bluuebunny/crossref_metadata_2025 huggingface dataset:
Prognostic Value of the Intratumoral Lymphocyte to Monocyte Ratio and M0 Macrophage Enrichment in the Melanoma Immune Microenvironment
Authors: Jairath Neil , Farha Mark , Jairath Ruple , Harms Paul , Tsoi Lam , Tejasvi Trilokraj
Published: September 2020

Background: Cutaneous Melanoma (SKCM) is characterized by significant heterogeneity in its molecular, genomic, and immunologic characteristics. Methods: Whole transcriptome RNAseq data from The Cancer Genome Atlas of SKCM (n=328) was utilized. The immune microenvironment was characterized using CIBERSORTX to identify immune cell type composition. Unsupervised hierarchical clustering was performed based on immune cell type content. Samples were separated into those obtained from the primary tumor site and regional skin or soft tissue (locoregional), or distant metastasis and regional lymph node (metastatic). Analysis of overall survival (OS) was performed using Kaplan-Meier estimates and Cox-regression multivariable analyses. Results: Four immune clusters were identified, largely defined by lymphocyte:monocyte (L:M) ratio, monocyte-enrichment, and M0-macrophage-enrichment (L:MLow, MonocyteHigh, M0High; L:MLow, MonocyteMid, M0Low; L:MMid, MonocyteLow, M0Low; L:MHigh, MonocyteLow, M0Low). The L:MLow, MonocyteHigh, M0High cluster demonstrated significantly worse OS than clusters 2-4 in the locoregional group (HR 2.804, 95% CI 1.262–6.234, p=0.0114). Membership in the L:MLow, MonocyteHigh, M0High cluster was an independently poor prognostic factor for survival (HR 3.03, 95% CI 1.12–8.20, p=0.029). The L:MLow, MonocyteHigh, M0High cluster correlated with higher rates of metastasis and decreased predicted response to immune checkpoint blockade compared to the other clusters as determined by the Tumor Immune Dysfunction and Exclusion tool (TIDE). Conclusion: Distinct tumor immune clusters with a M0-macrophage-enriched, L:M ratio low phenotype in the primary melanoma tumor site independently characterize an aggressive phenotype that may differentially respond to treatment.
Characteristics and Prognosis of COVID-19 in Patients with COPD
Authors: Graziani Desirée , Soriano Joan B , Del Rio-Bermudez Carlos , Morena Diego , Díaz Teresa , Castillo María , Alonso Miguel , Ancochea Julio , Izquierdo José Luis
Published: September 2020

Patients with COPD have a higher prevalence of coronary ischemia and other factors that put them at risk for COVID-19-related complications. We aimed to explore the impact of COVID-19 in a large population-based sample of patients with COPD in Castilla-La Mancha, Spain. We analyzed clinical data in electronic health records from January 1st to May 10th, 2020 by using Natural Language Processing through the SAVANA Manager® clinical platform. Out of 31,633 COPD patients, 793 had a diagnosis of COVID-19. The proportion of patients with COVID-19 in the COPD population (2,51%; CI95% 2,33 – 2,68) was significantly higher than in the general population aged > 40 years (1,16%; 95%CI 1,14 – 1,18); P < .001. Compared with COPD-free individuals, COPD patients with COVID-19 showed significantly poorer disease prognosis, as evaluated by hospitalizations (31,1 % vs 39,8%: OR 1,57; 95%CI 1,14 – 1,18) and mortality (3,4% vs 9,3%: OR 2,93; 95%CI 2,27 – 3,79). Patients with COPD and COVID-19 were significantly older (75 vs. 66 years), predominantly male (83% vs 17%), smoked more frequently, and had more comorbidities than their non-COPD counterparts. Pneumonia was the most common diagnosis among COPD patients hospitalized due to COVID-19 (59%); 19% of patients showed pulmonary infiltrates suggestive of pneumonia and heart failure. Mortality in COPD patients with COVID-19 was associated with older age and prevalence of heart failure (P<0.05). COPD patients with COVID-19 showed higher rates of hospitalization and mortality, mainly associated with pneumonia. This clinical profile is different from exacerbations caused by other respiratory viruses in the winter season.
Detection of Recombinant Hare Myxoma Virus in Wild Rabbits (Oryctolagus cuniculus algirus)
Authors: Abade dos Santos Fábio A. , Carvalho Carina L. , Pinto Andreia , Rai Ranjit , Monteiro Madalena , Carvalho Paulo , Mendonça Paula , Peleteiro Maria C. , Parra Francisco , Duarte Margarida D.
Published: September 2020

In late 2018, an epidemic myxomatosis outbreak emerged on the Iberian Peninsula leading to high mortality in Iberian hare populations. Soon, a recombinant virus (MYXV-Tol or ha-MYXV) was identified, harboring a 2.8 kb insertion containing evolved duplicates of M060L, M061L, M064L, and M065L from MYXV. Since 2017, 1616 rabbits and 82 hares were tested by a qPCR directed to M000.5L/R gene, conserved in MYXV and MYXV-Tol/ ha-MYXV strains. A subset (20%) of the positive samples was tested for the insert with MYXV being detected in rabbits and recombinant MYXV in hares. Recently, two wild rabbits found dead in South Portugal, showing skin oedema and pulmonary lesions tested positive for the 2.8 Kb insert. Sequencing showed 100% similarity with the insert sequences described in Iberian hares from Spain. Viral particles were observed in the lungs of both rabbits by electron microscopy, and isolation in RK13 cells showed virus infectivity. Despite the analysis of recombinant MYXV genomes may predict its ability to infect rabbit, routine analyses showed species segregation for the circulation of MYXV and recombinant MYXV in wild rabbit and in Iberian hares, respectively. This study demonstrates, however, that recombinant MYXV can effectively infect and cause myxomatosis in wild rabbits and domestic rabbits, which raises serious concerns for the future of the Iberian wild leporids and emphasizes the need to continue monitoring MYXV and recombinant MYXV in both species.
Моделирование течений многокомпонентных газовых смесей с использованием метода двойного потока
Authors: Борисов Виталий Евгеньевич , Borisov Vitaly Evgenyevich , Рыков Юрий Германович , Rykov Yuri Germanovich
Published: September 2020

Статья посвящена численному моделированию течений многокомпонентных газовых смесей в рамках расширенной системы уравнений Эйлера с помощью модифицированной явной схемы годуновского типа. Особенностью используемого алгоритма является учет возможности появления сильных скачков в решениях, что выражается в использовании точных решений соответствующей задачи Римана, а также учет появления нефизичных осцилляций давления на контактных границах, для исключения которых применялся метод «двойного потока». Проведенное численное исследование демонстрирует работоспособность разработанной методики, результаты расчетов одномерных и двумерных течений хорошо согласуются с данными расчетов других авторов и лабораторных экспериментов.
Математическая модель резонатора плазмонного нанолазера с учетом эффекта нелокальности
Authors: Еремин Юрий Александрович , Eremin Yurii Aleksandrovich , Свешников Алексей Георгиевич , Sveshnikov Aleksei Georgievich
Published: September 2020

На основе метода Дискретных источников разработана и реализована математическая модель резонатора плазмонного нанолазера, располагающегося на поверхности призмы в активной среде, позволяющая учитывать эффект нелокальности
(ЭН) в плазмонном материале. Проведена оптимизация характеристик резонатора,
позволяющая получить усиление поля непосредственно на внешней поверхности
резонатора более чем на два порядка. Исследовано влияние ЭН на коэффициент
усиления в спектральном диапазоне длин волн. Показано, что учет ЭН приводит к
существенному снижению интенсивности ближнего поля.
Моделирование развития неустойчивости Рихтмайера-Мешкова с использованием разрывного метода Галеркина на локально-адаптивных сетках
Authors: Жалнин Руслан Викторович , Zhalnin Ruslan V. , Масягин Виктор Федорович , Masyagin Victor Fedorovich , Пескова Елизавета Евгеньевна , Peskova Elizaveta Evgenievna , Тишкин Владимир Федорович , Tishkin Vladimir Fedorovich
Published: September 2020

Представлен численный алгоритм для решения уравнений многокомпонентной газовой динамики с помощью разрывного метода Галеркина на локально-адаптивных сетках. В численном алгоритме используется структура данных и алгоритм динамической локальной адаптации сетки из библиотеки p4est. В работе используются численные потоки Лакса-Фридрихса-Русанова и HLLC. Для избавления от нефизических осцилляций применяется лимитер Барта-Йесперсена. В результате исследования было проведено моделирование развития неустойчивости Рихтмайера-Мешкова, проведено сравнение полученных результатов с результатами эксперимента и известными численными решениями данной задачи. Сделан вывод о хорошем совпадении расчетных и экспериментальных данных. В дальнейшем предполагается исследование данного процесса с использованием модели, учитывающей явления вязкости и теплопроводности.
Age Differences in Pet Sensitization by Pet Ownership
Authors: Won Jun Yeon , Kwon Jea-Woo , Hong Seung-No , Lee Woo Hyun
Published: September 2020

Objectives. The association between pet sensitization and pet ownership remains unclear. Therefore, we aimed to elucidate the association between pet sensitization and pet ownership by age.Methods. We retrospectively reviewed 2,883 patients who visited our allergy clinic for nasal symptoms from January 2003 to December 2014, of whom 1,957 patients with data on skin-prick tests and questionnaire responses were included and divided into adults (age >19 years) and children (age ≤19 years). The association between pet sensitization and pet ownership was evaluated in both groups.Results. Among children, dog and cat sensitization showed no associations with dog and cat ownership, respectively. However, among adults, dog sensitization was significantly associated with dog ownership (odds ratio [OR], 3.283; P<0.001), and cat sensitization with cat ownership (OR, 13.732; P<0.001). After adjustment for age, sex, familial history of allergy, sinusitis, diabetes mellitus, other pet ownership, and non-pet sensitization, significant associations remained between dog sensitization and dog ownership (adjusted OR [aOR], 3.881; P<0.001), and between cat sensitization and cat ownership (aOR, 10.804; P<0.001) among adults. Dog ownership did not show any association with allergic rhinitis, asthma, or atopic dermatitis, whereas atopic dermatitis had a significant association with cat ownership in adults (aOR, 4.840; P<0.001).Conclusion. Pet ownership in adulthood increased the risk of pet sensitization. However, pet ownership was not associated with the prevalence of atopic disorders, regardless of age, except for atopic dermatitis and cat ownership in adults.
Initial Experience With Robotic Modified Radical Neck Dissection Using the da Vinci Xi System Through the Bilateral Axillo-Breast Approach
Authors: Choi Yun Suk , Hong Yong Tae , Yi Jin Wook
Published: September 2020

Objectives. The bilateral axillo-breast approach (BABA) to robotic thyroidectomy has been extended to modified radical neck dissection (MRND). This study assessed outcomes in patients who underwent robotic MRND through BABA using the da Vinci Xi system.Methods. The medical records of 40 patients who underwent total thyroidectomy, bilateral central neck dissection, and MRND from September 2018 to March 2020 were reviewed retrospectively, including 12 who underwent robotic surgery and 28 who underwent open surgery. All operations were performed by a single endocrine surgeon.Results. The operation time was significantly longer in the robotic group than in the open group (277.08±32.64 vs. 191.43± 60.43 minutes, respectively, P<0.01), but the number of retrieved lymph nodes did not differ significantly (32.58± 9.31 vs. 34.54±10.90, respectively, P=0.569). The incidence of transient hypoparathyroidism was significantly lower in the robotic group (16.7% [2/12] vs. 53.6% [15/28], P=0.041). The mean hospital stay was shorter (3.92±0.90 vs. 4.71±1.63 days) and the pain score on the first postoperative day was lower (2.92±0.29 vs. 3.18±0.67) in the robotic group. Six of the 12 patients (50%) in the robotic group had stimulated thyroglobulin levels <1.0 ng/mL.Conclusion. Robotic MRND through BABA has several advantages, including excellent cosmetic outcomes and a lower incidence of transient hypoparathyroidism than is the case for open MRND. Robotic MRND through BABA may be a promising surgical approach compared with conventional open MRND.
Analisis Kelayakan Usaha Produksi Biji Kopi Sangrai dan Jasa Penyangraian: Studi Kasus pada Java Sumedang Coffee
Authors: Thoriq Ahmad , Sampurno Rizky Mulya , Imaduddin Luthfie Hafidz
Published: September 2020

The development of specialty coffee roasted beans business and coffee roasting services is currently quite rapid, but often that the business is not based on the feasibility analysis. This study aims to analyze the feasibility level of the production of specialty coffee roasted beans and roasting service of coffee beans. This study was carried out beginning from November 2019 until February 2020 with case study method at Java Sumedang Coffee (JSC) in Genteng Village, Sukasari District, Sumedang Regency, West Java Province.  Primary data was collected based on test results and interviews directly with the business manager of JSC, while secondary data were obtained from published scientific articles. The results of this study show that with the use of a roasted machine for 5 hours per day or 1200 hours per year at an interest rate of 7% per year, the business of specialty roasted coffee beans production at JSC are feasible with an assumption of a minimum selling price of Rp.128,500/kg. The indicators of business feasibility are NPV (Net Present Value) Rp. 111,759,128.10; BCR (Benefit Cost Ratio) of 1.02%; IRR (Internal Rate of Return) of 6.21%; capital returned in the 17th month. While, in the coffee bean roasting service business are feasible if the minimum roasting service cost is Rp. 14,000/kg, with feasibility indicators are NPV Rp. 112,286,86; BCR of 1.23; IRR of 6.25% per month; and PBP occurred in the 17th month.
Penampilan Fenotipik, Keragaman, dan Heritabilitas Sembilan Genotipe Teh [Camellia sinensis (L.) O. Kuntze]
Authors: Wicaksono Ilham Nur Ardhi , Martono Budi
Published: September 2020

The estimated value of genotype variability, phenotype variability, environmental variability, and heritability have an important role in breeding activities of tea in order to create the superior varieties. The objective of this study was to investigate the phenotypic performance, genotype and phenotype variation, and heritability value of nine genotypes of tea. The study was conducted at Pemandangan block, Tambi Plantation Unit,  Wonosobo, Central Java, from April 2013 until April 2014. The Randomized Complete Block Design (RBD) with nine treatments and three replications was used in this study. The 9th of treatments consisted of 2 genotypes of tea resulting from a cross (GMB 3 and GMB 4), 2 introduced genotypes (TRI 2024 and TRI 2025), and 5 local genotypes resulting from selection (Cin 143, Kiara 8, RB 3, Tambi 1, and Tambi 2). The results showed that the genotype of GMB 3 more higher than other genotypes in pecco length, leaf length, leaf width, length of leaf stalk, and length of leaf internodes characters, whereas Tambi 2, GMB 3, and GMB 4 more higher in fresh weight of P+2 and P+3. The production of fresh shoot of GMB 4 more higher than the other genotypes, but not significant with GMB 3 and RB 3. The leaf length and fresh shoot production characters has a wide of genotype and phenotype variability, whereas the high of heritability value were found in all characters observed. The selection based on leaf length and fresh shoot production characters will be effective because both characters have a high genotypes variability and heritability.
Metodología para el análisis integrado de peligros asociados a la inundación: propuesta adaptada a la ordenación territorial en regiones mediterráneas
Authors: Gallegos Reina Antonio , Perles Roselló María Jesús
Published: September 2020

El objetivo del presente trabajo es presentar una propuesta metodológica de análisis de inundabilidad, incorporando peligros asociados, para adaptar la evaluación de la inundabilidad a las particularidades del área geográfica del litoral mediterráneo español como región-riesgo. Se pretende con ello dar un enfoque territorial al análisis de la inundabilidad, siguiendo los nuevos requisitos introducidos por la legislación en materia de riesgos naturales e inundaciones, orientándolo de manera directa a la gestión y ordenación territorial para escalas locales y regionales, y buscando una estimación más fiable de su estudio en regiones mediterráneas. La normativa española en la actualidad establece el estudio hidrológico-hidráulico como documento que evalúa el riesgo de inundación de una zona. La metodología propone incorporar a este estudio un análisis de la potencial generación de aportes al caudal por erosión de suelos en la cuenca, así como por movimientos en masa, incluyendo así información tanto cuantitativa como cualitativa sobre el aporte de partículas sólidas al flujo de inundabilidad. Los resultados, tras su aplicación en una cuenca piloto en el litoral malacitano, muestran una mejor estimación de la lámina de inundación de la propuesta metodológica con respecto a la metodología convencional.
Drusen Characteristics of Type 2 Macular Neovascularization in Age-related Macular Degeneration
Authors: Ahmed Daniel , Stattin Martin , Haas Anna-Maria , Graf Alexandra , Krepler Katharina , Ansari-Shahrezaei Siamak
Published: September 2020

BackgroundType 2 macular neovascularization (MNV) is supposed to be a rare condition in age-related macular degeneration (AMD). The main purpose of this study was to assess accompanying factors of type 2 MNV in AMD.MethodsRetrospective data analysis of eyes previously diagnosed with neovascular AMD in a tertiary eye care center (Medical Retina Unit, Rudolf Foundation Hospital, Vienna, Austria) between June 2008 and December 2017. Drusen subtypes, fibrosis, atrophy and subfoveal choroidal thickness (SFCT) of both eyes in patients with type 2 MNV lesions were categorized based on multimodal imaging.ResultsType 2 MNV was diagnosed in 27 (3.2%) of 835 eyes (749 patients). Drusen characteristics in type 2 MNV were observed as followed: drusen < 63 mm in 2 eyes (7.4%), drusen ≥ 63 mm in 10 eyes (37%), subretinal drusenoid deposits (SDD) in 8 eyes (29.6%), cuticular drusen in 2 eye (7.4%) and no drusen were evident in 10 eyes (37%). Drusen distribution in 23 fellow eyes was detected as followed: drusen < 63 mm in 2 eyes (8.7%), drusen ≥ 63 mm in 9 eyes (39.1%), SDD in 5 eyes (21.7%), cuticular drusen in 1 eye (4.3%) and no drusen were evident in 9 eyes (39.1%). Mean SFCT was 140 ± 49 mm in affected eyes and 152 ± 41 mm in the fellow eyes. Patients with drusen or SDD were significantly younger (mean 70.88 ± 6.85, p=0.04) than patients without deposits (mean 77.40 ± 5.74). ConclusionsType 2 MNV remains a rare entity in AMD. It was frequently seen in the absence ofdrusen, a hallmark of AMD. These findings contribute to the heterogeneity of phenotypes related to pure type 2 lesions.
Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars
Authors: Ding Haisheng , Liu Min , zhou Changfan , You Xiangbin , Su Tao , Yang Youbing , Xu Dequan
Published: September 2020

Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 ( PLCβ1) gene was verified to be a target of ssc-mir-423-5p . Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.
Transcriptome analysis of the hypothalamus and pituitary of turkey hens with low and high egg production
Authors: Brady Kristen , Liu Hsiao-Ching , Hicks Julie , Long Julie A , Porter Tom E
Published: September 2020

Background: High egg producing hens (HEPH) show increased hypothalamic and pituitary gene expression related to hypothalamo-pituitary-gonadal (HPG) axis stimulation as well as increased in vitro responsiveness to gonadotropin releasing hormone (GnRH) stimulation in the pituitary when compared to low egg producing hens (LEPH). Transcriptome analysis was performed on hypothalamus and pituitary samples from LEPH and HEPH to identify novel regulators of HPG axis function. Results: In the hypothalamus and pituitary, 4644 differentially expressed genes (DEGs) were identified between LEPH and HEPH, with 2021 genes up-regulated in LEPH and 2623 genes up-regulated in HEPH. In LEPH, up-regulated genes showed enrichment of the hypothalamo-pituitary-thyroid (HPT) axis. Beta-estradiol was identified as an upstream regulator regardless of tissue. When LEPH and HEPH samples were compared, beta-estradiol was activated in HEPH in 3 of the 4 comparisons, which correlated to the number of beta-estradiol target genes up-regulated in HEPH. In in vitro pituitary cell cultures from LEPH and HEPH, thyroid hormone pretreatment negatively impacted gonadotropin subunit mRNA levels in cells from both LEPH and HEPH, with the effect being more prominent in HEPH cells. Additionally, the effect of estradiol pretreatment on gonadotropin subunit mRNA levels in HEPH cells was negative, whereas estradiol pretreatment increased gonadotropin subunit mRNA levels in LEPH cells.Conclusions: Up-regulation of the HPT axis in LEPH and upstream beta-estradiol activation in HEPH may play a role in regulating HPG axis function, and ultimately ovulation rates. Thyroid hormone and estradiol pretreatment impacted gonadotropin mRNA levels following GnRH stimulation, with the inhibitory effects of thyroid hormone more detrimental in HEPH and estradiol stimulatory effects more prominent in LEPH. Responsiveness to thyroid hormone and estradiol may be due to desensitization to thyroid hormone and estradiol in LEPH and HEPH, respectively, due to up-regulation of the HPT axis in LEPH and of the HPG axis in HEPH. Further studies will be necessary to identify possible target gene desensitization mechanisms and elicit the regulatory role of the HPT axis and beta-estradiol on ovulation rates in turkey hens.
Multiplex and On-site PCR detection of swine diseases based on the microfluidic chip system
Authors: Jiang Yan , Jiang Shan , Wu Yue , Zhou Bin , Wang Kaiming , Jiang Luyan , Long Yunfeng , Chen Gan , Zeng Dexin
Published: September 2020

Background： At present, the process of inspection and quarantine starts with sampling at the customs port, continues with transporting the samples to the central laboratory for inspection experiments, and ends with the inspected results being fed back to the port. This process had the risks of degradation of biological samples and generation of pathogenic microorganisms and did not meet the rapid on-site detection demand because it took a rather long time. Therefore, it is urgently needed to develop a rapid and high-throughput detection assay of pathogenic microorganisms at the customs port. The aim of this study was to develop a microfluidic chip to rapidly detect swine pathogenic microorganisms with high-throughput and higher accuracy. Moreover, this chip will decrease the risk of spreading infection during transportation.Results: A series of experiments were performed to establish a microfluidic chip. The resulting data showed that the positive nucleic acid of four swine viruses were detected by using a portable and rapid microfluidic PCR system, which could achieve a on-site real-time quantitative PCR detection. Furthermore, the detection results of eight clinical samples were obtained within an hour. The detection limit of this microfluidic PCR detection system was as low as 1 copies/μL. The results showed that the high sensitivity and specificity of this chip system in disease detection played an important role in customs inspection and quarantine during customs clearance.Conclusion: The microfluidic PCR detection system established in this study could meet the requirement for rapid detection of samples at the customs port. This chip could avoid the risky process of transporting the samples from the sampling site to the testing lab, and drastically reduce the inspection cycle. Moreover, it would enable parallel inspections on one chip, which greatly raised the efficiency of inspection.
Prenatally undetected major heart defects: clinical findings and time of diagnosis
Authors: Pavlicek Jan , Klaskova Eva , Kapralova Sabina , Palatova Alzbeta , Piegzova Alicja , Spacek Richard , Gruszka Tomas
Published: September 2020

Background: Severe or critical congenital heart defects (CHDs) constitute one third of the heart defect cases detected only after birth. These prenatally unrecognised defects usually manifest as cyanotic or acyanotic lesions and are diagnosed postnatally at various times. The aim of the study was to identify their clinical symptoms and determine individual risk periods for CHD manifestation. Methods: Data were assessed retrospectively based on a cohort of patients born between 2009 and 2018 in a population of 175,153 live births. Occurrence of the first symptoms of CHD was classified into: early neonatal (0–7 days), late neonatal (8–28 days), early infancy (1–6 months), or late infancy (6–12 months). The first symptom for which the child was referred to a paediatric cardiologist was defined as a symptom of CHD. Results: There were 598 major CHDs diagnosed in the studied region, and 70% were isolated anomalies. A concomitant genetic disorder was diagnosed in 20% of the cases, while 10% presented extracardiac pathology with a normal karyotype. In total, 47% (282/598) of all CHDs were not identified prenatally. Of these, 74% (210/282) were diagnosed as early neonates, 16% (44/282) as late neonates, and 10% (28/282) as infants. The most common symptoms leading to the diagnosis of CHD were heart murmur (53%, 149/282) and cyanosis (24%, 69/282). Diagnosis after discharge from the hospital occurred in 12% (72/598) of all major CHDs. Most delayed diagnoses consisted of ventricular septal defect and coarctation of the aorta. Conclusions: In conclusion, murmur and cyanosis are the most common manifestations of prenatally undetected CHDs. Although most children with major CHDs are diagnosed as neonates, some patients are still discharged from the maternity hospital with an unidentified defect.
The algal selenoproteomes
Authors: Jiang Liang , Lu Yiqian , Zheng Lin , Li Gaopeng , Chen Lianchang , Zhang Maona , Ni Jiazuan , Liu Qiong , Zhang Yan
Published: September 2020

Background:Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec, but also the SECIS element in mRNA and the conservation of the Sec flanking region. These unique features have led to developing a series of bioinformatics methods to predict and research selenoprotein genes. There are some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, is very limited.Results:In this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to hold these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families.Conclusions:This study reveals the primordial state of the eukaryotic selenoproteome. It is an important clue to explore the significance of selenium for primordial eukaryotes and to build the whole evolutionary spectrum of selenoproteins for all life.
Detection of copy number variants in African goats using whole genome sequence data
Authors: Nandolo Wilson , Mészáros Gábor , Wurzinger Maria , Banda Liveness J. , Gondwe Timothy N. , Mulindwa Henry A. , Nakimbugwe Helen N. , Clark Emily L. , Woodward-Greene M. Jennifer , Liu Mei , Liu George E. , Tassell Curtis P. Van , Rosen Benjamin D. , Sölkner Johann
Published: September 2020

Background Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. Results A total of 253,553 CNV (244,876 deletions and 8,677 duplications) were identified, corresponding to an overall average of 1,393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6,231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. Conclusions This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.
Assessing the Impact of Biologically Synthesized ZnO Nanoparticles as Source of Nutrient on the Growth of Zea mays L.
Authors: Sabir Sumera , Zahoor Muhammad Asif , waseem Muhammad , Siddique Muhammad Hussnain , Shafique Muhammad , Imran Muhammad , Hayat Sumreen , Malik Imran Riaz , Muzammil Saima
Published: September 2020

The authors have withdrawn this preprint due to erroneous posting.
Evaluation of antiparasitic therapy directly administered for the control of canine echinococcosis in an endemic area of hydatidosis.
Authors: Montalvo Raul , Huiza Alaina , Clemente Johana , Castañeda Lorena , Ccente Yoli , Nuñez Mayori , Arteaga Lizet , Balbuena Lizzeth , Inga Cristhian
Published: September 2020

Background: Echinococcosis remains endemic despite attempts to reduce the prevalence of this disease. The objective of the study was to evaluate the results of an intervention program based on antiparasitic therapy directly administered to the dogs for the control of Echinococcus in an endemic area of ​​ cystic echinococcosis (CE). Methods: The dog faeces were analyzed by coproantigen using the immunoenzymatic technique for the diagnosis of echinococcosis before and after the direct and observed administration of praziquantel 5mg by kg orally in three doses every 30 days each cycle was 2 times at year for two consecutive years. Results: A total of 252 dogs entered the study, of them 119 (47%) dogs had positive results for Echinococcus at the beginning of the intervention. The adverse effects that occurred with the administration of prazicuantel were vomiting (13%), diarrhea (2.4%) and lethargy (2%); 229 dogs completed the 4 cycles of praziquantel treatment. The presence of a positive coproantigen was evident in 03 (1.3%) dogs at the end of the study. Conclusions: Antiparasitic chemotherapy administered directly to the dogs periodically managed to reduce the prevalence of canine echinococcosis.
Single-cell RNA seq analysis identifies the biomarkers and differentiation of chondrocyte in human osteoarthritis
Authors: Zhang Xiaolu , Huang Nianlai , Huang Rongfu , Wang Liangming , Ke Qingfeng , Cai Liquan , Wu Shiqiang
Published: September 2020

Background: Single-cell RNA sequencing (scRNA-seq) was recently adopted for exploring molecular programmes and lineage progression patterns of pathogenesis of important diseases. In this study, scRNA-seq was used to identify potential markers for chondrocytes in osteoarthritis (OA) and to explore the function of different types of chondrocytes in OA. Methods: Here we aimed to identify the biomarkers and differentiation of chondrocyte by Single-cell RNA seq analysis. GeneOntology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to identify the function of candidate marker genes in chondrocytes. Protein-protein interaction (PPI) network was constructed to find the hub genes in 3 types of chondrocyte respectively. We also used qRT-PCR to detect the expression level of the candidate marker genes in different types of chondrocyte. Results: In this study, we characterized the single-cell expression profiling of 480 chondrocyte samples and found hypertrophic chondrocyte (HTC), homeostatic chondrocyte (HomC) and fibrocartilage chondrocyte (FC) respectively. The results of GO and KEGG analysis showed the candidate marker genes made specific function in these chondrocytes to regulate the development of OAs respectively. We further revealed the differential expression of top 10 marker genes in 3 types of chondrocyte. The marker genes of HTC and FC were mainly expressed in their cell subset respectively. The marker genes of HomC did not have obviously differential expression among different types of chondrocyte. Last, we predicted the key genes in each cell subset. CD44, JUN and FN1 were predicted tightly related to the proliferation and differentiation of chondrocytes in OAs and could be regarded as biomarkers to estimate the development of OA. Conclusion: Our results provide new insights into exploring the roles of different types of chondrocyte in OA. The biomarkers of chondrocyte were also valuable for estimating OA progression.
The development and validation of a Questionnaire in Bahasa Malaysia to assess problems of vision or feelings about vision among patients with cataracts.
Authors: Thevi Thanigasalam , Abas Adinegara Lutfi , Chang Stephanie Yen Li
Published: September 2020

Background We conducted the study to compare the validation properties of the English version of the Questionnaire and the Bahasa Malaysia (Malay Language) version regarding the Quality of Life of patients with cataracts.Methods We carried out a cross-sectional study collecting data between June 2017 and March 2018 in the pre-operative Eye Clinic of Hospital Melaka. The Malay version was translated by two independent translators who were well versed in both languages. Methods used to validate the standard questionnaire included the use of construct validity via factor analysis and the deployment of reliability test through assessment of internal consistency via Cronbach’s alpha. Results We observed both English and Bahasa Malaysia versions to have high reliability with Cronbach’s alpha values of 0.90 and above in factors on difficulty with activities and responses to vision problems.Exploratory factor analysis performed revealed that the three-factor model fits the data well for the English version of the questionnaire - difficulty with activities (23.81% of variance), responses to vision problem (22.22% of variance) and general health and vision (14.68% of variance). The Bahasa Malaysia version of the questionnaire produced three factors with two of the factors resembling the factors from the original version of the questionnaire - difficulty with activities (24.28% of variance) and responses to vision problem (23.66% of variance). Conclusion The present study observed that both the English and Bahasa Malaysia versions of the NEI VFQ-25 have comparable construct validity to the original American version. With high validity and reliability, the tool shall be able to provide health care providers the assessment of impact due to cataract and other ophthalmic conditions on the vision-related quality of life of ophthalmic patients.
An analytic perspective of a mixed methods study during humanitarian crises in South Sudan: translating facility- and community-based newborn guidelines into practice
Authors: Sami Samira , Amsalu Ribka , Dimiti Alexander , Jackson Debra , Kenneth Kemish , Kenyi Solomon , Meyers Janet , Mullany Luke C , Scudder Elaine , Tomczyk Barbara , Kerber Kate
Published: September 2020

Background: The civil war in 2016 led to mass displacement in Juba that rapidly spread to other regions of the country. Access to health care was limited because of attacks against health facilities and workers and pregnant women and newborns were among the most vulnerable. Translation of newborn guidelines into public health practice, particularly during periods of on-going violence, are not well studied during humanitarian emergencies. During 2016 to 2017, we assessed the feasibility of delivering a package of community- and facility-based newborn health interventions in displaced person camps to understand implementation outcomes. This case study describes the methodology for conducting a mixed methods study during periods of sudden violence.Discussion: Challenges unique to conducting research in South Sudan included violent attacks against humanitarian aid workers that required research partners to modify study plans on an ongoing basis to ensure staff and patient safety. South Sudan faced devastating cholera and measles outbreaks that shifted programmatic priorities. Costs associated with traveling study staff and transporting equipment kept rising due to hyperinflation and, after the July 2016 violence, the study team was unable to convene in Juba for some months to conduct refresher trainings or monitor data collection. Strategies used to address these challenges were: collaborating with non-research partners to identify operational solutions; maintaining a locally-based study team; maintaining flexible budgets and timelines; using mobile data collection to conduct timely data entry and remote quality checks; and utilizing a cascade approach for training field staff. Conclusions: The study provides lessons that are applicable to other humanitarian settings including the need for flexible research methods, budgets and timelines; innovative training and supervision; and a local team from the study sites with careful consideration of sociopolitical factors that impact their access and safety. Engagement of national and local stakeholders can ensure health services and data collection continue and findings translate to public health action, even in contexts facing severe and unpredictable insecurity. Word count: 314/350
Healthcare disparities in cardio oncology: patients receive same level of surveillance regardless of race at a safety net hospital
Authors: Chen Crystal , Dalsania Raj , Hamad Eman A
Published: September 2020

Background: Cardiotoxicity remains a dreaded complication for patients undergoing chemotherapy with human epidermal growth factor (HER)-2 receptor antagonists and anthracyclines. Though many studies have looked at racial disparities in heart failure patients, minimal data is present for the cardio-oncology population. Methods: We queried the echocardiogram database at a safety net hospital, defined by a high proportion of patients with Medicaid or no insurance, for patients who received HER2 receptor antagonists and/or anthracyclines from January 2016 to December 2018. Patient demographics, clinical characteristics, and treatment outcomes were collected. Based on US census data in 2019, home ZIP codes were used to group patients into quartiles based on median annual household income. The primary end point studied was referral rate to cardiology for patients undergoing chemotherapy. Results: We identified 149 patients who had echocardiograms and also underwent treatment with HER2 receptor antagonists and/or anthracyclines, of which 70 (47.0%) were referred to the cardio-oncology program at our institution. Basic demographics were similar, but white patients were more likely to live in ZIP codes with higher income quartiles (p<0.00001). Comparing between racial groups, there was no statistical difference in the percentage of patients that had a reduction in ejection fraction (EF) (p=0.75). There was no statistical difference between racial groups in the number of cardiology or oncology appointments attended, number of appointments cancelled, average number of echocardiograms received, additional cardiac imaging received. Black patients were more likely to receive ACEI/ARB post chemotherapy (p=0.047). A logistic regression model was created using race, age, gender, insurance, income quartile by home ZIP code, comorbidities (hypertension, hyperlipidemia, coronary artery disease, arrhythmia, diabetes mellitus, smoking, family history, age >65), procedures (coronary stents, cardiac surgery), medications pre-chemotherapy, cancer type, cancer stage, and chemotherapy. This model found that there was an increased referral rate among patients from higher income quartiles (p=0.017 for quartile 3, p=0.049 for quartile 4), patients with a history of hypertension (p<0.0001), and patients with breast cancer (p=0.02). Conclusions: The results of this study suggest that patients of our cardio-oncology population at a safety net hospital receive the same level of surveillance and treatment, and develop drop in ejection fraction at similar rates regardless of their race. However, patients that reside in ZIP codes associated with higher income quartiles, with hypertension, and with breast cancer, are associated with increased rate of referral.
Integrity, Use and Care of Long-Lasting Insecticidal Nets in Kirinyaga County, Kenya
Authors: Nyangi Mary Wanjiku , Kigondu Elizabeth Mumbi , Irungu Beatrice , Nganga Margaret , Gachanja Anthony , Kinyanjui Martin , Nyangacha Ruth , Muniu Erastus , Kamau Luna , Gathirwa Jeremiah
Published: September 2020

Background: Vector control is an essential component in prevention and control of malaria in malaria endemic areas. Insecticide treated nets is one of the standard tools recommended for malaria vector control. The objective of the study was to determine physical integrity and insecticidal potency of long-lasting insecticidal nets (LLINs) used in control of malaria vector in Kirinyaga County, Kenya.Method: The study targeted households in an area which had received LLINs during mass net distribution in 2016 from Ministry of Health. A total of 420 households were sampled using systematic sampling method, where the household heads consented to participate in the study. A semi-structured questionnaire was administered to assess care and use while physical examination was used to determine integrity. Chemical potency was determined by gas chromatography mass spectroscopy (GC-MS). Data analysis was done using Statistical Package for Social Sciences (SPSS) version 19. Results: After eighteen months of use, 96.9% (95% CI: 95.2% – 98.6%) of the distributed nets were still available. Regarding the net utilization, 94.1% of household heads reported sleeping under an LLIN the previous night. After physical examination, 49.9% (95% CI: 43% - 52.8%) of the bed nets had at least one hole. The median number of holes of any size was 2[interquartile range (IQR) 1-4], and most holes were located on the lower part of the nets, [median 3 (IQR 2-5)]. Only 15% of the nets with holes had been repaired. The median concentration for alpha-cypermethrin was 7.15mg/m2 (IQR 4.25-15.31) and 0.00mg/g (IQR 0.00-1.99) for permethrin. Based on pHI, Chi-square test varied significantly with the manufacturer (X (6, N=389) = 29.14, p = 0.04). There was no significant difference between nets with different number of washes (X2(2) = 4.55, p = 0.103).Conclusion: More than three-quarters of the nets supplied had survived and insecticidal potency was adequate in vector control. Studies for validated field evaluation of surface insecticidal content available to a mosquito after landing on a net to rest should be developed.
Antiviral effect of baicalin on Marek’s disease virus in CEF cells
Authors: Yang Fan , Feng Chun , Yao Yongxiu , Qin Aijian , Shao Hongxia , Qian Kun
Published: September 2020

Background: Baicalin, the main metabolic component of Scutellaria baicalensis Georgi, has various pharmacological properties including anti-inflammatory, anti-oxidant, anti-apoptotic, anti-bactericidal and anti-viral. The purpose of this study was to investigate the anti-Marek’s disease virus (MDV) activities of baicalin in CEF cells. Results: Here, we showed that baicalin could inhibit viral mRNA, protein levels and overall plaque formation in a time-dependent manner. We also found that baicalin could consistently inhibit MDV replication and directly affect the virus infectivity. Moreover, baicalin treatment has no effect on expression level of antiviral cytokine and inflammatory cytokines in MDV infected CEFs. Conclusions: These results demonstrate that baicalin could be a potential drug against MDV infection.
Circulating Tumor Cells to Predict Microvascular Invasion and Dynamical Detection Indicate Prognosis of Hepatocellular Carcinoma
Authors: Zhou Jiangmin , Zhang Zhiwei , Zhou Honghao , Leng Chao , Hou Bingwu , Zhou Chenyang , Hu Xinsheng , Wang Jinlin , Chen Xiaoping
Published: September 2020

Background: The number of preoperative circulating tumor cell (CTC) was correlated with the presence of microvascular invasion (MVI). The change of postoperative CTC count can predict the prognosis of patients. But the change trend of postoperative CTC is controversial.Methods: A total of 137 patients were recruited for the study. Preoperative blood samples of all patients were collected to detect CTC. The time points for blood collection were before the operation, during operation, and at one week, one month, two months, three months, six months, and one year after surgery. The power of predicting the presence of MVI was analyzed by the receiver operating characteristic curve (ROC). According to the survival status, 137 patients were divided into three groups: no recurrence, early recurrence, and non-early recurrence. Results: A threshold CTC value of 5 showed the most significant power to predict the existence of MVI. In a multivariate analysis, the parameters of preoperative CTCs, alpha-fetoprotein (AFP) and tumor diameter were independent predictors of MVI (P < 0.05). A CTC value greater than or equal to 5 has better predictive value than AFP > 400μg/L or tumor diameter > 5 cm. The number of intraoperative CTCs in the three groups did not increase compared to before surgery (P > 0.05). The number of CTC in the non-recurrent group and the non-early recurrent group decreased significantly one week after surgery compared with intraoperative values (P < 0.001), although there was no statistical significance in the group with early recurrence (P = 0.95). Patients with mean CTC ≥ 5 had significantly worse long-term outcome than those with mean CTC < 5 (P <0.001). Conclusion: The preoperative CTC counts in peripheral blood of patients with HCC is closely correlated to MVI. Intraoperative manipulation for the lesion by the surgeon does not increase the number of CTC in peripheral blood. Surgical removal of the tumor decreases the number of CTC. The persistence of CTC at a high level (≥ 5) after surgery suggests a risk of early recurrence.