Performance of high-throughput DNA quantification methods

BACKGROUND: The accuracy and precision of estimates of DNA concentration are critical factors for efficient use of DNA samples in high-throughput genotype and sequence analyses. We evaluated the performance of spectrophotometric (OD) DNA quantification, and compared it to two fluorometric quantification methods, the PicoGreen(® )assay (PG), and a novel real-time quantitative genomic PCR assay (QG) specific to a region at the human BRCA1 locus. Twenty-Two lymphoblastoid cell line DNA samples with an initial concentration of ~350 ng/uL were diluted to 20 ng/uL. DNA concentration was estimated by OD and further diluted to 5 ng/uL. The concentrations of multiple aliquots of the final dilution were measured by the OD, QG and PG methods. The effects of manual and robotic laboratory sample handling procedures on the estimates of DNA concentration were assessed using variance components analyses. RESULTS: The OD method was the DNA quantification method most concordant with the reference sample among the three methods evaluated. A large fraction of the total variance for all three methods (36.0–95.7%) was explained by sample-to-sample variation, whereas the amount of variance attributable to sample handling was small (0.8–17.5%). Residual error (3.2–59.4%), corresponding to un-modelled factors, contributed a greater extent to the total variation than the sample handling procedures. CONCLUSION: The application of a specific DNA quantification method to a particular molecular genetic laboratory protocol must take into account the accuracy and precision of the specific method, as well as the requirements of the experimental workflow with respect to sample volumes and throughput. While OD was the most concordant and precise DNA quantification method in this study, the information provided by the quantitative PCR assay regarding the suitability of DNA samples for PCR may be an essential factor for some protocols, despite the decreased concordance and precision of this method

Analysis and Intellectual Structure of the Multi-Factor Authentication in Information Security

This study presents the current state of research on multi-factor authentication. Authentication is one of the important traits in the security domain as it ensures that legitimate users have access to the secure resource. Attacks on authentication occur even before digital access is given, but it becomes quite challenging with remote access to secure resources. With increasing threats to single authentication schemes, 2Factor and later multi-factor authentication approaches came into practice. Several studies have been done in the multi-factor authentication discipline, and most of them proposed the best possible approaches, but there are very limited studies in the area that can comprehend all these innovative and effective approaches. Using Web of Science data of the research publications on the topic, the study adopted the bibliometric approach to find the evolution of authentication in the security domain, especially multi-factor authentication. This study finds the impact of the research in the selected domain using bibliometric analysis. This research also identifies the key research trends that most of the researchers are paying attention to. The highest number of publications on multi-factor authentication were published in 2019 while the highest number of citations were received in 2014. United States, India, and China are the leading countries publishing the most on multi-factor authentication

Identification of bioactive compounds with GC–Q-TOF–MS in the extracts from Clinacanthus nutans using subcritical carbon dioxide extraction

Subcritical carbon dioxide Soxhlet extraction of biologically active compounds from Clincanthus nutans was investigated by full factorial design to identify and optimize the factors (particle size and co-solvent) affecting extract yield, antioxidant activity, total phenolic content, total flavonoid content, and α-glucosidase inhibitory activity. An average of 3.103% yield, 98.90% antioxidant activity, 49.40 mg/g (GAE) TPC, 43.76 mg/g (RE), and 88.58% AGI activity can be achieved using the optimum levels of independent variables. The GC-Q-TOF MS identification of optimized extract shown that different classes of phytoconstituents were successfully separated by CO2-Soxhlet to produce potential antioxidant and α-glucosidase inhibitory activity

Identification of bioactive compounds with GC Q-TOF MS in the extracts from Clinacanthus nutans using subcritical carbon dioxide extraction

Subcritical carbon dioxide Soxhlet extraction of biologically active compounds from Clincanthus nutans was investigated by full factorial design to identify and optimize the factors (particle size and co-solvent) affecting extract yield, antioxidant activity, total phenolic content, total flavonoid content, and α-glucosidase inhibitory activity. An average of 3.103% yield, 98.90% antioxidant activity, 49.40 mg/g (GAE) TPC, 43.76 mg/g (RE), and 88.58% AGI activity can be achieved using the optimum levels of independent variables. The GC-Q-TOF MS identification of optimized extract shown that different classes of phytoconstituents were successfully separated by CO2-Soxhlet to produce potential antioxidant and α-glucosidase inhibitory activity

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

The impact of surgical delay on resectability of colorectal cancer: An international prospective cohort study

AIM: The SARS-CoV-2 pandemic has provided a unique opportunity to explore the impact of surgical delays on cancer resectability. This study aimed to compare resectability for colorectal cancer patients undergoing delayed versus non-delayed surgery. METHODS: This was an international prospective cohort study of consecutive colorectal cancer patients with a decision for curative surgery (January-April 2020). Surgical delay was defined as an operation taking place more than 4 weeks after treatment decision, in a patient who did not receive neoadjuvant therapy. A subgroup analysis explored the effects of delay in elective patients only. The impact of longer delays was explored in a sensitivity analysis. The primary outcome was complete resection, defined as curative resection with an R0 margin. RESULTS: Overall, 5453 patients from 304 hospitals in 47 countries were included, of whom 6.6% (358/5453) did not receive their planned operation. Of the 4304 operated patients without neoadjuvant therapy, 40.5% (1744/4304) were delayed beyond 4 weeks. Delayed patients were more likely to be older, men, more comorbid, have higher body mass index and have rectal cancer and early stage disease. Delayed patients had higher unadjusted rates of complete resection (93.7% vs. 91.9%, P = 0.032) and lower rates of emergency surgery (4.5% vs. 22.5%, P < 0.001). After adjustment, delay was not associated with a lower rate of complete resection (OR 1.18, 95% CI 0.90-1.55, P = 0.224), which was consistent in elective patients only (OR 0.94, 95% CI 0.69-1.27, P = 0.672). Longer delays were not associated with poorer outcomes. CONCLUSION: One in 15 colorectal cancer patients did not receive their planned operation during the first wave of COVID-19. Surgical delay did not appear to compromise resectability, raising the hypothesis that any reduction in long-term survival attributable to delays is likely to be due to micro-metastatic disease

Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance

<p>Abstract</p> <p>Background</p> <p>Whole genome amplification (WGA) promises to eliminate practical molecular genetic analysis limitations associated with genomic DNA (gDNA) quantity. We evaluated the performance of multiple displacement amplification (MDA) WGA using gDNA extracted from lymphoblastoid cell lines (N = 27) with a range of starting gDNA input of 1–200 ng into the WGA reaction. Yield and composition analysis of whole genome amplified DNA (wgaDNA) was performed using three DNA quantification methods (OD, PicoGreen^®and RT-PCR). Two panels of N = 15 STR (using the AmpF<it>l</it>STR^®Identifiler^®panel) and N = 49 SNP (TaqMan^®) genotyping assays were performed on each gDNA and wgaDNA sample in duplicate. gDNA and wgaDNA masses of 1, 4 and 20 ng were used in the SNP assays to evaluate the effects of DNA mass on SNP genotyping assay performance. A total of N = 6,880 STR and N = 56,448 SNP genotype attempts provided adequate power to detect differences in STR and SNP genotyping performance between gDNA and wgaDNA, and among wgaDNA produced from a range of gDNA templates inputs.</p> <p>Results</p> <p>The proportion of double-stranded wgaDNA and human-specific PCR amplifiable wgaDNA increased with increased gDNA input into the WGA reaction. Increased amounts of gDNA input into the WGA reaction improved wgaDNA genotyping performance. Genotype completion or genotype concordance rates of wgaDNA produced from all gDNA input levels were observed to be reduced compared to gDNA, although the reduction was not always statistically significant. Reduced wgaDNA genotyping performance was primarily due to the increased variance of allelic amplification, resulting in loss of heterozygosity or increased undetermined genotypes. MDA WGA produces wgaDNA from no template control samples; such samples exhibited substantial false-positive genotyping rates.</p> <p>Conclusion</p> <p>The amount of gDNA input into the MDA WGA reaction is a critical determinant of genotyping performance of wgaDNA. At least 10 ng of lymphoblastoid gDNA input into MDA WGA is required to obtain wgaDNA TaqMan^®SNP assay genotyping performance equivalent to that of gDNA. Over 100 ng of lymphoblastoid gDNA input into MDA WGA is required to obtain optimal STR genotyping performance using the AmpF<it>l</it>STR^®Identifiler^®panel from wgaDNA equivalent to that of gDNA.</p

Incidence and molecular characterization of extended-spectrum beta-lactamase (ESBL)-producing <i>Salmonella enterica</i> and <i>Escherichia coli</i> of avifauna origin in Pakistan

Members of Enterobacteriaceae are known to produce extended-spectrum beta-lactamases (ESBL) which hydrolyze the beta-lactam group of antibiotics. The existence of ESBL-producing Salmonella enterica (S. enterica) and Escherichia coli (E. coli) harbored by urban avifauna was investigated in this study. Dropping samples (n= 180) were collected from six different bird species in the district Jhang, Punjab province, Pakistan. Isolation and identification of ESBL isolates were made by using cefotaxime- (4 mg/L) supplemented MacConkey agar and double disc synergy test (DDST). Polymerase chain reaction (PCR) was performed for the detection of four different ESBL genes including bla CTX-M, bla TEM, bla SHV and bla OXA. A total of 42.69% isolates were confirmed as ESBL via DDST including 30.64% S. enterica and 49.54% E. coli. The incidence of ESBL S. enterica and ESBL E. coli was found highest in egret (Ardea alba) and pigeon (Columba livia) as 64.28% and 78.95%, respectively. The bla CTX-M gene was detected in 57.89% and 64.81% of isolates of S. enterica and E. coli, respectively. Among other genes in S. enterica and E. coli, bla TEM (21.05%, 20.4%); bla SHV (15.78%, 9.26%), and bla OXA (5.26%, 5.56%) were detected, respectively. All of the tested isolates were found resistant to at least one of the thirteen antimicrobial agents except meropenem. To the best of our knowledge, this is the first study reporting the incidence and genetic diversity of ESBL bacteria associated with urban avifauna in Pakistan. The urban avifauna can serve as a potential subject of bio-surveillance to monitor the emergence of antimicrobial-resistant bacteria

Analysis and Intellectual Structure of the Multi-Factor Authentication in Information Security

This study presents the current state of research on multi-factor authentication. Authentication is one of the important traits in the security domain as it ensures that legitimate users have access to the secure resource. Attacks on authentication occur even before digital access is given, but it becomes quite challenging with remote access to secure resources. With increasing threats to single authentication schemes, 2Factor and later multi-factor authentication approaches came into practice. Several studies have been done in the multi-factor authentication discipline, and most of them proposed the best possible approaches, but there are very limited studies in the area that can comprehend all these innovative and effective approaches. Using Web of Science data of the research publications on the topic, the study adopted the bibliometric approach to find the evolution of authentication in the security domain, especially multi-factor authentication. This study finds the impact of the research in the selected domain using bibliometric analysis. This research also identifies the key research trends that most of the researchers are paying attention to. The highest number of publications on multi-factor authentication were published in 2019 while the highest number of citations were received in 2014. United States, India, and China are the leading countries publishing the most on multi-factor authentication