bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of volatile compounds in different parts of fresh Amomum villosum Lour. from different geographical areas using cryogenic grinding combined HS–SPME–GC–MS
Authors: Chen Ling-Xiao , Lai Yun-Feng , Zhang Wei-Xiong , Cai Jing , Hu Hao , Wang Ying , Zhao Jing , Li Shao-Ping 
Published: September 2020

Abstract
Background
The essential oil is one of the main active ingredients of Amomum villosum Lour. However, volatile compounds are easily lost during the drying, storage and even sample preparation procedure. Therefore, using fresh samples can obtain more accurately data for qualitative and comparative analysis.

Methods
In this study, the volatile compounds in different parts of fresh A. villosum from different origins were systemic analyzed and compared by using cryogenic grinding combined HS–SPME–GC–MS for the first time. GC–MS analyses were performed on a 6890 Series GC instrument coupled to a 5973 N mass spectrometer. The volatile compounds were extracted by the SPME fiber (100 μm PDMS). Analytes separation was achieved on a HP-5MS capillary column. The oven temperature was initially programmed at 70 °C, then raised 4 °C/min to reach 125 °C and then programmed at 0.5 °C/min to 133 °C, then at 6 °C/min to 170 °C and finally, at 20 °C/min to 280 °C held for 2 min. The temperatures of the injection port, ion source and transfer line were set at 250 °C, 230 °C and 280 °C, respectively.

Results
Forty-eight main compounds were identified in different parts of fresh A. villosum. The most abundant components in fresh fruit samples were camphor (3.91%), bornyl acetate (10.53%), caryophyllene (8.70%), β-bisabolene (11.50%), (E)-nerolidol (14.82%) and cubenol (10.04%). This is quite different with that of dried samples analyzed in our previous work. As different parts of the same plant, many common components with biological activities were detected in fruit and other parts. In principle components analysis (PCA) and hierarchical clustering analysis (HCA), four parts of A. villosum were divided into different groups clearly. Additionally, fruit and root samples also could be divided into two subgroups (HCA) in accordance with their regions.

Conclusion
The developed method was successfully used for qualitative and comparative analysis of volatile compounds in fresh A. villosum samples. Additionally, using fresh samples can obtain much more information which is helpful for their performance in the fields of functional foods, agriculture and biomedical industry. Furthermore, our research is helpful for comprehensive utilization and quality control of A. villosum.
COCOA: coordinate covariation analysis of epigenetic heterogeneity
Authors: Lawson John T. , Smith Jason P. , Bekiranov Stefan , Garrett-Bakelman Francine E. , Sheffield Nathan C. 
Published: September 2020

AbstractA key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across individuals and a database of region sets to annotate epigenetic heterogeneity. COCOA is the first such tool for DNA methylation data and can also analyze any epigenetic signal with genomic coordinates. We demonstrate COCOA’s utility by analyzing DNA methylation, ATAC-seq, and multi-omic data in supervised and unsupervised analyses, showing that COCOA provides new understanding of inter-sample epigenetic variation. COCOA is available on Bioconductor (http://bioconductor.org/packages/COCOA).
Alignment and mapping methodology influence transcript abundance estimation
Authors: Srivastava Avi , Malik Laraib , Sarkar Hirak , Zakeri Mohsen , Almodaresi Fatemeh , Soneson Charlotte , Love Michael I. , Kingsford Carl , Patro Rob 
Published: September 2020

AbstractBackgroundThe accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been shown to be important, considerably less attention has been given to comparing the effect of various read alignment approaches on quantification accuracy.ResultsWe investigate the influence of mapping and alignment on the accuracy of transcript quantification in both simulated and experimental data, as well as the effect on subsequent differential expression analysis. We observe that, even when the quantification model itself is held fixed, the effect of choosing a different alignment methodology, or aligning reads using different parameters, on quantification estimates can sometimes be large and can affect downstream differential expression analyses as well. These effects can go unnoticed when assessment is focused too heavily on simulated data, where the alignment task is often simpler than in experimentally acquired samples. We also introduce a new alignment methodology, called selective alignment, to overcome the shortcomings of lightweight approaches without incurring the computational cost of traditional alignment.ConclusionWe observe that, on experimental datasets, the performance of lightweight mapping and alignment-based approaches varies significantly, and highlight some of the underlying factors. We show this variation both in terms of quantification and downstream differential expression analysis. In all comparisons, we also show the improved performance of our proposed selective alignment method and suggest best practices for performing RNA-seq quantification.
Acupuncture treatment for carotid atherosclerotic plaques: study protocol for a pilot randomized, single blinded, controlled clinical trial
Authors: Zhou Junhe , Zhao Lin , Meng Lingcui , Liang Huitao , Zhou Ting , Ye Siting , Qi Zhiqi , Huang Xichang , Zhou Peng , Fu Wenbin 
Published: September 2020

Abstract
Background
Carotid atherosclerosis disease (CAD) is generally associated with the occurrence of cardiovascular and cerebrovascular accidents. However, CAD has not been taken seriously enough in the clinic, which, coupled with the single treatment and prevention of CAD, has led to a generally low level of patient compliance. Therefore, acupuncture is expected to be a safe and effective therapy that can be maintained in the long term for patients with CAD. The study objective is to evaluate the efficiency and reliability of acupuncture to relieve CAD and provide a new therapeutic idea for the clinical treatment of CAD.

Methods
This is a three-arm randomized clinical trial in China. Three groups (TA, SA, and MC) will be randomly allocated at a 1:1:1 ratio. The study will enrol 105 cervical atherosclerosis plaque patients in total on a voluntary basis, with 35 patients in each group. The treatment will last for 12 weeks, with two treatments per week for twenty-four treatments in total.

Results
Two 3D ultrasound indicators will be measured as the primary outcomes: the total plaque volume (PV) of the carotid artery on each side and the grey-scale median (GSM). The secondary outcomes will include intima-media thickness (IMT), lipid levels, apolipoprotein A-IV level, platelet count (PLT), fibrinogen (FIB), and platelet aggregation rate (PAR). All the outcomes will be assessed before treatment, after treatment, and after a 12-week follow-up period. This study will utilize per-protocol (PP) and intention-to-treat (ITT) analysis principles.

Conclusions
This trial is to evaluate the efficacy and reliability of acupuncture in relieving carotid atherosclerotic plaques by establishing acupuncture (TA), sham acupuncture (SA), and medication (MC) groups.

Ethics and dissemination
This study was approved by the Institutional Ethics Committee of Guangdong Provincial Hospital of Traditional Chinese Medicine (no. YF2018-107-01). All data and findings will be provided by the principal investigator via email.

Trial registration
ChiCTR, ChiCTR1800019259. Registered on 1 November 2018—retrospectively registered, http://www.chictr.org.cn/index.aspx
Dexamethasone in the era of COVID-19: friend or foe? An essay on the effects of dexamethasone and the potential risks of its inadvertent use in patients with diabetes
Authors: Alessi Janine , de Oliveira Giovana B. , Schaan Beatriz D. , Telo Gabriela H. 
Published: September 2020

AbstractBackgroundThe disclosure in the media of a benefit with the use of dexamethasone in patients with COVID-19 infection sets precedents for self-medication and inappropriate use of corticosteroids.MethodsThis is a critical interpretive synthesis of the data available in the literature on the effects of the use of corticosteroids and the impact that their indiscriminate use may have on patients with diabetes. Reviews and observational and experimental studies published until June 18, 2020 were selected.ResultsCorticosteroids are substances derived from cholesterol metabolism that interfere with multiple aspects of glucose homeostasis. Interactions between corticoid receptors and target genes seem to be among the mechanisms responsible for the critical functions of glucocorticoids for survival and anti-inflammatory effects observed with these medications. Corticosteroids increase hepatic gluconeogenesis, reduce peripheral use of glucose and increase insulin levels. Previous studies have shown that glucocorticoids have a pro-adipogenic function, increasing deposition of abdominal fat, and lead to glucose intolerance and hypertriglyceridemia. In addition, these drugs play a role in controlling liver metabolism and can lead to the development of hepatic steatosis. Glucocorticoids reduce the recruitment of osteoblasts and increase the number of osteoclasts, which results in increased bone resorption and greater bone fragility. Moreover, these medications cause water and sodium retention and increase the response to circulating vasoconstrictors, which results in increased blood pressure levels. Chronic or high-dose use of corticosteroids can, by itself, lead to the onset of diabetes. For those who were already diagnosed with diabetes, studies show that chronic use of corticosteroids leads to a 94% higher risk of hospitalization due to diabetes complications. In addition to the direct effects on glycemic control, the effects on arterial pressure control, lipids and bone metabolism also have a potential for severe consequences in patients with diabetes.ConclusionFear and uncertainty toward a potentially serious infection may lead people to self-medication and the inappropriate and abusive use of corticosteroids. More than ever, it is necessary for health professionals to be alert and able to predict damages related to the use of these drugs, which is the first step to minimize the potential damages to come.
A study on input noise second-order filtering and smoothing of linear stochastic discrete systems with packet dropouts
Authors: Zhao Huihong , Li Zhifang , Li Bin , Li Tongxing 
Published: September 2020

AbstractWe investigate non-Gaussian noise second-order filtering and fixed-order smoothing problems for non-Gaussian stochastic discrete systems with packet dropouts. We present a novel Kalman-like nonlinear non-Gaussian noise estimation approach based on the packet dropout probability distribution and polynomial filtering technique. By means of properties of Kronecker product we first introduce a second-order polynomial extended system and then analyze the means and variances of the Kronecker powers of the extended system noises. To generate noise estimators in forms of filtering and smoothing, we use the innovation approach. We give an example to illustrate that the presented algorithm has better robustness against packet dropouts than conventional linear minimum variance estimation.
Why are supercentenarians so frequently found in French Overseas Departments? The cases of Guadeloupe and Martinique
Authors: Vallin Jacques 
Published: September 2020

AbstractMany more cases of supercentenarians are observed in the French Départements d’Outre-Mer (DOM) than in metropolitan France. A first possible explanation is that the standard French protocol for validating age does not sufficiently cover DOMs. However, if additional checks can confirm the verity of this phenomenon, forming explanatory hypotheses can be relevant and quite interesting. Thanks to an INED research funding, a special protocol of deep age checking has been established to be applied to the two DOMs where the phenomenon is the most pronounced: Guadeloupe and Martinique. First results not only show that combining several additional checks does not leave much room for further doubting the ages of supercentenarians but they also support some arguments in favor of a possible fundamental explanation: genetic selection due to the extreme severity of mortality inflicted on their slave ancestors.
Effects of maternal depression and prenatal SSRI exposure on executive functions and susceptibility to household chaos in 6-year-old children: prospective cohort study
Authors: Dhaliwal Gurpreet , Weikum Whitney M. , Jolicoeur-Martineau Alexia , Brain Ursula , Grunau Ruth E. , Oberlander Tim F. 
Published: September 2020

Background
Maternal depressed mood during pregnancy may shape a child's adaptation to their environment and engagement in goal-directed behaviour such as executive functions. Whether everyday household context also alters executive functions in children with prenatal selective serotonin reuptake inhibitor (SSRI) antidepressant exposure remains to be determined.

Aims
To examine the impact of prenatal depressed maternal mood and SSRI exposure on child executive functions and to determine whether these exposures shape a susceptibility to household chaos.

Method
A prospective cohort study of mothers and their children (118 mother–children dyads (47 SSRI-exposed, 71 non-exposed)) followed from the second trimester to 6 years. Regression models examined relationships between maternal depressed mood and household chaos on maternal report of child executive functions. Competitive-confirmatory regression models examined whether children were susceptible to household chaos or were positively influenced by less chaos.

Results
Prenatal SSRI exposure, third-trimester maternal depressed mood and household chaos in a three-way interaction were associated with executive functions within a model of differential susceptibility. When household chaos was low, children of non-prenatally depressed mothers had better executive function than children of prenatally depressed mothers, regardless of whether the mothers were SSRI-treated. However, when household chaos was high, SSRI-exposed children of mothers who were not depressed during pregnancy had poorer executive functions at 6 years of age compared with SSRI-exposed children whose mothers were symptomatic during pregnancy.

Conclusions
The impact of household chaos depended on whether mothers were prenatally depressed and whether mothers were SSRI-treated.
Imagery rescripting and eye movement desensitisation and reprocessing as treatment for adults with post-traumatic stress disorder from childhood trauma: randomised clinical trial
Authors: Boterhoven de Haan Katrina L. , Lee Christopher W. , Fassbinder Eva , van Es Saskia M. , Menninga Simone , Meewisse Marie-Louise , Rijkeboer Marleen , Kousemaker Margriet , Arntz Arnoud 
Published: September 2020

BackgroundInvestigation of treatments that effectively treat adults with post-traumatic stress disorder from childhood experiences (Ch-PTSD) and are well tolerated by patients is needed to improve outcomes for this population.AimsThe purpose of this study was to compare the effectiveness of two trauma-focused treatments, imagery rescripting (ImRs) and eye movement desensitisation and reprocessing (EMDR), for treating Ch-PTSD.MethodWe conducted an international, multicentre, randomised clinical trial, recruiting adults with Ch-PTSD from childhood trauma before 16 years of age. Participants were randomised to treatment condition and assessed by blind raters at multiple time points. Participants received up to 12 90-min sessions of either ImRs or EMDR, biweekly.ResultsA total of 155 participants were included in the final intent-to-treat analysis. Drop-out rates were low, at 7.7%. A generalised linear mixed model of repeated measures showed that observer-rated post-traumatic stress disorder (PTSD) symptoms significantly decreased for both ImRs (d = 1.72) and EMDR (d = 1.73) at the 8-week post-treatment assessment. Similar results were seen with secondary outcome measures and self-reported PTSD symptoms. There were no significant differences between the two treatments on any standardised measure at post-treatment and follow-up.ConclusionsImRs and EMDR treatments were found to be effective in treating PTSD symptoms arising from childhood trauma, and in reducing other symptoms such as depression, dissociation and trauma-related cognitions. The low drop-out rates suggest that the treatments were well tolerated by participants. The results from this study provide evidence for the use of trauma-focused treatments for Ch-PTSD.
Triangle of Knowledge “Extra-Day Educational Activity and Conditions of Its Realization in Education
Authors: Nazarova T. 
Published: September 2020

The article shows the methodological problems of the organization of extracurricular activities of schoolchildren in the context of the “knowledge triangle” concept, which includes interconnections in the triad “education - science - innovation” in order to systemically transform the school of a new generation in the conditions of information postmodernism. The homework of schoolchildren is presented as an extracurricular independent activity of a schoolchild, undergoing significant changes due to a breakthrough in the educational process of technical and technological innovations. The prerequisites of a new vision of the problems of organization and management of educational activity (cognition) of schoolchildren and their consideration in the conditions of developing innovations are shown. Technological innovations in the form of new electronic equipment and interdisciplinary humanitarian technologies affect the updating of the content of subject courses, which, when introduced into the context of educational activity, change the forms of information transmission, the structure of its activity organization and assimilation. Understanding this problem implies the knowledge of the researcher about the features of the content, self-organization operations, the resulting communicative relationships and the features of the translation of educational material. An analysis of educational development trends shows the desire of world communities to integrate and form a new global information society based on fundamental knowledge, science, technology, high technology, allowing to achieve an increase in the pace of economic development and favorable social transformations.
The factors of influence on the state of extracurricular work of schoolchildren, emerging didactic barriers in the real process of completing homework are considered. The views of domestic and foreign scientists on the problem of necessity and the abolition of homework are presented. The strategic guidelines of the organization of extracurricular activities are shown, designed to ensure the overcoming of negative influence factors through the development of instrumental-activity platforms, including digital ones, which provide rational forms of translation, perception, understanding and application of educational material.
Synovial plica of the elbow and its clinical relevance
Authors: Lubiatowski Przemysław , Wałecka Joanna , Dzianach Marcin , Stefaniak Jakub , Romanowski Leszek 
Published: September 2020

A synovial plica (fold) is normal anatomic finding, and occurs in 86–100% of cases; however, symptomatic plica is much less common (7.2–8.7% of all elbow arthroscopies). Synovial plica syndrome is a painful elbow condition related to symptomatic synovial plica. Synovial plica syndrome is diagnosed by clinical examination (lateral elbow pain) commonly accompanied by local tenderness, pain at terminal extension and/or painful snapping. Synovial plica syndrome may be mimicked by other elbow conditions, commonly tennis elbow, loose bodies, and degenerative arthritis. Magnetic resonance imaging or ultrasound scan may support diagnosis in correlation with clinical findings, but symptomatic plica may also be diagnosed as unexpected during elbow arthroscopy. The arthroscopic resection is effective and safe if conservative treatment fails. Cite this article: EFORT Open Rev 2020;5:549-557. DOI: 10.1302/2058-5241.5.200027
Literature review of the causes of pain following total knee replacement surgery: prosthesis, inflammation and arthrofibrosis
Authors: Li Cheuk Yin , Ng Cheong Chung Kenneth Jordan , Ali Omar M. E. , Chung Nicholas D. H. , Li Cheuk Heng 
Published: September 2020

Adverse knee pain occurs in 10–34% of all total knee replacements (TKR), and 20% of TKR patients experience more pain post-operatively than pre-operatively. Knee pain is amongst the top five reasons for knee replacement revision in the United Kingdom. The number of TKRs is predicted to continue increasing due to the ageing population. A narrative literature review was performed on the different causes of pain following TKR. A database search on Scopus, PubMed, and Google Scholar was conducted to look for articles related to TKR, pain, and cause. Articles were selected based on relevance, publication date, quality of research and validation. Relevant sections were added to the review. One hundred and fourteen articles were identified and potential causes of TKR pain included: arthrofibrosis, aseptic loosening, avascular necrosis, central sensitization, component malpositioning, infection, instability, nerve damage, overstuffing, patellar maltracking, polyethylene wear, psychological factors and unresurfaced patella. It is important to tailor our approach to address the individual causes of pain. Certain controllable risk factors can be managed pre-operatively to minimize post-operative pain. Risk factors help to predict adverse pain outcomes and identify specific causes. There are multiple causes of pain following TKR. Some factors will require further extensive studies, and as pain is a commonly attributed reason for TKR revision, its underlying aetiologies should be explored. Understanding these factors helps to develop effective methods for diagnosis, prevention and management of TKR pain, which help to improve patient outcomes. Cite this article: EFORT Open Rev 2020;5:534-543. DOI: 10.1302/2058-5241.5.200031
A 324-years temperature reconstruction from Pinus latteri Mason at highland in Chiang Mai Province, Thailand
Authors: Lumyai Pichit , PALAKIT KITSADAPAN , DUANGSATHAPORN KHWANCHAI , WANTHONGCHAI KOBSAK 
Published: September 2020

Abstract. Lumyai P, Palakit K, Suangsathaporn K, Wanthongchai K. 2020. A 324-years temperature reconstruction from Pinus latteri Mason at highland in Chiang Mai Province, Thailand. Biodiversitas 21: 3938-3945. The objective of this study was to investigate the relationship between the growth of Pinus latteri and climate data in Chiang Mai Province, Thailand. Dendrochronological techniques were used to analyze 35 sample cores. The cross dated ring width data could be extended back for up to 324 years (1692-2015). The relationship between ring-width index and climate data indicated a significant correlation (p < 0.01) with the monthly rainfall in January, monthly temperature in August and September, extreme maximum temperature in August and mean maximum temperature in March and August. The reconstructed average monthly temperature in August was estimated at around 27.35 °C, a warming period could have occurred in 1694-1702, 1834-1844, 1848-1866, 1873-1876, 1884-1890, 1896-1902, 1911-1927, 1942-1958, and 1986-1990, with cooling periods occurring in 1703-1722, 1739-1752, 1865-1872, 1877-1883, 1891-1895, 1903-1910, 1928-1941, 1959-1961, and 1968-1970, which could explain the high fluctuations in temperature. Periods in the range 2.1-2.5, 10.1 , and 13.5 years were found to be common with the variations in El Niño-Southern Oscillation. In conclusion, the pine growth information can be used to monitor the variations in climate in Thailand.