bluuebunny/crossref_metadata_2025 huggingface dataset:
Know Place: Heaven’s Gate and American Gnosticism
Authors: Gutierrez Cathy
Published: November 2019

Bonnie Nettles and Marshall Applewhite, the founders of the millenarian movement Heaven’s Gate, began teaching at a retreat they called Know Place, where one came to “know thyself” in the “no-place of Utopia.” This initial phase set the stage for a process of self-recognition that would become the hallmark of conversion to the movement, much as Gnosticism employed in the first centuries of the common era. The parallels between late antique Gnosticism and Heaven’s Gate are remarkable. Both posited two breeds of humans, one a material husk and the other an enlightened soul temporarily trapped on earth. Both proposed radical gender equality and maintained a rigorous ascetic regime. Both proffered death as a return to a prior state of gnosis rather than a disjuncture into a new life and afterlife. This paper examines the rhetoric of self-verification employed by both movements as it relates to a modified monotheism.
Ainsliaea simplicissima (Asteraceae), a new species from southeast China and its phylogenetic position

Authors: ZHANG MEI-JIAO , YU WEI-JUN , LI HONG-QING
Published: November 2019

Ainsliaea simplicissima M. J. Zhang & H.-Q. Li, sp. nov., a new species (tribe Mutiseiae, Asteraceae) from Fujian, China, is described and illustrated based on morphological and molecular analyses. It can be distinguished by leaves situated in a basal rosette or aggregated at the lower part of the short stem, leaf blade narrowly elliptic or lanceolate, thick papyraceous, and capitulum bearing only one flower. The new species is morphologically similar to A. trinervis and molecularly sister to A. fragrans, both distributed nearby.
Trechispora yunnanensis sp. nov. (Hydnodontaceae, Basidiomycota) from China

Authors: XU TAI-MIN , CHEN YU-HUI , ZHAO CHANG-LIN
Published: November 2019

A new wood-inhabiting fungal species, Trechispora yunnanensis sp. nov., is proposed based on morphological characteristics and molecular phylogenetic analyses. The species is characterized by resupinate basidiomata, rigid and fragile up on drying, cream to pale greyish hymenial surface; a monomitic hyphal system with generative hyphae bearing clamp connections, IKI-, CB-; ellipsoid, hyaline, thick-walled, ornamented, IKI-, CB- basidiospores measuring as 7–8.5 × 5–5.5 µm. The internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood (ML), maximum parsimony (MP) and bayesian inference methods (BPP). The phylogenetic analyses based on molecular data of ITS+nLSU sequences showed that T. yunnanensis formed a monophyletic lineage with a strong support (100% ML, 100% MP, 1.00 BPP) and was closely related to T. byssinella and T. laevis. Both morphological characteristics and results of molecular phylogenetic analyses confirmed the placement of the new species in Trechispora.
Unusual Trapped Mountain Lee Waves with Deep Vertical Penetration and Significant Stratospheric Amplitude
Authors: Metz Johnathan J. , Durran Dale R. , Blossey Peter N.
Published: November 2019

Simulations of the weather over the South Island of New Zealand on 28 July 2014 reveal unusual wave activity in the stratosphere. A series of short-wavelength perturbations resembling trapped lee waves were located downstream of the topography, but these waves were in the stratosphere, and their crests were oriented north–south, in contrast to both the northeast–southwest orientation of the spine of the Southern Alps and the crests of trapped waves present in the lower troposphere. Vertical cross sections through these waves show a nodal structure consistent with that of a higher-order trapped-wave mode. Eigenmode solutions to the vertical structure equation for two-dimensional, linear, Boussinesq waves were obtained for a horizontally homogeneous sounding representative of the 28 July case. These solutions include higher-order modes having large amplitude in the stratosphere that are supported by just the zonal wind component. Two of these higher-order modes correspond to trapped waves that develop in an idealized numerical simulation of the 28 July 2014 case. These higher-order modes are trapped by very strong westerly winds in the midstratosphere and are triggered by north–south-oriented features in the subrange-scale topography. In contrast, the stratospheric cross-mountain wind component is too weak to trap similar high-order modes with crest-parallel orientation.
Does the Arctic Stratospheric Polar Vortex Exhibit Signs of Preconditioning Prior to Sudden Stratospheric Warmings?
Authors: Lawrence Zachary D. , Manney Gloria L.
Published: November 2019

Characteristics of the Arctic stratospheric polar vortex are examined using reanalysis data with dynamic time warping (DTW) and a clustering technique to determine whether the polar vortex exhibits canonical signs of preconditioning prior to sudden stratospheric warmings (SSWs). The DTW and clustering technique is used to locate time series motifs in vortex area, vortex edge-averaged PV gradients, and vortex edge-averaged wind speeds. Composites of the motifs reveal that prior to roughly 75% of SSWs, in the middle to upper stratosphere, PV gradients and wind speeds in the vortex edge region increase, and vortex area decreases. These signs agree with prior studies that discuss potential signals of preconditioning of the vortex. However, similar motifs are also found in a majority of years without SSWs. While such non-SSW motifs are strongly associated with minor warming signals apparent only in the middle and upper stratosphere, only roughly half of these can be associated with later “significant disturbances” (SDs) that do not quite meet the threshold for major SSWs. The median lead time for sharpening vortex edge PV gradients represented in the motifs prior to SSWs and SDs is ~25 days, while the median lead time for the vortex area and edge wind speeds is ~10 days. Overall, canonical signs of preconditioning do appear to exist prior to SSWs, but their existence in years without SSWs implies that preconditioning of the vortex may be an insufficient condition for the occurrence of SSWs.
Comparison of Referral Pathways in Otolaryngology at a Public Versus Private Academic Center
Authors: Bertelsen Caitlin , Choi Janet S. , Jackanich Anna , Ge Marshall , Sun Gordon H. , Chambers Tamara
Published: November 2019

Objective:

Delayed medical care may be costly and dangerous. Examining referral pathways may provide insight into ways to reduce delays in care. We sought to compare time between initial referral and first clinic visit and referral and surgical intervention for index otolaryngologic procedures between a public safety net hospital (PSNH) and tertiary-care academic center (TAC).

Methods:

Retrospective cohort study of eligible adult patients undergoing one of several general otolaryngologic procedures at a PSNH (n = 216) and a TAC (n = 161) over a 2-year time period.

Results:

PSNH patients were younger, less likely to have comorbidities and more likely to be female, Hispanic or Asian, and to lack insurance. Time between referral and first clinic visit was shorter at the PSNH than the TAC (Mean 35.8 ± 47.7 vs 48.3 ± 60.3 days; P = .03). Time between referral and surgical intervention did not differ between groups (129 ± 90 for PSNH vs 141 ± 130 days for TAC, P = .30). On multivariate analysis, the TAC had more patient-related delays in care than the PSNH (OR: 3.75, P < .001). Time from referral to surgery at a PSNH was associated with age, source of referral, type of surgery, diagnostic workup and comorbidities, and at a TAC was associated with gender and type of surgery and comorbidities.

Conclusions:

Sociodemographic differences between PSNH and TAC patients, as well as differences in referral pathways between the types of institutions, influence progression of surgical care in otolaryngology. These differences may be targets for interventions to streamline care.

Level of Evidence:

2c
Finding latent groups in observed data: A primer on latent profile analysis in Mplus for applied researchers
Authors: Ferguson Sarah L. , G. Moore E. Whitney , Hull Darrell M.
Published: November 2019

The present guide provides a practical guide to conducting latent profile analysis (LPA) in the Mplus software system. This guide is intended for researchers familiar with some latent variable modeling but not LPA specifically. A general procedure for conducting LPA is provided in six steps: (a) data inspection, (b) iterative evaluation of models, (c) model fit and interpretability, (d) investigation of patterns of profiles in a retained model, (e) covariate analysis, and (f) presentation of results. A worked example is provided with syntax and results to exemplify the steps.
Cannibals, Colorful Birds, and Exuberant Nature: The Representation of Brazilian Nationalism and Its Tropical Modernity in the 2016 Rio Olympics
Authors: Malanski Daniel
Published: November 2019

Hosting the Olympics is a singular opportunity to build an updated narrative of the nation. Such a narrative is traditionally intended to emphasize the hosting country contributions toward the modern project through the displaying of key nationalistic accounts linking the country’s history to the development of western society. In the case of the 2016 Rio de Janeiro Olympics, its organizing committee has sought into Brazil’s history different elements that were central to both the formation of Brazilian identity and the discussion over current global issues. Therefore, the country’s enduring relation with nature as well as national narratives such as modernist Anthropophagy, the discourse of ethnic miscegenation, and the myth of Brazil as a racial democracy became historical credentials to use environmentalism and tolerance as the paramount features of Rio-2016’s aesthetics as well as a means to denounce xenophobia and the effects of the Anthropocene on the planet. We argue that the exposition of these two issues in the event’s ceremonies was a way to symbolically insert the country within modernity’s forefront. In this article, we examine the sociopolitical aspects that led to the creation and popularization of Brazilian nationalistic narratives that were later used during the Rio 2016 opening ceremony and the ways such aspects were internationally conveyed during the aforementioned theatrical presentation.
Finding a way with words: Delphi study to develop a discussion prompt list for paediatric palliative care
Authors: Ekberg Stuart , Herbert Anthony , Johns Kristi , Tarrant Gabrielle , Sansone Holly , Yates Patsy , Danby Susan , Bradford Natalie K
Published: November 2019

Background:

Effective communication is a cornerstone of quality paediatric palliative care. Families report struggling, however, to know what to discuss, with whom, and when. Although question prompt lists exist for adult palliative care, they do not suit the unique circumstances of paediatric palliative care.

Aim:

To develop a prompt list suitable for paediatric palliative care.

Design:

Underpinned by Delphi methodology, a six-phase procedure was adopted: (1) drafting items based on the findings of a literature review, (2) condensing the list of items based on group discussion, (3) refining items based on a survey of expert healthcare professionals, (4) additional refining of items based on another survey of professionals, (5) further refining of items based on cognitive interviews with family members, and (6) final review by healthcare professional and family member groups.

Participants:

Three participant groups were involved during various phases: (1) members of an Australasian paediatric palliative care national reference group, (2) healthcare professionals associated with a local paediatric palliative care service, and (3) family members who were users of the same local service.

Results:

Through multi-phase consultation across participant groups, the draft question prompt list was refined progressively to 28 items, split across two booklets to allow end-of-life items to be provided separately, and reconceptualised as a discussion prompt list rather than a question prompt list.

Conclusion:

By involving representatives of major stakeholder groups, this study has facilitated the design of a prompt list suited to the circumstances of paediatric palliative care. Future research should trial the effectiveness of this resource.
Legal geography II: Bodies and law
Authors: Jeffrey Alex
Published: November 2019

Building on the arguments of the first report concerning court materiality, this progress report examines the various ways in which bodies have become the focal point of legal geographic interest. This work strays across disciplinary boundaries, mirroring other areas of the geographic discipline in understanding bodies both in their corporeal terms (as fleshy and vital) and their discursive construction (emerging through constellations of language and power). The report examines four interlinked aspects of this work, examining (i) bodies and testimony, (ii) bodies as evidence; (iii) bodies as property, and (iv) law and animality.
Pre-clinical evaluation of surface coating performance in guidewire surrogates: Potential implications for coated interventional surgical devices
Authors: Shi Huiyu , Wang Jonathan , Vorvolakos Katherine , White Kathleen , Duraiswamy Nandini
Published: November 2019

Purpose

Polymer fragments have been identified from autopsy reports of patients who had at some point undergone intravascular procedures with medical devices (such as guidewires and catheters) with lubricious coatings. Coating separation on these devices may cause a range of adverse events, the most severe being patient death associated with undesired embolization of blood vessels by coating particles. The objective of the present study is to identify bench test methods for evaluation of hydrophobic and hydrophilic coatings to better understand the relationships between coating formulation and coating behavior, which in turn helps to determine safety and effectiveness of the coating on the device.

Methods

Hydrophilic or hydrophobic coatings were applied on prepared 304 V stainless steel guidewire surrogates. Coating integrity was assessed after exposing the surrogates to extended periods of soaking and rotary bend fatigue testing. Additionally, coating durability was evaluated by abrasion testing.

Results

Soaking tests showed deionized water can cause more changes to the microscopic appearance of the coating on the guidewire surrogates as compared to 0.9% saline at both room temperature and 37°C; however, soaking tests in either medium did not alter coating integrity after 11 hours. Rotary bend fatigue, which subjects the coatings to both tension and compression, did not affect coating integrity on the guidewire surrogates after three hours. The pad material used in abrasion testing can lead to markedly different performance predictions.

Conclusion

Soaking, bend fatigue test, and abrasion tests can provide valuable information on coating performance. Coating integrity and durability were affected during abrasion testing, a test method that can provide more useful information for evaluating bench coating performance. It remains to correlate these findings with clinical performance, but emphasis should be placed on comprehensive characterization. Further investigation is needed by multidisciplinary stakeholders: materials scientists, engineers, and clinicians, to properly inform next steps.
Inconsistency between records of δ18O and trace element ratios from stalagmites: Evidence for increasing mid–late Holocene moisture in arid central Asia
Authors: Liu Xiaokang , Liu Jianbao , Shen Chuan-Chou , Yang Yan , Chen Jianhui , Chen Shengqian , Wang Xianfeng , Wu Chung-Che , Chen Fahu
Published: November 2019

The interpretation of trace element/calcium ratios of speleothems as indicators of local hydroclimatic variability in the vicinity of caves has led to controversy in reconstructing the evolution of moisture conditions in arid central Asia (ACA) during the Holocene. Here we present records of Mg/Ca, Sr/Ca, Ba/Ca, and U/Ca from precisely dated stalagmites from Baluk cave in Xinjiang (northwest China), spanning the past 9370 years. The co-variations of the trace element ratios, together with the slopes of the regression lines of the corresponding logarithmically transformed data, suggest that they are dominated by prior calcite precipitation (PCP) and thus can be used as reliable proxies of changes in moisture/precipitation. The trace element ratios are relatively high during ~9 to 5 ka and lower from 5 ka to the present, indicating a trend of increasing mid–late Holocene moisture in ACA. The long-term trend of variation of the trace element ratios is correlative with two other records of speleothem trace element ratios from caves in ACA: Kesang cave (western Xinjiang) and Ton cave (Uzbekistan). This spatial coherency of the trend of inferred moisture conditions from three caves that are separated by hundreds of kilometers demonstrates that speleothem trace element ratios are indicative of large spatial scale rather than local hydroclimatic variability in ACA during the Holocene. However, the long-term trend of variation of the trace element ratios is the inverse of the corresponding oxygen isotope (δ18O) records from the same cave sites, which implies that Holocene speleothem δ18O records do not represent changes in the precipitation amount in ACA; rather, they most likely reflect moisture sources and related water vapor transport controlled by Northern Hemisphere summer insolation (NHSI). Our findings provide new evidence for a ‘westerlies-dominated climatic regime’, which influenced hydroclimatic changes in ACA during the Holocene.
Introduction to the special issue on generalisation from dialogical single case studies
Authors: Marková Ivana , Zadeh Sophie , Zittoun Tania
Published: November 2019

Drawing on historical, theoretical and cultural knowledge, this introduction explains and justifies the importance of generalisation from dialogical single case studies. We clarify the meaning of dialogism and dialogicality, differentiate between single case studies and dialogical single case studies, identify the dynamic and ethical features of dialogical single case studies, and articulate the problem of generalisation as it pertains to this topic. We suggest that the question of generalisation ought to be viewed as an effort to resituate knowledge and its dialogical features, for example values, ethical standards or levels of engagement, in other dialogical single case studies.
The Good, The Bad, and The Street: Does ‘street culture’ affect offender communication and reception in restorative justice?
Authors: Willis Roxana , Hoyle Carolyn
Published: November 2019

This article examines whether and how ‘street culture’ affects offender communication and reception in restorative justice. Drawing on an archival dataset of police-led restorative justice conferences, we analysed the relationship between street cultural capital and offenders’ ability to communicate during restorative justice. We explored how offenders’ social background, measured by street cultural capital, and/or communication abilities affect third-party perceptions of offender sincerity and their likelihood to reoffend. Results indicate that the embodiment of street cultural capital may affect offender participation in restorative justice. Socioeconomically disadvantaged offenders appeared more likely to experience communication difficulties, and were less likely to be perceived by third parties as sincere or willing to desist from offending. These findings are considered within a theoretical framework that draws on Bourdieu’s concept of cultural capital, Skeggs’ notion of inscription and Loftus’ research on ‘attitude tests’.
Fast Model for Evaluation of the Thyroid Dosimetry During Chest Tumor Radiotherapy
Authors: Wang Yiling , Zheng Min , He Ling , Xu Jinhui , Yin Gang , Zhou Jie , Zhao Yue , Jiang Ming , Wang Jie
Published: November 2019

Due to the reported high incidence of thyroid cancer induced by radiotherapy, dose assessment is significant to prevent thyroid late effects. Thyroid dosimetry can be evaluated either by entrance skin dose (ESD) measured with thermoluminescent dosimeter (TLD) arrays or by absorbed dose (AD) computed with treatment planning system. However, their correlation has hardly been reported in any publications. Moreover, the reported measurement procedures for thyroid ESD are usually inefficient. This study aims to provide a fast model for efficient acquisition of thyroid ESD and analyze the coherent relationship between ESD and AD. We conducted the study on the China radiation anthropomorphic phantom with intentionally delineated cancers, irradiated by a Varian 23EX linac. We have measured the ESD with TLD at 5 different points, while computed AD with the Oncentra Masterplan TPS. The ESD at the middle gorge of thyroid has exhibited significant linear correlation with those measured at other points. Furthermore, a regressive model has been proposed to predict thyroid AD from ESD. Consequently, it is recommended to only measure the ESD at the middle gorge of thyroid for an efficient dose assessment. The validity of the regressive model to predict thyroid AD from ESD has also been demonstrated.
Performing Law Into Being: How One Religious Community Remade State Law
Authors: Plitmann Yael
Published: November 2019

This paper considers the case of the Karaite sect in modern-day Israel as an instance where an insular and marginalized religious community reshaped official law through its members’ religious performances. Despite their failing political and legal campaigns to change Israeli family law to accommodate their distinct Judaism, the religiously committed Karaite community brought about official legal change. They did so by mimicking official law, embedding it into their sacred order, and living their original jurisprudence daily. Drawing on primary historical sources, this study reenacts the ways by which official state law and local religious law reciprocally change each other under a plural normative setting.
Awkward Black girls and post-feminist possibilities: Representing millennial Black women on television in Chewing Gum and Insecure
Authors: Sobande Francesca
Published: November 2019

Focusing on television depictions of ‘millennial’ Black women, this article explores how such on-screen identities are crafted through entwined issues concerning race, gender, sexuality and feminism. Theorising post-feminism in this contemporary context necessitates discussion of post-feminism’s (dis)connection to and from Black feminism and the politics of intersectionality. Thus, this article examines how Black feminist and post-feminist media sentiments push against each other in ways that may indicate a form of Black post-feminist television. It considers how ‘millennial’ Black women are depicted in Chewing Gum (2015–2017) and Insecure (2016–present) and analyses how feminist media discourse is implicated in these representations.
Leptin facilitates the differentiation of Th17 cells from MRL/Mp-Fas lpr lupus mice by activating NLRP3 inflammasome
Authors: Yu Yiyun , Fu Sisi , Zhang Xianglin , Wang Lingbiao , Zhao Li , Wan Weiguo , Xue Yu , Lv Ling
Published: November 2019

Both NLRP3 inflammasome and Th17 cells play important roles in the pathogenesis of systemic lupus erythematosus (SLE). Here we tried to investigate whether leptin promotes the differentiation of Th17 cells from lupus mice by activating the NLRP3 inflammasome. Th17 cells induced from MRL/Mp-Fas lpr mice splenocytes under Th17 polarizing condition were treated with leptin at scalar doses during the last 18 h of culture. The mRNA levels of IL-17A, IL-17F, RORγt, IL-1β, IL-18, NLRP3, ASC, and IL-1R1 were detected by quantitative PCR. IL-17A, IL-17F, IL-1β, and IL-18 were tested by ELISA, while the activity of caspase-1 and number of Th17 cells were counted by flow cytometry before/after inhibition of the NLRP3 inflammasome. We found that leptin pushed up the expression of IL-17A, IL-17F, NLRP3, and IL-1β and increased the number of Th17 cells in lupus mice, while the expression of IL-17A, RORγt, and IL-1β and the number of Th17 cells were decreased after inhibition of the NLRP3 inflammasome. Leptin promoted the differentiation of Th17 cells from lupus mice by activating the NLRP3 inflammasome.
Helping parents reexamine children’s emergent writing performance through parent–teacher portfolio sharing conferences
Authors: Hou Yu-Ju , Hsieh Ming-Fang
Published: November 2019

This study documented how the teacher conducted one-on-one portfolio sharing conferences with the parents to help them understand their children’s emergent writing performances. Data included the selection and analysis of children’s writing samples, parent–teacher conferences, and teacher interviews. The results indicated that parents’ perspectives on children’s writing reflect their concerns regarding their children’s transition to elementary education and limited understanding of emergent writing development. After the parent–teacher conferences, the parents demonstrated better understanding of emergent writing, became more confident about their children’s writing performance, and affirmed the benefits of parent–teacher sharing conferences. Lastly, the study increased teachers’ understanding about parents’ perspectives and improved the teacher–parent relationship.
A Near Miss and Salvage Management of Aortoesophageal Fistula Secondary to Cell Battery Ingestion
Authors: Bartkevics Maris , Stankovic Zoran , Schibli Susanne , Fluri Simon , Berger Steffen , Schmidli Juerg , Kadner Alexander
Published: November 2019

We report a case of an infant surviving aortoesophageal fistula secondary to lithium cell battery ingestion. In the setting of a delayed vascular complication, computed tomography and magnetic resonance imaging are essential to establishing the correct diagnosis and surgical management. Management of children after battery ingestion must be guided by a high index of clinical suspicion.
Pedicle Screws Challenged: Lumbar Cortical Density and Thickness Are Greater in the Posterior Elements Than in the Pedicles
Authors: Odeh Khalid , Rosinski Alexander , Leasure Jeremi , Kondrashov Dimitriy
Published: November 2019

Study Design:

Controlled laboratory study.

Objective:

To measure the total bone mineral density (BMD), cortical volume, and cortical thickness in seven different anatomical regions of the lumbar spine.

Methods:

Using computed tomography (CT) images, 3 cadaveric spines were digitally isolated by applying filters for cortical and cancellous bone. Each spine model was separated into 5 lumbar vertebrae, followed by segmentation of each vertebra into 7 anatomical regions of interest using 3-dimensional software modeling. The average Hounsfield units (HU) was determined for each region and converted to BMD with calibration phantoms of known BMD. These BMD measurements were further analyzed by the total volume, cortical volume, and cancellous volume. The cortical thickness was also measured. A similar analysis was performed by vertebral segment. St Mary’s Medical Center’s Institutional Review Board approved this study. No external funding was received for this work.

Results:

The lamina and inferior articular process contained the highest total BMD, thickest cortical shell, and largest percent volumes of cortical bone. The vertebral body demonstrated the lowest BMD. The BMDs of the L4 and L5 segments were lower; however, there were no statistically significant differences in BMD between the L1-L5 vertebral segments.

Conclusion:

Extrapedicular regions of the lumbar vertebrae, including the lamina and inferior articular process, contain denser bone than the pedicles. Since screw pullout strength relies greatly on bone density, the lamina and inferior articular processes may offer stronger fixation of the lumbar spine.
TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Authors: Alaimo Salvatore , Di Maria Antonio , Shasha Dennis , Ferro Alfredo , Pulvirenti Alfredo
Published: November 2019

Background

Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, requiring large bandwidth to download and special purpose data manipulation tools to extract subsets relevant for the specific analysis.

Results

TACITuS is a web-based system that supports rapid query access to high-throughput microarray and NGS repositories. The system is equipped with modules capable of managing large files, storing them in a cloud environment and extracting subsets of data in an easy and efficient way. The system also supports the ability to import data into Galaxy for further analysis.

Conclusions

TACITuS automates most of the pre-processing needed to analyze high-throughput microarray and NGS data from large publicly-available repositories. The system implements several modules to manage large files in an easy and efficient way. Furthermore, it is capable deal with Galaxy environment allowing users to analyze data through a user-friendly interface.
ImaGene: a convolutional neural network to quantify natural selection from genomic data
Authors: Torada Luis , Lorenzon Lucrezia , Beddis Alice , Isildak Ulas , Pattini Linda , Mathieson Sara , Fumagalli Matteo
Published: November 2019

Background

The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms underpinning human phenotypes. Popular methods of detecting such signals rely on compressing genomic information into summary statistics, resulting in the loss of information. Furthermore, few methods are able to quantify the strength of selection. Here we explored the use of deep learning in evolutionary biology and implemented a program, called , to apply convolutional neural networks on population genomic data for the detection and quantification of natural selection.

Results

enables genomic information from multiple individuals to be represented as abstract images. Each image is created by stacking aligned genomic data and encoding distinct alleles into separate colors. To detect and quantify signatures of positive selection, implements a convolutional neural network which is trained using simulations. We show how the method implemented in can be affected by data manipulation and learning strategies. In particular, we show how sorting images by row and column leads to accurate predictions. We also demonstrate how the misspecification of the correct demographic model for producing training data can influence the quantification of positive selection. We finally illustrate an approach to estimate the selection coefficient, a continuous variable, using multiclass classification techniques.

Conclusions

While the use of deep learning in evolutionary genomics is in its infancy, here we demonstrated its potential to detect informative patterns from large-scale genomic data. We implemented methods to process genomic data for deep learning in a user-friendly program called . The joint inference of the evolutionary history of mutations and their functional impact will facilitate mapping studies and provide novel insights into the molecular mechanisms associated with human phenotypes.
Exploratory analysis of transposable elements expression in the C. elegans early embryo
Authors: Ansaloni Federico , Scarpato Margherita , Di Schiavi Elia , Gustincich Stefano , Sanges Remo
Published: November 2019

Background

Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is becoming evident that TE have a role in several physiological and pathological processes. In particular, it has been shown that TE transcription is necessary for the correct development of mice embryos and that their expression is able to finely modulate transcription of coding and non-coding genes. Moreover, their activity in the central nervous system (CNS) and other tissues has been correlated with the creation of somatic mosaicisms and with pathologies such as neurodevelopmental and neurodegenerative diseases as well as cancers.

Results

We analyzed TE expression among different cell types of the Caenorhabditis elegans (C. elegans) early embryo asking if, where and when TE are expressed and whether their expression is correlated with genes playing a role in early embryo development. To answer these questions, we took advantage of a public C. elegans embryonic single-cell RNA-seq (sc-RNAseq) dataset and developed a bioinformatics pipeline able to quantify reads mapping specifically against TE, avoiding counting reads mapping on TE fragments embedded in coding/non-coding transcripts. Our results suggest that i) canonical TE expression analysis tools, which do not discard reads mapping on TE fragments embedded in annotated transcripts, may over-estimate TE expression levels, ii) Long Terminal Repeats (LTR) elements are mostly expressed in undifferentiated cells and might play a role in pluripotency maintenance and activation of the innate immune response, iii) non-LTR are expressed in differentiated cells, in particular in neurons and nervous system-associated tissues, and iv) DNA TE are homogenously expressed throughout the C. elegans early embryo development.

Conclusions

TE expression appears finely modulated in the C. elegans early embryo and different TE classes are expressed in different cell types and stages, suggesting that TE might play diverse functions during early embryo development.
Doxapram alleviates low SpO2 induced by the combination of propofol and fentanyl during painless gastrointestinal endoscopy
Authors: Gu Zhengfeng , Xin Lian , Wang Haoxing , Hu Chunxiao , Wang Zhiping , Lu Shunmei , Xu Jingjing , Qian Yiling , Wang Jun
Published: November 2019

Background

Painless gastrointestinal endoscopy under intravenous propofol anesthesia is widely applied in the clinical scenario. Despite the good sedation and elimination of anxiety that propofol provides, low SpO2 may also result. Doxapram is a respiratory stimulant with a short half-life. The primary aim of this study was to investigate the effects of doxapram on alleviating low SpO2 induced by the combination of propofol and fentanyl during painless gastrointestinal endoscopy.

Methods

In this prospective study, patients scheduled for painless gastrointestinal endoscopy were randomly assigned to group D or S with 55 patients per group. Initially, both groups received a combination of propofol and fentanyl. Patients in group D received 50 mg doxapram after propofol injection, while patients in group S received an equal volume of saline. Vital signs of the patients, propofol dose, examination duration, and incidences of low SpO2 were recorded.

Results

There were no statistical differences in propofol consumption and examination duration between the two groups. Twenty-six patients in group S experienced low SpO2 versus 10 in group D (P = 0.001). Nineteen patients in group S underwent oxygenation with a face mask in contrast to 8 in group D (P = 0.015). Eighteen patients in group S were treated with jaw lifting compared to 5 in group D (P = 0.002). Four patients in group S underwent assisted respiration compared to 2 in group D (without statistical difference). The average oxygen saturation in group S was significantly lower than that in group D at 1, 2 and 3 min after propofol injection (P < 0.001, P = 0.001 and P = 0.020, respectively). There were no statistical differences in oxygen saturation at other time points. There were no statistical differences in MAP and HR (except for the time point of 1 min after the induction) between the two groups.

Conclusions

Low dose of doxapram can effectively alleviate low SpO2 in painless gastrointestinal endoscopy with intravenous propofol, without affecting propofol consumption, examination duration, MAP, or HR.

Trail registration

The study was approved by the Institutional Ethics Committee of Clinical and New Technology of Wuxi People’s Hospital on 20th July, 2018 (KYLLH2018029) and registered in the Chinese Clinical Trial Register on 16th August, 2018 (
ChiCTR1800017832).
Can risk modelling improve treatment decisions in asymptomatic carotid stenosis?
Authors: Burke James F. , Morgenstern Lewis B. , Hayward Rodney A.
Published: November 2019

Background

Carotid endarterectomy (CEA) is routinely performed for asymptomatic carotid stenosis, yet its average net benefit is small. Risk stratification may identify high risk patients that would clearly benefit from treatment.

Methods

Retrospective cohort study using data from the Asymptomatic Carotid Atherosclerosis Study (ACAS). Risk factors for poor outcomes were included in backward and forward selection procedures to develop baseline risk models estimating the risk of non-perioperative ipsilateral stroke/TIA. Baseline risk was estimated for all ACAS participants and externally validated using data from the Atherosclerosis Risk in Communities (ARIC) study. Baseline risk was then included in a treatment risk model that explored the interaction of baseline risk and treatment status (CEA vs. medical management) on the patient-centered outcome of any stroke or death, including peri-operative events.

Results

Three baseline risk factors (BMI, creatinine and degree of contralateral stenosis) were selected into our baseline risk model (c-statistic 0.59 [95% CI 0.54–0.65]). The model stratified absolute risk between the lowest and highest risk quintiles (5.1% vs. 12.5%). External validation in ARIC found similar predictiveness (c-statistic 0.58 [0.49–0.67]), but poor calibration across the risk spectrum. In the treatment risk model, CEA was superior to medical management across the spectrum of baseline risk and the magnitude of the treatment effect varied widely between the lowest and highest absolute risk quintiles (3.2% vs. 10.7%).

Conclusion

Even modestly predictive risk stratification tools have the potential to meaningfully influence clinical decision making in asymptomatic carotid disease. However, our ACAS model requires target population recalibration prior to clinical application.
Profiling Mycobacterium tuberculosis transmission and the resulting disease burden in the five highest tuberculosis burden countries
Authors: Ragonnet Romain , Trauer James M. , Geard Nicholas , Scott Nick , McBryde Emma S.
Published: November 2019

Background

Tuberculosis (TB) control efforts are hampered by an imperfect understanding of TB epidemiology. The true age distribution of disease is unknown because a large proportion of individuals with active TB remain undetected. Understanding of transmission is limited by the asymptomatic nature of latent infection and the pathogen’s capacity for late reactivation. A better understanding of TB epidemiology is critically needed to ensure effective use of existing and future control tools.

Methods

We use an agent-based model to simulate TB epidemiology in the five highest TB burden countries—India, Indonesia, China, the Philippines and Pakistan—providing unique insights into patterns of transmission and disease. Our model replicates demographically realistic populations, explicitly capturing social contacts between individuals based on local estimates of age-specific contact in household, school and workplace settings. Time-varying programmatic parameters are incorporated to account for the local history of TB control.

Results

We estimate that the 15–19-year-old age group is involved in more than 20% of transmission events in India, Indonesia, the Philippines and Pakistan, despite representing only 5% of the local TB incidence. According to our model, childhood TB represents around one fifth of the incident TB cases in these four countries. In China, three quarters of incident TB were estimated to occur in the ≥ 45-year-old population. The calibrated per-contact transmission risk was found to be similar in each of the five countries despite their very different TB burdens.

Conclusions

Adolescents and young adults are a major driver of TB in high-incidence settings. Relying only on the observed distribution of disease to understand the age profile of transmission is potentially misleading.
The role of adipose triglyceride lipase in lipid and glucose homeostasis: lessons from transgenic mice
Authors: Trites Michael J. , Clugston Robin D.
Published: November 2019

The ability of mammals to store and draw on fat reserves has been a driving force throughout evolution in an environment with intermittent nutrient availability. The discovery of adipose triglyceride lipase (ATGL) as a triglyceride lipase provided a heightened understanding of the mechanisms governing mobilization of fat reserves from adipose tissue. ATGL catalyses the initial step in adipose triglyceride lipolysis, working in concert with other enzymes to mobilize triglyceride for energy production. In addition to the role of ATGL in adipose tissue triglyceride mobilization, ATGL plays crucial roles in regulating lipid homeostasis in other tissues. These roles have been characterized primarily using transgenic mice with tissue-specific ATGL ablation. For example, the global ATGL knockout induces a severe cardiac defect that results in premature mortality that is mimicked by inducible cardiomyocyte-specific ATGL knockout. Global- and adipose-specific ATGL ablation induces a whole-body shift from lipid metabolism to glucose metabolism to satisfy metabolic demand primarily facilitated by an increase in glucose uptake by skeletal muscle. Generation of liver-specific ATGL knockouts has implicated hepatic lipolysis as a critical component of normal liver function. Analysis of β-cell ATGL knockouts implicates the necessity of pancreatic ATGL in insulin secretion. The objective of this review is to discuss the contributions of ATGL to systemic lipid- and glucose-homeostasis discovered through the study of transgenic mice.
The proliferative effect of cortisol on bovine endometrial epithelial cells
Authors: Dong Junsheng , Li Jun , Li Jianji , Cui Luying , Meng Xia , Qu Yang , Wang Heng
Published: November 2019

Background

Bovine endometrial epithelial cells (BEECs) undergo regular regeneration after calving. Elevated cortisol concentrations have been reported in postpartum cattle due to various stresses. However, the effects of the physiological level of cortisol on proliferation in BEECs have not been reported. The aim of this study was to investigate whether cortisol can influence the proliferation properties of BEECs and to clarify the possible underlying mechanism.

Methods

BEECs were treated with different concentrations of cortisol (5, 15 and 30 ng/mL). The mRNA expression of various growth factors was detected by quantitative reverse transcription-polymerase chain reaction (qPCR), progression of the cell cycle in BEECs was measured using flow cytometric analysis, and the activation of the Wnt/β-catenin and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathways was detected with Western blot and immunofluorescence.

Results

Cortisol treatment resulted in upregulated mRNA levels of vascular endothelial growth factor (VEGF) and connective tissue growth factor (CTGF); however, it had no influence on transforming growth factor-beta1 (TGF-β1). Cortisol (15 ng/mL) accelerated the cell cycle transition from the G0/G1 to the S phase. Cortisol upregulated the expression of β-catenin, c-Myc, and cyclinD1 and promoted the phosphorylation of PI3K and AKT.

Conclusions

These results demonstrated that cortisol may promote proliferation in BEECs by increasing the expression of some growth factors and activating the Wnt/β-catenin and PI3K/AKT signaling pathways.
Focused cardiac ultrasound in preoperative assessment: the perioperative provider’s new stethoscope?
Authors: Lenk Tara , Whittle John , Miller Timothy E. , Williams David G. A. , Bronshteyn Yuriy S.
Published: November 2019

Focused cardiac ultrasound (FoCUS)—a simplified, qualitative version of echocardiography—is a well-established tool in the armamentarium of critical care and emergency medicine. This review explores the extent to which FoCUS could also be used to enhance the preoperative physical examination to better utilise resources and identify those who would benefit most from detailed echocardiography prior to surgery. Among the range of pathologies that FoCUS can screen for, the conditions it provides the most utility in the preoperative setting are left ventricular systolic dysfunction (LVSD) and, in certain circumstances, significant aortic stenosis (AS). Thus, FoCUS could help answer two common preoperative diagnostic questions. First, in a patient with high cardiovascular risk who subjectively reports a good functional status, is there evidence of LVSD? Second, does an asymptomatic patient with a systolic murmur have significant aortic stenosis? Importantly, many cardiac pathologies of relevance to perioperative care fall outside the scope of FoCUS, including regional wall motion abnormalities, diastolic dysfunction, left ventricular outflow obstruction, and pulmonary hypertension. Current evidence suggests that after structured training in FoCUS and performance of 20–30 supervised examinations, clinicians can achieve competence in basic cardiac ultrasound image acquisition. However, it is not known precisely how many training exams are necessary to achieve competence in FoCUS image interpretation. Given the short history of FoCUS use in preoperative evaluation, further research is needed to determine what additional questions FoCUS is suited to answer in the pre-operative setting.