level versus breast height); however, there were significant differences between ATBI plots. Tardigrade communities were not significantly different between mosses and lichens, but soil tardigrade communities were quite distinct from these moss/lichen communities. We analysed the impact of 17 environmental variables on community structure using partition tree analyses. SOx deposition explained most of the variation in species richness and evenness in moss tardigrades. Forest disturbance regime had the greatest impact on abundance in lichen tardigrades. Other environmental factors influencing community structure are discussed.
Resistance Against Melon Chlorotic Mosaic Virus and Tomato Leaf Curl New Delhi Virus in Melon
Authors: Romay Gustavo , Pitrat Michel , Lecoq Herve , Wipf-Scheibel Catherine , Millot Pauline , Girardot Gregory , Desbiez Cecile
Published: May 2019

Thirty-one melon accessions were screened for resistance to the begomoviruses Melon chlorotic mosaic virus (MeCMV) and Tomato leaf curl New Delhi virus (ToLCNDV). Five accessions presented nearly complete resistance to both viruses. Accession IC-274014, showing the highest level of resistance to both viruses, was crossed with the susceptible cultivar Védrantais. The F1, F2, F3/F4, and both backcross progenies were mechanically inoculated with MeCMV. Plants without symptoms or virus detection by enzyme-linked immunosorbent assay and/or PCR were considered as resistant. The segregations were compatible with two recessive and one dominant independent genes simultaneously required for resistance. Inheritance of resistance to ToLCNDV in the F2 was best explained by one recessive gene and two independent dominant genes simultaneously required. Some F3 and F4 families selected for resistance to MeCMV also were resistant to ToLCNDV, suggesting that common or tightly linked genes were involved in resistance to both viruses. We propose the names begomovirus resistance-1 and Begomovirus resistance-2 for these genes (symbols bgm-1 and Bgm-2). Resistance to MeCMV in IC-274014 was controlled by bgm-1, Bgm-2, and the recessive gene melon chlorotic mosaic virus resistance (mecmv); resistance to ToLCNDV was controlled by bgm-1, Bgm-2, and the dominant gene Tomato leaf curl New Delhi virus resistance (Tolcndv).