bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of gene amplifications related to drug resistance in Plasmodium falciparum using droplet digital PCR
Authors: Srisut Suttipat , Suwannasin Kanokon , Sugaram Rungirun , Dondorp Arjen M. , Imwong Mallika 
Published: November 2020

Abstract
Background: Copy number variations (CNVs) of the Plasmodium falciparum multidrug resistance 1 (pfmdr1), P. falciparum pfplasmepsin2 (pfplasmepsin2) and P. falciparum GTP cyclohydrolase 1 (pfgch1) genes are associated with antimalarial drug resistance in P. falciparum malaria. Droplet digital PCR (ddPCR) assays have been developed for accurate assessment of CNVs in several human genes. The aim of the present study was to develop and validate ddPCR assays for detection of the CNVs of P. falciparum genes associated with resistance to antimalarial drugs.Methods: The ddPCR assays were developed to detect the CNVs in the pfmdr1, pfplasmepsin2 and pfgch1 genes. The gene copy number (GCN) quantification limit, as well as the accuracy and precision of the ddPCR assays were determined and compared to conventional quantitative PCR (qPCR). In addition, the CNVs of genes of field samples collected from Thailand from 2015 to 2019 (n = 84) were assessed by ddPCR and results were compared to qPCR as the reference assay.Results: Based on the obtained gene copy number quantification limit, the accuracy and percent relative standard deviation (%RSD) value of the multiplex ddPCR assay were 95% and 5%, respectively, for detection of the CNV of the pfmdr1 gene, and 91% and 5% for detection of the CNV of the pfplasmepsin2 gene. The accuracy and %RSD value of the duplex ddPCR assay were 94.88% and 3.71, respectively, regarding pfgch1 GCN. In the P. falciparum field samples, pfmdr1 and pfplasmepsin2 GCNs were amplified in 15% and 27% of samples from Ubon Ratchathani, Thailand, while pfgch1 GCN was amplified in 50% of samples from Yala, Thailand. There was 100% agreement between the GCN results obtained from the ddPCR and qPCR assays (κ = 1.00). Conclusions: The developed ddPCR assays are simple, accurate, precise and cost-effective tools for detection of the CNVs in the pfmdr1, pfplasmepsin2 and pfgch1 genes of P. falciparum. The ddPCR assay is a useful additional tool for the surveillance of antimalarial drug resistance.
LINC00460 / DHX9/IGF2BP2 complex promotes colorectal cancer proliferation and metastasis by mediating HMGA1 mRNA stability depending on m6A modification
Authors: Hou Pingfu , Meng Sen , Li Minle , Lin Tian , Chu Sufang , Li Zhongwei , Zheng Junnian , Gu Yuming , Bai Jin 
Published: November 2020

Abstract
Background: Increasing studies have shown that long noncoding RNAs (lncRNAs) are pivotal regulators participating in carcinogenic progression and tumor metastasis in colorectal cancer (CRC). Although lncRNA long intergenic noncoding RNA 460 (LINC00460) has been reported in CRC, the role and molecular mechanism of LINC00460 in CRC progression still requires exploration.Methods: The expression levels of LINC00460 were analyzed by using a tissue microarray containing 498 CRC tissues and their corresponding non-tumor adjacent tissues. The correlations between the LINC00460 expression level and clinicopathological features were evaluated. The functional characterization of the role and molecular mechanism of LINC00460 in CRC was investigated through a series of in vitro and in vivo experiments.Results: LINC00460 expression was increased in human CRC, and high LINC00460 expression was correlated with poor five-year overall survival and disease-free survival. LINC00460 overexpression sufficiently induced the epithelial–mesenchymal transition and promoted tumor cell proliferation, migration, and invasion in vitro and tumor growth and metastasis in vivo. In addition, LINC00460 enhanced the protein expression of high-mobility group AT-hook 1 (HMGA1) by directly interacting with IGF2BP2 and DHX9 to bind the 3′ untranslated region (UTR) of HMGA1 mRNA and increased the stability of HMGA1 mRNA. In addition, the N6-methyladenosine (m6A) modification of HMGA1 mRNA by METTL3 enhanced HMGA1 expression in CRC. Finally, it suggested that HMGA1 was essential for LINCC046-induced cell proliferation, migration, and invasion.Conclusions: LINC00460 may be a novel oncogene of CRC through interacting with IGF2BP2 and DHX9 and bind to the m6A modified HMGA1 mRNA to enhance the HMGA1 mRNA stability. LINC00460 can serve as a promising predictive biomarker for the diagnosis and prognosis among patients with CRC.
Spatio-Temporal Variability and Trend of Rainfall and Its Association with Pacific Ocean Sea Surface Temperature in West Harerge Zone, Eastern Ethiopia
Authors: Tiruneh Getachew Bayable , Amare Gedamu , Alemu Getnet , Gashaw Temesgen 
Published: November 2020

Abstract
Background: Rainfall variability is a common characteristic in Ethiopia and it exceedingly affects agriculture particularly in the eastern parts of the country where rainfall is relatively scarce. Hence, understanding the spatio-temporal variability of rainfall is indispensable for planning mitigation measures during high and low rainfall seasons. This study examined the spatio-temporal variability and trends of rainfall in the West Harerge Zone, eastern Ethiopia.Method: The coefficient of variation (CV) and standardized anomaly index (SAI) was employed to analyze rainfall variability while Mann-Kendall (MK) trend test and Sen’s slop estimator were employed to examine the trend and magnitude of the rainfall changes, respectively. The association between rainfall and Pacific Ocean Sea Surface Temperature (SST) was also evaluated by the Pearson correlation coefficient (r).Results: The annual rainfall CV ranges from 12-19.36% while the seasonal rainfall CV extends from 15-28.49%, 24-35.58%, and 38-75.9% for average Kiremt (June-September), Belg (February-May), and Bega (October-January) seasons, respectively (1983-2019). On the monthly basis, the trends of rainfall decreased in all months except in July, October, and November. However, the trends of rainfall were not statistically significant (α = 0.05), unlike November. The annual rainfall trends showed a non-significant decreasing trend. On a seasonal basis, the trend of mean Kiremt and Belg seasons rainfall was decreased. But, it increased in Bega season although it was not statistically significant. Moreover, the correlation between rainfall and Pacific Ocean SST was negative for Kiremt while positive for Belg and Bega seasons. Besides, the correlation between rainfall and Pacific Ocean SST was negative at annual time scales.Conclusions: High spatial and temporal rainfall variability on monthly, seasonal, and annual time scales was observed in the study area. Seasonal rainfall has high inter-annual variability in the dry season (Bega) than other seasons. The trends in rainfall were decreased in most of the months. Besides, the trend of rainfall was increased annually and in the Bega season rather than other seasons. Generally, the occurrence of droughts in the study area was associated with ENSO events like most other parts of Ethiopia and East Africa.
Emotional impact of health personnel, medical students, and general population samples during COVID-19 pandemic in Lima, Peru: A cross-sectional study.
Authors: Pedraz-Petrozzi Bruno , Krüger-Malpartida Hever , Arevalo-Flores Martin , Salmavides-Cuba Frine , Anculle-Arauco Victor , Dancuart-Mendoza Mauricio 
Published: November 2020

Abstract
Background: Negative emotional effects were reported in different groups since the beginning of the COVID-19 pandemic. However, few studies compare those groups regarding the emotional effects of the COVID-19. To this end, this study's main objective is to compare the emotional effects of the COVID-19 between three different groups, namely health personnel, medical students, and the general population sample.Methods: We recruited 375 participants for this study, of which 125 were medical students (preclinical studies = 59, clinical studies = 66), 125 were health personnel (COVID-19 first-line personnel = 59, personnel not related with COVID-19 = 66), and 125 belonged to the general population. PHQ-9 (depression), GAD-7 (anxiety), and CPDI (COVID-19 related stress) were assessed to measure the emotional impact. A multinomial logistic regression was carried out to measure differences between groups, considering possible confounding factors. Results: Regarding CPDI values, all other groups showed reduced CPDI values compared to COVID-19 first-line personnel. However, the general population, preclinical medical students, and clinical medical students showed increased PHQ-9 values compared to COVID-19 first-line personnel. Finally, confounder factors, gender and age, correlated negatively with higher CPDI and PHQ-9 scores. Conclusions: Being COVID-19 first-line personnel is associated with more stress related to COVID-19. Depression is associated, however, with other groups not directly involved with the treatment of COVID-19 patients. Female and younger age participants correlated with depression and stress related to COVID-19.
Stunted Toddler in Eastern Indonesia
Authors: Laksono Agung Dwi , Wulandari Ratna Dwi 
Published: November 2020

Abstract
Background: Eastern is one of the regions that have a higher prevalence rate of stunted children than other regions in Indonesia. The study aims to analyze the risk factors for stunted toddlers in Eastern Indonesia.Methods: The study employed secondary data from the 2017 Indonesia Nutritional Status Monitoring. With the multi-stage cluster random sampling method, 24,103 toddlers in eastern Indonesia were sampled. Data were analyzed using a multinomial logistic regression test.Results: The results of the study found that toddlers living in urban areas had a 0.798 times chance compared to toddlers living in rural areas to experience severe stunted (OR 0.798; 95% CI 0.719-0.885). A toddler with a married mother is 0.706 times more likely than a toddler with a divorced/widowed mother to experience severe stunted (OR 0.706; 95% CI 0.547-0.911). The results of this multivariate analysis indicate that the better the level of education of a mother, the less likely it is to have stunted and severely stunted toddlers. Meanwhile, the analysis also found that toddler's age is a determinant of stunted and severe stunted toddlers.Conclusion: It concluded that 4 factors were found as risk factors for stunted toddlers in Eastern Indonesia. The four factors are living in rural areas, having a divorced/widowed mother, poor education, and a toddler's age.
Geographic information system methods tell spatiotemporal transmission and its drivers of COVID-19 in Wuhan, China at street-level
Authors: Liu Wei , Wang Wongming , Hua Shuiqiong , Xie Cong , Wang Bin , Qiu Weihong , Xu Tao , Ye Zi , Yu Linling , Yang Meng , Xiao Yang , Feng Xiaobing , Shi Tingming , Li Mingyan , Chen Weihong 
Published: November 2020

Abstract
Background: No study has revealed spatial transmission characteristics of COVID-19 in Wuhan, China. We aimed to analyze the spatiotemporal spread of COVID-19 in Wuhan and its influence factors.Methods: Information of 32,682 COVID-19 cases reported through March 18 were extracted from the national infectious disease surveillance system. Geographic information system methods were applied to analysis transmission of COVID-19 and its influence factors in different periods.Results: We found decrease in effective reproduction number (Rt) and COVID-19 related indicators through taking a series of effective public health measures including restricting traffic, centralized quarantine and strict stay-at home policy. The distribution of COVID-19 cases number in Wuhan showed an obvious global aggregation and a local aggregation in central urban areas, but such aggregations was decreased in the later period of the epidemic. In addition, the analysis at streets-level suggested population density and the number of hospitals were influence factors of spatial difference.Conclusions: The epidemic situation showed obvious global and local spatial aggregations. High population density and directional flow of the Population to hospitals may account for the aggregations. Strong quarantine measures and restrictions on movement of residents in Wuhan make the epidemic under control in a short time.
Time and the etiology of Acute Kidney Injury define prognosis in the course of COVID-19
Authors: Murt Ahmet , Dincer Mevlut Tamer , Karaca Cebrail , Trabulus Sinan , Karaali Ridvan , Balkan Ilker Inanc , Seyahi Nurhan , Altiparmak Mehmet Riza 
Published: November 2020

Abstract
Introduction Kidneys are among the affected organs in COVID-19 and there may be different etiologies resulting in acute kidney injury (AKI) in different stages of the disease. This study aimed to analyze AKI among hospitalized COVID-19 patients in relation to the time and etiologies of AKI.Materials & Methods 1056 patients who were hospitalized with COVID-19 diagnosis in our institution were retrospectively evaluated and 383 of them met the inclusion criteria. Eighty-nine patients who developed AKI were involved in the final analysis. As immunologic response is generally accepted to start with the second week of COVID-19 course, patients were classified into three groups, those who had AKI on admission, those who developed AKI in the first week and those who developed AKI starting from 7th day. Initial lymphocyte counts, creatinine levels and inflammatory markers as well as changes in these parameters were compared between the groups.Results AKI was seen in 23% of the patients and 23% of those who developed AKI died. Patients who developed AKI later had higher peak CRP and D-dimer levels with lower nadir lymphocyte counts (p=0,000, 0,004 and 0,003 respectively). Additionally, patients who died had higher initial inflammatory marker levels and lower lymphocyte counts than those who survived. Mortality of patients who had AKI on hospital admission (13%) was similar to the overall COVID-19 mortality for inpatients, however it was as high as 44% for those who developed AKI after 7th day.Conclusion Early AKI was more related to pre-renal causes and had a milder course. However, later AKIs were more related to immunologic response and had significantly higher mortality. Findings of this study suggest that AKI in COVID-19 is not of one kind. When developed, AKI should be evaluated in conjunction with the disease stage and possible etiologies.
Mathematical Understanding of Sequence Alignment and Phylogenetic Algorithms: A Comprehensive Review of Methods
Authors: Saif Rashid , Nadeem Sadia , Iftekhar Ali , Khaliq Alishba , Zia Saeeda 
Published: November 2020

Abstract
Context: Pairwise sequence alignment is one of the ways to arrange two biological sequences to identify regions of resemblance that may suggest the functional, structural, and/or evolutionary relationship (proteins or nucleic acids) between the sequences. There are two strategies in pairwise sequence alignment: Local sequence Alignment (Smith-waterman algorithm) and Global sequence Alignment (Needleman-Wunsch algorithm). In local sequence alignment, two sequences that may or may not be related are aligned to find regions of local similarities in large sequences whereas in global sequence alignment, two sequences same in length are aligned to identify conserved regions. Similarities and divergence between biological sequences identified by sequence alignment also have to be rationalized and visualized in the sense of phylogenetic trees. The phylogenetic tree construction methods are divided into distance-based and character-based methods. Evidence Acquisition: In this article, different algorithms of sequence alignment and phylogenetic tree construction were studied with examples and compared to establish the best among them to look into background of these methods for the better understanding of computational phylogenetics.Conclusions: Pairwise sequence alignment is a very important part of bioinformatics to compare biological sequences to find similarities among them. The alignment data is visualized through phylogenetic tree diagram that shows evolutionary history among organisms. Phylogenetic tree is constructed through various methods some are easier but does not provide accurate evolutionary data whereas others provide accurate evolutionary distance among organism but are computationally exhaustive.
Impact of SARS-CoV-2 on reperfusion therapies for acute ischemic stroke in Lombardy, Italy. The STROKOVID network
Authors: Pezzini Alessandro , Grassi Mario , Silvestrelli Giorgio , Locatelli Martina , Rifino Nicola , Beretta Simone , Gamba Massimo , Raimondi Elisa , Giussani Giuditta , Carimati Federico , Sangalli Davide , Corato Manuel , Gerevini Simonetta , Masciocchi Stefano , Cortinovis Matteo , Gioia Sara La , Barbieri Francesca , Mazzoleni Valentina , Pezzini Debora , Bonacina Sonia , Pilotto Andrea , Benussi Alberto , Magoni Mauro , Premi Enrico , Prelle Alessandro Cesare , Agostoni Elio Clemente , Palluzzi Fernando , De Giuli Valeria , Magherini Anna , Roccatagliata Daria Valeria , Vinciguerra Luisa , Puglisi Valentina , Fusi Laura , Xhani Rubjona , Pozzi Federico , Diamanti Susanna , Santangelo Francesco , Grampa Giampiero , Versino Maurizio , Salmaggi Andrea , Marcheselli Simona , Cavallini Anna , Giossi Alessia , Censori Bruno , Ferrarese Carlo , Ciccone Alfonso , Sessa Maria , Padovani Alessandro 
Published: November 2020

Abstract
Whether and how SARS-CoV-2 outbreak affected in-hospital acute stroke care system is still matter of debate. In the setting of the STROKOVID network, a collaborative project between the 10 centers designed as hubs for the treatment of acute stroke during SARS-CoV-2 outbreak in Lombardy, Italy, we retrospectively compared clinical features and process measures of patients with confirmed infection (COVID-19) and non-infected patients (non-COVID-19) who underwent reperfusion therapies for acute ischemic stroke. Between March 8 and April 30, 2020, 296 consecutive patients (median age, 74 [interquartile range (IQR), 62–80.75] years; males, 154 [52.0%]; 34 [11.5%] COVID-19) qualified for the analysis. Time from symptoms onset to treatment was longer in the COVID-19 group (230 [IQR, 200.5–270] minutes vs 190 [IQR, 150–245] minutes; p=0.007), especially in the first half of the study period. Patients with COVID-19 who underwent endovascular thrombectomy had more frequently absent collaterals or collaterals filling ≤50% of the occluded territory (50.0% vs 16.6%; OR, 5.05; 95% CI, 1.82–13.80) and a lower rate of good/complete recanalization of the primary arterial occlusive lesion (55.6% vs 81.0%; OR, 0.29; 95% CI, 0.10–0.80). Post-procedural intracranial hemorrhages were more frequent (35.3% vs 19.5%; OR, 2.24; 95% CI, 1.04-4.83) and outcome was worse among COVID-19 patients (in-hospital death, 38.2% vs 8.8%; OR, 6.43; 95% CI, 2.85-14.50). Our findings showed longer delays in the intra-hospital management of acute ischemic stroke in COVID-19 patients, especially in the early phase of the outbreak, that likely impacted patients outcome and should be the target of future interventions.
A systematic review of injectable corticosteroid for osteoarthritis of the first metatarsophalangeal joint&nbsp;
Authors: Reilly Ian , Bromley Gillian , Flanagan George 
Published: November 2020

Abstract
Intra articular steroid injection is a common treatment modality for relief of pain and inflammation associated with degenerative joint disease. Use of injectable steroid preparations is widely accepted as safe and effective for the treatment of osteoarthritis of the 1st metatarsophalangeal joint. Despite the frequency of use, literature specific to pathology of the 1st metatarsophalangeal joint is sparse. The aim of this systematic review was to determine if good quality research exists to enable clinicians to adopt an evidenced based approach to corticosteroid injection of the 1st metatarsophalangeal joint. Despite the frequency of use, this review found no high quality studies that support the use of intra articular corticosteroid injection of the 1st metatarsophalangeal joint in osteoarthritis.
Consumption of melatonin supplement improves cardiovascular disease risk factors and anthropometric indices in type 2 diabetes mellitus patients: A double-blind, randomized, placebo-controlled trial
Authors: Bazyar Hadi , Javid Ahmad Zare , Behbahani Hossein Bavi , Moradi Fardin , Poode Bahman Moradi , amiri parichehr 
Published: November 2020

Abstract
Background: Diabetes mellitus is a common chronic disease. Dyslipidemia and hypertension are two complications that may develop in diabetic patients if hyperglycemia, insulin resistance, and weight gain are not controlled. This study investigated the effects of melatonin supplementation on some cardiovascular disease risk factors and anthropometric indices in patients with type 2 diabetes mellitus (T2DM).Materials and Methods: In this double-blind, randomized, placebo-controlled trial, 50 T2DM patients were randomly allocated to intervention and control groups which received two tablets of either melatonin or placebo (250 mg) once a day for eight weeks. Mean arterial pressure (MAP), pulse pressure (PP), the atherogenic index of plasma (AIP), weight, body mass index (BMI), waist and hip circumference (WC, HC), body shape index (ABSI), abdominal volume index (AVI), body adiposity index (BAI), lipid accumulation product (LAP), conicity index, and waist-to-height ratio (WHR) were evaluated in all the patients pre- and post-intervention.Results: Melatonin supplementation for eight weeks significantly decreased the mean levels of MAP, PP, weight, BMI, WC, HC, BAI, AVI, conicity index, and WHR post-intervention (p<0.05). Also, the median changes of MAP, PP, weight, BMI, WC, HC BAI, AVI, and conicity index were significantly lower in the intervention group compared with the control group (p<0.05). A significant increase (p<0.001) was observed in the mean levels of ABSI in the intervention group. The median changes of ABSI were significantly greater in the intervention group compared with the control group (p<0.001).Conclusions: Consumption of melatonin supplement may be effective in controlling arterial pressure and anthropometric indices (as predictors of obesity) in T2DM patients.Trial registration: This trial was registered in the Iranian Registry of Clinical Trials website at 2019/5/17. (IRCT20190303042905N1).
Early childhood infections, antistreptococcal and basal ganglia antibodies in adult ADHD: A preliminary study
Authors: Oliva Francesco , Girolamo Giulia di , Malandrone Francesca , Iaia Noemi , Biasi Fiorella , Maina Giuseppe 
Published: November 2020

Abstract
Background: To explore the relationship between adult Attention Deficit/ Hyperactivity Disorder (ADHD), antistreptococcal titers, ABGA, and recurrent infections during early childhood.Method: Childhood history of recurrent infections and a blood sample were collected in a sample of DSM-IV adult outpatients with ADHD. The anti-streptolysin O (ASO), anti-deoxyribonuclease B (anti-DNase B), and anti-basal ganglia antibodies (ABGA) titers were determined in patient plasma by enzyme-linked immunosorbent assay (ELISA). Titers positivity was evaluated following manufacturer's specifications. Absolute titers were also collected as continuous variables.Results: Fourteen out of 22 (63.6%) have had recurrent infections in childhood (i.e., seven, 31.8%, have had tonsillitis or adenoiditis and seven, 31.8%, have had any other infections). Eighteen patients (81.9%) were positive for anti-DNase B, five (22.7%) for ASO, and 4 (18.2%) were positive for both of them. Five participants (22.7%) were ABGA positive, whereas only two (9.1%) were positive for all three antibodies.Conclusions: patients with ADHD might be more prone to infections during childhood and subclinical streptococcal infections during adulthood. Moreover, they seem to have an increased risk for basal ganglia autoimmunity in adulthood. Both infections and the ensuing acquired autoimmunity could influence the neurodevelopmental process, by contributing, at least in part, to the ADHD pathogenesis.