bluuebunny/crossref_metadata_2025_split huggingface dataset:
ARID1A&nbsp;Upregulation Predicts Poor Survival in Patients With Liver Cancer&nbsp;
Authors: Jiang Feng , Wei Ke , Wang Ming , Wu Chuyan 
Published: January 2021

Abstract
Objective: ARID1A has been identified as a possible biomarker for certain cancers. There is, however, some debate regarding its function in liver cancer. Methods: Associations between clinical variables and ARID1A were evaluated. Cox and Kaplan – Meier analysis were used to examine clinical pathological factors linked to overall survival of patients with liver cancer. Gene set enrichment analysis (GSEA) was conducted using the dataset of the cancer genome atlas(TCGA). Results: High expression of ARID1A was correlated with the gender and tumor topography (T) diagnosis of liver cancer. Patients with elevated ARID1A expression had poorer prognosis than those with low ARID1A expression. The study also showed that ARID1A was an independent risk factor for overall survival. GSEA established pathways involved in ERBB signaling, cancer, insulin signaling, mTOR signaling, MAPK signaling, VEGF signaling, Ubiquitin signaling, and Wnt signaling as differentially enriched in ARID1A-high expression liver cancer. Conclusion: ARID1A has been shown to be expressed at high rates of liver cancer and to represent a possible independent molecular marker for diagnosis and prognosis of liver cancer.
Identification of significant genes with invasive promotion in non-functional pituitary adenoma via bioinformatical analysis
Authors: Wang An Shuo , Xu Hao , Zeng Ming Hui , Wang Fei 
Published: January 2021

Abstract
Background

Non-functional pituitary adenoma (NFPA) is a disease with a high incidence, which accounts for a large part of pituitary tumors and plays a pivotal role. While invasive NFPAs which have not any endocrinology manifestations and space-occupying symptoms at early stages account for about 30 percent of NFPAs. The purpose of the present academic work was to identify significant genes with invasive promotion and their underlying mechanisms.
Methods

Gene expression profiles of GSE51618 was available from GEO database. There are 4 non-invasive NFPA tissues, 3 invasive NFPA tissues and 3 normal tissues in the profile datasets. Differentially expressed genes (DEGs) between non-invasive NFPA tissues and invasive NFPA tissues were picked out by GEO2R online tool. There were total of 226 up-regulated genes and 298 down-regulated genes. Next, we made use of the Database for Annotation, Visualization and Integrated Discovery (DAVID) to analyze Kyoto Encyclopedia of Gene and Genome (KEGG) pathway, gene ontology (GO) and Kaplan Meier Plotter. Then protein-protein interaction (PPI) of these DEGs was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). There were total of 141 up-regulated genes and 171 down-regulated genes. Of PPI network analyzed by Molecular Complex Detection (MCODE) plug-in, all 141 up-regulated genes were selected.
Results

After reanalysis of GO, five genes (ATP2B3, ADCYAP1R1, PTGER2, FSHβ, HTR4) were found to significantly enrich in the cAMP signaling pathway, Neuroactive ligand-receptor interaction and Renin secretion via reanalysis of DAVID.
Conclusions

We have identified five significant up-regulated DEGs with invasive promotion in invasive NFPAs on the basis of integrated bioinformatical methods, which could be potential therapeutic targets for invasive NFPAs patients.
Conventional Suture with Prolonged Timing of Drainage Is As Good As Quilting Suture In Preventing Seroma Formation at Pectoral Area After Mastectomy
Authors: Huang Juan , Wang Shouman , Wu Yuhui , Hai Jian , Mao Jie , Dong Xue , Xiao Z 
Published: January 2021

Abstract
BackgroundThe aim of this study was to compare conventional suture with prolonged timing of drainage with quilting suture on the formation of seroma at pectoral area after mastectomy (ME) with sentinel lymph nodes biopsy (SLN) or axillary lymph nodes dissection (ALND) for breast cancer.Methods388 consecutive breast cancer patients were retrospectively analyzed and categorized into three group. Patients in group 1 were with quilting suture, group 2 with conventional suture and 13-15 days drainage in situ, and group 3 with conventional suture and 20-22 days drainage. The primary outcome was the incidence of Grade 2 and 3 seroma at anterior pectoral area within one month postoperatively. Cox regression was used for analysis.ResultsThe incidence of Grade 2 and 3 seroma was comparable among groups (9.5% vs. 7.9% vs. 5.3%, p = 0.437), as well as late Grade 2 and 3 seroma among groups (4.3% vs. 2.9% vs. 1.5%, p = 0.412). Old age, high body mass index and hypertension were independently risk factors for Grade 2 and 3 seroma.ConclusionsProlonged timing of drainage to 13-15 days in conventional suture was long enough to decrease the incidence of Grade 2 and 3 seroma as lower as that in quilting suture group at pectoral area within one month after mastectomy.
Retroperitoneal Leiomyosarcoma with Left Hip Pain as its Clinical Manifestation: A Case Report and Literature Review
Authors: Shi Yunfu , Zhang Bing , Zhang Mingxia , Yang Wenjuan , Qi Yiming , Hong Xiufang 
Published: January 2021

Abstract
Background: Leiomyosarcoma is a malignant tumor that originates from smooth muscle tissue, and can occur in multiple organs and tissues of the abdominal cavity, and most often in the retroperitoneum. It can occur at any age, usually 40 to 70 years old, and it is more common in women. The main clinical manifestations were abdominal discomfort, abdominal mass, abdominal pain, weight loss, nausea, vomiting or edema of the lower limbs. It is easy to invasion, recurrence and metastasis, and its prognosis is poor. Surgical resection is the preferred treatment method. Case presentation: A 55-year-old woman had pain in the left hip more than 6 years. Abdominal enhanced CT and MR showed that the tumor was located on the left side of psoas major muscle. She underwent surgical treatment, and the postoperative pathology was leiomyosarcoma. No other treatment was performed after the operation. The patient has been followed up for 78 months and no tumor recurrence. Conclusions: Retroperitoneal leiomyosarcoma is a rare type of malignant tumor with no specific clinical manifestation. Because of its atypical clinical manifestations, particular attention should be paid to avoid misdiagnosis and missed diagnosis.
Cognitive Impairment At 3, 6 and 12 Month After the First-Ever Stroke Among Lebanese Survivors: Incidence and Risk Factors
Authors: Boutros Celina , Khazaal Walaa , Taliani Maram , Salameh Pascale , Hosseini Hassan , Sadier Najwane Said 
Published: January 2021

Abstract
Cognitive impairment is a prevalent outcome of stroke, affecting the quality of life and increasing the disability. Its risk factors are unknown in Lebanon. Therefore, the aims of this study were to evaluate the cognitive impairment incidence among Lebanese stroke survivors at 3, 6 and 12 month post stroke, and to identify the associated factors. A multicenter longitudinal prospective study was conducted in 10 hospitals of Beirut and Mount Lebanon among 150 subjects aged ≥ 18 years old between February 2018 until May 2019. The Mini-Mental State Examination assessed the cognitive function. Univariate and Multivariable analyses were performed to identify the predictors of the post stroke cognitive impairment. A p-value <0.05 was considered statistically significant. At 3 month post stroke, 74.8% were cognitively impaired versus 46.7% and 37.6% at 6 and 12 month post stroke respectively. Older age, past smoking, presence of a caregiver, sedentary ≥ 12 hours, aphasia at the time of stroke occurrence, the length of hospital stay, severe stroke, high disability degree, post stroke anxiety and depression, epileptic seizures and physical disorders were the risk factors inducing cognitive decline. Whereas, the high education level, the employment and the history of diabetes mellitus played a protective role for the cognitive function. Findings reveal levels of cognitive impairment post-stroke that are concerning. Thus, primary and secondary prevention is essential to reduce its incidence and to cope with its burden.
Thixotropy of A Transparent Clay Manufactured by Carbopol Simulate Marine Soil
Authors: SUN Zhiwen , KONG Gangqiang , ZHOU Yang , SHEN Yang , XIAO Hanyu 
Published: January 2021

Abstract
A transparent clay manufactured by Carbopol® UltrezTM 10 (simplified as U10) was introduced, and its manufacture processes were briefly described. Both relative transparency (RT) and modulation transfer function (MTF) methods were used to quantify the optical character variation via soil thickness. The transparency of this new transparent clay was comparative analyzed with traditional four previous transparent materials. The results show that this new transparent clay has relative higher optical transparency than majority of previous materials. The thixotropic properties of this synthetic transparent clay were measured in detail through laboratory vane test. Exponential function was used to describe the thixotropy and sensitivity of clay. The good fitting results shown similar development trend of thixotropy for synthetic transparent clay and natural one. Furthermore, sensitivity of transparent clay belongs to low to medium sensitivity, which can simulate marine soil. With the test results, Carbopol® UltrezTM 10 shows a great potential as a substitute for natural clay and is expected to be widely used in model tests.
Clinical Outcomes of Micropulse Transscleral Cyclophotocoagulation in Refractory Glaucoma
Authors: Seo Duri , Lee Taek June , Kim Joo Yeon , Choi Wungrak , Lee Sang Yeop , Seong Gong Je , Kim Chan Yun , Bae Hyoung Won 
Published: January 2021

Abstract
This study evaluated the clinical outcomes of first-time micropulse transscleral cyclophotocoagulation (MP-TSCPC) performed in cases of refractory glaucoma. This retrospective study analysed the patients with refractory glaucoma who underwent MP-TSCPC rom February 2018 to February 2020 at Yonsei University Severance Hospital. A total of 45 eyes of 43 Asian patients (aged 55.71±16.84 years) who underwent MP-TSCPC for the first time, were included in this study. The mean baseline intraocular pressure (IOP) was 25.96±9.27 mmHg. The most common diagnosis was secondary glaucoma (44.4%) with a mean logarithm of the minimum angle of resolution (logMAR) visual acuity of 1.19±1.02. There was a significant reduction (P<0.05) in IOP on 1 day 1,to 18.03±5.99 mmHg;, at 1 week, to 13.29±5.24 mmHg;, at 1 month, to 14.98±4.55 mmHg;, at 3 months, to 17.05±5.52 mmHg;, 6 months to 17.78±6.37 mmHg; and 12 months, to 16.56±5.96 mmHg. There was also a reduction (P<0.05) in the number of topical anti-glaucoma medications required to control IOP from baseline (3.69±0.63) at 1, 3, and 6 months. MP-TSCPC is an effective procedure that offers good results in reducing IOP and decreases the use of anti-glaucoma medications in patients with refractory glaucoma.
COVseq is a cost-effective workflow for mass-scale
SARS-CoV-2 genomic surveillance
Authors: Simonetti Michele , Zhang Ning , Harbers Luuk , Milia Maria Grazia , Nguyen Thi , Brossa Silvia , Bienko Magda , Sapino Anna , Sottile Antonino , Ghisetti Valeria , Crosetto Nicola 
Published: January 2021

Abstract
Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the spread and evolution of the virus across different populations, geographical regions and species. Here, we present a streamlined workflow—COVseq—based on the CUTseq method that we previously described, which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms, from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We validated COVseq on RNA extracted from the supernatant of a SARS-CoV-2 culture as well as from 85 RNA samples from nasopharyngeal swabs, demonstrating the ability of COVseq to achieve near complete genome coverage, including the S region encoding the spike protein. A cost analysis showed that COVseq could be used to sequence thousands of samples per week at less than 10 USD per sample, including library preparation and sequencing costs. COVseq is a versatile and scalable method that can be readily applied for genomic surveillance of the ongoing pandemic and easily adapted to other pathogens such as influenza viruses.
Arthroscopic reconstruction of anterior cruciate ligaments with allograft: Single-tunnel double-bundle versus single-tunnel single-bundle
Authors: Zhu Weimin , Zheng Yizi , Lu Wei , Xiong Jianyi , Wang Daping , Deng Zhenhan 
Published: January 2021

Abstract
Background: Arthroscopic reconstruction of anterior cruciate ligament (ACL) commonly adopted single-tunnel single-bundle (STSB) or double-tunnel double-bundle (DTDB) methods. Though single-tunnel double-bundle (STDB) has been used in clinical practice, the efficacy remains unclear. The objective of this study is to compare the clinical results of ACL reconstruction using the STDB and STSB techniques.Methods: Between March 2010 to June 2013, 78 patients with ACL rupture underwent arthroscopic STDB reconstruction (42 cases) or STSB reconstruction (36 cases) using anterior tibialis tendon allografts in our department. IKDC, Lysholm and Tegner scores were used to evaluate the subjective function of the knee joint during the postoperative follow-up. In addition, the Lachman test and pivot shift test were used to objectively assess the stability of the knee.Results: The average follow-up time is 24.2±5.7 months in the STDB group, and 24.8±6.6 months in the STSB group. Patients in both groups recovered to preoperative sports level with few complications. The postoperative Lysholm, IKDC, Tegner scores, and knee joint stability were significantly improved compared to preoperative status in both groups (P<0.05). However, no statistically significant difference was observed between the two groups at the final follow-up (P>0.05), except for the improvement of pivot shift test positive rate in the STDB group compared with STSB group (P<0.05).Conclusion: Both techniques can be used to restore the stability and function of the knee joint with satisfactory short-term efficacy, and STDB showed better rotational stability than STSB technique, indicating the STDB technique may also considered a reliable method for ACL reconstruction.
Comorbidities of COVID-19 Patients With Low Cycle Threshold (Ct) Value of Nucleocapsid (N) Gene: An Application to Cluster-Based Logistic Model.
Authors: RUDRA SUJAN , DAS SHUVA , HOQUE MD. EHSANUL , KALAM ABUL , RAHMAN MOHAMMAD ARIFUR , SHIZUKA SWAGATA NANDY , RAHMAN TAZRINA 
Published: January 2021

Abstract
Background: Coronavirus disease 2019 (COVID-19) is a health crisis throughout the world. The widely used Real-time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) method is most capable to demonstrate the patient’s condition. Comorbidities can make patients more critical.Materials and methods: In this study, we shed light on the low cycle threshold (Ct) value of the N gene in the rRT-PCR test of the COVID-19 patients who had comorbidities and their cure rate as well as the needfulness of ICU (Intensive Care Unit) management. We conducted the research in the Molecular Biology Laboratory of Chittagong Medical College between May and August 2020, then took the telephone interview with 300 positive patients who fulfilled the study criteria. We applied cluster-based logistic regression to analyze the data.Results: Low Ct value of the N gene was found 1.324 times more in Type 2 DM patients and 1.871 times higher in hypertensive patients. Hospitalized patients are 2.480 times more vulnerable to shift in ICU in case of low Ct value of the N gene. Conclusion: While infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) frequently causes severe diseases, suspected cases with comorbid conditions should go through the rRT-PCR as early as possible.
Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective
Authors: Ekpenyong Moses Effiong , Uzoka Faith-Michael , Edoho Mercy , Inyang Udoinyang G. , Udo Ifiok J , Uto Nseobong P. , Ekaidem Itemobong S. , Moses Anietie E. , Anwana Enoabasi D. , Tatfeng Youchou M. , Joseph Geoffery , Dan Emmanuel A. 
Published: January 2021

Abstract
Background: The increased number of accessible genomes has prompted large-scale comparative studies for decerning evolutionary knowledge of infectious diseases, but challenges such as non-availability of close reference sequence(s), incompletely assembled or large number of genomes, preclude real time multiple sequence alignment and sub-strain(s) discovery. This paper introduces a cooperatively inspired open-source framework, for intelligent mining of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes. We situate this study within the African context, to drive advancement on state-of-the-art, towards intelligent infectious disease characterization and prediction. The outcome is an enriched Knowledge Base, sufficient to provide deep understanding of the viral sub-strains’ identification problem. We also open investigation by gender, which to the best of our knowledge has been ignored in related research. Data for the study came from the Global Initiative on Sharing All Influenza Data database (https://gisaid.org) and processed for precise discovery of viral sub-strains transmission between and within African countries. To localize the transmission route(s) of each isolate excavated and provide appropriate links to similar isolate strain(s), a cognitive solution was imposed on the genome expression patterns discovered by unsupervised self-organizing map (SOM) component planes visualization. The Freidman-Nemenyi’s test was finally performed to validate our claim. Results: Evidence of inter- and intra-genome diversity was noticed. While some isolates (or genomes) clustered differently, implying different evolutionary source (or high-diversity), others clustered closely together, indicating similar evolutionary source (or less-diversity). SOM component planes analysis revealed multiple sub-strains patterns, strongly suggesting local- or intra-community and country to country transmissions. Cognitive maps of both male and female isolates revealed multiple transmission routes. Freidman’s test results showed highly significant difference (p<0.01) among the various isolate groups. Nemenyi’s test revealed groups that differed in their isolates.Conclusion: The proposed framework offers explanations to SARS-CoV-2 diversity and provides real time identification to disease transmission routes, as well as rapid decision support for facilitating inter- and intra-country contact tracing of infected case(s). Intermediate data produced in this paper are helpful to enrich the genome datasets for intelligent characterization and prediction of COVID-19 and related pandemics, as well as the construction of intelligent device for accurate infectious disease monitoring.
Characterizing and tailoring climate change adaptation practices into a diversified agroecosystem&nbsp;
Authors: Adego Tsega 
Published: January 2021

Abstract
Smallholder farmers require viable adaptation strategies for climate change. Adaptation project might be mal-practiced unless it considers the local diversity. This paper argued that the challenge of agriculture in developing countries in general and Ethiopia, in particular, is much diversified and thus interventions require a systematic shift to specific agro-ecosystems. In light of this, we used agro-ecosystem analysis to design locally appropriate adaptation strategies specific to Rib watershed in Ethiopia. The agro-ecosystem uses three inputs of agro-climatic zoning, soil type and terrain analysis, and farming systems. We used primary data collected from 383 randomly selected farm-households. The survey data was supplemented by key-informant interviews, focus group discussions and secondary data. We characterized and mapped the study area in two distinct groups of agro-ecosystems: Fogera plain and Libo-Farta highlands. The finding portrayed that across these agro-ecosystems, there was considerable difference in the: potentials, constraints, crop type, income distribution, and soil type. We found blanket application of the same strategies irrespective of these heterogeneities. The income distribution shows that the poorest 20 percent of the population share about 5 percent of the income. Relatively the plain has less income inequality with 38.3 as compared to the highlands Gini coefficient of 42.8. Looking only at the average distribution of income does not reveal the inequality. It is important to disaggregate into the specific agroecosystems. The study identified that drainage projects, fruit trees, and fishing are among the prioritized adaptation strategies for the plain while conservation structures, irrigation, agroforestry are tailored to the highland areas. It is important to consider diversities before intervention.
Assessment of Microscopic detection of Malaria with Nested Polymerase Chain Reaction in War-torn Federally Administered Tribal Areas of Pakistan
Authors: Nadeem Muhammad Faisal , Khattak Aamer Ali , Yaqoob Adnan , Awan Usman Ayub , Zeeshan Nadia 
Published: January 2021

Abstract
Background: Diagnostic accuracy of malaria is critical for early treatment, control, and elimination of malaria, especially in war-affected malaria endemic areas. Microscopic detection of Plasmodium species has been the gold standard in remote malaria-endemic regions. However, the diagnostic accuracy is still questioned, especially in discriminating mixed and submicroscopic parasitic levels. This study was designed to evaluate the diagnostic performance of microscopic examination against nested PCR analysis in war-torn malaria-endemic Federally Administered Tribal Areas (FATA) of Pakistan. Methods: Venous blood samples were collected from symptomatic patients for microscopic examination and nested PCR analysis from January 2016 - December 2016 from five Agencies (Bajaur, Mohmand, Khyber, Orakzai and Kurram Agency) and four Frontier Regions (Peshawar, Kohat, Bannu, and Dera Ismail Khan Frontier Region) of FATA. Malaria-positive isolates were confirmed by nested PCR (targeting Plasmodium small subunit ribosomal ribonucleic acid (ssrRNA) genes) for speciation. Results: Among enrolled participants, 762 were found positive for malaria parasite on microscopic examination of the blood film. P. vivax was found in 623, P. falciparum in 132 and 7 were diagnosed with mixed infection (P. vivax and P. falciparum coinfection). Nested PCR detected Plasmodium infection in 679 samples (523 P. vivax, 121 P. falciparum, and 35 mixed infections). Compared with microscopy, the sensitivity of nested PCR was 98.94%, and specificity was 98.27%, while the sensitivity and specificity of slide microscopy 89.34% and 87.99% respectively. Conclusion: The conventional microscopy method has low sensitivity to detect mixed infection as compared to nested PCR. High sensitivity and specificity observed in nested PCR makes this molecular tool a useful technique for monitoring, controlling, and eliminating malaria-endemic regions.