bluuebunny/crossref_metadata_2025_split huggingface dataset:
The chromosome-level wintersweet (Chimonanthus praecox) genome provides insights into floral scent biosynthesis and flowering in winter
Authors: Shang Junzhong , Tian Jingpu , Cheng Huihui , Yan Qiaomu , Li Lai , Jamal Abbas , Xu Zhongping , Xiang Lin , Saski Christopher A. , Jin Shuangxia , Zhao Kaige , Liu Xiuqun , Chen Longqing 
Published: August 2020

Abstract
Background
Wintersweet (Chimonanthus praecox), an important ornamental plant, has evolved unique fragrant aroma and winter-flowering properties, which are critical for its successful sexual reproduction. However, the molecular mechanisms underlying these traits are largely unknown in this species. In addition, wintersweet is also a typical representative species of the magnoliids, where the phylogenetic position of which relative to eudicots and monocots has not been conclusively resolved.

Results
Here, we present a chromosome-level wintersweet genome assembly with a total size of 695.36 Mb and a draft genome assembly of Calycanthus chinensis. Phylogenetic analyses of 17 representative angiosperm genomes suggest that Magnoliids and eudicots are sister to monocots. Whole-genome duplication signatures reveal two major duplication events in the evolutionary history of the wintersweet genome, with an ancient one shared by Laurales, and a more recent one shared by the Calycantaceae. Whole-genome duplication and tandem duplication events have significant impacts on copy numbers of genes related to terpene and benzenoid/phenylpropanoid (the main floral scent volatiles) biosynthesis, which may contribute to the characteristic aroma formation. An integrative analysis combining cytology with genomic and transcriptomic data reveals biological characteristics of wintersweet, such as floral transition in spring, floral organ specification, low temperature-mediated floral bud break, early blooming in winter, and strong cold tolerance.

Conclusions
These findings provide insights into the evolutionary history of wintersweet and the relationships among the Magnoliids, monocots, and eudicots; the molecular basis underlying floral scent biosynthesis; and winter flowering, and highlight the utility of multi-omics data in deciphering important ornamental traits in wintersweet.
A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex
Authors: Sabin Susanna , Herbig Alexander , Vågene Åshild J. , Ahlström Torbjörn , Bozovic Gracijela , Arcini Caroline , Kühnert Denise , Bos Kirsten I. 
Published: August 2020

Abstract
Background
Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605–d. 1679).

Results
A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent.

Conclusions
The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells
Authors: Arruda Nicole L. , Carico Zachary M. , Justice Megan , Liu Ying Frances , Zhou Junjie , Stefan Holden C. , Dowen Jill M. 
Published: August 2020

Abstract
Background
The three-dimensional organization of the genome in the nucleus plays an integral role in many biological processes, including gene expression. The genome is folded into DNA loops that bring together distal regulatory elements and genes. Cohesin, a ring-shaped protein complex, is a major player in the formation of DNA loops. Cohesin is composed of a core trimer and one of two variant STAG subunits, STAG1 or STAG2. It is not understood whether variant STAG proteins give rise to cohesin complexes with distinct functions. Recent studies have begun to characterize the roles of STAG1 and STAG2, with partially contradictory results.

Results
Here, we generate stable single-knockout embryonic stem cell lines to investigate the individual contributions of STAG1 and STAG2 in regulating cohesin chromosomal localization and function. We report both overlapping roles for STAG1 and STAG2 in cohesin localization and somewhat distinct roles in gene expression. STAG1 and STAG2 occupy the same sites across the genome, yet do not exist together in a higher order complex. Despite their shared localization, STAG1 and STAG2 have both distinct and redundant effects on gene expression. Loss of both STAG1 and STAG2 causes widespread transcriptome dysregulation, altered cohesin DNA occupancy, and reduced cell proliferation.

Conclusions
Together, this work reveals the requirement of at least one STAG protein for proper cohesin function. STAG1 and STAG2 have independent roles in cohesin localization and both overlapping and distinct roles in gene expression. The roles of STAG1 and STAG2 in mouse embryonic stem cells may be somewhat different than in other cell types, due to their relative expression levels. These results advance our understanding of the link between mammalian genome organization and gene expression during development and disease contexts.
Biospeckle optical coherence tomography in speedy visualizing effects of foliar application of plant growth hormone to Chinese chives leaves
Authors: Rajagopalan Uma Maheswari , Kabir Mahjabin , Lim Yiheng , Kadono Hirofumi 
Published: August 2020

Abstract
Objective
The aim of this study is to demonstrate the potential of applying the contrast of the speckles obtained as noise in optical coherence tomography (OCT) images to monitor short term activity changes during foliar application of phytohormones to a plant leaf. Plant growth hormone, gibberellic acid (GA3) was sprayed onto the leaf of Chinese chives and after 60 min, OCT images (1 frame: 512 × 2048 pixels) were recorded at ten frames per second for a few tens of seconds.

Results
Contrast across the temporal axis was calculated for each pixel of the structural images and biospeckle OCT contrast images were obtained under the conditions of before and after application of GA3 for different concentrations 0, 40, and 100 μM. Application of 40 μM GA3 failed to show any differences in the OCT structural images. However, bOCT contrast image was clearly different. Changes were found to be statistically significant. Although the mechanism for the contrast difference is not clear, it can be said there is a large change across the temporal scale with the application of GA3. Demonstration of OCT utilizing the speckle contrast is believed to have the potential as a promising tool in plant physiology.
Identification of symbiotic bacteria in the midgut of the medically important mosquito, Culiseta longiareolata (Diptera: Culicidae)
Authors: Ghahvechi Khaligh Fereshteh , Vahedi Mozaffar , Chavshin Ali Reza 
Published: August 2020

Abstract
Objective
The potential use of symbiotic bacteria for the control of mosquito-borne diseases has attracted the attention of scientists over the past few years. Culiseta longiareolata is among the medically important mosquitoes that transmit a wide range of vector-borne diseases worldwide. However, no extensive studies have been done on the identification of its symbiotic bacteria. Given the role of this species in the transmission of some important diseases and its widespread presence in different parts of the world, including northwestern parts and the West Azerbaijan Province in Iran, a knowledge about the symbiotic bacteria of this species may provide a valuable tool for the biological control of this mosquito. Accordingly, the present study was conducted to isolate and identify the cultivable isolates bacterial symbionts of Culiseta longiareolata using 16S rRNA fragment analysis.

Results
The midguts of 42 specimens of Cs. longiareolata were dissected, and the bacteria were cultured on agar plates. After the purification of the bacterial colonies, 16srRNA region amplification and gene sequence analysis were performed, and the sequences were confirmed by biochemical methods. In the present study, 21 isolates belonging to the genera Acinetobacter, Aerococcus, Aeromonas, Bacillus, Carnobacterium, Klebsiella, Morganella, Pseudomonas, Shewanella and Staphylococcus were identified.
Symptoms of burnout in intensive care unit specialists facing the COVID-19 outbreak
Authors: Azoulay Elie , De Waele Jan , Ferrer Ricard , Staudinger Thomas , Borkowska Marta , Povoa Pedro , Iliopoulou Katerina , Artigas Antonio , Schaller Stefan J. , Hari Manu Shankar , Pellegrini Mariangela , Darmon Michael , Kesecioglu Jozef , Cecconi Maurizio ,   ESICM
Published: August 2020

Abstract
Background
The COVID-19 pandemic has resulted in an unprecedented healthcare crisis with a high prevalence of psychological distress in healthcare providers. We sought to document the prevalence of burnout syndrome amongst intensivists facing the COVID-19 outbreak.

Methods
Cross-sectional survey among intensivists part of the European Society of Intensive Care Medicine. Symptoms of severe burnout, anxiety and depression were collected. Factors independently associated with severe burnout were assessed using Cox model.

Results
Response rate was 20% (1001 completed questionnaires were returned, 45 years [39–53], 34% women, from 85 countries, 12 regions, 50% university-affiliated hospitals). The prevalence of symptoms of anxiety and depression or severe burnout was 46.5%, 30.2%, and 51%, respectively, and varied significantly across regions. Rating of the relationship between intensivists and other ICU stakeholders differed significantly according to the presence of anxiety, depression, or burnout. Similar figures were reported for their rating of the ethical climate or the quality of the decision-making. Factors independently associated with anxiety were female gender (HR 1.85 [1.33–2.55]), working in a university-affiliated hospital (HR 0.58 [0.42–0.80]), living in a city of > 1 million inhabitants (HR 1.40 [1.01–1.94]), and clinician’s rating of the ethical climate (HR 0.83 [0.77–0.90]). Independent determinants of depression included female gender (HR 1.63 [1.15–2.31]) and clinician’s rating of the ethical climate (HR 0.84 [0.78–0.92]). Factors independently associated with symptoms of severe burnout included age (HR 0.98/year [0.97–0.99]) and clinician’s rating of the ethical climate (HR 0.76 [0.69–0.82]).

Conclusions
The COVID-19 pandemic has had an overwhelming psychological impact on intensivists. Follow-up, and management are warranted to assess long-term psychological outcomes and alleviate the psychological burden of the pandemic on frontline personnel.
Indicators of home-based hospitalization model and strategies for its implementation: a systematic review of reviews
Authors: Casteli Christiane Pereira Martins , Mbemba Gisèle Irène Claudine , Dumont Serge , Dallaire Clémence , Juneau Lucille , Martin Elisabeth , Laferrière Marie-Claude , Gagnon Marie-Pierre 
Published: August 2020

Abstract
Background
Home-based hospitalization (HBH) offers an alternative delivery model to hospital care. There has been a remarkable increase in pilot initiatives and deployment of this model to optimize services offered to a population with a variety of progressive and chronic diseases. Our objectives were to systematically summarize the indicators of HBH as well as the factors associated with the successful implementation and use of this model.

Methods
We used a two-stage process. First, five databases were consulted, with no date delimitation. We included systematic reviews of quantitative, qualitative, and mixed studies published in English, French, Spanish, or Portuguese. We followed guidance from PRISMA and the Cochrane Collaboration. Second, we used the Nursing Care Performance Framework to categorize the indicators, a comprehensive grid of barriers and facilitators to map the factors affecting HBH implementation, and a thematic synthesis of the qualitative and quantitative findings.

Results
Fifteen reviews were selected. We identified 26 indicators related to nursing care that are impacted by the use of HBH models and 13 factors related to their implementation. The most frequently documented indicators of HBH were cost of resources, problem and symptom management, comfort and quality of life, cognitive and psychosocial functional capacity, patient and caregiver satisfaction, hospital mortality, readmissions, and length of stay. Our review also highlighted new indicators, namely use of hospital beds, new emergency consultations, and use of healthcare services as indicators of resources of cost, and bowel complications, caregiver satisfaction, and survival time as indicators of change in the patient’s condition. The main facilitators for HBH implementation were related to internal organizational factors (multidisciplinary collaboration and skill mix of professionals) whereas barriers were linked to the characteristics of the HBH, specifically eligibility criteria (complexity and social situation of the patient).

Conclusion
To the best of our knowledge, this is the first review that synthesizes both the types of indicators associated with HBH and the factors that influence its implementation. Considering both the processes and outcomes of HBH will help to identify strategies that could facilitate the implementation and evaluation of this innovative model of care delivery.

Systematic review registration
PROSPERO CRD42018103380
Theory-based E-health literacy interventions in older adults: a systematic review
Authors: Pourrazavi Sara , Kouzekanani Kamiar , Bazargan-Hejazi Shahrzad , Shaghaghi Abdolreza , Hashemiparast Mina , Fathifar Zahra , Allahverdipour Hamid 
Published: August 2020

Abstract
Background
e-health literacy can facilitate the uptake of benefits of health for older adults. In this review, we aimed to tabulate the types and outcomes of the theory-based e-health interventions that had been applied to improve the e-health literacy of older adults.

Methods
In this systematic review, theory-based e-health literacy interventions that published up to April 2020 were retrieved from several online electronic databases, including Medline via PubMed, Cochrane Library, ProQuest, and EMBASE. The published papers were included in this study, if the study had been conducted on older adults, a theory-based intervention aimed at promoting e-health literacy, and had been written in English language in the timeframe of 2008–2020.

Results
A total of 1658 records were identified initially, of which, 12 articles met the inclusion criteria. The systematic review identified the using of variety of intrapersonal, interpersonal, and societal level conceptual models in enhancing of e-health literacy in older adults, and the concept of self-efficacy was applied in the most of interventions as the main conceptual theoretical framework.

Conclusions
Despite the paucity of conceptual models, which are specifically designed for e-health literacy interventions, based on our findings, we recommend self-efficacy as a powerful concept that can play an important role in improving e-health literacy in older adults.
Potential methanol toxicity and the importance of using a standardised alcohol-based hand rub formulation in the era of COVID-19
Authors: Dear K. , Grayson L. , Nixon R. 
Published: August 2020

Abstract
Objectives
Hand sanitisers are urgently needed in the time of COVID-19, and as a result of shortages, some people have resorted to making their own formulations, including the repurposing of distilleries. We wish to highlight the importance of those producing hand sanitisers to avoid methylated spirits containing methanol and to follow WHO recommended formulations.

Methods
We explore and discuss reports of methanol toxicity through ingestion and transdermal absorption. We discuss the WHO formulations and explain the rationale behind the chosen ingredients.

Short conclusion
We advise those producing hand sanitisers to follow WHO recommended formulations, and advise those producing hand sanitisers using methylated spirits, to avoid formulations which contain methanol.
Exploring the efficacy of transfer learning in mining image-based software artifacts
Authors: Best Natalie , Ott Jordan , Linstead Erik J. 
Published: August 2020

Abstract
Background
Transfer learning allows us to train deep architectures requiring a large number of learned parameters, even if the amount of available data is limited, by leveraging existing models previously trained for another task. In previous attempts to classify image-based software artifacts in the absence of big data, it was noted that standard off-the-shelf deep architectures such as VGG could not be utilized due to their large parameter space and therefore had to be replaced by customized architectures with fewer layers. This proves to be challenging to empirical software engineers who would like to make use of existing architectures without the need for customization.

Findings
Here we explore the applicability of transfer learning utilizing models pre-trained on non-software engineering data applied to the problem of classifying software unified modeling language (UML) diagrams. Our experimental results show training reacts positively to transfer learning as related to sample size, even though the pre-trained model was not exposed to training instances from the software domain. We contrast the transferred network with other networks to show its advantage on different sized training sets, which indicates that transfer learning is equally effective to custom deep architectures in respect to classification accuracy when large amounts of training data is not available.

Conclusion
Our findings suggest that transfer learning, even when based on models that do not contain software engineering artifacts, can provide a pathway for using off-the-shelf deep architectures without customization. This provides an alternative to practitioners who want to apply deep learning to image-based classification but do not have the expertise or comfort to define their own network architectures.
Early response assessment and prediction of overall survival after peptide receptor radionuclide therapy
Authors: Huizing Daphne M. V. , Aalbersberg Else A. , Versleijen Michelle W. J. , Tesselaar Margot E. T. , Walraven Iris , Lahaye Max J. , de Wit–van der Veen Berlinda J. , Stokkel Marcel P. M. 
Published: August 2020

Abstract
Background
Response after peptide receptor radionuclide therapy (PRRT) can be evaluated using anatomical imaging (CT/MRI), somatostatin receptor imaging ([68Ga]Ga-DOTA-TATE PET/CT), and serum Chromogranin-A (CgA). The aim of this retrospective study is to assess the role of these response evaluation methods and their predictive value for overall survival (OS).

Methods
Imaging and CgA levels were acquired prior to start of PRRT, and 3 and 9 months after completion. Tumour size was measured on anatomical imaging and response was categorized according to RECIST 1.1 and Choi criteria. [68Ga]Ga-DOTA-TATE uptake was quantified in both target lesions depicted on anatomical imaging and separately identified PET target lesions, which were either followed over time or newly identified on each scan with PERCIST-based criteria. Response evaluation methods were compared with Cox regression analyses and Log Rank tests for association with OS.

Results
A total of 44 patients were included, with median follow-up of 31 months (IQR 26–36 months) and median OS of 39 months (IQR 32mo-not reached)d. Progressive disease after 9 months (according to RECIST 1.1) was significantly associated with worse OS compared to stable disease [HR 9.04 (95% CI 2.10–38.85)], however not compared to patients with partial response. According to Choi criteria, progressive disease was also significantly associated with worse OS compared to stable disease [HR 6.10 (95% CI 1.38–27.05)] and compared to patients with partial response [HR 22.66 (95% CI 2.33–219.99)]. In some patients, new lesions were detected earlier with [68Ga]Ga-DOTA-TATE PET/CT than with anatomical imaging. After 3 months, new lesions on [68Ga]Ga-DOTA-TATE PET/CT which were not visible on anatomical imaging, were detected in 4/41 (10%) patients and in another 3/27 (11%) patients after 9 months. However, no associations between change in uptake on 68Ga-DOTA-TATE PET/CT or serum CgA measurements and OS was observed.

Conclusions
Progression on anatomical imaging performed 9 months after PRRT is associated with worse OS compared to stable disease or partial response. Although new lesions were detected earlier with [68Ga]Ga-DOTA-TATE PET/CT than with anatomical imaging, [68Ga]Ga-DOTA-TATE uptake, and serum CgA after PRRT were not predictive for OS in this cohort with limited number of patients and follow-up time.
A paleomagnetic record of the early Matuyama chron including the Réunion subchron and the onset Olduvai boundary: High-resolution magnetostratigraphy and insights from transitional geomagnetic fields
Authors: Konishi Takumi , Okada Makoto 
Published: August 2020

AbstractWe present a novel paleomagnetic record for the lower Matuyama chronozone, which includes the Réunion subchronozone and the lower Olduvai polarity reversal, from a continuous section of a 168-m-thick on-land marine succession in the southernmost part of the Boso Peninsula, central Japan. In this section, the Réunion subchronozone and the lower Olduvai reversal are observed at 38.6–44.6 m and 142.0 m, respectively. The average sedimentation rates between the lower and upper Réunion boundaries and between the upper Réunion boundary and lower Olduvai boundary are calculated as 25 cm/ky and 57 cm/ky, respectively. The virtual geomagnetic pole (VGP), observed in the Boso Peninsula, at both the upper and lower Réunion boundaries passed across the equator within a similar longitudinal band over Africa. Immediately below the upper boundary, between 43.0 and 43.5 m, the VGP settled in a cluster area around China. Relative paleointensity (RPI) values for the entire Réunion interval are generally lower than the average for the entire interval from the Réunion to the lower Olduvai subchronozone. Conversely, the VGP for the lower Olduvai reversal boundary did not pass across the equator within a narrow longitudinal band but settled in several cluster areas; i.e., the southern Indian Ocean, North America, and the southern South Pacific Ocean off South America. The VGP then moved rapidly between the clusters. The locations of VGP cluster areas in the lower Olduvai reversal seem to coincide with areas where a vertical component of the present geomagnetic non-axial dipole (NAD) field is dominant. During the reversal, the RPI declined rapidly and recovered slowly as the VGP moved rapidly between cluster areas. Our new paleomagnetic data are one of the most detailed records for those geomagnetic reversals from marine sediments, and will, therefore, help to understand the dynamics of the geomagnetic reversals.