Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproductive number of coronavirus: A systematic review and meta-analysis based on global level evidence

Background The coronavirus (SARS-COV-2) is now a global concern because of its higher transmission capacity and associated adverse consequences including death. The reproductive number of coronavirus provides an estimate of the possible extent of the transmission. This study aims to provide a summary reproductive number of coronavirus based on available global level evidence. Methods A total of three databases were searched on September 15, 2020: PubMed, Web of Science, and Science Direct. The searches were conducted using a pre-specified search strategy to record studies reported the reproductive number of coronavirus from its inception in December 2019. It includes keywords of coronavirus and its reproductive number, which were combined using the Boolean operators (AND, OR). Based on the included studies, we estimated a summary reproductive number by using the meta-analysis. We used narrative synthesis to explain the results of the studies where the reproductive number was reported, however, were not possible to include in the meta-analysis because of the lack of data (mostly due to confidence interval was not reported). Results Total of 42 studies included in this review whereas 29 of them were included in the meta-analysis. The estimated summary reproductive number was 2.87 (95% CI, 2.39–3.44). We found evidence of very high heterogeneity (99.5%) of the reproductive number reported in the included studies. Our sub-group analysis was found the significant variations of reproductive number across the country for which it was estimated, method and model that were used to estimate the reproductive number, number of case that was considered to estimate the reproductive number, and the type of reproductive number that was estimated. The highest reproductive number was reported for the Diamond Princess Cruise Ship in Japan (14.8). In the country-level, the higher reproductive number was reported for France (R, 6.32, 95% CI, 5.72–6.99) following Germany (R, 6.07, 95% CI, 5.51–6.69) and Spain (R, 3.56, 95% CI, 1.62–7.82). The higher reproductive number was reported if it was estimated by using the Markov Chain Monte Carlo method (MCMC) method and the Epidemic curve model. We also reported significant heterogeneity of the type of reproductive number- a high-value reported if it was the time-dependent reproductive number. Conclusion The estimated summary reproductive number indicates an exponential increase of coronavirus infection in the coming days. Comprehensive policies and programs are important to reduce new infections as well as the associated adverse consequences including death.
Modeling and simulation of atrazine biodegradation in bacteria and its effect in other living systems

Abstract Atrazine is the most commonly used herbicide worldwide in the agricultural system. The increased environmental concentration of the atrazine showed the toxic effects on the non-target living species. Biodegradation of the atrazine is possible with the bacterial systems. The present study investigated biodegradation potential of atrazine degrading bacteria and the impact of atrazine on environmental systems. Model of atrazine fate in ecological systems constructed using the cell designer. The used model further analyzed and simulated to know the biochemistry and physiology of the atrazine in different cellular networks. Topological analysis of the atrazine degradation confirmed the 289 nodes and 300 edges. Our results showed that the overall biomagnification of the atrazine in the different environmental systems. Atrazine is showing toxic effects on humans and plants, whereas degraded by the bacterial systems. To date, no one has analyzed the complete degradation and poisonous effects of the atrazine in the environment. Therefore, this study is useful for overall system biology based modeling and simulation analysis of atrazine in living systems. Communicated by Ramaswamy H. Sarma
Exergaming and Aquatic Exercises Affect Lung Function and Weight Loss in Obese Children

Abstract We investigated the effect of exergames and aquatic exercises on lung function and weight loss in obese children. Sixty-one obese male primary-school children were randomly allocated to video game, aquatic exercise, and control groups. Lung functions and anthropometric variables were measured before and after the intervention and after one month (follow-up). In the video game group, an Xbox Kinect game was played for 60 min during three sessions a week. The aquatic aerobic exercise was performed three times per week and consisted of a warm-up, main exercises, and a cool down phase. For the video game group, there was a significant reduction in body weight between (i) pre- and (ii) post-intervention and follow-up. In the aquatic exercise group, there was a significant reduction in body weight between pre- and post-intervention and between pre-intervention and follow-up. Both exercise groups improved the waist/hip ratio index compared to the control group. Forced vital capacity was significantly improved in the follow-up of the video game group and the aquatic exercise group compared to the control group. A significant improvement was found in forced expiratory volume in the first second at post-intervention and follow-up in the video game and the aquatic exercise groups. Exergames and aquatic exercises improved weight loss and lung function in obese children.
Clinical characteristics of breast ductal carcinoma in situ with microinvasion: a narrative review

Ductal carcinoma in situ (DCIS) with microinvasion (DCIS-MI) is defined as the extension of cancer cells beyond the basement membrane into adjacent tissue with no focus larger than 1 mm or a maximum diameter of less than 1 mm for multiple invasive foci. DCIS-MI constitutes approximately 1% of all breast cancer cases and 5% to 10% of cases of DCIS. The current literature is controversial concerning the clinical prognostic features and management of DCIS-MI. This narrative review described recently reported literature regarding the characteristics, diagnosis, treatment, and prognosis of DCIS-MI.
P.F508del editing in cells from cystic fibrosis patients

Development of genome editing methods created new opportunities for the development of etiology-based therapies of hereditary diseases. Here, we demonstrate that CRISPR/Cas9 can correct p.F508del mutation in the CFTR gene in the CFTE29o- cells and induced pluripotent stem cells (iPSCs) derived from patients with cystic fibrosis (CF). We used several combinations of Cas9, sgRNA and ssODN and measured editing efficiency in the endogenous CFTR gene and in the co-transfected plasmid containing the CFTR locus with the p.F508del mutation. The non-homologous end joining (NHEJ) frequency in the CFTR gene in the CFTE29o- cells varied from 1.25% to 2.54% of alleles. The best homology-directed repair (HDR) frequency in the endogenous CFTR locus was 1.42% of alleles. In iPSCs, the NHEJ frequency in the CFTR gene varied from 5.5% to 12.13% of alleles. The best HDR efficacy was 2.38% of alleles. Our results show that p.F508del mutation editing using CRISPR/Cas9 in CF patient-derived iPSCs is a relatively rare event and subsequent cell selection and cultivation should be carried out.
Circulating Tumor Cells and Biomarker Modulation with Olaratumab Monotherapy Followed by Olaratumab plus Doxorubicin: Phase Ib Study in Patients with Soft-Tissue Sarcoma

This phase Ib study enumerated whole blood circulating tumor cells (CTC) and evaluated biomarkers in patients with potentially resectable soft-tissue sarcoma (STS) treated with olaratumab monotherapy (20 mg/kg) for one cycle followed by up to six cycles of olaratumab (20 mg/kg, cycles 1–2; 15 mg/kg, cycles 3–7) plus doxorubicin (75 mg/m2 on day 1). CTCs, platelet-derived growth factor receptors (PDGFR), and PDGF ligand expression in tumor tissue pre- and post-olaratumab monotherapy were evaluated. Antitumor activity, safety, pharmacokinetics, and PET/biomarker association with clinical outcome were assessed. Of 51 treated patients, 35, 43, and 37 were evaluable for CTC enumeration, PDGFRs, and PDGF ligand expression, respectively. An increase in CTCs at cycle 1 day 8 was observed, followed by a significant reduction by cycle 3 day 1 or 30-day follow-up. Decrease in CTC counts after olaratumab monotherapy was higher in patients with disease control than without disease control (57.9% vs. 31.2%). Baseline IHC expression was positive in most patients for PDGFRα [n = 31 (72.1%)] and PDGFRβ [n = 36 (83.7%)]. Similar rates were observed post-olaratumab monotherapy [PDGFRα, n = 30 (69.8%); PDGFRβ, n = 33 (76.7%)]. Eleven patients (29.7%) showed a 30% reduction by RT-PCR in PDGFRα at cycle 2. PDGFR expression and PET response showed no correlation with clinical outcome. Safety and pharmacokinetic profiles were consistent with previous reports. This study, the first to use a validated method for CTC detection, confirms that CTC enumeration in STS is feasible. However, no correlation was observed between PDGFRα expression and clinical outcome.
New insights on Bidens herzogii (Coreopsideae, Asteraceae), an endemic species from the Cerrado biogeographic province in Bolivia

The morphological limits among some Coreopsideae genera in the Asteraceae family are complex. An example is Bidens herzogii, a taxon first described as a member of the genus Cosmos, but recently transferred to Bidens. The species is endemic to Eastern Bolivia and it grows on the Cerrado biogeographic province. Recently collected specimens, analysis of herbarium specimens, and revisions of literature lead us to propose new data on morphological description and a chromosome counts for the species, a tetraploid, where x = 12, 2n = 48. Lastly, we provide data on geographic distribution and niche modeling of B. herzogii to predict areas of endemism in Eastern Bolivia. This area is already known for this pattern of endemism, and the evidence generated can be used to direct conservation efforts.
Mid to late‐life scores of depression in the cognitively healthy are associated with cognitive status and Alzheimer's disease pathology at death

Early diagnosis of Alzheimer's disease (AD) is essential for early interventions. Symptoms of depression could represent a prodromal stage of AD. Very early mood alterations may help to stratify those at highest risk of late‐life AD. We aim to investigate associations between baseline/longitudinal scores for depression, presence of cognitive impairment and/or AD pathology at death.
Is periodontal disease a risk indicator for colorectal cancer? A systematic review and meta-analysis.

AIMS Existing epidemiological studies have suggested that periodontal disease (PD) may be a risk indicator for colorectal cancer (CRC). However, no formal systematic review and meta-analysis has been performed. Therefore, we aimed to evaluate the association between PD and CRC risk in this study. MATERIALS AND METHODS We used the PubMed, EMBASE, Cochrane Library and Web of Science to search for related articles published from January 1, 1966 to July 16, 2020. Stata (Version 15) software was used to calculate the total risk ratio (RR) and 95% confidence interval (CI) of the included studies through the random effects model to assess the association PD and CRC risk. RESULTS Nine studies were included in the narrative synthesis, and seven studies were included in the meta-analysis. Results showed that PD significantly increased the risk of CRC by 44% (RR, 1.44; 95% CI, 1.18-1.76; I2 , 55.2%). CONCLUSION We found an association between PD and CRC. PD can be a potential risk indicator for the occurrence and development of CRC, further studies are needed to assess causality. Hence, effective periodontal treatment could be a valuable preventive measure for CRC.
The validity of an isiZulu speech reception threshold test for use with adult isiZulu speakers

Background This study continued the development of an isiZulu speech reception threshold (zSRT) test for use with first language, adult speakers of isiZulu. Objectives The objective of this study was to determine the convergent and concurrent validity of the zSRT test. Methods One hundred adult isiZulu first-language speakers with normal hearing and 76 first-language, adult isiZulu speakers with conductive or sensorineural hearing losses ranging from mild to severe were assessed on pure tone audiometry and a newly developed isiZulu SRT test. Convergent validity was established through agreement of the zSRT scores with pure tone average (PTA) scores. Concurrent validity was assessed by examining the steepness of the psychometric curve for each word in the zSRT test for each type and degree of hearing loss. Results Intraclass correlation coefficient analyses showed zSRT scores were in substantial to very high agreement with PTA scores for the normal hearing and hearing loss groups (NH – right ear ICC consistency = 0.78, left ear ICC = 0.67; HL – right ear ICC consistency = 0.97, left ear ICC consistency = 0.95). The mean psychometric slope (%/dB) at 50% correct perception for all words in the zSRT test was 4.92%/dB for the mild conductive hearing loss group, 5.26%/dB for the moderate conductive hearing loss group, 2.85%/dB for the moderately severe sensorineural hearing loss group and 2.47%/dB for the severe sensorineural hearing loss group. These slopes were appropriate for the degree of hearing loss observed in each group. Conclusion The zSRT test showed convergent and concurrent validity for assessing SRT in first language, adult speakers of isiZulu.
Micro‐anatomy of the ear of the southern white rhinoceros (Ceratotherium simum simum)

The white rhinoceros is the largest of the five extant rhinoceros species. The population is declining rapidly because of intense poaching. However, normal anatomical descriptions in this species are lacking. The purpose of this study is to describe the osseous anatomy of the middle and inner ear of the southern white rhinoceros using micro‐focus X‐ray computed tomography imaging. Four temporal bones obtained from two 1‐day old southern white rhinoceros preserved in 10% formalin were scanned. Tri‐dimensional reconstructions were obtained and volumes of the middle ear ossicles and inner ear structures were calculated. Excellent high spatial resolution 3D images were obtained for all samples and virtual models of the auditory ossicles and bony labyrinth were generated. Visualization of the tympanic membrane, middle ear and inner ear structures was possible in all samples. Whereas the stapes and incus had a shape similar to their human or equine counterparts, the malleus showed a unique appearance with a long rostral branch projecting latero‐distally to the manubrium. The cochlea described 2 turns rostro‐laterally around its axis, with a medial direction of rotation. However, identification of the soft tissue structures of the middle ear was sometimes difficult and visualization of the small structures of the membranous labyrinth was not possible using this formalin fixation and alternative techniques should be investigated. Further investigations are needed in order to provide a complete virtual model including both soft and bone tissues of this difficultly accessible region.
COMMENTSTime to Stop the Tragedy in Spanish Nursing Homes During the COVID‐19 Pandemic

particularly vulnerable geriatric population, increased video visit adoption exponentially and rapidly through a combination of national structural interventions and local changes addressing provider capability, opportunities, and motivation. This paper shows how these changes were operationalized on a local level, shedding light on national trends. Similar clinics may likewise benefit from changes enacted in various domains and levels to decrease the digital divide for patients. Future steps will focus on addressing behavior change from the patient perspective.
Downregulation of lncRNA ZFAS1 inhibits the hallmarks of thyroid carcinoma via the regulation of miR-302-3p on cyclin D1

At present, treatment options for thyroid carcinoma remain limited. The present study aimed to investigate the role of ZFAS1 in various major hallmarks of cancer and the underlying mechanisms in thyroid carcinoma cells. The interactions between long non-coding RNAs (lncRNAs), microRNAs (miRs) and target genes were predicted by bioinformatics and confirmed by performing dual-luciferase assays. The mRNA and protein expressions were determined by reverse transcription-quantitative PCR and western blotting. Cell invasion, migration, and viability were evaluated via Transwell, wound-healing and Cell Counting Kit-8 assays, respectively. The results demonstrated that lncRNA ZFAS1 expression was upregulated in thyroid carcinoma tissues, TT and SW579 cells, and was associated with the proliferation of these two cell lines. Notably, downregulation ZFAS1 reduced migration and invasion, and reversed the promotive effects of miR-302a-3p inhibitor on the proliferation, migration and invasion of TT and SW579 cells. Moreover, cyclin D1 (CCND1) is targeted by miR-302a-3p, and was regulated by ZFAS1. In addition, the downregulation of ZFAS1 not only reversed the promotive effects of miR-302a-3p inhibitor on CCND1 expression and the epithelial-mesenchymal transition (EMT) of TT and SW579 cells, but also targeted and increased the expression of miR-302a-3p, and further reduced the expression of CCND1, resulting in suppression of the proliferation, migration, invasion and EMT of thyroid carcinoma cells.
Genetic and phenotypic determinants of resistance to antibiotics in Aeromonas spp., strains isolated from pediatric patients.

INTRODUCTION Intestinal and extraintestinal infections by Aeromonas spp. , remain controversial, due to the existence of healthy carriers of Aeromonas spp. In children under five years old, the diarrhea of infectious origin constitutes the second cause of mortality and remains a major concern for public health. The aim of this work was to detect the pheno/genotype of β-lactamases and class 1 integrons in Aeromonas spp. , strains isolated from pediatric patients in a tertiary referral hospital in Mexico. METHODOLOGY Sixty-six strains of Aeromonas spp. , were isolated from clinical samples of pediatric origin and were identified by RFLP-PCR 16S rRNA. Resistance phenotype according to CLSI, genetic and phenotypic detection of extended-spectrum β-lactamases (ESBL) and metallo-b-lactamases (MBL) was performed. Finally, characterization of class 1 integrons was performed. RESULTS Aeromonas spp. , strains of diarrheic origin were more predominant. A wide heterogeneity was detected, where A. caviae was the predominant specie. Second-generation cephalosporins, fluoroquinolones, and nitrofurans had best antimicrobial activity; moreover, antibiotics of the β-lactamic and lincosamides families showed lower inhibitory activity. Phenotypically, prevalences of 4.55% and 3.03% were detected for MBL (intestinal origin) and ESBL (extraintestinal origin), respectively. blaIMIS-cphA and blaTEM-1 genes, and nineteen class 1 integrons carrying two variants of cassettes corresponding to adenylyl transferases (aadA), and dihydrofolate reductases (dfrA). Monogenic array with aadA1 cassette was predominantly. CONCLUSIONS ESBL and class 1 integrons, in Aeromonas collected from pediatric patients, determines a major detection challenge for the clinical microbiology laboratory and represents a remarkable epidemiological risk of nosocomial spread of multidrug-resistant determinants.
Functional role of pax6 in eye and central nervous system development in the annelid Capitella teleta

The transcription factor Pax6 is an important regulator of early animal development. Loss of function mutations of pax6 in a range of animals results in a reduction or complete loss of the eye, a reduction of a subset of neurons, and defects in axon growth. There are no studies focusing on the role of pax6 during development of any lophotrochozoan representative, however, expression of pax6 in the developing eye and nervous system in a number of species suggest that pax6 plays a highly conserved role in eye and nervous system formation. We investigated the functional role of pax6 during development of the marine annelid Capitella teleta. Expression of pax6 transcripts in C. teleta larvae is similar to patterns found in other animals, with distinct subdomains in the brain and ventral nerve cord as well as in the larval and adult eye. To perturb pax6 function, two different splice-blocking morpholinos were used. Larvae resulting from injections with either morpholino show a reduction of the pax6 transcript, and development of both the larval eyes and the central nervous system architecture are highly disrupted. Preliminary downstream target analysis confirms disruption in expression of some components of the retinal gene regulatory network, as well as disruption of genes involved in nervous system development. Results from this study, taken together with studies from other species, reveal an evolutionarily conserved role for pax6 in eye development, and in neural specification and development.
Effects of course design (curves and elevation undulations) on marathon running performance: a comparison of Breaking 2 in Monza and the INEOS 1:59 Challenge in Vienna

ABSTRACT Eliud Kipchoge made two attempts to break the 2-hour marathon, in Monza and then Vienna. Here we analyse only the effects of course elevation profile and turn curvatures on his performances. We used publicly available data to determine the undulations in elevation and the radii of the curves on the course. With previously developed equations for the effects of velocity, slope, and curvature on oxygen uptake, we performed simulations to quantify how much the elevation changes and curves of the Vienna course affect a runner’s oxygen uptake (at a fixed velocity) or velocity (at a fixed oxygen uptake). We estimate that, after the initial downhill benefit, the course led to an overall oxygen uptake penalty of only 0.03%. When compared to a perfectly level straight course, we estimate that the combined effects of the undulations and curves of the Vienna course incurred a penalty of just 1.37 seconds. Kipchoge ran 2:00:25 in Monza Italy. Comparison with the Monza course profile indicates a 46.2 second (1.09% oxygen uptake) advantage of Vienna’s course while the fewer curves of Vienna contributed ~ 1 second. The Vienna course was very well-chosen because it minimized the negative effects of elevation changes and curves. Abbreviations: CoT: Oxygen cost of transport; C O2: Curved rate of oxygen consumption; O2: Rate of oxygen consumption; WA: World Athletics
Epigenetically inactivated RASSF1A as a tumor biomarker

RASSF1A, one of the eight isoforms of the RASSF1 gene, is a tumor suppressor gene that influences tumor initiation and development. In cancer, RASSF1A is frequently inactivated by mutations, loss of heterozygosity, and, most commonly, by promoter hypermethylation. Epigenetic inactivation of RASSF1A was detected in various cancer types and led to significant interest; current research on RASSF1A promoter methylation focuses on its roles as an epigenetic tumor biomarker. Typically, researchers analyzed genomic DNA (gDNA) to measure the amount of RASSF1A promoter methylation. Cell-free DNA (cfDNA) from liquid biopsies is a recent development showing promise as an early cancer diagnostic tool using biomarkers, such as RASSF1A. This review discusses the evidence on aberrantly methylated RASSF1A in gDNA and cfDNA from different cancer types and its utility for early cancer diagnosis, prognosis, and surveillance. We compared methylation frequencies of RASSF1A in gDNA and cfDNA in various cancer types. The weaknesses and strengths of these analyses are discussed. In conclusion, although the importance of RASSSF1A methylation to cancer has been established and is included in several diagnostic panels, its diagnostic utility is still experimental.