bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the Effect of D614g, N501y and S477n Mutation in Sars-Cov-2 through Computational Approach
Authors: Mathavan Sarmilah , Kumar Suresh
Published: December 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an outbreak of COVID-19 disease in humans with the aid of spike protein. It consists of a receptor-binding domain (RBD) that recognizes and binds to the host receptor angiotensin-converting enzyme 2 (ACE2). The aim of this study was to examine the mutational effect of spike protein on the sequence through an interaction study of the mutant spike protein and the human ACE2 protein at the structural level. A total of 17,227 spike proteins from Asia, Africa, Europe, Oceania, South America, and North America were compared to the Wuhan spike protein reference sequence (Wuhan-Hu-1). The structural and stability implications of D614G, N501Y, and S477N mutations were evaluated. The binding affinity between mutated RBD and human ACE2 protein was also studied. The D614G mutation may have originated in Germany, Europe based on the date of the first sample collection report. It is now widely circulated all over the world with most occurrences in North America. The mutations N501Y and S477N may have originated from Oceania based on the date of the first sample collection report and also have the highest occurrences in Oceania. Based on the computational analysis of mutational effects, the D614G, N501Y, and S477N mutations decreased stability and were tolerated. For disease propensity prediction, N501Y was more prone to disease compared to D614G, while S477N was not prone to disease. The mutation of D to G at position 614 and S to N at position 477 for secondary structure prediction shows no changes in secondary structure while remaining in the coil region, whereas the mutation of N to Y at position 501 changes from coil structure to extended strand. N501Y mutation has a higher affinity to human ACE2 protein compared to D614G and S477N based on a docking study. D614G spike mutation was identified to exist between the two hosts based on a comparison of SARS-CoV-2 derived between the mink and human. Further research is needed on the link between the mink mutation N501T and the mutation N501Y in humans, which has evolved as a separate variant.
Keragaman Jenis Bambu di Kawasan Ekosistem Leuser, Kecamatan Tenggulun, Kabupaten Aceh Tamiang, Aceh
Authors: Ritonga Muhammad Azli , Navia Zidni Ilman , Arico Zulfan , Damayanto I Putu Gede P.
Published: December 2020

Informasi keragaman jenis bambu di Kawasan Ekosistem Leuser, terutama di wilayah Kecamatan Tenggulun, Kabupaten Aceh Tamiang, Aceh belum terdokumentasi dengan baik. Tujuan penelitian ini adalah menyediakan informasi keragaman jenis bambu di Kecamatan Tenggulun, Kabupaten Aceh Tamiang, Aceh. Penelitian dilakukan menggunakan metode pengumpulan data taksonomi melalui kegiatan eksplorasi dengan menjelajahi lokasi penelitian di Kecamatan Tenggulun pada bulan Januari–Maret 2019. Selama eksplorasi, sampel material bambu dikoleksi untuk dibuatkan spesimen herbarium dan disimpan di Herbarium Bogoriense (BO). Data pendukung seperti titik koordinat, ketinggian, nama lokal, kegunaan, dan foto bambu yang masih segar juga didokumentasikan. Material bambu diidentifikasi berdasarkan literatur dan koleksi spesimen herbarium yang telah tersimpan
di BO. Data dianalisis secara deskriptif dengan menjabarkan pertelaan dari setiap jenis bambu. Kunci identifikasi serta analisis hubungan kemiripan antarjenis bambu juga dilakukan. Sebanyak 29 karakter morfologi (vegetatif) dipilih untuk membentuk dendogram menggunakan metode UPGMA dengan bantuan program PAUP*. Terdapat delapan jenis bambu ditemukan di Kecamatan Tenggulun, yakni Bambusa heterostachya, B. multiplex, B. spinosa, B. vulgaris, Dendrocalamus asper, Gigantochloa
apus, G. atter, dan Schizostachyum zollingeri). Dendogram menunjukkan bahwa semua anggota jenis Bambusa dan satu jenis Schizostachyum mengumpul dalam satu kelompok yang sama. Sementara itu, jenis Dendrocalamus dan Gigantochloa mengumpul dalam kelompok lainnya. Hasil penelitian ini dapat digunakan sebagai data dasar penentuan kegiatan pengelolaan bambu di Kawasan Ekosistem Leuser.
Cendawan Penghasil Mikotoksin pada Komoditas Pertanian
Authors: Susilowati Dwi Ningsih , Sukmawati Dalia , Suryadi Yadi
Published: December 2020

Mikotoksin adalah metabolit sekunder beracun dengan bobot molekul rendah yang dihasilkan oleh cendawan berfilamen. Cendawan penghasil mikotoksin menginfeksi berbagai komoditas mulai dari kacang-kacangan, sampai komoditas pertanian lainnya seperti jagung, padi, buah-buahan, kopi, kakao, biji pala, dan gandum. Meskipun bukan merupakan penyebab utama penyakit tanaman, namun beberapa cendawan penghasil mikotoksin perlu diwaspadai karena dapat mengakibatkan kerusakan pada beberapa tanaman dan produknya. Infeksi cendawan penghasil mikotoksin dapat mengakibatkan penurunan kualitas hasil pertainan karena sifat mikotoksin yang karsinogenik, nefrotoksik, hepatotoksin, dan berbahaya bagi kesehatan. Sehubungan dengan tingginya keragaman jenis cendawan penghasil mikotoksin dan dampak negatifnya terhadap komoditas pertanian, maka perlu diketahui deskripsi beberapa jenis cendawan penghasil mikotoksin, jenis mikotoksin yang dihasilkan, efek, dan solusi penanganannya.
Hal ini perlu sebagai bahasan karena sejumlah mikotoksin pada produk pertanian dapat menimbulkan risiko kesehatan yang bervariasi dari reaksi alergi hingga kematian pada manusia dan hewan, serta permasalahan ekonomi. Ulasan ini menekankan pada status terkini kontaminasi mikotoksin pada komoditas pertanian dan strategi pengendalian lebih lanjut yang direkomendasikan untuk mitigasi mikotoksin.
The Determinants of Sustainable Agricultural Technology Adoption
Authors: Ashari NFN , Saliem Handewi Purwati , Maulana Mohammad , Ariningsih Ening , Septanti Kartika Sari
Published: December 2020

Pertanian memiliki peran penting karena lebih dari 60% populasi dunia bergantung pada pertanian sebagai mata pencaharian. Salah satu faktor penyumbang  besar terhadap pertumbuhan produktivitas pertanian adalah penerapan teknologi baru.  Teknologi baru pertanian diharapkan berperan sebagai jalan penting untuk keluar dari kemiskinan di sebagian besar negara berkembang. Namun, realita menunjukkan tingkat adopsi teknologi pertanian dianggap masih relatif rendah. Makalah ini merupakan scientific review yang merangkum dan menganalisis hasil-hasil penelitian tentang adopsi teknologi pertanian. Tujuan makalah adalah untuk mengamati pengalaman di sejumlah negara terkait adopsi teknologi pertanian dan menentukan faktor-faktor yang memengaruhi adopsi serta keberlanjutan suatu adopsi teknologi. Hasil studi mengungkapkan bahwa keputusan petani untuk mengadopsi teknologi baru bergantung pada interaksi dinamis antara karakteristik teknologi dan kondisi lingkungannya. Beberapa aspek yang memengaruhi adopsi teknologi pertanian antara lain aspek teknologi, ekonomi dan keuangan, sosial dan kelembagaan, serta usaha pertanian dan karakteristik rumah tangga petani. Namun, penentu adopsi teknologi pertanian tidak selalu tunggal, melainkan kombinasi dari beberapa faktor sehingga untuk memacu adopsi teknologi harus memperhitungkan semua faktor penentunya. Pendekatan yang komprehensif menjadi pilihan terbaik untuk menyebarluaskan teknologi baru pertanian. Pemerintah dapat menjadi fasilitator untuk adopsi teknologi dan memastikan teknologi yang disebarkan bermanfaat bagi petani.
Estrategias metodológicas docentes en comprensión lectora y rendimiento académico en el área de Comunicación
Authors: Choquichanca Lavado Rosa Eufemia , Inga Arias Miguel Gerardo
Published: December 2020

La base para el futuro educativo del estudiante es la  educación temprana. Con esa premisa se implementaron  el Programa Integral de Educación Temprana con Base en  la Familia (Pietbaf), el Programa de Atención Integral de  Grupos de Madres (Paigruma), las Salas de Educación Tem prana (SET) y Cuna Más. Todos son importantes, pero se  ha logrado muy poco, porque aún continúa la enseñanza  tradicional. Por ello, el objetivo de esta investigación fue  establecer si existe relación entre las estrategias metodológicas del docente en comprensión lectora y el rendimiento académico de los niños de 5 años en tres instituciones educativas (IE) de San Juan de Miraflores. Mediante  el estadígrafo rho de Spearman encontramos que existe  relación significativa positiva respecto a las estrategias de  las dimensiones para la comprensión lectora, como los juegos de lenguaje, la lectura grupal en voz alta de cuentos infantiles, el teatrino, la observación-descripción-creación, la poesía y la expresión-imaginación-creatividad, y el  rendimiento académico.
The physiological demands of Singing for Lung Health compared to treadmill walking
Authors: Philip Keir , Lewis Adam , Buttery Sara , McCabe Colm , Manivannan Bishman , Fancourt Daisy , Orton Christopher , Polkey Michael , Hopkinson Nicholas
Published: December 2020

Participating in singing is considered to have a range of social and psychological benefits. However, the physiological demands of singing, whether it can be considered exercise, and its intensity as a physical activity are not well understood. We therefore compared cardiorespiratory parameters while completing components of Singing for Lung Health (SLH) sessions, with treadmill walking at differing speeds (2, 4, and 6km/hr). Eight healthy adults were included, none of whom reported regular participation in formal singing activities. Singing induced physiological responses that were consistent with moderate intensity activity (METS: median 4.12, IQR 2.72 - 4.78), with oxygen consumption, heart rate, and volume per breath above those seen walking at 4km/hr. Minute ventilation was higher during singing (median 22.42L/min, IQR 16.83 - 30.54) than at rest (11L/min, 9 - 13), lower than 6km/hr walking (30.35L/min, 26.94 - 41.11), but not statistically different from 2km/hr (18.77L/min, 16.89 - 21.35) or 4km/hr (23.27L/min, 20.09 - 26.37) walking. Our findings suggest the metabolic demands of singing may contribute to the health and wellbeing benefits attributed to participation. However, if physical training benefits result remains uncertain. Further research including different singing styles, singers, and physical performance impacts when used as a training modality is encouraged.
Stabilization of S3O4 at High Pressure-Implications for the Sulfur Excess Paradox
Authors: Liu Siyu , Lv Jian , Gao Pengyue , Hermann Andreas , Yang Guochun , Wang Yanchao , Ma Yanming
Published: December 2020

The geological conundrum of “sulfur excess” refers to the finding that predicted amounts of sulfur, in the form of SO2, discharged in volcanic eruptions much exceeds the sulfur available for degassing from the erupted magma. Exploring the source of the excess sulfur has been the subject of considerable interest. Here, from a systematic computational investigation of sulfur oxygen compounds under pressure, a hitherto unknown S3O4 compound containing a mixture of sulfur oxidation states +II and +IV emerges and is predicted to be stabilized above a pressure of 79 GPa. We predict that S3O4 can be produced via multiple redox reactions involving subducted S bearing minerals (e.g., sulfates and sulfides) at high pressure and temperature conditions relevant to the deep lower mantle, and conversely be decomposed into SO2 and S at shallow depths of Earth. Therefore, S3O4 can be considered as a key intermediate compound to promote the decomposition of sulfates to release SO2, which offers an alternative source of the excess sulfur released during explosive eruptions. These findings provide a possible resolution to the geological paradox of “excess sulfur degassing” and a viable mechanism for understanding of S exchange between Earth’s surface and the lower mantle for the deep sulfur cycle.
General Versus Regional Anaesthesia for Caesarean Section Indicated for Acute Foetal Distress: A Retrospective Cohort Study
Authors: Metogo Junette Arlette , Nana Theophile , Ngongheh Brian , Nyuydzefon Emelinda , Adjahoung Christoph , Tochie Joel , Minkande Jacqueline
Published: December 2020

BackgroundAcute foetal distress (AFD) is a life-threatening foetal condition complicating 2% of all pregnancies and accounting for 8.9% of caesarean sections (CS) especially in developing nations. Despite the severity of the problem, no evidence exists as to the safest anaesthetic technique for the mother and foetus couple undergoing CS for AFD. We aimed to compare general anaesthesia (GA) versus regional (spinal and epidural) anaesthesia in terms of their perioperative maternal and foetal outcomes.MethodsWe carried out a retrospective cohort study by reviewing the medical records of all women who underwent CS indicated for AFD between 2015 to 2018 at the Douala General Hospital, Cameroon. Medical records of neonates were also reviewed. We sought to investigate the association between GA, and regional anaesthesia administered during CS for AFD and foetal and maternal outcomes. The threshold of statistical significance was set at 0.05. ResultsWe enrolled the medical records of 117 pregnant women who underwent CS indicated for AFD. Their mean age and mean gestational age were 30.5 ± 4.8 years and 40 weeks respectively. Eighty-three (70.9%), 29 (24.8%) and 05 (4.3%) pregnant women underwent CS under SA, GA and EA respectively. Neonates delivered by CS under GA were more likely to have a significantly low APGAR score at both the 1st (RR = 1.93, p = 0.014) and third-minute (RR = 2.52, p = 0.012) and to be resuscitated at birth (RR = 2.15, p = 0.015).Past CS, FHR pattern on CTG didn’t affect these results in multivariate analysis. Adverse maternal outcomes are shown to be higher following SA when compared to GA ConclusionThe study infers an association between CS performed for AFD under GA and fetal morbidity. This, however, failed to translate into a difference in perinatal mortality when comparing GA vs RA. This finding does not discount the role of GA, but we emphasize the need for specific precautions like adequate anticipation for neonatal resuscitation in order to reduce neonatal complications associated with CS performed for AFD under GA.
Association between Severe Acute Malnutrition during Childhood and Variability in Blood Pressure during Adulthood in Low- and Middle-income Countries: The Lwiro Cohort Study in the Democratic Republic of the Congo
Authors: Mwene-Batu Pacifique , Lemogoum Daniel , Hoye Laurène de le , Bisimwa Ghislain , Hermans Michel , Minani Jimmy , Amani Gaylord , Mateso Guy-Quesney , Cikomola Justin , Dramaix Michelle , Donnen Phillipe
Published: December 2020

Introduction: Little is known about the long-term outcomes of Severe Acute Malnutrition (SAM) during childhood. As such, this study aims to explore the association between childhood SAM and blood pressure (BP) variability in adulthood in a context without nutrition transition. Methodology: We identified 524 adults (Median age: 22 years) who were treated for SAM during childhood in Eastern DRC between 1988 and 2007. They were compared with 407 community unexposed age-and-sex matched with no history of SAM. The variables examined for this study were the systolic (SBP), diastolic (DBP), mean (MBP) and pulse (PP) blood pressures, as well as high blood pressure (HBP) in adulthood. For comparison, linear and logistic regression models were used for analysing continuous and dichotomous variables, respectively. Results: Of the 524 exposed located, 145 exposed were selected according to age. A total of 97 unexposed were recruited. Compared to unexposed, exposed had slightly higher SBP and PP after adjusting [SBP = 1.4 mm Hg (-2.2, 4.8) and PP = 2.6 mm Hg (-0.3, 6.0)]. However, their mean DBP was lower that of among the unexposed [ -1.6 mm Hg (-4.6, 1.5)]. MBP and creatinine levels were comparable between the two groups. The prevalence of HBP adjusted for age was higher among exposed than unexposed (9.7% vs 5.3%). In addition, the odds of having HBP was higher among exposed than unexposed, however the difference was not statistically significant [ORa 1.9 (0.7, 5.6)]. Finally, using multiple regression, although the effect was not significant, SAM was a major contributor to HBP [OR 3.1 (0.9,10.9), p = 0.064], while being male and higher BMI were the only independent predictors among the young population of this study. Conclusions: There was no significant impact from an episode of SAM during childhood on BP variability in young adults in a context without nutrition transition. However, people who experienced a period of SAM had a higher prevalence of HBP and a much higher risk of developing HBP than unexposed. Additional multicentre studies involving a larger cohort would provide greater understanding of the impact of SAM on the overall risk of BP disorders during adulthood.
Total, Gender- and Age-specific Incidence Rates of Upper Extremity Nerve Injuries in Finland
Authors: Wiman Kirsi , Hulkkonen Sina , Miettunen Jouko , Auvinen Juha , Karppinen Jaro , Ryhänen Jorma
Published: December 2020

Nerve injuries of the upper extremity can cause significant motor and sensory deficits that may lead to personal suffering and work disability with increased healthcare costs. The aim of this study was to describe the epidemiology of nerve injuries of the upper extremity in the whole population of Finland (1998–2016). Data based on diagnosis codes were obtained from the Care Register for Health Care, including incident cases of median, radial, ulnar, musculocutaneous, axillary, and digital nerves. Age- and gender-specific incidence rates, both crude and standardised (for the European normal population in 2011), were calculated as well as the level of the nerve injuries in the upper extremity. Our study included 13,458 patients with upper extremity nerve injury. The mean standardised incidence rate of any upper extremity nerve injury was 1.18 among men and 0.05 among women per 100,000 person-years over the study period. The incidence peaked among men at working age. The most common nerve injury level was the fingers and thumb, with 5,533 cases and mean standardised incidence rates per 100,000 person-years of 0.51 among men and 0.19 among women.
TrancriptomeReconstructoR, A Data-Driven Annotation of Complex Transcriptomes
Authors: Ivanov Maxim , Sandelin Albin , Marquardt Sebastian
Published: December 2020

Background: The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines for de novo transcriptome annotation. Ideally, gene and transcript models should be called from a limited set of key experimental data. Results: We developed TranscriptomeReconstructoR, an R package which implements a pipeline for automated transcriptome annotation. It relies on integrating features from independent and complementary datasets: i) full-length RNA-seq for detection of splicing patterns and ii) high-throughput 5' and 3' tag sequencing data for accurate definition of gene borders. The pipeline can also take a nascent RNA-seq dataset to supplement the called gene model with transient transcripts.We reconstructed de novo the transcriptional landscape of wild type Arabidopsis thaliana seedlings as a proof-of-principle. A comparison to the existing transcriptome annotations revealed that our gene model is more accurate and comprehensive than the two most commonly used community gene models, TAIR10 and Araport11. In particular, we identify thousands of transient transcripts missing from the existing annotations. Our new annotation promises to improve the quality of A.thaliana genome research.Conclusions: Our proof-of-concept data suggest a cost-efficient strategy for rapid and accurate annotation of complex eukaryotic transcriptomes. We combine the choice of library preparation methods and sequencing platforms with the dedicated computational pipeline implemented in the TranscriptomeReconstructoR package. The pipeline only requires prior knowledge on the reference genomic DNA sequence, but not the transcriptome. The package seamlessly integrates with Bioconductor packages for downstream analysis.
A Network Pharmacology Approach to Determine the Mechanisms of Action of Shuangshen Granules in Suppressing Pancreatic Cancer Precursor Lesions
Authors: Jiang Juling , Zhang Zhenhua , Yuan Yixin , Qi Runzhi , Chen Shuntai , Zhang Xiwen , Zhang Xing , Xi Yupeng , Guo Qiujun , Zheng Honggang , Hua Baojin , Liu Rui
Published: December 2020

Background and purpose: Pancreatic cancer is an insidious and highly lethal disease. Recognition and treatment of pancreatic cancer precursor lesions (PCPL) are important measures and can improve patient survival rate. Shuangshen Granules (SSG) have been prescribed for use in clinical practice for more than seven years and are widely used to treat the precursor lesions of various tumours. In this study, we used network pharmacology to explore the pharmacological mechanisms through which SSG suppress PCPL. We aimed to provide a basis for further research and the development of small, molecular, natural chemical drugs.Methods: We first searched databases and screened the bioactive components of SSG and the related targets acting on PCPL to construct a component-target network. Then, network topology analysis was used to analyse the hub target of SSG acting on PCPL. Enrichment analyses of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were also performed to determine the potential pathways. Finally, molecular docking simulations were carried out to investigate the interactions between PCPL-target proteins and the active components of SSG.Results: Seven of the main components of SSG affected PCPL, with 100 key targets including 16 hub targets. In addition, GO and KEGG enrichment analysis revealed that SSG regulated 111 molecular functions, 46 cellular components, 2334 biological processes, and 144 related signalling pathways, of which 26 were closely related to PCPL. Results of molecular docking analysis showed that the PCPL-related targets had strong binding properties with the active components of SSG, quercetin, and ginsenoside rh2, mainly TNF, IL-6, AKT1, TP53, and EGFR.Conclusion: This study has revealed the pharmacological and molecular mechanisms through which SSG acts on PCPL. It also provides powerful evidence to support the exploration of the pharmacological mechanisms of action and clinical applications of traditional Chinese medicine.
General Anaesthesia Related Mortality in a Limited Resource Settings Region: A Retrospective Study in Two Teaching Hospitals of Butembo
Authors: Pascal Furaha Nzanzu Blaise , Malisawa Agnes , Barratt-Due Andreas , Namboya Felix , Pollach Gregor
Published: December 2020

Background: General anaesthesia (GA) in developing countries is still a high-risk practice, especially in Africa, accompanied with high morbidity and mortality. No study has yet been conducted in Butembo to determine the mortality related to GA practice. The main objective of this study was to assess mortality related to GA in Butembo. Methods: This study was a retrospective analytic study of patients who underwent surgery under GA in the 2 main teaching hospitals of Butembo from January 2011 to December 2015. Data were collected from patients file, anaesthesia registries and were analysed with SPSS 26. Results: From a total of 921patients, male and female patients were 539 (58.5%) 382 (41.5%) respectively. A total of 83 (9.0%) patients died. The overall perioperative mortality rate was 90 per 1,000. From the 83 deaths, 38 occurred within 24h representing GA related mortality of 41 per 1,000. There was a global drop in mortality from 2011 to 2015. The risk factors of death were neonate and senior adult age, emergency operation, ASA physical status more than 2 and single deranged vital sign preoperatively. The occurrence of any complication during GA increased the risk of death. Anaesthesia duration more than 120 minutes increased mortality as well as visceral surgeries/laparotomies. Ketamine was the most employed agent. Conclusion: GA related mortality is very high in Butembo. Improved GA services and outcomes can be obtained by training more anaesthesia providers, proper patients monitoring, enhanced the infrastructure, better equipment and drugs procurement.
Plasma vanin-1 as a novel biomarker of sepsis for trauma patients: a prospective multicenter cohort study
Authors: Lu Hongxiang , Zhang Anqiang , Wen Dalin , Du Juan , Sun Jianhui , Qiao Liang , Du Dingyuan , Gu Wei , Jiang Jianxin
Published: December 2020

BackgroudVanin-1 plays a pivotal role in oxidative stress and the inflammatory response. However, its relationship with traumatic sepsis remains unknown. The aim of our study was to evaluate whether plasma vanin-1 expression can be used to predict traumatic sepsis in an early time.MethodsIn this three-stage prospective cohort study, severe trauma patients admitted to two hospitals from January 2015 to October 2018 were enrolled. Clinical data during hospitalization and APACHE II score were collected. Plasma vanin-1 levels were measured by enzyme linked immunosorbent assay. The associations among variables and traumatic sepsis were identified by logistic regression model. The receiver-operating characteristic curve was analyzed to evaluate the diagnostic efficiency of the selected factors.ResultsA total of 426 trauma patients (22 patients in the discovery cohort, 283 patients in the internal test cohort, and 121 patients in the external validation cohort) and 16 healthy volunteers were enrolled. The plasma vanin-1 level of trauma patients was significantly higher than that of healthy volunteers (P < 0.05), and sepsis patients had higher plasma vanin-1 than non-sepsis patients in the discovery trauma cohort (P < 0.05). In the internal test cohort, plasma vanin-1 levels at day 1 after trauma were significantly associated with the incidence of sepsis (OR = 3.92, 95% CI = 2.68–5.72, P = 1.62⊆10− 12). As a predictive biomarker, vanin-1 obtained a better area under the curve (AUC) (0.82, 95% CI = 0.77–0.87) than C-reaction protein (CRP) (0.62, 95% CI = 0.56–0.68, P < 0.0001), procalciton in (PCT) (0.66, 95% CI = 0.60–0.71, P < 0.0001), and Acute Physiology and Chronic Health Evaluation II (APACHE II) (0.71, 95% CI = 0.65–0.76, P = 6.70⊆10− 3). In addition, the clinical relevance between plasma vanin-1 and traumatic sepsis was validated in the external validation cohort (OR = 4.26, 95% CI = 2.22–8.17, P = 1.28⊆10− 5). The AUC of vanin-1 was 0.83 (95% CI = 0.75–0.89), which was better than that of CRP, PCT, and APACHE II.ConclusionsOur study demonstrated that plasma vanin-1 increased among trauma patients and was independently associated with the risk of sepsis. Vanin-1 might be a potential biomarker for the early prediction of traumatic sepsis.Trial registrationClinicaltrials.gov Identifier NCT01713205. Registered 24 October 2012.
Age Related Changes in the Circulating Leukocyte Transcriptome in Dairy Cows
Authors: Buggiotti Laura , Cheng Zhangrui , Salavati Mazdak , Wathes Claire D.
Published: December 2020

Background: Previous studies of ageing have identified many pathways which are consistently altered in humans and model organisms. Dairy cows are often culled at quite young ages due to an inability to cope adequately with metabolic and infectious diseases, resulting in reduced milk production and infertility. Improved longevity is therefore a desirable trait which would benefit both farmers and their cows. This study analysed the transcriptome derived from RNA-seq data of leukocytes obtained from Holstein cows in early lactation with respect to lactation number. Results: Samples were divided into three age groups for analysis: i) primiparous (PP, n = 53), ii) multiparous in lactations 2-3 (MP 2-3, n = 121), and iii) MP in lactations 4-7 (MP>3, n = 55). Leukocyte expression was compared between PP vs MP>3 cows with MP 2-3 as background using DESeq2 followed by weighted gene co-expression network analysis (WGCNA). Seven modules were significantly correlated (r ≥ 0.25) to the trait age. Genes from the modules which were more highly expressed in either the PP or MP>3 cows were pooled, and the gene lists subjected to David functional annotation cluster analysis. The top three clusters from modules more highly expressed in the PP cows all involved regulation of gene transcription, particularly zinc fingers. Another cluster included genes encoding enzymes in the mitochondrial beta-oxidation pathway. Top clusters up-regulated in MP>3 cows included the terms Glycolysis/Gluconeogenesis, C-type lectin, and Immunity. Differentially expressed candidate genes for ageing previously identified in the human blood transcriptome up-regulated in PP cows were mainly associated with T-cell function (CCR7, CD27, IL7R, CAMK4, CD28), mitochondrial ribosomal proteins (MRPS27, MRPS9, MRPS31), and DNA replication and repair (WRN). Those up-regulated in MP>3 cows encoded immune defence proteins (LYZ, CTSZ, SREBF1, GRN, ANXA5, ADARB1). Conclusions: Genes and pathways associated with age in cows were identified for the first time to date, and we found that many were comparable to those known to be associated with ageing in humans and model organisms. We also detected changes in energy utilization and immune responses in leukocytes with age.
Extraskeletal Osteosarcoma After Postoperative Radiotherapy for a Keloid: a Case Report
Authors: Aramaki-Hattori Noriko , Watanabe Itsuo , Okabe Keisuke , Sakai Shigeki , Morioka Hideo , Kishi Kazuo
Published: December 2020

Background: The current standard treatment for keloids is a combination of surgery and postoperative radiotherapy with 8–25 Gy. Case presentation: Our case was a 75-year-old patient who developed a swollen mass in her chest 20 years after excision of a chest keloid followed by 32 Gy postoperative radiotherapy. After resection of the swollen mass, pathology indicated extraskeletal osteosarcoma. Conclusions: Six putative cases of carcinogenesis after postsurgical radiotherapy for keloid have been reported over the last 70 years. To our knowledge, this is the first case of post-keloid radiotherapy carcinogenesis that meets the definition of a radiation-induced sarcoma. The risk of secondary carcinogenesis after postsurgical radiotherapy for keloid is small but must be explained to the patient.
Machine Learning-based in-hospital Mortality Prediction Models for Patients With Acute Coronary Syndrome
Authors: Ke Jun , Chen Yiwei , Wang Xiaoping , Wu Zhiyong , Zhang qiongyao , Lian Yangpeng , Chen Feng
Published: December 2020

BackgroundThe purpose of this study is to identify the risk factors of in-hospital mortality in patients with acute coronary syndrome (ACS) and to evaluate the performance of traditional regression and machine learning prediction models.MethodsThe data of ACS patients who entered the emergency department of Fujian Provincial Hospital from January 1, 2017 to March 31, 2020 for chest pain were retrospectively collected. The study used univariate and multivariate logistic regression analysis to identify risk factors for in-hospital mortality of ACS patients. The traditional regression and machine learning algorithms were used to develop predictive models, and the sensitivity, specificity, and receiver operating characteristic curve were used to evaluate the performance of each model.ResultsA total of 7810 ACS patients were included in the study, and the in-hospital mortality rate was 1.75%. Multivariate logistic regression analysis found that age and levels of D-dimer, cardiac troponin I, N-terminal pro-B-type natriuretic peptide (NT-proBNP), lactate dehydrogenase (LDH), high-density lipoprotein (HDL) cholesterol, and calcium channel blockers were independent predictors of in-hospital mortality. The study found that the area under the receiver operating characteristic curve of the models developed by logistic regression, gradient boosting decision tree (GBDT), random forest, and support vector machine (SVM) for predicting the risk of in-hospital mortality were 0.963, 0.960, 0.963, and 0.959, respectively. Feature importance evaluation found that NT-proBNP, LDH, and HDL cholesterol were top three variables that contribute the most to the prediction performance of the GBDT model and random forest model.ConclusionsThe predictive model developed using logistic regression, GBDT, random forest, and SVM algorithms can be used to predict the risk of in-hospital death of ACS patients. Based on our findings, we recommend that clinicians focus on monitoring the changes of NT-proBNP, LDH, and HDL cholesterol, as this may improve the clinical outcomes of ACS patients.
EZH2 Promotes Extracellular Matrix Degradation via Nuclear Factor-kB(NF-kB)and p38 signaling Pathways in Pulpitis.
Authors: He jie , Qin Man , Chen Yingyi , Hu Ziqi , Ye Ling , Hui Tianqian
Published: December 2020

Background: Pulpitis is a complicated chronic inflammatory process which in a dynamic balance between damage and repair. Extracellular matrix plays an important regulatory role in wound healing and tissue repair. The aim of this study was to explore role of the epigenetic mark, enhancer of zeste homolog 2 (EZH2) on the degradation of extracellular matrix during pulpitis. Methods : Quantitative polymerase chain reaction was used to assess the expression of matrix metalloproteinases (MMPs) and type I collagen in HDPCs upon EZH2 and EI1 stimulation. The mechanism of EZH2 affecting extracellular matrix was explored through quantitative polymerase chain reaction and Western blot. A rat model of dental pulp inflammation was established, and the expression of type I collagen in dental pulp under EZH2 stimulation was detected by immunohistochemical staining. Results :EZH2 upregulated the expression of MMP-1, MMP-3, MMP-8 and MMP-10 and decreased the production of type I collagen in HDPCs, while EI1 had the opposite effect .EZH2 activated the Nuclear Factor-kB(NF-kB)and p38 signaling Pathways in HDPCs, the inhibition of which reversed the induction of MMPs and the suppression of type I collagen .EZH2 can downregulated the type I collagen levels in an experimental model of dental pulpitis in rats. Conclusion: EZH2 promotes extracellular matrix degradation via Nuclear Factor-kB(NF-kB)and P38 signaling pathways in pulpitis.EZH2 can decrease the type I collagen levels in vivo and vitro.
MRI Contributes to Accurate and Early Diagnosis of Non-Radiographic HLA-B27 Negative Axial Spondyloarthritis
Authors: LU CHUN-CHI , Huang Guo-Shu , Lee Tony Szu-Hsien , Chao En , Chen Hsiang-Cheng , Yong-Si Guo , Shi-Jye Chu , Feng-Cheng Liu , Kao San-Yuan , Hou Tsung-Yun , Chen Chen-Hung , Chang Deh-Ming , Lyu Sin-Yi
Published: December 2020

BackgroundStructural changes to sacroiliac joints cannot be adopted to confirm active sacroiliitis on magnetic resonance imaging in the absence of bone marrow edema (BME). However, less than half of Asian patients with axial spondyloarthritis were characterized by BME. We aim to define the best methodology for accurate diagnosis, especially in the area with less common bone marrow edema and serum human leukocyte antigen-B27 (HLA-B27). Methods We included 103 patients with inflammatory back pain and morning stiffness in this prospective study. No radiograph met the definition of positive modified New York criteria. Inflammation and structural damage on magnetic resonance imaging were evaluated. Serum c-reactive protein and HLA-B27 levels were collected. Correlations between the various collected variables were analyzed. Results We demonstrated a positive association between inflammatory lesions and structural damage in the 58 ASAS-defined nr-axSpA subjects. BME on magnetic resonance imaging is moderately correlated with sclerosis and focal joint space widening (fJSW) (phi score of 0.372 and 0.319, p = 0.005 and 0.015, respectively). A moderately positive correlation between either the severity of BME and fJSW (p = 0.004) in 36 patients who had BME and met Assessment of Spondyloarthritis international Society criteria. There is a positive correlation between BME and fJSW across the whole cohort (phi score of 0.389; p < 0.001). We also identified a positive correlation between fJSW and BME in patients with non-radiographic axial spondyloarthritis and normal serum c-reactive protein levels (phi score of 0.362 and p = 0.001). Conclusion Severe erosions like fJSW on MRI-SIJs is positively correlated with development of BME on MRI and helps contribute to accurate diagnosis of non-radiographic axial spondyloarthritis either in the absence of HLA-B27 or normal serum inflammatory biomarkers, which might be used alternatively for early diagnosis of non-radiographic axial spondyloarthritis in Asian people who are characterized by less prevalence of BME and HLA-B27.
A new type of disordered CP12 protein in the marine diatom Thalassiosira pseudonana
Authors: Shao Hui , Huang Wenmin , Avilan Luisana , Receveur-Brechot Veronique , Puppo Carine , Puppo Rémy , Lebrun Régine , Gontero Brigitte , Launay Helene
Published: December 2020

Background
CP12 is a small chloroplast protein that is widespread in various photosynthetic organisms and is often involved in the redox metabolic on/off switch of the Calvin Benson Bassham (CBB) cycle. The gene encoding this protein is conserved in many diatoms, but the protein has been overlooked in these organisms, despite their ecological predominance and their complex and still enigmatic evolutionary background.
Methods
A combination of biochemical, bioinformatics and biophysical methods including electrospray ionization-mass spectrometry, circular dichroism, nuclear magnetic resonance and small X ray scattering spectroscopy, was used to characterize a diatom CP12.
Results
Here, we demonstrate that CP12 is expressed in the marine diatom Thalassiosira pseudonana constitutively in dark-treated and in continuous light-treated cells as well as in all growth phases. This CP12 behaves abnormally under gel electrophoresis, is heat resistant and lacks a structural core, all features of intrinsically disorder family similarly to its homologues in other species. By contrast, unlike other known CP12 proteins that are monomers, this protein is a dimer as shown by native electrospray ionization-mass spectrometry and small angle X-ray scattering. In addition, small angle X-ray scattering showed that this CP12 is an elongated cylinder with kinks. Circular dichroism spectra indicated that CP12, though it has features of disordered proteins, has a high content of α-helices. Nuclear magnetic resonance spectroscopy showed that these helices are unstable and dynamic within a millisecond timescale. Together with in silico predictions, these results suggest that T. pseudonana CP12 has both coiled-coil and disordered regions.
Conclusions
These findings bring new insights into the large family of intrinsically disordered proteins increasing the diversity of known CP12 proteins. This raises questions about the role of this protein in addition to the well-established regulation of the CBB cycle.
Hsa_circ_001659 serves as a diagnostic and prognostic biomarker for colorectal cancer
Authors: He Baoyu , Chao Wei , Huang Zhizhuo , Zeng Jianchao , Yang Jie , Luo Delan , Huang Shishun , Pan Hongli , Hao Yujun
Published: December 2020

Background: Colorectal cancer (CRC) is prevalent worldwide and novel diagnostic and prognostic biomarkers are needed to improve precision medicine. Circulating circular RNAs (circRNAs) are currently being considered as emerging tumor biomarkers. Methods: Candidate circRNA was selected by integrating analysis of Gene Expression Omnibus (GEO) database using GEO2R program. The expression data of serum circ_001659 were obtained from the quantitative real-time polymerase chain reaction (qRT-PCR). Receiver operating characteristic curves were applied to evaluate the clinical applications of circ_001659. Finally, biological functions and potential mechanisms of circ_001659 in tumor progression were investigated in CRC progression. Results: The results showed that the diagnostic performance of serum circ_001659 were excellent for CRC detection. The predictive values and likelihood ratios were satisfactory for the diagnosis of CRC, including patients in early-stage disease or patients with carcinoembryonic antigen (CEA)-negative status. Serum levels of circ_001659 declined significantly 3 months after surgery in both preoperative CEA-positive and CEA-negative patients. Functionally, circ_001659 influenced tumor cell metastasis via regulating epithelial-mesenchymal transition (EMT) and cytoskeleton organization. Conclusion: Our findings demonstrate that circ_001659 could be a useful serum biomarker for CRC diagnosis and prognosis. Targeting circ_001659 and its pathway may be meaningful for treating patients with CRC.
Mismatch repair deficiency is associated with specific morphologic features and frequent loss of ARID1A expression in ovarian clear cell carcinoma
Authors: Ge Huijuan , Xiao Yaoxin , Qin Guangqi , Gu Yanzi , Cai Xu , Jiang Wenhua , Tu Xiaoyu , Yang Wentao , Bi Rui
Published: December 2020

Background
Ovarian clear cell carcinoma (OCCC) is the second subtype of ovarian epithelial carcinoma reported to be closely related to Lynch syndrome (LS). ARID1A mutation is an important pathogenetic mechanism in OCCC that leads to loss of ARID1A expression in approximately half of OCCCs. However, the correlation of MMR status and ARID1A deficiency is unclear. The current study aimed to identify the clinical and histopathological characteristics of OCCC associated with dMMR and to further explore the association between dMMR and ARID1A deficiency.
Methods
A cohort of 176 primary OCCC patients was enrolled and review included histological characteristics (nuclear atypia, necrosis, mitosis, stromal hyalinization, and background precursors) and host inflammatory response (tumor-infiltrating lymphocytes, peritumoral lymphocytes, intratumoral stromal inflammation and plasma cell infiltration). Immunohistochemical staining of MLH1, PMS2, MSH2, MSH6 and ARID1A was performed using tissue microarrays.
Results
dMMR was detected in 10/176 tumors (6%), followed by MSH2/MSH6 (6/176), MLH1/PMS2 (3/176), and MSH6 (1/176). The average age of patients with dMMR was younger than the patients with intact MMR (46 y vs 53 y). Tumors with diffuse intratumoral stromal inflammation remained a significant association after multivariate analysis. ARID1A expression was absent in 8 patients with dMMR (8/10), which is a significantly higher frequency than that observed in patients with intact MMR (80% vs. 43.2%).
Conclusion
Our study indicates that diffuse intratumoral stromal inflammation of OCCCs is associated with dMMR, with loss of MSH2/MSH6 expression being most frequent. dMMR is strongly associated with loss of ARID1A expression in OCCC.
Peptide barcodes in dogs with pulmonary hypertension secondary to mitral valve disease using MALDI-TOF MS and LC-MS/MS
Authors: Riengvirodkij Nattapon , Roytrakul Sittiruk , Jaresitthikunchai Janthima , Phaonakrop Narumon , Charoenlappanich Sawanya , Sakcamduang Walasinee
Published: December 2020

Background

Pulmonary hypertension (PH) is an important complication in dogs with cardiorespiratory diseases. The most common underlying disease of PH has been described to be mitral valve disease (MVD), which is the most frequent acquired heart disease found in dogs. Doppler echocardiography is generally used in routine practice for identifying PH; however, there are several limitations to this method in practical use. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique that can characterize specific patterns of peptide mass called peptide barcodes from various samples. In addition, in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS), potential peptide sequences associated with specific conditions could be identified. The present study aimed to use MALDI-TOF coupled with LC-MS/MS to characterize specific peptide barcodes and potential peptide candidates in serum samples from healthy dogs (normal control), dogs with MVD stage B (MVD B) (asymptomatic stage), MVD stage C (MVD C) (symptomatic stage), MVD stage B with PH (MVD B PH) and MVD stage C with PH (MVD C PH).
Results

Discrete clusters of the 5 sample groups were identified by 3D plot analysis. Peptide barcodes also revealed differences in peptide patterns among the 5 groups. Six amino acid sequences of peptide candidates at 1,225.60, 1,363.85, 1,688.71, 1789.52, 2020.21 and 2156.42 Da were identified as part of the proteins CLCN1, CLUL1, EDNRA, PTEN, SLC39A7, and CLN6, respectively. The network interactions between these discovered proteins and common cardiovascular drugs were also investigated.
Conclusion

The present study revealed distinct clusters and different peptide barcodes for the MVD B, MVD C, MVD B PH, MVD C PH and normal control groups using MALDI-TOF MS. These results demonstrate that MALDI-TOF MS has promise as a technique for diagnosing dogs affected by asymptomatic and symptomatic stages of MVD with and without PH. Additionally, with MALDI-TOF MS in combination with LC-MS/MS, potential peptide candidates related to diseases were also identified. Further studies are required to identify peptide barcodes in dogs with other diseases to create peptide barcode databases in veterinary medicine before using this method as a novel diagnostic tool in the future.
Is Expected Substance Type Associated With Timing of Drug Checking Service Utilization?: a Cross-sectional Study
Authors: Beaulieu Tara , Wood Evan , Tobias Samuel , Lysyshyn Mark , Patel Priya , Matthews Jennifer , Ti Lianping
Published: December 2020

Background: Drug checking is a harm reduction intervention aiming to reduce substance use-related risks by improving drug user knowledge of the composition of unregulated drugs. With increasing fears of fentanyl adulteration in unregulated drugs, this study sought to examine whether the expected type of drug checked (stimulant vs. opioid) was associated with timing of drug checking service utilization (pre-consumption vs. post-consumption).Methods: Data were derived from drug checking sites in British Columbia between October 31, 2017 and December 31, 2019. Pearson’s Chi-square test was used to examine the relationship between expected sample type (stimulant vs. opioid) and timing of service utilization. Odds ratios (OR) were calculated to assess the strength of this relationship. The Mantel-Haenszel (MH) test was used to adjust for service location. Results: 3,561 unique stimulant and opioid samples were eligible for inclusion, including 691 (19.40%) stimulant samples; and 2,222 (62.40%) samples that were tested pre-consumption. Results indicated a positive association between testing stimulant samples and testing pre-consumption (OR = 1.45; 95% CI: 1.21 – 1.73). Regions outside of the epicenter of the province’s drug scene showed a stronger association with testing pre-consumption (ORMH = 2.33; 95% CI: 1.51 - 3.56) than inside the epicenter (ORMH = 1.33; 95% CI: 1.09 - 1.63).Conclusion: Stimulant samples were more likely to be checked pre-consumption as compared with opioid samples, and stimulant samples were more likely to be tested pre-consumption in regions outside the epicenter of the province’s drug scene. This pattern may reflect a concern for fentanyl-adulterated stimulant drugs.