bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effectiveness of applying for Formative Assessment Objective Structured Clinical Examination (OSCE)for Undergraduate Students in Faculty of Medicine King Abdul Aziz University, Jeddah, Kingdom of Saudi Arabia
Authors: Allhiani Rajaa , Abdulwahab Sumaiah , Alamri Sultan Hassan
Published: June 2020

The use of formative and summative assessment for students have been always a concern for medical professionals such as teachers and students especially when students are at graduating level. This can be supported with increasing the effectiveness and comprehensiveness of the students with appropriate clinical training using a defined structure with questionnaire-based system defined in the methodology to support student’s skills using clinical competencies to form perspective. It has been found that with Objective Structured Clinical Examination can be used as the method to assess the adequacy to support clinical skills of medical students following their competence level. This can be used to support a variety of tests to work on underpinning emergency procedures to interpret investigational data to ensure in-depth and breadth coverage of clinical skills following 5th-year medical students.
SARS-CoV-2 and mosquitoes: an extreme challenge
Authors: Huang Yan-Jang S. , Vanlandingham Dana L. , Bilyeu Ashley N. , Sharp Haelea M. , Hettenbach Susan M. , Higgs Stephen
Published: June 2020

The research addresses public speculation that SARS-CoV-2 might be transmitted by mosquitoes. The World Health Organization has stated “To date there has been no information nor evidence to suggest that the new coronavirus could be transmitted by mosquitoes”. Here we provide the first experimental data to the capacity of SARS-CoV-2 to infect and be transmitted by mosquitoes. Using three species of mosquitoes from both genera involved in transmission of most arboviruses that infect humans we demonstrate that SARS-CoV-2 virus is unable to replicate in mosquitoes and therefore cannot be transmitted to people.
Testing pipelines for genome-wide SNP calling from Genotyping-By-Sequencing (GBS) data for Pinus ponderosa
Authors: Shu Mengjun , Moran Emily V.
Published: June 2020

Background

Single Nucleotide Polymorphism (SNP) markers have rapidly gained popularity due to their abundance in most genomes and their amenability to high-throughput genotyping techniques. Reduced-representation restriction-enzyme-based sequencing methods (GBS or RADseq) have been demonstrated to be robust and cost-effective genotyping methods. While previous studies have shown that alignment of the short-read fragments to a genome sequence results in better SNP calling than de novo approaches, only a few tree species - and few conifers in particular - have an annotated sequence. While these could be used to align sequence fragments from related species, sequence divergence might result in SNPs being missed if they are in fragments that don't align properly. Producing a new annotated genome sequence for every conifer species before SNP analyses are conducted is still prohibitive, as many conifer genomes are huge (> 19 GB) and include a large proportion of repeat sequences, making assembly difficult. Here we compare four bioinformatics pipelines, two of which require a reference genome (TASSEL-GBS V2 and Stacks), two of which are de novo pipelines (UNEAK and Stacks). We used Illumina sequence data from 94 ponderosa pines, with loblolly pine as the reference genome.
Results

The number of SNPs called was much lower without a reference genome (62–196 thousand vs. 2.1–2.7 million SNPs). UNEAK was the fastest overall and identified more SNPs than Stacks de novo. Stacks with a reference genome produced the highest number of SNPs with lowest proportion of paralogs, while SNPs identified by TASSEL-GBS V2 exhibited the highest heterozygosity, minor allele frequency, and proportion of paralogs. More SNPs were uniquely identified by Stacks than TASSEL, though there was high overlap between methods.
Conclusion

The present case study provides a comprehensive comparison between four commonly-used SNP calling pipelines, and identifies the Stacks reference-based approach as the best overall for conifers (or other species with large repetitive genomes) that do not have a published reference genome for the same species. However, all four pipelines had distinct benefits and limitations, with Stacks for instance being less user-friendly than some of the other pipelines. In addition, researchers studying other conifer species using similar approaches should be prepared to analyze very large numbers of SNPs.
The Relationship Between Padi4 -94G/A Polymorphism and Rheumatoid Arthritis: A Meta-analysis in Multi Ethnic Groups
Authors: Jian Changchun , Pu Jingsong
Published: June 2020

Background: A number of studies have reported the association between peptidylarginine deiminase 4 (PADI4) -94G/A polymorphisms and rheumatoid arthritis (RA) risk in different populations, however, the results remained inconclusive. Objecitve: We therefore aim to address this association by performed an updated meta-analysis in multi ethnic groups. Methods: The PubMed and Chinese related databases were searched up to January 2019. The strength of association between PADI -94G/A polymorphism and RA susceptibility was assessed with odds ratios (ORs) and 95% confidence intervals (CIs). Results: A total of 22 studies with 14514 RA cases and 21138 controls were finally included in the analysis. Six ethnic groups such as China, Japan, USA, UK, Sweden and Spain were contained. In the overall population, it revealed that PADI -94G/A polymorphism was significantly associated with an increased risk of RA. In the subgroup analyses by ethnicity, significant association was found in China as well as in Japan and USA. Conclusions: This meta-analysis demonstrates that the PADI4 -94G/A polymorphisms may represent a significant risk factor for RA in China, in Japan and USA. Further studies are needed to clarify this finding, since most available studies were conducted among Chinese and Japanese in this study.
Autophagy-related signature as Indicators for the Prognosis of Hepatocellular carcinoma
Authors: Ye Wen , Shi Zhehao , Zhang Zhongjing , Zhou Yi , Chen Bicheng , Zhang Qiyu
Published: June 2020

Background

Hepatocellular carcinoma (HCC) is the most common and deadly type of liver cancer. Autophagy is the process of transporting damaged or aging cellular components into lysosomes for digestion and degradation. There is an accumulative evidence implies that autophagy is a key factor of the progression of cancer. The aim of this study was to determine a panel of a novel autophagy-related prognostic marker for liver cancer.
Methods

We conducted a comprehensive analysis of ARGs expression profiles and corresponding clinical information based on The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) database. The univariate Cox proportional regression model was used to screen candidate autophagy-related prognostic genes. In addition, the multivariate Cox proportional regression model were helped to prove five key prognostic autophagy-related genes (ATIC, BAX, BIRC5, CAPNS1 and FKBP1A), which were used to construct prognostic signature.
Results

Based on the prognostic signature, liver cancer patients were significantly divided into high-risk and low-risk groups in terms of overall survival (OS). Further multivariate Cox regression analysis indicated that the prognostic signature remained as an independent prognostic factor for OS. The prognostic signature in possession of a better Area Under Curves (AUC) has a better performance in predicting the survival of patients with HCC, compared with other clinical parameters.
Conclusion

This study provides a prospective biomarker for monitoring the outcomes in the patients with HCC.
Reconstruction of time-consistent species trees
Authors: Lafond Manuel , Hellmuth Marc
Published: June 2020

Background: The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way.Results: In this contribution, we consider event-labeled gene trees that contain speciations, duplications as well as horizontal gene transfer (HGT) and we assume that the species tree is unknown. Although many problems become NP-hard as soon as HGT and time-consistency are involved, we show, in contrast, that the problem of finding a time-consistent species tree for a given event-labeled gene can be solved in polynomial-time. We provide a cubic-time algorithm to decide whether a "time-consistent" species for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity.
Discovery of a potent angiotensin converting enzyme 2 inhibitor from Chinese Medicinal and Edible Plant via Docking-based Virtual Screening
Authors: Zi Cheng-Ting , Zhang Ning , Yang Liu , Wang Li-Xia , Wu Yi-Long , Su Yin-Shan , Wang Xuan-Jun
Published: June 2020

COVID-19 has outbreaked in Wuhan city, Hubei province of China since December 30th 2019, and spread nationwide and widely spilled over to other countries around the world that has been declared a public health emergency. However, there is no specific drug for the treatment of the disease. Therefore, identifying effective antiviral drugs to combat the disease is urgently needed. Angiotensin converting enzyme 2 (ACE2) has become the promising target to discovery new antiviral drugs to treat COVID-19, we have attempted to discover novel ACE2 inhibitors through ligand-based virtual screening. Finally, eight compounds were selected and tested ACE2 kinase inhibitory assay using fluorescence assays method. The results showed that four compounds (monoammonium glycyrrhizinate, glycyrrhizic acid methyl ester, ginsenoside Rg6 and ginsenoside F1) from 101 kinds of Chinese medicinal and edible plants which could inhibit ACE2 activity in vitro. Further efforts on chemical modification of these lead compounds are undergoing can lead to discover better agents against COVID-19.
Functional Conservation of Mitochondrial RNA Levels Despite Divergent mtDNA Organization
Authors: Held James P , Patel Maulik R
Published: June 2020

Objective: Mitochondria-encoded ribosomal RNA (rRNA) genes in humans are expressed at a higher rate than protein coding genes of the mitochondria. The organization of the human mitochondrial genome (mtDNA) is amenable to differential expression of rRNAs as it contains a promoter specific to the transcription of the two rRNAs. However, mtDNA is not organized in the same way as humans in all metazoans. In the nematode, Caenorhabditis elegans, the rRNA genes are on opposite sides of the mtDNA molecule and there are no obvious promoter sequences specific to the rRNA genes. Thus, we asked whether rRNA levels are higher relative to mRNAs in mitochondria of C. elegans as they are in humans.Results: Using droplet digital PCR, we discovered that steady-state mitochondrial rRNA transcript levels are approximately 120 times higher than the levels of mitochondrial mRNAs. These data demonstrate that despite the lack of conservation in mitochondrial genome organization, a high mitochondrial rRNA-to-mRNA ratio is a conserved feature of metazoans.
Performance Assessment of Two Motion Management Systems for Frameless Stereotactic Radiosurgery
Authors: Wang Hao , Xu Zhiyong , Grantham Kevin , Zhou Yongkang , Cui Taoran , Zhang Yin , Liu Bo , Wang Xiao , Vergalasova Irina , Reyhan Meral , Weiner Joseph Paul , Shabbar Danish , Yue Ning , Nie Ke
Published: June 2020

Background/PurposeFrameless stereotactic radiosurgery (SRS) requires dedicated systems to monitor patient motion in order to avoid inaccurate radiation delivery due to involuntary shifts. The purpose of this study is to assess the accuracy and sensitivity of two distinct motion monitoring systems used for frameless SRS.MethodsA surface image-guided system known as Optical Surface Monitoring System (OSMS), and a fiducial marker-based system known as High Definition Motion Management (HDMM) as part of the latest Gamma Knife Icon® were compared with each other. A 3D printer-based cranial motion phantom was developed to evaluate the accuracy and sensitivity of these two systems in terms of: (1) the capability to recognize predefined shifts up to 3 cm, and (2) the capability to recognize predefined speeds up to 3 cm/s. The performance of OSMS, in terms of different reference surfaces, was also evaluated.ResultsTranslational motion could be accurately detected by both systems, with an accuracy of 0.3 mm for displacement up to 1 cm, and 0.5 mm for larger displacements. The reference surface selection had an impact OSMS performance, with flat surface resulting in less accuracy. HDMM was in general more sensitive when compared with OSMS in capturing the motion, due to its faster frame rate, but a delay in response was observed with faster speeds. Both systems were less sensitive in detection of superior-inferior motion when compared to lateral or vertical displacement directions.ConclusionTranslational motion can be accurately and sensitively detected by OSMS and HDMM real-time monitoring systems. However, performance variations were observed along different motion directions, as well as amongst the selection of reference images. Caution is needed when using real-time monitoring systems for frameless SRS treatment.
Magnetic properties, anticancer and antibacterial effectiveness of sonochemically produced Ce3+/Dy3+ co-activated Mn-Zn nanospinel ferrites
Authors: almessiere munirah , Slimani Yassine , Rehman Suriya , Khan Firdos A. , Guner S. , Shirsath Sagar E. , Baykal Abdulhadi
Published: June 2020

Some new types of Ce3+ and Dy3+ co-doped manganese-zinc nanospinel ferrites (CDMZNSFs) of the form (Mn0.5Zn0.5)[Fe2 − 2xCexDyx]O4 (with 0.0 ≤ x ≤ 0.1) were sonochemically produced and characterized. The structure, morphology, optical and magnetic behaviors of these NSFs were determined as a function of co-dopant (Ce3+ and Dy3+) contents. In addition, the bactericidal (on the gram-positive and gram-negative bacterial strains) and anti-cancerous effectiveness of these NSFs were assessed. The cancer cells' growth inhibitory action of these NSFs was tested against both normal (HEK-293) and cancerous (HCT-116) human cells. The direct optical band gap energies of the studied NSFs were ranged from 1.54 to 1.85 eV. The measured hysteresis loop and temperature-dependent magnetization of the NSFs disclosed a phase transformation from the superparamagnetic (SPM) at room temperature (RT) to ferromagnetic (FM) below the blocking temperature (TB). The saturation magnetization and TB were decreased with the increase in co-dopant contents. After 48 h of treatment of the cancerous cells with the NSFs, their population was significantly dropped as shown by the MTT assay, indicating the selective inhibition of the cancer cells growth by the proposed NSFs. Conversely, the non-cancerous cells (HEK-293) population remained unaffected. The IC50 values of the NSFs-treated cancerous cells (HCT-116) were in the range of 0.74–2.35 µg/mL. The results of the MIC and MBC assays revealed the reasonable antibacterial efficacy (growth inhibitory activity) of these NSFs when tested against the E. coli and S. aureus bacterial strains. It is established that the proposed Ce3+/Dy3+ co-activated CDMZNSFs may be beneficial for the anti-cancerous and bactericidal applications.
Micropapillary pattern of pathologic IIIA-N2 lung adenocarcinoma is a prognostic factor after adjuvant chemoradiotherapy.
Authors: Zeng Jian , Cui Xiaoying , Cheng Lei , Chen Ying , Du Xianghui , sheng liming
Published: June 2020

Objectives: Lung adenocarcinoma with a micropapillary pattern is a highly aggressive disease and related to locoregional recurrence after surgery. This study aims to investigate the role of micropapillary pattern in pathologic IIIA-N2 lung adenocarcinoma after adjuvant chemoradiotherapy. Methods: A total of consecutive 257 patients with pathologic IIIA-N2 lung adenocarcinoma who received adjuvant chemoradiotherapy were enrolled in this retrospective study. Patients were classified into three groups based on the proportion of micropapillary components: micropapillary negative (MPN), micropapillary minor component (MPM, positive but not predominant), and micropapillary predominant component (MPP, positive and predominant). The disease-free survival (DFS) and overall survival (OS) were analyzed using SPSS software. Results: The five-year DFS and OS rates in the whole population were 41.0% and 62.7%, respectively. MPP group had the shortest median DFS time and OS time, compared with the MPM group and the MPN group (Median DFS time: 27 months Vs. 39 months Vs. 62 months, p=0.032; Median OS time: 54 months Vs. 64 months Vs. not reached, p=0.004). Furthermore, the micropapillary pattern was an independent prognostic factor for DFS and OS by multivariate analysis (p＜0.05). Conclusion: Micropapillary pattern of pathologic IIIA-N2 lung adenocarcinoma was related to the earlier treatment failure and worse prognosis after adjuvant chemoradiotherapy.
Efficacy and Toxicity of Re-irradiation for Esophageal Cancer Patients with Locoregional Recurrence: a retrospective analysis
Authors: Zhao Kaikai , Si Youjiao , Sun Liangchao , Meng Xiangjiao , Yu Jinming
Published: June 2020

Introduction: There is no standard treatment for locoregional recurrent (LR) esophageal squamous cell carcinoma (ESCC) patients treated with radiotherapy (RT) previously. This retrospective study aimed to examine the efficacy and toxicity of re-irradiation (re-RT) for ESCC patients with LR. Patients and Methods: A total of 252 patients were enrolled. Gross tumor volumes for re-RT were defined using contrast enhanced computed tomography and/or positron emission tomography/computed tomography. Overall survival (OS), after recurrence survival (ARS) and toxicities were assessed. Results: Through a median follow-up of 38 months, the median OS and ARS were 39.0 and 13.0 months, respectively. The 6-, 12-, and 24-month ARS rates were 81.9%, 50.5%, and 21.8%, respectively. Multivariate analyses showed that chemotherapy, esophageal stenosis and RFI may be independent prognostic factors for ARS. The incidence of esophageal fistula/ perforation, radiation-induced pneumonitis and esophagorrhagia was 21.4%, 12.8% and 9.1%, respectively. RFI≤12 months, esophageal stenosis and fat space between tumor and adjacent tissue disappeared were independent risk factors for the development of EP after re-RT. Conclusions: Re-RT was feasible for LR ESCC patients after RT initially, the complications occurred in re-RT is acceptable. Patients with RFI≤12 months, esophageal stenosis and fat space between tumor and adjacent tissue disappeared should be closely observed during and after re-RT.
The construction and visualization of the transmission networks for COVID-19: A potential solution for contact tracing and assessments of epidemics
Authors: Luo Caiying , Ma Yue , Jiang Pei , Zhang Tao , Yin Fei
Published: June 2020

The WHO described coronavirus disease 2019 (COVID-19) as a pandemic due to the speed and scale of its transmission. Without effective interventions, the rapidly increasing number of COVID-19 cases would greatly increase the burden of clinical treatments. Identifying the transmission sources and pathways is of vital importance to block transmission and allocate limited public health resources. According to the relationships among cases, we constructed disease transmission network graphs for the COVID-19 epidemic through a visualization technique based on individual reports of epidemiological data. We proposed an analysis strategy of the transmission network with the epidemiological data in Tianjin and Chengdu. The transmission networks showed different transmission characteristics. In Tianjin, an imported case can produce an average of 2.9 secondary infections and ultimately produce up to 4 generations of infections, with a maximum of 6 cases generated before being identified. In Chengdu, 45 noninformative cases and 24 cases with vague exposure information made it difficult to provide accurate information by the transmission network. The proposed analysis framework of visualized transmission networks can trace the transmission source and contacts, assess the current situation of transmission and prevention, and provide evidence for the global response and control of the COVID-19 pandemic.
Dercum’s Disease: Estimating the prevalence of a rare painful loose connective tissue disease
Authors: Munguia Natalie Corina , Mozayeni B. Robert , Wright Thomas , Herbst Karen L.
Published: June 2020

Background
In the United States (US), the Orphan Drug Act of 1983 defines a rare disease as affecting less than 200,000 individuals. In Europe, a rare disease or disorder is defined as affecting 5 individuals in 10,000 which the European commission reports to be approximately 246,000 individuals. Dercum’s disease, also known as Adiposis Dolorosa, is a rare loose connective (fat) tissue disease that is characterized by painful lipomas (fatty masses). Orphanet, the National Organization for Rare Disease (NORD) and the United States National Institutes of Health (NIH) have classified Dercum’s disease as a rare disorder. The prevalence of Dercum’s disease is not well studied or understood. The objective of this paper is to estimate the prevalence of Dercum’s disease, whether it is in fact a rare disease, and increase awareness for this painful disease.
Results
An in-depth literature review was conducted in PubMed, the UK Biobank, the U.S. Agency for Health Research and Quality Healthcare Cost and Utilization, by incidence of disease in medical practice, in social media forums and by internet search in order to understand, estimate and determine the prevalence of Dercum’s disease. The prevalence of Dercum’s disease was found to range from 150 to 150,000 in the US population.
Conclusion
The data collected in this paper meet the requirements of the Orphan Drug Act which requires 200,000 individuals or less to be affected by a disorder for it to be classified as rare. These conclusions may apply to Europe as supporting data was utilized from both Sweden and the UK. Further research must be conducted to better understand subclassifications of this rare disorder.
Correcting the baseline drift without human knowledge
Authors: Liu Yuanjie
Published: June 2020

Baseline drift occurs universally in many sorts of analytical chemistry data, such as in MALDI-TOF, Raman, infrared and XRD spectra. In the era of big data, automatic correcting methods are eagerly demanded. However, traditional baseline correction methods are impossible to execute fully automatically. They always depend on some preset parameters. To build parameter-free methods, utilizing current intelligent algorithms is the best choice. However, it is a great challenge to provide a huge number of labeled samples which are required for effective training. In this article, a novel strategy has been developed to train a deep neural network successfully for baseline correction. The impossible mission of preparing millions of manually processed training samples was avoided. Under the new scheme, the power of deep learning was freely applied to achieve straightforward full automation in baseline recognition. Numerical experiments on authentic datasets indicated that the new intelligent model outperformed traditional methods.
Clinical Impact of Hypofractionated Carbon Ion Radiotherapy on Locally Advanced Hepatocellular Carcinoma
Authors: Shiba Shintaro , Shibuya Kei , Okamoto Masahiko , Okazaki Shohei , Komatsu Shuichiro , Kubota Yoshiki , Nakano Takashi , Ohno Tatsuya
Published: June 2020

Background
Hepatocellular carcinoma (HCC) involving a major branch of the portal or hepatic vein is in a locally advanced stage and remains difficult to cure. This study aimed to evaluate the clinical effects of carbon ion radiotherapy (C-ion RT) in locally advanced HCC (LAHCC).
Methods
Consecutive 11 patients with LAHCC who received C-ion RT were analyzed. The C-ion RT doses of 52.8 Gy (relative biological effectiveness [RBE]) and 60.0 Gy (RBE) were delivered in four fractions for standard cases and the 60.0 Gy dose was delivered in 12 fractions for close-to-gastrointestinal-tract cases. Survival and local control probabilities were calculated using the Kaplan-Meier method.
Results
The median follow-up duration after C-ion RT was 36.4 months. The median age at the time of registration of C-ion RT was 76 years. The median tumor size was 53 mm. The number of treatment-naïve and recurrent HCC patients was 1 and 10, respectively. Direct invasion of the major branch of the portal vein, hepatic vein, or both the portal and hepatic veins was observed in three, five, and three patients, respectively. The 3-year overall survival, local control, and progression-free survival rates were 64%, 78%, and 18%, respectively. No patient developed radiation-induced liver diseases or grade 3 or higher toxicities of acute and late phases.
Conclusions
C-ion RT showed favorable clinical outcomes with a high rate of local control and minimal toxicities in LAHCC. Our findings suggest that C-ion RT is a promising multidisciplinary treatment option in LAHCC.
Spike protein modeling and single amino acid variant analysis might suggest reduced transmitability of SARS-CoV-2 in Jordan, Middle East
Authors: Al-Zyoud Walid , Haddad Hazem
Published: June 2020

Spike protein (approx. 180 kDa) is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the interaction of the virus with human endothelial cell receptors on the cell membrane to be engulfed causing COVID-19 disease after binding with the angiotensin-converting enzyme 2 (ACE2) with an evident activation by type II transmembrane protease TMPRSS2 . Therefore, mutations and amino acid variants analysis are essential in characterizing the mechanism of binding of spike protein with its receptor, which totally gives insights on possibilities to design a peptide or nucleotide-based vaccine for COVID-19. Here, we employed Iterative Threading Assembly Refinement (I-TASSER) and Multiple Alignment using Fast Fourier Transform (MAFFT) to predict the three-dimensional structure and to analyze the amino acid variants for spike protein sequences of SARS-CoV-2 from GISAID database of samples collected from Jordan to try to find a justification for low number of confirmed COVID-19 in Jordan, Middle East. Our findings showed the molecules structurally close to the spike glycoprotein from the Enzyme Commission (EC) numbers and active sites included Isoleucyl-tRNA synthetase, Crystal structure of the tricorn protease (hydrolase); Crystal structure of the T. Thermophilus RNA polymerase holoenzyme (transferase); Crystal structure of the complex between pyruvate-ferredoxin oxidoreductase from Desulfovibrio africanus and pyruvate (oxidoreductase); and Reovirus core (virus). Our MAFFT findings showed that Four Amino Acid Variants (SAV) founded in 20 samples of SARS-CoV-2 were not conserved residues in spike glycoprotein. What is equal to 5% of samples showed tyrosine (polar) deletion at Y144 , 62% of samples showed aspartate (polar, acidic) substitution to glycine (nonpolar) at D614G, 5% of samples showed aspartate (polar, acidic) substitution to tyrosine (polar) at D1139Y and 5% of samples showed glycine (nonpolar) substitution to serine (polar) at G1167S respectively. By using Phyre2, our findings have shown lower sensitive mutational that cannot affect the pocket region or alpha and beta-sheet in all mutations except for D614G, which has the highest mutational sensitivity score (5 out of 9) indicating a bigger effect on the function of spike protein. This might suggest, in general, a reduced transmitability of SARS-CoV-2 in Jordan, Middle East. As the crystal structure of spike protein is not revealed yet, it was not possible to compare the predicted modes versus each other.
The relation between ACEI/ARB use and COVID-19 severity in RT-PCR–confirmed cases: A retrospective case-control study
Authors: Amaouche Sabrina , Letaief Ziad , Buls Nico , Allard Sabine , Mey Johan de
Published: June 2020

One hypothesis suggests that patients undergoing Angiotensin Converting Enzyme inhibitor (ACEI) or Angitensin Receptor Blocker (ARB) treatment might be at greater risk for severe COVID-19 disease. This retrospective study aims to elucidate whether patients with reverse transcription-polymerase chain reaction (RT-PCR)–confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection undergoing ACEI or ARB treatment present with a more severe clinical presentation or more severe lung injury than other patients, as evaluated by CT thorax scans. Comorbidities related to ACEI or ARB use, including arterial hypertension (AHT), heart disease (HD), and diabetes mellitus (DM), were found to be more frequent (p < 0.05 ) in the ACEI or ARB users’ group. The odds ratio of ACEI or ARB users for having a more severe clinical presentation was 1.12 (95% [CI] 0.59–2.13, p = 0.741). For having a severe CT severity score (with a cut-off of 12.5 on a total score of 25), the odds ratio was 1.46 (95% [CI] 0.73–2.94, p = 0.287). Furthermore, the odds ratio of the mortality outcome was 1.1 (95% [CI] 0.49–2.48, p = 0.824). Although the group of ACEI or ARB users had more comorbidities, we found no significant association between CT severity, clinical severity, or mortality and the use of these drugs. These findings bolster the argument against ACEI or ARB withdrawal in COVID-19 patients.
Computational approach for the design of potential spike protein binding natural compounds in SARS- CoV2
Authors: Basu Anamika , Sarkar Anasua , Maulik Ujjwal
Published: June 2020

Angiotensin converting enzyme 2 (ACE2) (EC:3.4.17.23) is a transmembrane protein which is considered as receptor for spike protein binding of novel coronavirus (SARS-CoV2). Since no specific medication is available to treat COVID-19, designing of new drug is important and essential. In this regard, in silico method plays an important role as it is rapid, cost effective, compared to the trial and error methods using experimental studies. Natural products are safe and easily available to treat coronavirus effected patients, in the present alarming situation. In this paper five phytochemicals which belong to flavonoid and anthraquinone subclass, selected as small molecules in molecular docking study of spike protein of SARS-CoV2 with its human receptor ACE2 molecule. From the detail analysis of their molecular binding site on spike protein binding site with its receptor, hesperidin, emodin and chrysin are selected as competent natural products from both Indian and Chinese medicinal plants, to treat COVID-19.
TAŞINMAZ ÜZERİNDE GERİ ALIM HAKKI
Authors: GÜZEL Pınar
Published: June 2020

Özel hukukta geri alım hakkı, malike sattığı malı belirli koşullar ve bir bedel karşılığında tek taraflı irade beyanı ile geri alabilmesi imkânını bahşeden yenilik doğurucu bir haktır. Söz konusu bu hak Türk hukukunda özellikle taşınmaz mallar açısından önem arz eder. Geri alım hakkı çoğunlukla sözleşme ile doğar ve satış sözleşmesinin içinde, bir yan anlaşma olarak veya bir ek anlaşma olarak öngörülebilir. Türk Medenî Kanunu’nda ve Türk Borçlar Kanunu’nda taşınmazları konu edinen geri alım hakkını kuran sözleşmenin geçerliliğinin resmî şekilde kurulmasına bağlı olduğu ve geri alım hakkının azamî on yıl için kurulabileceği düzenlenmektedir. Geri alım hakkı bir nispî hak olup, Türk Medenî Kanunu uyarınca tapu siciline şerh edilebilir. Şerh edilmiş geri alım hakkı taşınmaz üzerinde şerhten sonra aynî hak iktisap eden kişilere karşı da ileri sürülebilir. Geri alım hakkı, uygulamada çoğunlukla teminat fonksiyonu icra etmektedir ve kanunda açıkça yer verilmiş bir hak olması sebebiyle lex commissoria yasağını ihlâl etmediği kabul edilmektedir.
ESKİ VAKIFLARDA TOPRAK MÜLKİYETİNDEN DOĞAN SORUNLARIN GÜNÜMÜZE YANSIYAN BİÇİMLERİ: TAVİZ BEDELİ
Authors: ÇAK Murat , ÇAK Demet
Published: June 2020

743 sayılı Türk Kanuni Medenisinin yürürlüğe girmesinden önce kurulmuş bulunan vakıfların, Vakıflar Genel Müdürlüğü tarafından temsil ve idare edilenlerine mazbut vakıflar adı verilmektedir. Mazbut vakıflar, mülk sayılan arazilerin ve bunlardan elde edilen gelirlerin insanlığın hayrına olacak şekilde vakfa bağışlanmasıyla oluşturulabildiği gibi; miri arazilerden bir kısmının vergi ve sair gelirlerinin hayır şartına vakfedilmesiyle de kurulabilmekteydi. Bunlardan ilki sahih vakıfları meydana getirirken, ikincisi ise gayrisahih vakıfları oluşturmaktadır. Günümüzde ise sahih mazbut vakıflara ait, mukataa ve icareteyn usulleriyle kiraya verilen arazilerin şahıslar veya kurumlar adına serbest tasarrufa geçirilmesi esnasında 5737 sayılı Vakıflar Kanunu’nun 18. maddesi uyarınca taviz bedeli adı altında, taşınmazın emlak vergisi değerinin %10’una denk bir bedel tahsil edilmektedir. Taviz bedeli tahsilatı, şahıslar ve kurumlarla, Vakıflar Genel Müdürlüğü arasında ihtilafa neden olmakta ve bu ihtilaf yargı mercilerinde çözüme kavuşturulmaktadır. Bu çalışmamızda kökeninde Selçuklu ve Osmanlı Devletlerinin toprak sistemlerindeki arazi çeşitleriyle mülkiyet esaslarının yer aldığı taviz bedeli sorununun, yargı aşamasında çözümünde izlenecek yöntem ele alınmaktadır.
Hacia la construcción interdisciplinaria de una antropología del dolor en perspectiva franciscana
Authors: Sánchez Sánches Luis Fernando , Alzate Mejía Nicolás Alberto , Arbeláez Castaño Enrique León , Zapata Muriel Fernando Antonio , Benítez Arias Luis Fernando
Published: June 2020

El propósito general de este trabajo investigativo ha sido realizar un estudio sistemático en torno al sentido del dolor en perspectiva interdisciplinaria, con el fin de hacer aproximaciones a una nueva visión que favorezca el significado del dolor. Se presenta la validez y la vigencia de la mirada evangélica del dolor en Francisco de Asís a través de un estudio hermenéutico y de análisis documental. Discusión: el dolor nos hace tomar conciencia de nuestro existir en el mundo, de la individualidad, de los límites y de la corporeidad. Todo ser humano ha experimentado alguna vez el dolor, por ello se afirma que es algo inherente e intrínseco a la condición humana, aunque no se apetezca, no se busque, se le quiera huir o evadir, a pesar de ser, en algunos casos, algo inevitable. El método a seguir es el documental, guiado por la hermenéutica, con el fin de congregar las diversas verdades construidas desde las diferentes disciplinas que acuden al estudio de este tópico. Conclusión: el dolor no se puede reducir a un hecho neurológico ni orgánico exclusivamente. El dolor humano requiere de un tratamiento interdisciplinar si lo que se busca es aportar un valor antropológico en favor de una mirada integral con la que se reconozca el aporte de múltiples intencionalidades epistemológicas y de las ciencias humanas que acuden al estudio del dolor.
Bone Marrow Culture Yield for the Diagnosis of Opportunistic Diseases in Patients with AIDS and Disseminated Kaposi Sarcoma
Authors: Cornejo-Juárez P. , Islas-Muñoz B. , Ramírez-Ibargüen A.F. , Rosales-Pedraza G. , Chávez-Mazari B. , Martínez-Orozco A. , Volkow-Fernández P.
Published: June 2020

Background:

Disseminated Kaposi sarcoma (DKS) is present in patients with advanced HIV infection in whom co-infection with other opportunistic pathogens can occur. Bone marrow (BM) aspirate and biopsy comprises a robust diagnostic tool in patients with fever, cytopenias, and abnormal liver tests. However, the yield in patients with DKS has not been determined.

Objective:

The aim of this study was to evaluate the utility of BM aspirate and biopsy in patients with DKS.

Methods:

We included 40 male patients with recent diagnosis of DKS. BM aspirate and biopsy was performed as part of the workup to rule out co-infections.

Results:

In four patients, Mycobacterium avium complex (MAC) was recovered from culture. In another four patients, intracellular yeasts were observed in the Grocott stain, diagnosed as Histoplasma. The yield of BM was calculated in 20%. Only 12 patients (30%) had fever and 11 (27.5%) had pancytopenia. Alkaline phosphatase (ALP) above normal values and C-reactive protein (CRP) were higher in patients with positive results for BM than in those with negative results (63% vs. 21.9%, and 3.0 vs. 1.2 mg/L; p = 0.03 in both comparisons). No differences were found on comparing complete blood-count abnormalities.

Conclusion:

We recommend performing a BM aspirate for stains, culture, and biopsy in all HIV patients with DKS, as this will permit the early diagnosis of co-infections and prevent further complications in those who receive chemotherapy.
Agrochemicals Residues in Human Milk, Scientific Evidence or Overestimated Risk?
Authors: Raimundo Rodrigo D. , da Silva Tamara M. , Ferreira Amanda V. , Santos Bárbara S. , Carvalho Tatiana D. , Fonseca Ricardo L.A. , da Silva Odair R. , Castanha Cyntia S.C. , Daboin Blanca E.G. , Fonseca Fernando L.A.
Published: June 2020

Background:

Exposures to agrochemicals can be directly through the handling of
chemicals as well as indirectly when consuming food containing residues of them. Such exposure
may affect the health of the population if accumulated in the human body, including in human milk.

Objective:

This literature review aims to assess the potential impact of agrochemical residues in human
milk as a barrier to breastfeeding.

Methods:

The search followed PRISMA guidelines (Preferred Reporting Items for Systematic Reviews
and Meta Analyses), by selecting original articles published between 1995 and 2019, extracted
from the free access databases PubMed, Scielo, Web of Sciences and Scopus using as keywords: agrochemicals,
pesticides, breastfeeding, human milk, contamination and infant. Medical Subject Headings
(MeSH) were used as descriptors.

Results:

We selected 11 studies. Taking as inclusion criteria those most aligned with the objective of
our study.

Conclusion:

The studies presented in this review ratified the benefits of breastfeeding compensating
for the potential risks of agrochemical residues in human milk.
Liver Cirrhosis Complications Management at the Emergency Department
Authors: Scarpellini Emidio , Luigiano Carmelo , Svegliati-Baroni Gianluca , Dumitrascu Dan , Larussa Tiziana , Santori Valeria , Luzza Francesco , Abenavoli Ludovico
Published: June 2020

Background and Aims:

Liver cirrhosis (LC) of any origin has always been a source of
several emergencies for physicians working at the Emergency Department (ER). LC patients can
present with several complications that are sometimes difficult to recognize and treat.

Thus, we reviewed the literature evidence for the diagnosis and management of several LC related
emergencies.

Methods:

We conducted a search on the main medical databases for papers, reviews, metanalyses,
case series, and RCTs using the following keywords and their associations: liver cirrhosis, variceal
hemorrhage, ascites, hepatic encephalopathy, spontaneous bacterial peritonitis, hepato-renal syndrome,
emergency.

Results:

Main LC emergencies are upper gastrointestinal hemorrhage, decompensated ascites and
spontaneous bacterial peritonitis, hepatic encephalopathy, hepato-renal syndrome. Their management
is partly medical and interventional. Very often, the final cure of some complications, such as
hepato-renal syndrome, is represented by liver transplantation.

Conclusions:

Although LC prevalence is going to fall in the following years, due to HBV and HCV
optimized treatments, its complications represent a significant admission percentage at the ER and
challenge for physicians’ skills.
Topiramate Decelerates Bicarbonate-Driven Acid-Elimination of Human Neocortical Neurons: Strategic Significance for its Antiepileptic, Antimigraine and Neuroprotective Properties
Authors: Bonnet Udo , Wiemann Martin
Published: June 2020

Background:

Mammalian central neurons regulate their intracellular pH (pHi) strongly and even slight pHi-fluctuations
can influence inter-/intracellular signaling, synaptic plasticity and excitability.

Objective:

For the first time, we investigated topiramate´s (TPM) influence on pHi- behavior of human central neurons representing a
promising target for anticonvulsants and antimigraine drugs.

Methods:

In slice-preparations of tissue resected from the middle temporal gyrus of five adults with intractable temporal lobe epilepsy, BCECF-AM-loaded neocortical pyramidal-cells were investigated fluometrically. The pHi-regulation was estimated by using the
recovery-slope from intracellular acidification after an ammonium-prepulse (APP).

Results:

Among 17 pyramidal neurons exposed to 50 µM TPM, seven (41.24%) responded with an altered resting-pHi (7.02±0.12),
i.e. acidification of 0.01-0.03 pH- units. The more alkaline the neurons, the greater the TPM-related acidifications (r=0.7, p=0.001,
n=17). The recovery from APP-acidification was significantly slowed under TPM (p<0.001, n=5). Further experiments using nominal
bicarbonate-free (n=2) and chloride-free (n=2) conditions pointed to a modulation of HCO3(-)-driven pHi-regulation by TPM, favoring the stimulation of the passive Cl(-)/HCO3(-)- antiporter (CBT) - an acid-loader predominantly in more alkaline neurons.

Conclusion:

TPM modulated the bicarbonate-driven pHi-regulation just as previously described in adult guinea-pig hippocampal
neurons. We discussed the significance of the resulting subtle acidifications for beneficial antiepileptic, antimigraine and neuroprotective effects as well as for unwanted cognitive deficits.
Study Limitations: Although these results are the only available pHi-measurements of human brain neurons to this issue, to the best
of our knowledge, the study is limited by the small number of cells analyzed due to limited human material. Thus, the results presented here are preliminary data. Greater sample size is required to reach more reliable conclusions.”
The Role of Interferences in the Increasing Incidence of Vitamin D Deficiency
Authors: Gonel Ataman , Kirhan Idris , Koyuncu Ismail , Bayraktar Nihayet , Karadag Mujgan Ercan , Karadag Mehmet
Published: June 2020

Objective:

Lipemia is one of the causes of interference in immunoassay and LC-MS/MS
methods. Increased prevalence of vitamin D deficiency in the US, where obesity is gradually increasing,
raises the suspicion that high levels of fat diet and blood lipid levels interfere with vitamin D
measurement results. The focus of this study was to investigate the effect of blood lipid profiles on
vitamin D results and prevent the matrix effect.

Material and Methods:

In this study, 25OH vitamin D3 (25OHD3) levels of 100 samples consecutively
accepted to biochemistry laboratory regardless of age and sex were measured by the LC-MS/MS
method, and each sample was restudied after 1/10 dilution. After dilution restudy, two groups were
obtained-group 1 (results deviating below 20%) and group 2 (results deviating above 20%)—and the
difference between the groups was investigated. There were 79 patients in group 1 and 21 patients in
group 2. In our study, lipid profiles (triglyceride, total cholesterol, HDL, LDL) from the same samples
of consecutive vitamin D patients were studied.

Results:

It was observed that the triglyceride, total cholesterol HDL, LDL, and 25OHD3 measurements
of group 1 and group 2 were similar (p > 0.05). While the mean vitamin D value in the second
group was 9.94 ± 7.85, the mean vitamin D value after dilution was measured as 39.23 ± 18.13 and
was statistically significant. 25OHD3 concentrations of 21 patients out of 100 were found to be falsely
low. Measurements were repeated to confirm the results.

Conclusion:

The matrix effect caused by exogenous and endogenous interferences in the blood could
be a hidden factor increasing the prevalence of vitamin D deficiency by causing falsely low 25OHD3
values. Suspicious results should be remeasured by a dilution study.
Legal Issues and Challenges in Managing Kuala Lumpur as a Tourism Destination: A case study of the Silang Street
Authors: Sulaiman Siti Sarah , Rahmat Nur Ezan , Azizun Najwa
Published: June 2020

Kuala Lumpur is a historical city with heritage significance for tourism destination. However, the heritage significance of the city may be challenged by several issues. One of which is the number of immigrants who have manipulated business activities in the busy street which is known as Silang Street. The issue of immigrants at Silang Street is not only on the matter of licence to operate business, but also involved the immigration aspect. This paper highlights the challenges faced by the stakeholders in regulating business activities conducted by the immigrants at Silang Street and possible improvements are suggested.   
Keywords: heritage; Kuala Lumpur; legal issues; tourism destination.   
eISSN: 2398-4287 © 2020. The Authors. Published for AMER ABRA cE-Bs by e-International Publishing House, Ltd., UK. This is an open access article under the CC BYNC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer–review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians) and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Malaysia.   DOI: https://doi.org/10.21834/ebpj.v5iSI1.2321
Securing Proprietary Rights for Buyers of Unascertained Fungible Goods in a Bulk in Malaysia
Authors: Chuah John  Chong Oon , Khalid Azlena
Published: June 2020

The research aims to ascertain the most effective methods to protect the rights of buyers of unascertained fungible goods who have paid under a contract of sale subject to the Malaysian Sale of Goods Act 1957. The research method is doctrinal. The findings reveal that in the event the seller becomes insolvent, the buyer as unsecured creditors would need to compete with the other creditors for the price of the goods. The trust device and the adoption of section 20A and 20B of the English Sale of Goods Act 1979 could provide adequate protection by conferring proprietary rights to buyers.   
Keywords: Contract; Sale of unascertained goods; Proprietary rights; Trusts.   
eISSN: 2398-4287 © 2020. The Authors. Published for AMER ABRA cE-Bs by e-International Publishing House, Ltd., UK. This is an open access article under the CC BYNC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer–review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians) and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Malaysia.   DOI: https://doi.org/10.21834/ebpj.v5iSI1.2323
Exploring the Determinant Factors of Food Related Fatwa Issuances based on ‘Urf
Authors: Ruzulan Zulaipa , Ab Rahman Suhaimi , Saidon Rafeah , Fathullah Harun Hanifah Musa
Published: June 2020

There are queries on the halal status of food among Muslim consumers due to the accessibility of halal knowledge via mass media, and this needs for the jurists’ clarification (fatwa). Thus, this paper seeks to examine the determinant factors of fatwa’s decisions on food-related issues based on the approach of ‘urf. A qualitative approach which involved document analysis technique was applied from various authoritative sources. Furthermore, content analysis and constant comparative methods were used to analyze the data. This study will assist policymakers in dealing with food-related issues and help the public in identifying the rationale of the fatwa’s decisions.   
Keywords: Fatwa; halal food; istiṭābah; ‘urf.   
eISSN: 2398-4287 © 2020. The Authors. Published for AMER ABRA cE-Bs by e-International Publishing House, Ltd., UK. This is an open access article under the CC BYNC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer–review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians) and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Malaysia.   DOI: https://doi.org/10.21834/ebpj.v5iSI1.2325