Comparison of commercially available target enrichment methods for next-generation sequencing. J. Biomol. Tech. 24, 73 (2013). Article CAS Google Scholar Meienberg, J. et al. New insights into the ...

An enrichment method to increase cell-free fetal DNA fraction and significantly reduce false negatives and test failures for non-invasive prenatal screening: A feasibility study

Abstract. Docking-based virtual screening (DBVS) is well placed in modern drug discovery and is widely applied with many success cases by both pharmaceutical companies and academic groups. The recent advances in scoring functions, search algorithms, consensus scoring, protein flexibility and enrichment represent a new era of …

Accordingly, the goal of this study is to evaluate a new low-volume enrichment method for rapid screening and isolation of lytic phages from environmental sources that has automation potential, is not labor intensive, and is faster than conventional methods [22]. ... Enrichment methods select for phages in a sample that target the …

To detect TB, numerous methods screening Mycobacterium tuberculosis (MTB) have been developed. However, the methods still have challenges of rapid and specific enrichment of MTB. In this study, we present a novel specific enrichment method of MTB using a microfabricated tip.

Based upon a review of enrichment methods presented in Table 1, five combinations of three simple methods of enrichment were selected and performed on 1 mL aliquots of the artificial sample as follows; low-speed centrifugation in a microfuge at 6000 × g for 10 min at 4 °C, sterile syringe filtration at 0.45 μm, nuclease treatment …

We demonstrate that using an all-atom molecular mechanics force field combined with an implicit solvent model for scoring protein-ligand complexes is a promising approach for improving inhibitor enrichment in the virtual screening of large compound databases. The rring method is evaluated by the …

Our observation that ABFE calculations outperform docking in virtual compound screening would not be very meaningful if we were comparing it with an unreliable docking method. However, our docking calculations do yield good enrichment metrics for the focused Tier 1 and Tier 2 sets, as assessed by the AUC statistic (Table 1 ).

a) target ligand, which the aptamer must bind b) method of altering the sequence of the ssDNA or ssRNA c) method to. Suppose you want to identify an aptamer that bind vitamin D3. Aptamers are identified by the Systemic Evolution of Ligands by Exponential Enrichment (SELEX) method. All of the following are necessary for a SELEX …

DNA-encoded libraries are a powerful tool to identify hit compounds for drug discovery. Now, two papers have reported new advances in this technology. One paper reports a method to screen for ...

Introduction. Over the past decade, high-throughput virtual screening has become a popular method for discovering hit compounds in the field of drug design 1–3.When a receptor's three-dimensional (3D) structure is available, molecular docking is used to identify potential binders for the target pocket 4.However, due to the simplifications …

After expanding the cells from the first round and subjecting them to a second round of CRISPRa enrichment screening, we observed a further robust increase of IL-2 tetramer positive from 13.3 to 95% IL-2 …

All three of the data mining methods at hand tolerated increasing levels of false positives even when the ratio of misclassified compounds to true active compounds was 5:1 in the training set. False negatives in the ratio of 1:1 were tolerated as well. SVM outperformed the other two methods in capturing active compounds and scaffolds in the top 1%.

The results showed that the enrichment factor (EF) 1% of ENS-VS was 6 times higher than that of Autodock vina. Compared with the newest virtual screening method SIEVE-Score, the mean EF 1% and ... present a target-speci c virtual screening method based on ensemble learning named ENS-VS, which has the following three innovations. Firstly, we ...

The results demonstrated that the use of selective enrichment broth followed by PCR targeting the atr gene is a highly sensitive, specific and accurate test for GBS screening in pregnant women, allowing the detection of the bacteria even in lightly colonized patients. Group B Streptococcus (GBS) is the most common cause of life …

The inclusion of such a large amount of analogues makes ligand enrichment much easier than the real-world screening, thus causes the "analogue bias" during benchmarking evaluations. Cleves and Jain compared the performances of GSIM-2D similarity search with Surflex-Dock based on DUD (PPAR-gamma case which originally …

Methods: 100 screening samples were cultured onto each of MSCA, CESB, and MAC-Mero. ... Both media were evaluated alongside a broth enrichment method recommended by the CDC for isolation of CPE ...

Microfiltration enrichment methods process whole blood through a range of microscale constrictions to capture target cells based on their size or a combination of size and deformability. ... and cancer screening. The interpretation of such metrics is quite challenging because of some major limiting factors such as the volume of blood used, …

The affinity module requires rapid enrichment of sequences with high affinity for the target and is therefore suitable for homogeneous screening; the specificity module requires a screening method that facilitates the isolation of complexes in an environment with interfering substances; and the final applicability module uses cell-SELEX to ...

A screening for optimal selenium enrichment additives for selenium-enriched fish production: Application of a HPLC-ICP-MS method Food Chem X. 2023 Dec 21:21:101088. doi: 10.1016/j.fochx.2023.101088. eCollection 2024 …

The new enrichment method yielded Bt from 44 out of 58 samples. Contrarily, Bt was isolated only from 16 and 18 samples by sodium acetate selection and dry heat pretreatment methods, respectively. Moreover, the percentages of Bt colonies isolated by the enrichment method were higher comparatively. Vegetative whole cell protein profile …

In this study, ultrafiltration, nitrocellulose membrane enrichment and saturated ammonium sulfate precipitation were used to process 10 mL urine samples from five healthy volunteers and five bladder cancer patients. The urine proteins were enriched and separate by SDS-PAGE to compare the purification efficiency of different methods. …

Conclusion: Group B streptococcal antigen detection by latex agglutination after 5 h enrichment is a reliable, easy, and relatively rapid method for screening of GBS carriage in pregnant woman not in labor. Latex agglutination after 18-24 h enrichment can be used alternative to standard subculture method for screening GBS carriage.

Over the past decade, high-throughput virtual screening has become a popular method for discovering hit compounds in the field of drug design 1, 2, 3 . When a receptor's three-

Therefore, we developed a simple and effective separation method, improved NIPS (iNIPS), that enriches the fetal fraction and improves the accuracy of NIPS for fetal aneuploid detection. We adopted a novel strategy to achieve enrichment of 125-135 bp cell-free DNA (cfDNA) by e-gel electrophoresis.

Therefore, we recommend applying this method of addition of liquid enrichment media as part of a culture protocol routine for CRE screening. Keywords ... to compare the efficacy of a rectal sample culture technique on two different selective growth media targeted for CRE screening prior enrichment and after enrichment with …

the method D (two fractions) was 22 (D1) and 18 (D2) spots; the method B (three fractions) was total spots of 19 (B1), 15 (B2), Method E and 17 (B3); the method E was 15 spots, whereas for the control of the Piperine (three spots) and spot spread use than any other Acid-base extraction method using Wagner method [21] with comparison eluent ...

Here, we describe three enrichment methods for obtaining Burkholderia thailandensis persisters: (1) flow sorting for persisters from exponentially dividing cultures by fluorescent staining of bacterial cells with a translational membrane depolarization-specific DiBAC 4 (3) dye, (2) antibiotic lysis of nonpersisters, and (3) culture aging to ...

The results showed that the enrichment factor (EF) 1% of ENS-VS was 6 times higher than that of Autodock vina. Compared with the newest virtual screening method SIEVE-Score, the mean EF 1% and AUC of ENS-VS (mean EF 1% = 52.77, AUC = 0.982) were statistically significantly higher than those of SIEVE-Score (mean EF 1% …

Therefore, enrichment of Nanobodies from periplasmic extract and removal of periplasmic extract matrix can be crucial to design a robust functional-based screening assay. In order to do this, the antigen of interest can be immobilized on a solid carrier (e.g., a 96-well plate coated with NHS functional groups (as described below)), followed by ...