bluuebunny/crossref_metadata_2025_split huggingface dataset:
INSM1 Expression in Chordomas
Authors: Dridi Maroa , Boutonnat Jean , Dumollard Jean Marc , Peoc’h Michel , Karpathiou Georgia 
Published: October 2020

Abstract

Objectives
Chordomas are rare malignant tumors with a broad differential diagnosis, including chondrosarcomas and metastatic carcinomas. Recently, insulinoma-associated protein 1 (INSM1) has gained great interest regarding the diagnosis of neuroendocrine tumors but also extraskeletal myxoid chondrosarcomas. However, its expression in chordomas remains largely unknown.

Methods
We retrospectively examined 57 chordomas for INSM1 expression.

Results
INSM1 expression was found in only 5% of tumors.

Conclusions
This marker is rarely expressed in this type of tumor, raising questions about neuroendocrine differentiation.
Evaluation of AccuFIT 9000: A Novel Apparatus for Quantitative Fit Testing of Particulate Respirators
Authors: Grinshpun Sergey A , Yermakov Michael , Kano Minoru 
Published: October 2020

Abstract
Various strategies developed for protecting frontline workers and the general public from the novel coronavirus, SARS-CoV-2, largely rely on respiratory protective devices (RPDs), especially considering recent evidence about the aerosol transmission route of COVID-19. Performance of an RPD primarily depends on how well the protective device fits the wearer. Therefore, quantitative fit testing of particulate respirators is crucial for achieving the intended protection level. Millions of fit tests are conducted every year using a US OSHA-accepted standard protocol involving a PortaCount® (TSI Inc., Shoreview, MN, USA) which measures a respirator fit factor. Recently, several alternative fit testing instruments have been developed and introduced to the market. Among them is an AccuFIT 9000 (Kanomax-Japan Inc., Suita-city, Osaka, Japan), which, like the PortaCount®, utilizes the condensation particle counting principle, but features an advanced saturation chamber design allowing for a longer residence time and greater flow stability. It is also claimed to have a more cost-efficient assembly than its predecessors. In this study, the novel AccuFIT apparatus was extensively evaluated against the PortaCount® (the reference instrument) using the traditional standard fit testing protocol and following the American National Standards Institute (ANSI) standard (Z88.10-2010 Annex A2). The evaluation was performed with three types of respirators, N95 filtering facepiece respirator (FFR), P100 FFR, and half-mask elastomeric facepiece, of different models and manufacturers donned on 25 subjects. The comparative testing and analysis showed that the AccuFIT 9000 is capable of identifying an inadequate fit of the tested respirators with a sensitivity 0.95 and specificity of 0.97, which meets the ANSI requirement of ≥0.95. The other ANSI requirements/recommendations were also met. It was concluded that the novel fit testing apparatus demonstrated an acceptable performance and, thus, can be successfully deployed for the quantitative respirator fit testing.
Development, Spanish Normative Data, and Validation of a Social Cognition Battery in Prodromal Alzheimer’s Disease and Multiple Sclerosis
Authors: Delgado-Álvarez Alfonso , Pytel Vanesa , Delgado-Alonso Cristina , Olbrich-Guzmán Carmen María , Cortés-Martínez Ana , Moreno-Ramos Teresa , Montero-Escribano Paloma , Matías-Guiu Jorge , Matias-Guiu Jordi A 
Published: October 2020

Abstract

Objectives
The assessment of social cognition changes may be challenging, especially in the earliest stages of some neurodegenerative diseases. Our objective was to validate a social cognition battery from a multidomain perspective. In this regard, we aimed to adapt several tests, collect normative data, and validate them in prodromal Alzheimer’s disease (AD) and multiple sclerosis (MS).

Methods
A total of 92 healthy controls, 25 prodromal AD, and 39 MS patients were enrolled. Age-, gender-, and education-matched control groups were created for comparisons. Social cognition battery was composed of an emotion-labeling task developed from FACES database, the Story-based Empathy test (SET), the Faux Pas test, and the Interpersonal Reactivity Index. Patients were also evaluated with a comprehensive cognitive battery to evaluate the other cognitive domains. Automatic linear modeling was used to predict each social cognition test’s performance using the neuropsychological tests examining other cognitive domains.

Results
The reliability of the battery was moderate-high. Significant intergroup differences were found with medium-large effect sizes. Moderate correlations were found between social cognition battery and neuropsychological tests. The emotion labeling task and SET showed moderate correlations with age and education, and age, respectively. Regression-based norms were created considering the relevant demographic variables. Linear regression models including other neuropsychological tests explained between 7.7% and 68.8% of the variance of the social cognition tests performance.

Conclusions
Our study provides a battery for the assessment of social cognition in prodromal AD and MS with Spanish normative data to improve the evaluation in clinical and research settings.
An update: mechanisms of microRNA in primary open-angle glaucoma
Authors: Wang Yuanping , Niu Lingzhi , Zhao Jing , Wang Mingxuan , Li Ke , Zheng Yajuan 
Published: October 2020

AbstractGlaucoma is a disease with characteristic optic neuropathy and loss of vision, leading to blindness, and primary open-angle glaucoma (POAG) is the most common glaucoma type throughout the world. Genetic susceptibility is the main factor in POAG, and most susceptibility genes cause changes in microRNA expression and function, thereby leading to POAG occurrence and development. Increasing evidence indicates that many microRNAs are involved in the regulation of intraocular pressure (IOP) and play an important role in the increase in IOP in POAG. Additionally, microRNA is closely related to optic nerve damage factors (mechanical stress, hypoxia and inflammation). This review discusses the effect of single-nucleotide polymorphisms in POAG-related genes on microRNA and the value of microRNA in the diagnosis and treatment of POAG.
Network principal component analysis: a versatile tool for the investigation of multigroup and multiblock datasets
Authors: Codesido Santiago , Hanafi Mohamed , Gagnebin Yoric , González-Ruiz Víctor , Rudaz Serge , Boccard Julien 
Published: October 2020

Abstract

Motivation
Complex data structures composed of different groups of observations and blocks of variables are increasingly collected in many domains, including metabolomics. Analysing these high-dimensional data constitutes a challenge, and the objective of this article is to present an original multivariate method capable of explicitly taking into account links between data tables when they involve the same observations and/or variables. For that purpose, an extension of standard principal component analysis called NetPCA was developed.

Results
The proposed algorithm was illustrated as an efficient solution for addressing complex multigroup and multiblock datasets. A case study involving the analysis of metabolomic data with different annotation levels and originating from a chronic kidney disease (CKD) study was used to highlight the different aspects and the additional outputs of the method compared to standard PCA. On the one hand, the model parameters allowed an efficient evaluation of each group’s influence to be performed. On the other hand, the relative relevance of each block of variables to the model provided decisive information for an objective interpretation of the different metabolic annotation levels.

Availability and implementation
NetPCA is available as a Python package with NumPy dependencies.

Supplementary information
Supplementary data are available at Bioinformatics online.
Effects of Temperature on Development and Survival of NymphalLycorma delicatula(Hemiptera: Fulgoridae)
Authors: Kreitman Devin , Keena Melody A , Nielsen Anne L , Hamilton George 
Published: October 2020

AbstractLycorma delicatula (White), an invasive planthopper originally from Asia, is an emerging pest in North America. It is important to understand its phenology in order to determine its potential range in the United States. Lycorma delicatula nymphs were reared on Ailanthus altissima (Miller) (Sapindales: Simaroubaceae) at each of the following constant temperatures: 5, 10, 15, 20, 25, 30, 35, and 40°C. The time spent in each instar and survival was recorded. Developmental rate increased with temperature from 15 to 30°C for all instars, then declined again at higher temperatures. Nymphal survival was lower at 35°C than between 15 and 30°C for all instars, and first instars placed at 5, 10, and 40°C all died without molting. This suggests that L. delicatula survival and development may be affected in the Southern United States by high temperatures and developmental delays will occur under cool spring conditions. The lower developmental threshold was found to be 13.00 ± 0.42°C for first instars, 12.43 ± 2.09°C for second instars, 8.48 ± 2.99°C for third instars, and 6.29 ± 2.12°C for fourth instars. The degree-day (DD) requirement for nymphs in the previous instar to complete development to reach the second instar, third instar, fourth instar, and adult was 166.61, 208.75, 410.49, and 620.07 DD (base varied), respectively. These results provide key data to support the development of phenology models and help identify the potential range of L. delicatula in North America.
Computed tomography imaging needs for novel transcatheter tricuspid valve repair and replacement therapies
Authors: Hell Michaela M , Emrich Tilman , Kreidel Felix , Kreitner Karl-Friedrich , Schoepf U Joseph , Münzel Thomas , von Bardeleben Ralph Stephan 
Published: October 2020

Abstract
Transcatheter tricuspid valve therapies are an emerging field in structural heart interventions due to the rising number of patients with severe tricuspid regurgitation and the high risk for surgical treatment. Computed tomography (CT) allows exact measurements of the annular plane, evaluation of adjacent structures, assessment of the access route, and can also be used to identify optimal fluoroscopic projection planes to enhance periprocedural imaging. This review provides an overview of current transcatheter tricuspid valve repair and replacement therapies and to what extent CT can support these interventions.
A scoping review of qualitative research on perceptions of one’s own alcohol use
Authors: Morris Stephanie , Stewart Duncan , Madden Mary , McCambridge Jim 
Published: October 2020

Abstract

Background
This scoping review aims to map the extent, range and nature of qualitative research on people’s ‘perceptions’ of their own alcohol consumption.

Methods
A systematic search of five electronic databases was conducted. A total of 915 abstracts were screened and 452 full texts examined, of which 313 papers met the inclusion criteria (including a report of qualitative data on perceptions, experiences or views of people’s own drinking in peer-reviewed journals published in English).

Results
This study maps the available literature assembled over approximately 30 years, which was found to be extensive and diverse. Many existing studies are focused largely on people’s ‘experiences’ of their own drinking behaviours, particularly when they were drinking in ways commonly understood as heavy, risky or problematic. Fewer studies focused on populations whose drinking was not heavy or was risky in less obvious ways, such as older adults prescribed medications for chronic health conditions. Most studies were conducted since 2010, with the rate of publications increasing since 2014.

Conclusions
This review identifies gaps in the evidence regarding people’s perceptions of their own drinking and opportunities for qualitative studies to make valuable contributions to alcohol research. Gaps discussed include patterns of drinking that are less obviously problematic, and in relation to consumption of alcohol in those parts of the world where overall consumption and harms from alcohol are high. Such studies could usefully be informed by existing studies in the evidence mapping.
A Direct Measure of Stand Density Based on Stand Growth
Authors: Dean Thomas J , D’Amato Anthony W , Palik Brian J , Battaglia Mike A , Harrington Constance A 
Published: October 2020

Abstract
Standardizing gross volume increment on periodic height increment of the dominant trees is a means of minimizing the effects of site quality and age in growth–growing-stock relations; however, volume increment per height increment contains more information than just a normalization method for fitting growth models. This study builds on previous work suggesting that the cumulative sum of the ratios between individual-tree volume increment and height increment may be a direct measure of stand density. We used data from several levels of growing-stock studies for Douglas-fir, ponderosa pine, and red pine to explore this hypothesis. Regression analysis indicated that the sum of the ratios is proportional to(Dqx⋅N), the underlying equation form of Reineke’s stand density index. Stem growth is a function of canopy dynamics, and additional analyses showed that volume added per unit of height growth was also related to canopy architecture, increasing with decreasing live-crown ratio and increasing foliage density. The linkages between growth, canopy architecture, intermediary canopy dynamics, and (Dqx⋅N) support the hypothesis that the sum of the tree ratios between volume increment and height increment is a direct measure of site occupancy due to its association between growth and corresponding resource use.
Prediction of single-cell gene expression for transcription factor analysis
Authors: Behjati Ardakani Fatemeh , Kattler Kathrin , Heinen Tobias , Schmidt Florian , Feuerborn David , Gasparoni Gilles , Lepikhov Konstantin , Nell Patrick , Hengstler Jan , Walter Jörn , Schulz Marcel H 
Published: October 2020

Abstract

Background
Single-cell RNA sequencing is a powerful technology to discover new cell types and study biological processes in complex biological samples. A current challenge is to predict transcription factor (TF) regulation from single-cell RNA data.

Results
Here, we propose a novel approach for predicting gene expression at the single-cell level using cis-regulatory motifs, as well as epigenetic features. We designed a tree-guided multi-task learning framework that considers each cell as a task. Through this framework we were able to explain the single-cell gene expression values using either TF binding affinities or TF ChIP-seq data measured at specific genomic regions. TFs identified using these models could be validated by the literature.

Conclusion
Our proposed method allows us to identify distinct TFs that show cell type–specific regulation. This approach is not limited to TFs but can use any type of data that can potentially be used in explaining gene expression at the single-cell level to study factors that drive differentiation or show abnormal regulation in disease. The implementation of our workflow can be accessed under an MIT license via https://github.com/SchulzLab/Triangulate.
Toward quantitative electromagnetic field imaging by differential-phase-contrast scanning transmission electron microscopy
Authors: Seki Takehito , Ikuhara Yuichi , Shibata Naoya 
Published: October 2020

Abstract
Differential-phase-contrast scanning transmission electron microscopy (DPC STEM) is a technique to directly visualize local electromagnetic field distribution inside materials and devices at very high spatial resolution. Owing to the recent progress in the development of high-speed segmented and pixelated detectors, DPC STEM now constitutes one of the major imaging modes in modern aberration-corrected STEM. While qualitative imaging of electromagnetic fields by DPC STEM is readily possible, quantitative imaging by DPC STEM is still under development because of the several fundamental issues inherent in the technique. In this report, we review the current status and future prospects of DPC STEM for quantitative electromagnetic field imaging from atomic scale to mesoscopic scale.
“They’re Constantly Cycling Through”: Lessons about Turnover and Collaborative Forest Planning
Authors: Coleman Kimberly J , Butler William H , Stern Marc J , Beck Samantha L 
Published: October 2020

AbstractWithin forest planning and management, collaboration has becoming increasingly widespread. Many collaborative projects take place over long time periods, and thus personnel turnover is inevitable within these groups. Scholars from the fields of business and organizational science have long studied strategies that organizations can use to prepare for and address turnover successfully. We draw from that literature and use it to examine the Collaborative Forest Landscape Restoration Program (CFLRP), a federal program aimed at bringing diverse stakeholders together to address the increasing costs, severity, and prevalence of wildfires in the United States. We conducted qualitative analysis of interviews, archival documents, and memos to explore what strategies are used within CFLRP groups to address turnover. We discuss our findings in light of the existing literature from business and organizational science and present insights about which strategies may be adaptable to collaborative natural resource management and which may require further research to assess their applicability to collaborative groups.
Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis
Authors: Liu Nannan , Du Yuanhao , Warburton Marilyn L , Xiao Yingjie , Yan Jianbing 
Published: October 2020

Abstract
Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in this area to date. In the present study, we established a population of 976 maize F1 hybrids by crossing 488 diverse inbred lines with two elite testers. Genome-wide association study identified hundreds of quantitative trait loci associated with phenotypic plasticity variation across diverse F1 hybrids, the majority of which contributed very little variance, in accordance with the polygenic nature of these traits. We identified several quantitative trait locus regions that may have been selected during the tropical-temperate adaptation process. We also observed heterosis in terms of phenotypic plasticity, in addition to the traditional genetic value differences measured between hybrid and inbred lines, and the pattern of which was affected by genetic background. Our results demonstrate a landscape of phenotypic plasticity in maize, which will aid in the understanding of its genetic architecture, its contribution to adaptation and heterosis, and how it may be exploited for future maize breeding in a rapidly changing environment.
Characterizing benefit from temozolomide in MGMT promoter unmethylated and methylated glioblastoma: a systematic review and meta-analysis
Authors: Alnahhas Iyad , Alsawas Mouaz , Rayi Appaji , Palmer Joshua D , Raval Raju , Ong Shirley , Giglio Pierre , Murad Mohammad Hassan , Puduvalli Vinay 
Published: October 2020

Abstract

Background
The current standard of care for the management of patients with newly diagnosed glioblastoma (GBM) includes maximal safe resection followed by radiotherapy (RT) with concurrent and adjuvant temozolomide (TMZ). While it is well established that TMZ has better efficacy in patients with MGMT promoter methylation, it remains an area of debate whether TMZ should be omitted when treating GBM patients with unmethylated MGMT.

Methods
We conducted a systematic review and meta-analysis to provide separate estimates of median overall survival (OS) and progression-free survival (PFS) for patients with methylated and unmethylated GBM treated with RT with or without TMZ. We searched multiple databases from inception to January 13, 2020.

Results
The median OS for patients with unmethylated GBM treated with RT/TMZ pooled from 5 phase III studies (N = 655) was 14.11 months (95% confidence interval [CI], 13.18–15.04) with a median PFS of 4.99 months (95% CI, 4.25–5.72). In contrast, the median OS for patients with methylated GBM pooled from 6 studies (N = 753) was 24.59 months (95% CI, 22.19–26.99) with a median PFS pooled from 7 studies (N = 805) of 9.51 months (95% CI, 7.41–11.61). There is a paucity of prospective data pertaining to OS/PFS in unmethylated patients treated with RT only and therefore a direct comparison was not possible.

Conclusions
This meta-analysis provides estimates of survival for patients with MGMT methylated or unmethylated GBM treated with RT/TMZ. Further research is needed to delineate whether TMZ should be withheld for patients with unmethylated GBM outside of the setting of clinical trials.
Effects of drought on nitrogen uptake and carbon dynamics in trees
Authors: Joseph Jobin , Luster Jörg , Bottero Alessandra , Buser Nathalie , Baechli Lukas , Sever Krunoslav , Gessler Arthur 
Published: October 2020

Abstract
Research on drought impact on tree functioning is focussed primarily on water and carbon (C) dynamics. Changes in nutrient uptake might also affect tree performance under drought and there is a need to explore underlying mechanisms. We investigated effects of drought on (a) in situ nitrogen (N) uptake, accounting for both, N availability to fine roots in soil and actual N uptake, (b) physiological N uptake capacity of roots and (c) the availability of new assimilates to fine roots influencing the N uptake capacity using 15N and 13C labelling. We assessed saplings of six different tree species (Acer pseudoplatanus L., Fagus sylvatica L., Quercus petraea (Mattuschka) Liebl., Abies alba Mill., Picea abies (L.) H.Karst. and Pinus sylvestris L.). Drought resulted in significant reduction of in situ soil N uptake in deciduous trees accompanied by reduced C allocation to roots and by a reduction in root biomass available for N uptake. Although physiological root N uptake capacity was not affected by drought in deciduous saplings, reduced maximum ammonium but not nitrate uptake was observed for A. alba and P. abies. Our results indicate that drought has species-specific effects on N uptake. Even water limitations of only 5 weeks as assessed here can decrease whole-plant inorganic N uptake, independent of whether the physiological N uptake capacity is affected or not.
HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification
Authors: Kist Nicolaas C , Lambert Ben , Campbell Samuel , Katzourakis Aris , Lunn Daniel , Lemey Philippe , Iversen Astrid K N 
Published: October 2020

AbstractPathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong positive correlation between ethnic diversity in African countries and both human immunodeficiency virus (HIV)-1 p24gag and subtype diversity. We demonstrate that ethnic HLA-allele differences between populations have influenced HIV-1 subtype diversification as the virus adapted to escape common antiviral immune responses. The evolution of HIV Subtype B (HIV-B), which does not appear to be indigenous to Africa, is strongly affected by immune responses associated with Eurasian HLA variants acquired through adaptive introgression from Neanderthals and Denisovans. Furthermore, we show that the increasing and disproportionate number of HIV-infections among African Americans in the USA drive HIV-B evolution towards an Africa-centric HIV-1 state. Similar adaptation of other pathogens to HLA variants common in affected populations is likely.