Effects of the number of aligned mammalian species on the TFBS detection accuracy

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools"</p><p>http://genomebiology.com/2007/8/10/R225</p><p>Genome Biology 2007;8(10):R225-R225.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2246299.</p><p></p> Each panel shows the performance of a tool in aligning a different number of species. Human and baboon were used for the two species alignment, mouse was added for the three species alignment, and all five species but cow were used for four species alignment. While all tools have almost the same performance for aligning the two closely related species human and baboon, MUSCLE and DIALIGN performed better than other tools in maintaining or improving performance when adding more species to the alignment

The average TFBS sensitivity of five tools in aligning TFBS in five mammalian species

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools"</p><p>http://genomebiology.com/2007/8/10/R225</p><p>Genome Biology 2007;8(10):R225-R225.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2246299.</p><p></p> The average TFBS sensitivity of all functional TFBSs. The average TFBS sensitivity with the subset of non-turnover sites among all TFBSs. The relative order of TFBS sensitivity for the five tools is almost the same as the order of their TFBS detection accuracy (Figure 10d)

Detection accuracy of individual TFBSs on five-way mammalian alignments

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools"</p><p>http://genomebiology.com/2007/8/10/R225</p><p>Genome Biology 2007;8(10):R225-R225.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2246299.</p><p></p> All five tools perform better at detecting YY1E2F and Pax6, which have low RTRs and short restricted distance for translocation, than IRF2 and ROAZ, which have high RTR and long restricted distance for translocation. MUSCLE shows an overall better performance than the other four tools. MLAGAN performs better than DIALIGN on YY1E2F, PAX6, PPARG and ROZA, while DIALIGN shows a better performance than MLAGAN on TP53 and PPARG, which have a long restricted distance for translocation but a relatively low RTR

P(NMe₂)₃‑Mediated Regioselective N‑Alkylation of 2‑Pyridones via Direct Deoxygenation of α‑Keto Esters

A practical and regioselective direct N-alkylation of 2-pyridones is enabled by use of α-keto esters in the P(NMe2)3-mediated deoxygenation process. The reaction proceeds under mild conditions to produce N-alkylated 2-pyridones with high selectivity and generality, and the protocol is shown to be applicable for the scale-up synthesis, which makes it promising for practical applications

Antimicrobial susceptibility of the 41 CR-KP isolates to 17 common antimicrobial agents.

<p>Antimicrobial susceptibility of the 41 CR-KP isolates to 17 common antimicrobial agents.</p

Antimicrobial resistance of 41 CR-KP isolates against antimicrobial agents among different sequence type.

<p>Antimicrobial resistance of 41 CR-KP isolates against antimicrobial agents among different sequence type.</p

Distribution of STs in the clonal complexes.

<p>The eBURST application of the MLST data from all of the isolates analyzed in this study. The purple and green numbers represent 16 STs which are found in 41 CR-KP isolates. STs that are linked by a line belong to the same cluster. Circle sizes are proportional to the number of strains within the ST.</p

Drug resistance gene distribution among the molecular types of 41 CR-KP isolates from pediatric patients.

<p>Drug resistance gene distribution among the molecular types of 41 CR-KP isolates from pediatric patients.</p

Sequential <i>In Situ</i>-Formed Kukhtin–Ramirez Adduct and P(NMe₂)₃‑Catalyzed <i>O</i>‑Phosphination of α‑Dicarbonyls with P(O)–H

O-Phosphination of α-dicarbonyls via sequential in situ formation of a Kukhtin–Ramirez adduct and a P(NMe2)3-catalyzed process has been exploited for the synthesis of α-phosphoryloxy carbonyls. A range of P(O)–H derivatives, including diarylphosphine oxides, arylphosphinates, and phosphinates, are competent candidates to be introduced into the α-dicarbonyls in this transformation, and various α-phosphoryloxy carbonyls are obtained. This approach possesses advantages of mild conditions, simple operations, atom economy, high efficiency, and gram-scale synthesis, which make it promising in the synthesis toolbox

Data_Sheet_2_Molecular Characteristics of Community-Associated Staphylococcus aureus Isolates From Pediatric Patients With Bloodstream Infections Between 2012 and 2017 in Shanghai, China.xls

<p>Staphylococcus aureus is known as an invasive human pathogen, resulting in significant morbidity and mortality worldwide; however, information on community-associated S. aureus (CA-SA) from bloodstream infections (BSI) in children in China remains scarce. This study aimed to investigate the molecular characteristics of 78 CA-SA isolates recovered from pediatric patients with BSI between 2012 and 2017 in Shanghai. All isolates including 51 (65.4%) methicillin-susceptible S. aureus (MSSA) and 27 (34.6%) methicillin-resistant S. aureus (MRSA) isolates were characterized based on antimicrobial resistance, virulence genes, multilocus sequence typing (MLST), spa, and SCCmec typing. A total of 18 distinct sequence types (STs) and 44 spa types were identified. ST188 and ST7 were the predominant MSSA clones and ST59-MRSA-SCCmecIV/V was the most common MRSA clone. Spa t189 (9.0%, 7/78) was the most common spa type. SCCmec types IV and V were observed at frequencies of 59.3 and 40.7%, respectively. Notably, 40 (51.3%) S. aureus BSI strains were multidrug resistant (MDR), and these were mostly resistant to penicillin, erythromycin, and clindamycin. MRSA strains were associated with substantially higher rates of resistance to multiple antibiotics than MSSA strains. Fifty (64.1%, 50/78) isolates, including 19 (70.3%) MRSA isolates, harbored ≥ 10 tested virulence genes, as evaluated in this study. Ten (37.0%) MRSA isolates and four (7.8%) MSSA isolates harbored the gene encoding Panton–Valentine leukocidin (PVL). Virulence genes analysis showed diversity in different clones; the seb-sek-seq genes were present in all ST59 strains, whereas the seg-sei-sem-sen-seo genes were present in different clones including ST5, ST20, ST22, ST25, ST26, ST30, ST121, and ST487 strains. In conclusion, this study revealed that community-associated S. aureus strains from BSI in children demonstrated considerable genetic diversity, and identified major genotypes of CA-MRSA and CA-MSSA, with a high prevalence of CA-MRSA. Furthermore, major genotypes were frequently associated with specific antimicrobial resistance and toxin gene profiles. Understanding the molecular characteristics of those strains might provide further insights regarding the spread of BSI S. aureus among children between communities in China.</p