Node Positivity Among Sonographically Suspicious but FNA-Negative Axillary Nodes.

BACKGROUND: Fine needle aspiration (FNA) of sonographically suspicious axillary lymph nodes is helpful to clinically stage patients and guide consideration of neoadjuvant therapy in breast cancer. However, data are limited for suspicious nodes that are FNA negative. Our goal is to compare the frequency of node positivity between patients with negative axillary ultrasound (AUSneg) versus suspicious AUS with negative FNA (FNAneg). METHODS: With IRB approval, we identified all clinically node-negative (cN0) patients with invasive breast cancer treated with upfront surgery at our tertiary care center between 2016 and 2021. AUS is routinely performed with FNA of suspicious lymph node(s). We compared clinicopathologic characteristics and nodal positivity rates between AUSneg and FNAneg groups. RESULTS: A total of 1580 cN0 patients with invasive breast cancer were analyzed, including 1240 AUSneg and 340 FNAneg patients. The FNAneg group was younger (median age 59.7 years versus 63.5 years, p < 0.001) and had higher clinical T (cT) category (29.1% versus 21.7% with cT2-cT4 disease, p = 0.005). Final axillary pathologic node positivity did not differ significantly between the AUSneg and FNAneg groups (16.5% versus 19.1%, p = 0.25). Among FNAneg patients, 58/340 (17.1%) had a clip placed, with retrieval confirmed in 28/58 (48.3%). Of the 28 retrieved clipped nodes, 27 were sentinel nodes. Final pathologic nodal status (pN+%) did not differ between patients in whom retrieval of the clipped node was confirmed versus not confirmed (28.6% versus 16.7%, p = 0.28). CONCLUSIONS: Both patients with sonographically suspicious node(s) and negative FNA and patients with negative AUS have a similarly low chance of positive nodes. Additionally, routine targeted excision of FNA-negative clipped nodes is not warranted.

A Hierarchical Genotyping Framework Using DNA Melting Temperatures Applied to Adenovirus Species Typing.

Known genetic variation, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. Increased taxonomic detail may be used by clinicians and public health decision-makers to observe circulation patterns, monitor for outbreaks, and inform testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of assay design and sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays to increase classification accuracy. An illustrative hierarchical classification model for human adenovirus (HAdV) species was developed and demonstrated ~95% cross-validated accuracy on a labeled dataset. The model was then applied to a near-real-time surveillance dataset in which deidentified adenovirus detected patient test data from 2018 through 2021 were classified into one of six adenovirus species. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence.

Intraoral Herniation of a Sinonasal Polyp: An Underreported Complication of Maxillary Extraction?

PURPOSE: The aim of the present study was to increase awareness of an underreported surgical complication by presenting the relevant findings of cases of herniated oroantral sinonasal polyp (OASNP) identified from our biopsy service and from previously reported cases. MATERIALS AND METHODS: The present study was a retrospective descriptive case series with a review of the reported data. Cases of OASNP were identified from our biopsy service, and the clinical, radiographic, surgical, and demographic information was retrieved. Previously reported cases of OASNP were also reviewed. RESULTS: We identified 14 cases of OASNP in our biopsy service and an additional 10 reported cases. Overall, OASNP was more prevalent in males (71%). The age range was 19 to 85 years (overall mean, 46.6 years; median, 43.5 years). OASNP typically presented as a red polypoid mass that was frequently pedunculated with a smooth or granular surface. The lesions were located on the maxillary alveolus in the molar region. The most commonly implicated tooth was a maxillary first molar (74%). In some cases, the OASNP had been mistaken for a tumor or pyogenic granuloma. Almost all were at least 1 cm in the greatest dimension, with 43% measuring at least 2 cm in size, and 1 lesion reaching 5 cm in diameter. The reported period for development of the lesion ranged from 2 days to 5 years, with 60% developing within 2 months of the extraction. All lesions had undergone surgical excision. Antibiotic use and surgical closure of the oroantral communication had been described for some of the cases. CONCLUSIONS: The results from our study suggest that herniation of a sinonasal polyp through an oroantral defect could be an underreported complication of maxillary exodontia. Additional research would help to enhance our knowledge and understanding of this interesting condition.

A- and B-site Codoped SrFeO3 Oxygen Sorbents for Enhanced Chemical Looping Air Separation.

Chemical-looping air separation has numerous potential benefits in terms of energy saving and emission reductions. The current study details a combination of density functional theory calculation and experimental efforts to design A- and B-site codoped SrFeO3 perovskites as "low-temperature" oxygen sorbents for chemical-looping air separation. Substitution of the SrFeO3 host structure with Ca and Co lowers oxygen vacancy formation energy by 0.24-0.46 eV and decreases the oxygen release temperature. As a result, Sr1-x Cax Fe1-y Coy O3 (SCFC; x=0.2, 0.0

The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography.

The crystal structure of the trans-acyltransferase (AT) from the disorazole polyketide synthase (PKS) was determined at room temperature to a resolution of 2.5 Å using a new method for the direct delivery of the sample into an X-ray free-electron laser. A novel sample extractor efficiently delivered limited quantities of microcrystals directly from the native crystallization solution into the X-ray beam at room temperature. The AT structure revealed important catalytic features of this core PKS enzyme, including the occurrence of conformational changes around the active site. The implications of these conformational changes for polyketide synthase reaction dynamics are discussed.

Roles of Conserved Active Site Residues in the Ketosynthase Domain of an Assembly Line Polyketide Synthase.

Ketosynthase (KS) domains of assembly line polyketide synthases (PKSs) catalyze intermodular translocation of the growing polyketide chain as well as chain elongation via decarboxylative Claisen condensation. The mechanistic roles of ten conserved residues in the KS domain of Module 1 of the 6-deoxyerythronolide B synthase were interrogated via site-directed mutagenesis and extensive biochemical analysis. Although the C211A mutant at the KS active site exhibited no turnover activity, it was still a competent methylmalonyl-ACP decarboxylase. The H346A mutant exhibited reduced rates of both chain translocation and chain elongation, with a greater effect on the latter half-reaction. H384 contributed to methylmalonyl-ACP decarboxylation, whereas K379 promoted C-C bond formation. S315 played a role in coupling decarboxylation to C-C bond formation. These findings support a mechanism for the translocation and elongation half-reactions that provides a well-defined starting point for further analysis of the key chain-building domain in assembly line PKSs.

Protein-Protein Interactions, Not Substrate Recognition, Dominate the Turnover of Chimeric Assembly Line Polyketide Synthases.

The potential for recombining intact polyketide synthase (PKS) modules has been extensively explored. Both enzyme-substrate and protein-protein interactions influence chimeric PKS activity, but their relative contributions are unclear. We now address this issue by studying a library of 11 bimodular and 8 trimodular chimeric PKSs harboring modules from the erythromycin, rifamycin, and rapamycin synthases. Although many chimeras yielded detectable products, nearly all had specific activities below 10% of the reference natural PKSs. Analysis of selected bimodular chimeras, each with the same upstream module, revealed that turnover correlated with the efficiency of intermodular chain translocation. Mutation of the acyl carrier protein (ACP) domain of the upstream module in one chimera at a residue predicted to influence ketosynthase-ACP recognition led to improved turnover. In contrast, replacement of the ketoreductase domain of the upstream module by a paralog that produced the enantiomeric ACP-bound diketide caused no changes in processing rates for each of six heterologous downstream modules compared with those of the native diketide. Taken together, these results demonstrate that protein-protein interactions play a larger role than enzyme-substrate recognition in the evolution or design of catalytically efficient chimeric PKSs.

Structure and mechanism of assembly line polyketide synthases.

Assembly line polyketide synthases (PKSs) are remarkable biosynthetic machines with considerable potential for structure-based engineering. Several types of protein-protein interactions, both within and between PKS modules, play important roles in the catalytic cycle of a multimodular PKS. Additionally, vectorial biosynthesis is enabled by the energetic coupling of polyketide chain elongation to the channeling of intermediates between successive modules. A combination of high-resolution analysis of smaller PKS components and lower resolution characterization of intact modules and bimodules has yielded insights into the structure and organization of a prototypical assembly line PKS. This review discusses our understanding of key structure-function relationships in this family of megasynthases, along with a recap of key unanswered questions in the field.

A Turnstile Mechanism for the Controlled Growth of Biosynthetic Intermediates on Assembly Line Polyketide Synthases.

Vectorial polyketide biosynthesis on an assembly line polyketide synthase is the most distinctive property of this family of biological machines, while providing the key conceptual tool for the bioinformatic decoding of new antibiotic pathways. We now show that the action of the entire assembly line is synchronized by a previously unrecognized turnstile mechanism that prevents the ketosynthase domain of each module from being acylated by a new polyketide chain until the product of the prior catalytic cycle has been passed to the downstream module from the corresponding acyl carrier protein domain. The turnstile is closed by virtue of tight coupling to the signature decarboxylative condensation reaction catalyzed by the ketosynthase domain of each polyketide synthase module. Reopening of the turnstile is coupled to the eventual chain translocation step that vacates the module. At the maximal rate of substrate turnover, one would expect the chain release step to initiate a cascade of chain translocation events that sequentially migrate back upstream, thereby repriming each module and setting up the assembly line for the next round of polyketide chain elongation.

The origin of regional failure in oral cavity squamous cell carcinoma with pathologically negative neck metastases.

IMPORTANCE: Squamous cell carcinoma of the oral cavity (OSCC) is a common malignant tumor worldwide. OBJECTIVE: To determine if regional failure in patients with OSCC and pathologically negative neck nodes (pN-) is due to an incomplete sampling procedure during surgery. DESIGN, SETTING, AND PARTICIPANTS: We retrospectively reviewed the medical records of 2258 patients from 11 cancer centers worldwide who underwent neck dissection for OSCC (1990-2011) and who were pN-. Of those, 345 had clinical evidence of nodal metastases (cN+) on radiologic workup. The neck specimens were available for reanalysis in 193 patients. Survival rates were calculated using the Kaplan-Meier graphs and analyzed by multivariable analysis. MAIN OUTCOMES AND MEASURES: Five-year overall survival (OS), disease-specific survival (DSS), and disease-free survival (DFS). RESULTS: Resectioning and analysis of the neck dissection specimens in the cN+/pN- subgroup revealed false-negative results in 29 (15%) of 193 patients. The negative predictive value of the initial pathologic examination was 85%. The 5-year OS and DSS in the cN-/pN- group were 77.6% and 87.2%, respectively. The 5-year OS and DSS of the cN+/pN- group were 62.6% and 78.5%, respectively (P < .001). In multivariable analysis, cN+ classification was significantly associated with poor OS (hazard ratio [HR], 1.7; 95% CI, 1.1-3.8; P = .03) and poor DSS (HR, 1.46; 95% CI, 1.1-4.1; P = .04). A cN+ classification was associated with lower DFS (66.3% vs 76.2%; P = .05) and lower regional recurrence-free survival (68.6% vs 78.8%; P = .02) but not with local (P = .20) or distant recurrence (P = .80). CONCLUSIONS AND RELEVANCE: Pathologic staging underestimates the incidence of nodal metastases in cN+ disease. After correction for pathologically missed nodal metastases, radiologic evidence of neck nodes is an independent predictor of outcome, suggesting that traditional sampling during surgery might miss metastases, and this fact might explain the origin of treatment failure in these patients.

Comparative analysis of the substrate specificity of trans- versus cis-acyltransferases of assembly line polyketide synthases.

Due to their pivotal role in extender unit selection during polyketide biosynthesis, acyltransferase (AT) domains are important engineering targets. A subset of assembly line polyketide synthases (PKSs) are serviced by discrete, trans-acting ATs. Theoretically, these trans-ATs can complement an inactivated cis-AT, promoting introduction of a noncognate extender unit. This approach requires a better understanding of the substrate specificity and catalytic mechanism of naturally occurring trans-ATs. We kinetically analyzed trans-ATs from the disorazole and kirromycin synthases and compared them to a representative cis-AT from the 6-deoxyerythronolide B synthase (DEBS). During transacylation, the disorazole AT favored malonyl-CoA over methylmalonyl-CoA by >40000-fold, whereas the kirromycin AT favored ethylmalonyl-CoA over methylmalonyl-CoA by 20-fold. Conversely, the disorazole AT had broader specificity than its kirromycin counterpart for acyl carrier protein (ACP) substrates. The presence of the ACP had little effect on the specificity (k(cat)/K(M)) of the cis-AT domain for carboxyacyl-CoA substrates but had a marked influence on the corresponding specificity parameters for the trans-ATs, suggesting that these enzymes do not act strictly by a canonical ping-pong mechanism. To investigate the relevance of the kinetic analysis of isolated ATs in the context of intact PKSs, we complemented an in vitro AT-null DEBS assembly line with either trans-AT. Whereas the disorazole AT efficiently complemented the mutant PKS at substoichiometric protein ratios, the kirromycin AT was considerably less effective. Our findings suggest that knowledge of both carboxyacyl-CoA and ACP specificity is critical to the choice of a trans-AT in combination with a mutant PKS to generate novel polyketides.

In vitro reconstitution and analysis of the 6-deoxyerythronolide B synthase.

Notwithstanding an extensive literature on assembly line polyketide synthases such as the 6-deoxyerythronolide B synthase (DEBS), a complete naturally occurring synthase has never been reconstituted in vitro from purified protein components. Here, we describe the fully reconstituted DEBS and quantitatively characterize some of the properties of the assembled system that have never been explored previously. The maximum turnover rate of the complete hexamodular system is 1.1 min(-1), comparable to the turnover rate of a truncated trimodular derivative (2.5 min(-1)) but slower than that of a bimodular derivative (21 min(-1)). In the presence of similar concentrations of methylmalonyl- and ethylmalonyl-CoA substrates, DEBS synthesizes multiple regiospecifically modified analogues, one of which we have analyzed in detail. Our studies lay the foundation for biochemically interrogating and rationally engineering polyketide assembly lines in an unprecedented manner.

Cyanide detection using a triazolopyridinium salt.

A triazolopyridinium salt chemodosimeter has been developed that displays a 60-fold enhancement in fluorescence upon reaction with cyanide. The novel, fast, selective and sensitive reaction-based indicator relies on the pseudopericyclic ring opening of the bridgehead nitrogen-containing detector.

"I wouldn't look at it as stress": conceptualizations of caregiver stress among low-income families of children with asthma.

Low-income caregivers of children with asthma experience multiple stressors, likely worsening family health. As part of Community Action Against Asthma's community-based participatory research partnership, researchers conducted 40 qualitative semi-structured interviews and quantitative surveys with low-income caregivers of children with asthma in Detroit, Michigan. Participants described daily childhood asthma experiences and completed scales including the Peds Quality of Life Family Impact Module and Zarit Burden Caregiver Scale. Quantitative scale findings suggested participants are moderately stressed or affected by their child's illness. While there was some accordance between qualitative and quantitative findings, qualitative findings additionally captured many relevant life stressors, seemingly overlooked or conflated in scale responses. Many participants described asthma as part of childrearing, rather than as a stressor or burden. Findings encourage improvement of clinical, psychometric assessments used to measure and address stressors that shape health for many families with children with asthma.

FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection.

The ideal clinical diagnostic system should deliver rapid, sensitive, specific and reproducible results while minimizing the requirements for specialized laboratory facilities and skilled technicians. We describe an integrated diagnostic platform, the "FilmArray", which fully automates the detection and identification of multiple organisms from a single sample in about one hour. An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis. Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time. These features make the system well-suited for molecular detection of infectious agents. Validation of the FilmArray technology was achieved through development of a panel of assays capable of identifying 21 common viral and bacterial respiratory pathogens. Initial testing of the system using both cultured organisms and clinical nasal aspirates obtained from children demonstrated an analytical and clinical sensitivity and specificity comparable to existing diagnostic platforms. We demonstrate that automated identification of pathogens from their corresponding target amplicon(s) can be accomplished by analysis of the DNA melting curve of the amplicon.

Mathematically modeling PCR: an asymptotic approximation with potential for optimization.

A mathematical model for PCR (Polymerase Chain Reaction) is developed using the law of mass action and simplifying assumptions regarding the structure of the reactions. Differential equations are written from the chemical equations, preserving the detail of the complementary DNA single strand being extended one base pair at a time. The equations for the annealing stage are solved analytically. The method of multiple scales is used to approximate solutions for the extension stage, and a map is developed from the solutions to simulate PCR. The map recreates observed PCR well, and gives us the ability to optimize the PCR process. Our results suggest that dynamically optimizing the extension and annealing stages of individual samples may significantly reduce the total time for a PCR run. Moreover, we present a nearly optimal design that functions almost as well and does not depend on the specifics of a single reaction, and so would work for multi sample and multiplex applications.