Making an accurate diagnosis of anterior mediastinal lesions: a proposal for a new diagnostic algorithm from the BTOG Thymic Malignancies Special Interest Group

Due to the rising demand in cross-sectional thoracic imaging, anterior mediastinal lesions are being identified with increasing frequency. Following iterative and multidisciplinary discussions, the BTOG Thymic Malignancies Special Interest Group have developed an algorithm to standardise the diagnostic approach for these relatively uncommon but important conditions which span from benign (thymic remnant, thymic hyperplasia and thymic cysts) to suspected localised thymomas to suspected more aggressive malignancy (thymic carcinoma, lymphoma and germ cell tumours). For each condition, we provide a brief description, an overview of the key radiological findings and a description of the proposed algorithm including the rationale behind the recommendations. We also highlight the role of magnetic resonance (MR) imaging for the characterisation of anterior mediastinal masses in specific indications when the necessary local resources and expertise exist. In addition, we hope this provides the rationale for service development in MR of the anterior mediastinum where current resource and expertise requires development. Through this standardised pathway, we hope to drive improvements in patient care by rationalising surveillance schedules, avoiding unnecessary resections of benign entities with their associated morbidity and optimising the diagnostic work-up prior to the appropriate treatment of anterior mediastinal malignancies.

The exocyst complex and intracellular vesicles mediate soluble protein trafficking to the primary cilium

The efficient transport of proteins into the primary cilium is a crucial step for many signaling pathways. Dysfunction of this process can lead to the disruption of signaling cascades or cilium assembly, resulting in developmental disorders and cancer. Previous studies on the protein delivery to the cilium were mostly focused on the membrane-embedded receptors. In contrast, how soluble proteins are delivered into the cilium is poorly understood. In our work, we identify the exocyst complex as a key player in the ciliary trafficking of soluble Gli transcription factors. In line with the known function of the exocyst in intracellular vesicle transport, we demonstrate that soluble proteins, including Gli2/3 and Lkb1, can use the endosome recycling machinery for their delivery to the primary cilium. Finally, we identify GTPases: Rab14, Rab18, Rab23, and Arf4 that are involved in vesicle-mediated Gli protein ciliary trafficking. Our data pave the way for a better understanding of ciliary transport and uncover transport mechanisms inside the cell.

Reducing the vicissitudes of heterologous prochiral substrate catalysis by alcohol dehydrogenases through machine learning algorithms

Alcohol dehydrogenases (ADHs) are popular catalysts for synthesizing chiral synthons a vital step for active pharmaceutical intermediate (API) production. They are grouped into three superfamilies namely, medium-chain (MDRs), short-chain dehydrogenase/reductases (SDRs), and iron-containing alcohol dehydrogenases. The former two are used extensively for producing various chiral synthons. Many studies screen multiple enzymes or engineer a specific enzyme for catalyzing a substrate of interest. These processes are resource-intensive and intricate. The current study attempts to decipher the ability to match different ADHs with their ideal substrates using machine learning algorithms. We explore the catalysis of 284 antibacterial ketone intermediates, against MDRs and SDRs to demonstrate a unique pattern of activity. To facilitate machine learning we curated a dataset comprising 33 features, encompassing 4 descriptors for each compound. Subsequently, an ensemble of machine learning techniques viz. Partial Least Squares (PLS) regression, k-Nearest Neighbors (kNN) regression, and Support Vector Machine (SVM) regression, was harnessed. Moreover, the assimilation of Principal Component Analysis (PCA) augmented precision and accuracy, thereby refining and demarcating diverse compound classes. As such, this classification is useful for discerning substrates amenable to diverse alcohol dehydrogenases, thereby mitigating the reliance on high-throughput screening or engineering in identifying the optimal enzyme for specific substrate.

Increased odds for COVID-19 infection among individuals with periodontal disease

OBJECTIVES

Periodontal disease has been linked to multiple systemic conditions, but the relationship with COVID-19 still needs to be elucidated. We hypothesized that periodontal disease may be associated with COVID-19 infection.

MATERIALS AND METHODS

This study utilized cross-sectional data to establish the strength of the association between periodontal disease and COVID-19 infection. The University of Florida Health Center's i2b2 patient's registry was used to generate patient counts through ICD-10 diagnostic codes. Univariate descriptive statistics of the patient population and logistic regression to estimate odds ratios of associations between periodontal disease and COVID-19 infection were used for analysis.

RESULTS

Patients with periodontal disease were 4.4 times more likely to be positively diagnosed with COVID-19 than patients without PD. Associations remained similar and robust (P value < 0.0001) after adjustment for age (OR = 4.34; 95% CI, 3.68-5.09), gender (OR = 4.46; 95% CI, 3.79-5.23), and smoking status (OR = 4.77; 95% CI, 4.04-5.59). Associations were smaller but remained robust (P value < 0.0001) after adjusting for race (OR = 2.83; 95% CI, 2.40-3.32), obesity (OR = 2.53; 95% CI, 2.14-2.98), diabetes (OR = 3.32; 95% CI, 2.81-3.90), and cardiovascular disease (OR = 2.68; 95% CI, 2.27-3.14).

CONCLUSIONS

Periodontal disease is significantly associated with increased odds for COVID-19 infection.

CLINICAL RELEVANCE

With the caveat of a cross-sectional study design, these results suggest that periodontal disease may increase the odds for COVID-19 infection.

A curated list of targeted optimized promiscuous ketoreductases (TOP-K)

Enzymes are either specific or promiscuous catalysts in nature. The latter is portrayed by protein families like CYP450Es, Aldo-ketoreductases and short/medium-chain dehydrogenases which participate in detoxification or secondary metabolite production. However, enzymes are evolutionarily 'blind' to an ever-increasing synthetic substrate library. Industries and laboratories have circumvented this by high-throughput screening or site-specific engineering to synthesize the product of interest. However, this paradigm entails cost and time-intensive one-enzyme, one-substrate catalysis model. One of the superfamilies regularly used for chiral alcohol synthesis are short-chain dehydrogenases/reductases (SDRs). Our objective is to determine a superset of promiscuous SDRs that can catalyze multiple ketones. They are typically classified into shorter 'Classical' and longer 'Extended' type ketoreductases. However, current analysis of modelled SDRs reveals a length-independent conserved N-terminus Rossmann-fold and a variable substrate-binding C-terminus substrate-binding region for both categories. The latter is recognized to influence the enzyme's flexibility and substrate promiscuity and we hypothesize these properties are directly linked with each other. We tested this by catalyzing ketone intermediates with the essential and specific enzyme: FabG_E, as well as non-essential SDRs such as UcpA and IdnO. The experimental results confirmed this biochemical-biophysical association, making it an interesting filter for ascertaining promiscuous enzymes. Hence, we created a dataset of physicochemical properties derived from the protein sequences and employed machine learning algorithms to examine potential candidates. This resulted in 24 targeted optimized ketoreductases (TOP-K) from 81 014 members. The experimental validation of select TOP-Ks demonstrated the correlation between the C-terminal lid-loop structure, enzyme flexibility and turnover rate on pro-pharmaceutical substrates.

The conundrum of bacteria-specific antibiotics

There is a continual debate on the pros and cons of broad-spectrum versus pathogen-specific antibiotics. The unmet need for a solution for antimicrobial resistance (AMR) has put this argument into sharper focus. A shortage of clinically differentiated antibiotics in late-stage clinical development coupled with the global unmet need in the face of the AMR onslaught has exacerbated the treatment options of drug-resistant bacterial infections. An added dimension to this problem is the current understanding of dysbiosis caused by antibiotics, often leading to negative fallout in immunocompromised patients. We attempt to deconstruct the nuances of this debate from an antibiotics discovery and a clinical standpoint.

SELF-SUPERVISED LEARNING WITH RADIOLOGY REPORTS, A COMPARATIVE ANALYSIS OF STRATEGIES FOR LARGE VESSEL OCCLUSION AND BRAIN CTA IMAGES

Scarcity of labels for medical images is a significant barrier for training representation learning approaches based on deep neural networks. This limitation is also present when using imaging data collected during routine clinical care stored in picture archiving communication systems (PACS), as these data rarely have attached the high-quality labels required for medical image computing tasks. However, medical images extracted from PACS are commonly coupled with descriptive radiology reports that contain significant information and could be leveraged to pre-train imaging models, which could serve as starting points for further task-specific fine-tuning. In this work, we perform a head-to-head comparison of three different self-supervised strategies to pre-train the same imaging model on 3D brain computed tomography angiogram (CTA) images, with large vessel occlusion (LVO) detection as the downstream task. These strategies evaluate two natural language processing (NLP) approaches, one to extract 100 explicit radiology concepts (Rad-SpatialNet) and the other to create general-purpose radiology reports embeddings (DistilBERT). In addition, we experiment with learning radiology concepts directly or by using a recent self-supervised learning approach (CLIP) that learns by ranking the distance between language and image vector embeddings. The LVO detection task was selected because it requires 3D imaging data, is clinically important, and requires the algorithm to learn outputs not explicitly stated in the radiology report. Pre-training was performed on an unlabeled dataset containing 1,542 3D CTA - reports pairs. The downstream task was tested on a labeled dataset of 402 subjects for LVO. We find that the pre-training performed with CLIP-based strategies improve the performance of the imaging model to detect LVO compared to a model trained only on the labeled data. The best performance was achieved by pre-training using the explicit radiology concepts and CLIP strategy.

Identification of key amino acid residues in OqxB mediated efflux of fluoroquinolones using site-directed mutagenesis

OqxB belongs to the RND (Resistance-Nodulation-Division) efflux pump family, recognized widely as a major contributor towards enhancing antimicrobial resistance. It is known to be predominantly present in all Klebsiella spp. and is attributed for its role in increasing resistance against an array of antibiotics like nitrofurantoin, quinolones, β-lactams and colistin. However, the presence of oqxB encoding this efflux pump is not limited only to Klebsiella spp., but is also found to occur via horizontal gene transfer in other bacterial genera like Escherichia coli, Enterobacter cloacae and Salmonella spp. Recently, we reported the crystal structure of OqxB and its structure-function relationship required for the efflux of fluoroquinolones. Extending these findings further, we characterized the structural architecture of this efflux pump along with identifying some critical amino acids at the substrate binding domain of OqxB. Based on our in silico modelling studies, both, hydrophobic residues (F180, L280, L621, F626) and polar residues (R48, E50, E184, R157, R774) were found to be located at this site. The present work reports the importance of these key amino acid residues and the crucial ion-pair interactions at the substrate-binding pocket, thereby establishing their role in OqxB mediated efflux and the resultant resistance development against fluoroquinolones.

"It's a decision I have to make": Patient perspectives on smoking and cessation after lung cancer screening decisions

Few studies exist showing that involvement in lung cancer screening (LCS) leads to a change in rates of cigarette smoking. We investigated LCS longitudinally to determine whether teachable moments for smoking cessation occur downstream from the initial provider-patient LCS shared decision-making discussion and self-reported effects on smoking behaviors. We performed up to two successive semi-structured interviews to assess the experiences of 39 individuals who formerly or currently smoked cigarettes who underwent LCS decision-making discussions performed during routine care from three established US medical center LCS programs.

The majority of those who remembered hearing about the importance of smoking cessation after LCS-related encounters did not report communication about smoking influencing their motivation to quit or abstain from smoking, including patients who were found to have pulmonary nodules. Patients experienced little distress related to LCS discussions. Patients reported that there were other, more significant, reasons for quitting or abstinence. They recommended clinicians continue to ask about smoking at every clinical encounter, provide information comparing the benefits of LCS with those of quitting smoking, and have clinicians help them identify triggers or other motivators for improving smoking behaviors. Our findings suggest that there may be other teachable moment opportunities outside of LCS processes that could be utilized to motivate smoking reduction or cessation, or LCS processes could be improved to integrate cessation resources.

Tracking the source of contaminant lead in children's blood

Pb isotope ratios are used for apportioning the sources of Pb in the blood of children (ages 1-6) screened for high blood Pb levels (>5 μg/dL) surrounding urban areas of Kansas City, MO. We compared Pb isotope ratios measured in the child's blood with those of the most likely sources of Pb in that child's home environment. The environmental sources sampled consisted of topsoils, paints, occupational sources (e.g., oil rig workers' uniforms, mechanics' clothes), indoor air filters, dusts, and dietary sources (e.g., spices). Blood lead levels (BLL) ranged from 2.9 to 12.7 μg/dL in children from the five homes participating in this study. Measurements of ²⁰⁶Pb/²⁰⁴Pb, ²⁰⁷Pb/²⁰⁴Pb and ²⁰⁸Pb/²⁰⁴Pb isotope ratios were made by multi-collector ICP-MS. Comparison of the Pb isotope ratios in home environment samples versus those in the child's blood in each home allowed the identification of possible sources of a child's Pb exposure in three homes. In five homes investigated, children's blood Pb levels were most likely to be derived from dusts inside, and topsoil outside, the homes, or a mixture thereof. In one case, blood Pb was derived from turmeric spice and, in another, the Pb was derived from paint. It is not always possible to directly link high BLLs to the environmental sources collected when Pb isotope ratios of the environmental samples did not overlap with those of the blood.

Search for Subsolar-Mass Binaries in the First Half of Advanced LIGO's and Advanced Virgo's Third Observing Run

We report on a search for compact binary coalescences where at least one binary component has a mass between 0.2  M_{⊙} and 1.0  M_{⊙} in Advanced LIGO and Advanced Virgo data collected between 1 April 2019 1500 UTC and 1 October 2019 1500 UTC. We extend our previous analyses in two main ways: we include data from the Virgo detector and we allow for more unequal mass systems, with mass ratio q≥0.1. We do not report any gravitational-wave candidates. The most significant trigger has a false alarm rate of 0.14  yr^{-1}. This implies an upper limit on the merger rate of subsolar binaries in the range [220-24200]  Gpc^{-3} yr^{-1}, depending on the chirp mass of the binary. We use this upper limit to derive astrophysical constraints on two phenomenological models that could produce subsolar-mass compact objects. One is an isotropic distribution of equal-mass primordial black holes. Using this model, we find that the fraction of dark matter in primordial black holes in the mass range 0.2  M_{⊙}<m_{PBH}<1.0  M_{⊙} is f_{PBH}≡Ω_{PBH}/Ω_{DM}≲6%. This improves existing constraints on primordial black hole abundance by a factor of ∼3. The other is a dissipative dark matter model, in which fermionic dark matter can collapse and form black holes. The upper limit on the fraction of dark matter black holes depends on the minimum mass of the black holes that can be formed: the most constraining result is obtained at M_{min}=1  M_{⊙}, where f_{DBH}≡Ω_{DBH}/Ω_{DM}≲0.003%. These are the first constraints placed on dissipative dark models by subsolar-mass analyses.

Validated In Silico Population Model of Escherichia coli

Flux balance analysis (FBA) and ordinary differential equation models have been instrumental in depicting the metabolic functioning of a cell. Nevertheless, they demonstrate a population's average behavior (summation of individuals), thereby portraying homogeneity. However, living organisms such as Escherichia coli contain more biochemical reactions than engaging metabolites, making them an underdetermined and degenerate system. This results in a heterogeneous population with varying metabolic patterns. We have formulated a population systems biology model that predicts this degeneracy by emulating a diverse metabolic makeup with unique biochemical signatures. The model mimics the universally accepted experimental view that a subpopulation of bacteria, even under normal growth conditions, renders a unique biochemical state, leading to the synthesis of metabolites and persister progenitors of antibiotic resistance and biofilms. We validate the platform's predictions by producing commercially important heterologous (isobutanol) and homologous (shikimate) metabolites. The predicted fluxes are tested in vitro resulting in 32- and 42-fold increased product of isobutanol and shikimate, respectively. Moreover, we authenticate the platform by mimicking a bacterial population in the presence of glyphosate, a metabolic pathway inhibitor. Here, we observe a fraction of subsisting persisters despite inhibition, thus affirming the signature of a heterogeneous populace. The platform has multiple uses based on the disposition of the user.

A Systems Approach to Remediating Human Exposure to Arsenic and Fluoride From Overexploited Aquifers

In semiarid agricultural regions, aquifers have watered widespread economic development. Falling water tables, however, drive up energy costs and can make the water toxic for human consumption. The study area is located in central Mexico, where arsenic and fluoride are widely present at toxic concentrations in well water. We simulated the holistic outcomes from three pumping scenarios over 100 years (2020-2120); (S1) pumping rates increase at a similar rate to the past 40 years, (S2) remain constant, or (S3) decrease. Under scenario S1, by 2120, the depth to water table increased to 426 m and energy consumption for irrigation increased to 4 × 10⁹ kWh/yr. Arsenic and fluoride concentrations increased from 14 to 46 μg/L and 1.0 to 3.6 mg/L, respectively. The combined estimated IQ point decrements from drinking untreated well water lowered expected incomes in 2120 by 27% compared to what they would be with negligible exposure levels. We calculated the 100-year Net Present Value (NPV) of each scenario assuming the 2020 average crop value to water footprint ratio of 0.12 USD/m³. Without drinking water mitigation, S1 and S3 yielded relative NPVs of -5.96 × 10⁹ and 1.51 × 10⁹ USD, respectively, compared to the base case (S2). The relative NPV of providing blanket reverse osmosis treatment, while keeping pumping constant (S2), was 11.55 × 10⁹ USD and this gain increased when combined with decreased pumping (S3). If a high value, low water footprint crop was substituted (broccoli, 1.51 USD/m³), the net gains from increasing pumping were similar in size to those of implementing blanket drinking water treatment.

Validated In Silico Model for Biofilm Formation in Escherichia coli

Using Escherichia coli as the representative biofilm former, we report here the development of an in silico model built by simulating events that transform a free-living bacterial entity into self-encased multicellular biofilms. Published literature on ∼300 genes associated with pathways involved in biofilm formation was curated, static maps were created, and suitably interconnected with their respective metabolites using ordinary differential equations. Precise interplay of genetic networks that regulate the transitory switching of bacterial growth pattern in response to environmental changes and the resultant multicomponent synthesis of the extracellular matrix were appropriately represented. Subsequently, the in silico model was analyzed by simulating time-dependent changes in the concentration of components by using the R and python environment. The model was validated by simulating and verifying the impact of key gene knockouts (KOs) and systematic knockdowns on biofilm formation, thus ensuring the outcomes were comparable with the reported literature. Similarly, specific gene KOs in laboratory and pathogenic E. coli were constructed and assessed. MiaA, YdeO, and YgiV were found to be crucial in biofilm development. Furthermore, qRT-PCR confirmed the elevation of expression in biofilm-forming clinical isolates. Findings reported in this study offer opportunities for identifying biofilm inhibitors with applications in multiple industries. The application of this model can be extended to the health care sector specifically to develop novel adjunct therapies that prevent biofilms in medical implants and reduce emergence of biofilm-associated resistant polymicrobial-chronic infections. The in silico framework reported here is open source and accessible for further enhancements.

Blood pressure variability in hypertension patients in Indian clinical settings

Funding Acknowledgements

Type of funding sources: None.

Background

 Blood pressure variability (BPV) is a potential predictor for complications such as coronary artery disease, heart failure, stroke, and all-cause death, independently of mean blood pressure (BP) in patients with hypertension.(1)

Objective

 The survey was carried out to seek the opinion of Indian clinicians on the burden, measurement  and management of BPV in patients with hypertension.

Method

 This PAN-India survey used a structured web-based objective questionnaire that was administered to 200 clinicians via google forms. The responses were analyzed descriptively.

Results

 This study suggests that &gt;80% of the clinicians reported that 10-40% of their hypertensive patients experience BPV while 13% and 6.5% respectively, reported having BPV issues in &lt;10% and &gt;40% of their patients.

A large majority of the clinicians (88.5%) agreed that effective control of BPV in hypertensive patients exerts benefits to prevent complications like target organ damage, cardiovascular disease and mortality.

A combination of home and office BP monitoring was the most recommended approach for the measurement of BPV by 28% of the clinicians, followed by home monitoring (23%) &gt; ambulatory monitoring (22.5%) &gt; combination of ambulatory and office monitoring (21%) &gt; office monitoring (4.5%) of BP. A majority of clinicians opted for angiotensin receptor blocker (ARB) + calcium channel blocker (CCB), ARB + beta blocker (BB) and ARB + diuretic as most preferred antihypertensive combination for effective control of BP and BPV (Figure 1). In particular, the clinicians opined for Telmisartan + Amlodipine (45.5%) &gt; Telmisartan + Chorthalidone (27%) &gt; Telmisartan + Cilnidipine (14%) &gt; Telmisartan + Hydrochlorothiazide (13%) as the preferred antihypertensive combinations.

41% and 30.5% of the clinicians reported that they would shift their patients with high BPV to a dual and a triple combination of antihypertensives, respectively followed by increasing the antihypertensive dose (18%) and shifting to new antihypertensive medication (8.5%).

Conclusion

 The survey underlined the considerable prevalence of BPV in hypertensive individuals and that its control can be beneficial in reducing the risk of future complications. The study also reflects that both home and office BP monitoring are important to identify BPV while ARBs particularly, Telmisartan in combination with CCB or a diuretic is the preferred regimen for effective control of BP and BPV. Abstract Figure 1

BSAC Vanguard Series: The future of drug development and the tension between access and excess

There is a crying need for a new broad-spectrum antibiotic. The global unmet need has energized governments and researchers alike. We may soon have the next antibiotics coming to the aid of patients after a drought of over half a century. However, we need to traverse a complex causeway between access to new antibiotics and their overuse. In an ICU setting where time is premium, identifying the causative organism and its resistance pattern in the time window is often impossible; physicians may be forced to prescribe the latest antibiotics. This practice in the long term may give rise to a rapid spread of resistance among microbes. There is an urgent need to do a cost-benefit analysis of easy access and use of the new antibiotics.

Novel non intrusive continuous use ZeBox technology to trap and kill airborne microbes

Preventing nosocomial infection is a major unmet need of our times. Existing air decontamination technologies suffer from demerits such as toxicity of exposure, species specificity, noxious gas emission, environment-dependent performance and high power consumption. Here, we present a novel technology called “ZeBox” that transcends the conventional limitations and achieves high microbicidal efficiency. In ZeBox, a non-ionizing electric field extracts naturally charged microbes from flowing air and deposits them on engineered microbicidal surfaces. The surface’s three dimensional topography traps the microbes long enough for them to be inactivated. The electric field and chemical surfaces synergistically achieve rapid inactivation of a broad spectrum of microbes. ZeBox achieved near complete kill of airborne microbes in challenge tests (5–9 log reduction) and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$>90\%$$\end{document}>90% efficiency in a fully functional stem cell research facility in the presence of humans. Thus, ZeBox fulfills the dire need for a real-time, continuous, safe, trap-and-kill air decontamination technology.

Azaindole Based Potentiator of Antibiotics against Gram-Negative Bacteria

We discovered azaindole-based compounds with weak innate activity that exhibit substantial potentiation of antibacterial activities of different antibiotics, viz., rifampicin, erythromycin, solithromycin, and novobiocin in Gram-negative bacteria. In the presence of the azaindole derivatives, these antibiotics exhibited submicromolar minimum inhibitory concentrations (MICs) against Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. The fold improvements in MIC of these antibiotics that were otherwise weak or inactive on their own against these bacteria were also observed against drug-resistant clinical isolates. Our studies indicate that this selective potentiation is probably through destabilization of the outer membrane's integrity, known to be regulated by the lipopolysaccharides (LPS). Thus, the azaindole based compounds described here open opportunities for those antibiotics that are otherwise ineffective due to LPS mediated entry barriers in Gram-negative bacteria.

41 Low Flow Priapism as A Complication of Covid-19 Infection

On 12 March 2020 the World Health Organisation (WHO) declared a pandemic of SARS-COV-2(Covid 19). We report a case of a 58-year-old man who presented with dyspnoea, pyrexia and a dry cough. Upon admission he was noted to be in a severe Type 1 Respiratory Failure with Bi-lateral pulmonary infiltrates suggestive of Covid 19 infection. Rapid transfer to ITU ensued with Intubation, Ventilation and Inotropic support. Priapism was noted a day into admission which was subsequently aspirated by the Urology team, achieving detumescence. Priapism is a state of persistent penile erection that continues for 4 hours beyond sexual stimulation. We describe the role of thrombosis, dysregulation of the clotting cascade and acute disseminated intravascular coagulation (DIC) as shared pathologies in priapism and Covid 19 infection. We highlight the importance of vigilance for extra-pulmonary manifestations of Covid-19 and feel that the pro-thrombotic phenomena exhibited by Covid-19 infection affects distal vasculature in the same manner as Low Flow Priapism and hence explains why our patient suffered from this particular urological complication

1097 17 Years of Treating Deep Sternal Wound Infections at A Single Institution: Outcomes and Lessons Learned

Introduction

Deep sternal wound infections (DSWI) are a serious complication following cardiac surgery that comprise of any infection penetrating the subcutaneous tissue of the sternum. DSWI have been found to increase mortality and worsen prognostic outcomes following surgery.

Method

We conducted a retrospective cohort study using hospital e-records from 2000 to 2017 of all adult patients operated on with a median sternotomy at our institution. Univariate and multivariate analysis along with mortality and Kaplan-Meier survival curves compared the DSWI population against the remaining study population, using SPSS-25 software.

Results

Of 15521 total patients in the study, 145 (0.9%) suffered a DSWI. Variables that were associated with DSWI included age at operation (p = 0.019), gender (p = 0.007), BMI (p = 0.001), diabetes (p &lt; 0.0001), renal disease (p = 0.008), operative urgency (p = 0.007), type of operation (p = 0.02), Euroscore (p = &lt;0.0001), bypass-time (p = 0.038) and crossclamp-time (p = 0.008). A logistic regression encompassing significant variables revealed that gender (p = 0.031 CI 1.45-1.96), BMI (p &lt; 0.0001 CI 1.03-1.10), diabetes (p = 0.007 CI 1.20-3.67) and type of operation (p = 0.018 CI 1.23-1.87) remained significant when covariate contribution was eliminated. DSWI subgroup mortality was insignificant at 30 days (3.4%vs2.9%, p = 0.68) but significantly worse at 90 days (8.3%vs3.7%, p = 0.004) and at 1 year (17.2%vs5.4%, p &lt; 0.0001). Kaplan-Meier analysis depicted a significantly worse survival distribution for the DSWI population compared to rest of study (Log-Rank&lt;0.05).

Conclusions

At our centre, DSWI are attributable to certain modifiable and set demographics and contribute heavily to medium-term mortality. A better understanding of DSWI risk factors may pinpoint those at risk and benefit the multidisciplinary team to ultimately reduce the rate of DSWI.

Clinical standards for the assessment, management and rehabilitation of post-TB lung disease

BACKGROUND: Increasing evidence suggests that post-TB lung disease (PTLD) causes significant morbidity and mortality. The aim of these clinical standards is to provide guidance on the assessment and management of PTLD and the implementation of pulmonary rehabilitation (PR).METHODS: A panel of global experts in the field of TB care and PR was identified; 62 participated in a Delphi process. A 5-point Likert scale was used to score the initial ideas for standards and after several rounds of revision the document was approved (with 100% agreement).RESULTS: Five clinical standards were defined: Standard 1, to assess patients at the end of TB treatment for PTLD (with adaptation for children and specific settings/situations); Standard 2, to identify patients with PTLD for PR; Standard 3, tailoring the PR programme to patient needs and the local setting; Standard 4, to evaluate the effectiveness of PR; and Standard 5, to conduct education and counselling. Standard 6 addresses public health aspects of PTLD and outcomes due to PR.CONCLUSION: This is the first consensus-based set of Clinical Standards for PTLD. Our aim is to improve patient care and quality of life by guiding clinicians, programme managers and public health officers in planning and implementing adequate measures to assess and manage PTLD.

Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae

OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.

Learnings from past failures: Future routes of antimicrobial drug discovery

Despite the unprecedented unmet need to discover new antibiotics, only a few molecules have been registered for clinical use. This shortage is primarily based on the scientific failure in the postgenomic era of drug discovery. It appears counterintuitive that knowledge of the bacterial genome was followed by the failure to produce new antibiotics using the paradigm of target-driven drug discovery. Here, I discuss the causes of the failures and also describe how small biotech is mitigating these risks and moving forward using new strategies to identify new antibiotics.

The Influence of Local Strain Distribution on the Effective Electrical Resistance of Carbon Black Filled Natural Rubber

A monotonous relation between strain and measured electric resistance is highly appreciated in stretchable elastomer sensors. In real-life application the voids or technological holes of strained samples often induce non-homogeneous local strain. The present article focused on studying the effect of non-homogeneous local strain on measured direct current (DC) effective electric resistance (EER) on samples of natural rubber (NR), reinforced with 50, 60 and 70 phr of carbon black (CB). Samples were imparted geometrical inhomogeneities to obtain varied local strains. The resulting strain distribution was analyzed using Digital Image Correlation (DIC). EER exhibited a well-detectable influence of locations of inhomogeneities. Expectedly, the EER globally decreased with an increase in CB loading, but showed a steady increase as a function of strain for 50 and 60 phr over the complete testing protocol. Interestingly, for 70 phr of CB, under the same testing conditions, an alternating trend in EER was encountered. This newly observed behavior was explained through a novel hypothesis—“current propagation mode switching phenomenon”. Finally, experimentally measured EERs were compared with the calculated ones, obtained by summing the global current flow through a diversity of strain dependent resistive domains.

A Comparison of Web-Based Cancer Risk Calculators That Inform Shared Decision-making for Lung Cancer Screening

INTRODUCTION

To align patient preferences and understanding with harm-benefit perception, the Centers for Medicare & Medicaid Services (CMS) mandates that providers engage patients in a collaborative shared decision-making (SDM) visit before LDCT. Nonetheless, patients and providers often turn instead to the web for help making decisions. Several web-based lung cancer risk calculators (LCRCs) provide risk predictions and screening recommendations; however, the accuracy, consistency, and subsequent user interpretation of these predictions between LCRCs is ambiguous. We conducted a systematic review to assess this variability.

DESIGN

Through a systematic Internet search, we identified 10 publicly available LCRCs and categorized their input variables: demographic factors, cancer history, smoking status, and personal/environmental factors. To assess variance in LCRC risk prediction outputs, we developed 16 hypothetical patients along a risk continuum, illustrated by randomly assigned input variables, and individually compared them to each LCRC against the empirically validated "gold-standard" PLCO risk model in order to evaluate the accuracy of the LCRCs within identical time-windows.

RESULTS

From the inclusion criteria, 11 calculators were initially identified. The analyzed calculators also vary in output characteristics and risk depiction for hypothetical patients. There were 13 total instances across ten hypothetical patients in which the sample standard error exceeded the mean risk percentage across all general samples and set standard calculations. The largest measured difference is 16.49% for patient 8, and the smallest difference is 0.01% for patient 2. The largest measured difference is 16.49% for patient 8, and the smallest difference is 0.01% for patient 2.

CONCLUSION

Substantial variability in the depiction of lung cancer risk for hypothetical patients exists across the web-based LCRCs due to their respective inputs and risk prediction models. To foster informed decision-making in the SDM-LDCT context, the input variables, risk prediction models, risk depiction, and screening recommendations must be standardized to best practice.

302 Is Age Just A Number in Cardiac Surgery? Evaluating Outcomes of An Octogenarian Cohort at A Single Cardiac Centre

Introduction

Cardiac surgery in octogenarians contains many age-specific perioperative risk factors and outcomes yet to be fully understood.

Method

All adults (N = 4957) undergoing cardiac surgery between 2011-2017 at our institution were retrospectively studied, encompassing 312 octogenarians. Data was evaluated with univariate and multivariate testing and mortality with Kaplan-Meier and cox-regression analyses.

Results

Compared to septuagenarians, octogenarians revealed more patients having previous surgery (p = 0.016), less diabetic patients (p = 0.034), lower BMI (0.002), and longer hospital stay (p &lt; 0.000). Compared to rest of study, octogenarians contained more females (p = 0.012), a greater Euroscore (p &lt; 0.000), spent longer in ITU (p = 0.001) and contained more ITU readmissions (p = 0.023). The octogenarians did not contain significant 30- and 90-day mortality but revealed significant mortality at 1-year versus septuagenarians (p = 0.039) and rest of study (p = 0.001). Variables testing significant in a multivariate regression were inserted into a cox-regression that found octogenarian group-membership to be insignificant (p = 0.051) in a 12-covariate model. Independent risk factors for mortality included emergency surgery (p = 0.04), reoperation (p &lt; 0.000), cardiac procedure (p = 0.007), ITU time (p = 0.041) and diabetes (p = 0.023).

Conclusions

We report specific differences for octogenarians in perioperative characteristics along with promising short- and medium-term survival. Such outcomes must constantly be monitored so that cardiac surgery can be further tailored to this elderly cohort.

Cropland trees need to be included for accurate model simulations of land-atmosphere heat fluxes, temperature, boundary layer height, and ozone

Trees significantly impact land-atmosphere feedbacks through evapotranspiration, photosynthesis and isoprene emissions. These processes influence the local microclimate, air quality and can mitigate temperature extremes and sequester carbon dioxide. Despite such importance, currently only 5 out of 15 atmospheric chemistry climate models even partially account for the presence of cropland trees. We first show that the tree cover over intensely farmed regions in Asia, Australia and South America is significantly underestimated (e.g. only 1-3% tree cover over north-India) in the Model of Emissions of Gases and Aerosol from Nature (MEGAN) and absent in Noah land-surface module of the Weather Research and Forecasting (WRF-Chem) Model. By including the actual tree cover (~10%) over the north-west Indo Gangetic Plain in the Noah land-surface module of the WRF-Chem and the MEGAN module, during the rice growing monsoon season in August, we find that the latent heat flux alone increases by 100%-300% while sensible heat flux reduces by 50%-100%, leading to a reduction in daytime boundary layer height by 200-400 m. This greatly improves agreement between the modelled and measured temperature, boundary layer height and surface ozone, which were earlier overestimated and isoprene and its oxidation products which were earlier underestimated. Mitigating peak daytime temperatures and ozone improves rice production by 10 to 20%. Our findings from north west Indo-Gangetic Plain establish that such plantations mitigate heat stress, and have beneficial effects on crop yields while also sequestering carbon. Expanding agroforestry practices to 50% of the cropland area could result in up to 40% yield gain regionally. Implementing such strategies globally could increase crop production and sequester 0.3-30 GtC per year, and therefore future climate mitigation and food security efforts should consider stakeholder participation for increased cropland agroforestry in view of its beneficial effects.

Post-tuberculosis lung health: perspectives from the First International Symposium

ALTHOUGH CURABLE, TB frequently leaves the individual with chronic physical and psycho-social impairment, but these consequences have been largely neglected. The 1^st International Post-Tuberculosis Symposium (Stellenbosch, South Africa) was held to discuss priorities and gaps in addressing this issue. A barrier to progress has been the varied terminology and nomenclature, so the Delphi process was used to achieve consensus on definitions. Lack of sufficient evidence hampered definitive recommendations in most domains, including prevention and treatment of post-TB lung disease (PTLD), but the discussions clarified the research needed. A consensus was reached on a toolkit for future PTLD measurement and on PTLD patterns to be considered. The importance of extra-pulmonary consequences and progressive impairment throughout the life-course was identified, including TB recurrence and increased mortality. Patient advocates emphasised the need to address the psychological and social impacts post TB and called for clinical guidance. More generally, there is an urgent need for increased awareness and research into post-TB complications.

"We Just Never Have Enough Time": Clinician Views of Lung Cancer Screening Processes and Implementation

RATIONALE

Despite a known mortality benefit, lung cancer screening (LCS) implementation has been unexpectedly slow. New programs face barriers to implementation, which may include lack of clinician engagement or beliefs that the intervention is not beneficial.

OBJECTIVE

To evaluate diverse clinician perspectives on their views of LCS and their experience with LCS implementation and processes.

METHODS

We performed a qualitative study of clinicians participating in LCS. Clinicians were drawn from three medical centers, representing diverse specialties and practice settings. All participants practiced at sites with formal lung cancer screening programs. We performed semi-structured interviews with probes designed to elicit opinions of LCS, perceived evidence gaps, and recommendations for improvements. Transcribed interviews were iteratively reviewed and coded using directed content analysis.

RESULTS

Participants (n=24) included LCS coordinators, pulmonologists, physician and non-physician primary care providers (PCPs), a surgeon, and a radiologist. Most clinicians expressed that the evidence supporting LCS was adequate to support clinical adoption, though most PCPs had little direct knowledge and based decisions on local recommendations or endorsement by the US Preventative Services Task Force (USPSTF). Many PCPs endorsed lack of knowledge of eligibility requirements and screening strategy (e.g. annual while eligible). Clinicians with more lung cancer screening knowledge, including several PCPs, identified a number of gaps in the current evidence that tempered enthusiasm, including: unclear ideal screening interval, populations with high cancer risk that do not qualify under USPSTF, indications to stop screening, and the role of serious comorbidities. Support for centralized programs and LCS coordinators was strong, but not uniform. Clinicians were frustrated by time limitations during a patient encounter, costs to the patient, and issues with insurance coverage. Many gaps in informatics support were identified. Clinicians recommended working to improve informatics support, continuing to clarify clinician responsibilities, and working on increasing public awareness of LCS.

CONCLUSIONS

Despite working within programs that have adopted many recommended care processes to support LCS, clinicians identified a number of issues in providing high-quality LCS. Many of these issues are best addressed by improved support of LCS within the electronic health record and continued education of staff and patients.

Release of extracellular vesicle miR-494-3p by ARPE-19 cells with impaired mitochondria

BACKGROUND

Mitochondrial function in retinal pigmented epithelial (RPE) cells and extracellular vesicle (EV) formation/release are related through the lysosomal and exocytotic pathways that process and eliminate intracellular material, including mitochondrial fragments. We propose that RPE cells with impaired mitochondria will release EVs containing mitochondrial miRNAs that reflect the diminished capacity of mitochondria within these cells.

METHODS

We screened ARPE-19 cells for miRNAs that localize to the mitochondria, exhibit biological activity, and are present in EVs released by both untreated cells and cells treated with rotenone to induce mitochondrial injury. EVs were characterized by vesicle size, size distribution, presence of EV biomarkers: CD81, CD63, and syntenin-1, miRNA cargo, and number concentration of EVs released per cell.

RESULTS

We found that miR-494-3p was enriched in ARPE-19 mitochondria. Knockdown of miR-494-3p in ARPE-19 cells decreased ATP production and mitochondrial membrane potential in a dose-dependent manner, and decreased basal oxygen consumption rate and maximal respiratory capacity. Increased number of EVs released per cell and elevated levels of miR-494-3p in EVs released from ARPE-19 cells treated with rotenone were also measured.

CONCLUSIONS

ARPE-19 mitochondrial function is regulated by miR-494-3p. Elevated levels of miR-494-3p in EVs released by ARPE-19 cells indicate diminished capacity of the mitochondria within these cells.

GENERAL SIGNIFICANCE

EV miR-494-3p is a potential biomarker for RPE mitochondrial dysfunction, which plays a central role in non-neovascular age-related macular degeneration, and may be a diagnostic biomarker for monitoring the spread of degeneration to neighboring RPE cells in the retina.

Abstract P3-14-10: Intralesional steroid injection: A novel method to treat the symptoms of idiopathic granulomatous mastitis

Background: Idiopathic granulomatous mastitis (IGM) is a chronic, inflammatory breast condition of benign nature that can clinically mimic breast cancer. Patients frequently present with a large, painful breast mass with associated inflammatory changes of the skin, and possible ulceration or fistula of the breast. Attempted methods for symptomatic relief include surgical excision and medical therapies including oral corticosteroids. Due to the success of treating dermatologic conditions with intralesional steroid injections, it was hypothesized that injecting the subdermal lesions of IGM may benefit patients with this disease. The use of intralesional steroid injections for the treatment of IGM has not been previously described in the literature.

Methods: Retrospective chart review was performed on a series of four patients with IGM who received intralesional steroid injections between August 2017 and April 2018. Patients were selected for treatment with injections based on their subjective report of painful breast lesions, lesion characteristics including size and depth, and the patient's desire to stop oral steroid therapy due to side effects despite active or residual disease. Data were collected on demographics, initial physical examination findings, prior and current treatments, characteristics of disease, details of injections performed, objective and subjective response to treatment, and recurrence.

Results: All patients presented with breast pain and either a mass, swelling, or hardness of the breast. Each patient received between one and three injection treatments, with one to four lesions treated in each session. Patients demonstrated improvement in subjective and objective symptoms after 87.5% of injection sessions (7 out of 8) by the subsequent follow-up visit (21-34 days). During the study period, three patients experienced resolution of at least one breast lesion within about 2 months (31-139 days, mean 68 days) without recurrence. One patient had four breast lesions that completely resolved (35-217 days, mean 88 days), but three of them recurred (63-217 days, mean 149 days).

Conclusion: In a small group of patients with idiopathic granulomatous mastitis, intralesional steroid injections were associated with an improvement in both subjective symptomatic relief and objective breast lesion characteristics in most cases. This treatment was associated with a good rate of lesion resolution and a low short-term recurrence rate.

Citation Format: Manst DJ, Ganschow PS, Marcus EA, Holden C, Datta S. Intralesional steroid injection: A novel method to treat the symptoms of idiopathic granulomatous mastitis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-14-10.

A strategy to identify a ketoreductase that preferentially synthesizes pharmaceutically relevant (S)-alcohols using whole-cell biotransformation

Introduction

Chemical industries are constantly in search of an expeditious and environmentally benign method for producing chiral synthons. Ketoreductases have been used as catalysts for enantioselective conversion of desired prochiral ketones to their corresponding alcohol. We chose reported promiscuous ketoreductases belonging to different protein families and expressed them in E. coli to evaluate their ability as whole-cell catalysts for obtaining chiral alcohol intermediates of pharmaceutical importance. Apart from establishing a method to produce high value (S)-specific alcohols that have not been evaluated before, we propose an in silico analysis procedure to predict product chirality.

Results

Six enzymes originating from Sulfolobus sulfotaricus, Zygosaccharomyces rouxii, Hansenula polymorpha, Corynebacterium sp. ST-10, Synechococcus sp. PCC 7942 and Bacillus sp. ECU0013 with reported efficient activity for dissimilar substrates are compared here to arrive at an optimal enzyme for the method. Whole–cell catalysis of ketone intermediates for drugs like Aprepitant, Sitagliptin and Dolastatin using E. coli over-expressing these enzymes yielded (S)-specific chiral alcohols. We explain this chiral specificity for the best-performing enzyme, i.e., Z. rouxii ketoreductase using in silico modelling and MD simulations. This rationale was applied to five additional ketones that are used in the synthesis of Crizotinib, MA-20565 (an antifungal agent), Sulopenem, Rivastigmine, Talampanel and Barnidipine and predicted the yield of (S) enantiomers. Experimental evaluation matched the in silico analysis wherein ~ 95% (S)-specific alcohol with a chemical yield of 23–79% was obtained through biotransformation. Further, the cofactor re-cycling was optimized by switching the carbon source from glucose to sorbitol that improved the chemical yield to 85–99%.

Conclusions

Here, we present a strategy to synthesize pharmaceutically relevant chiral alcohols by ketoreductases using a cofactor balanced whole-cell catalysis scheme that is useful for the industry. Based on the results obtained in these trials, Zygosaccharomyces rouxii ketoreductase was identified as a proficient enzyme to obtain (S)-specific alcohols from their respective ketones. The whole–cell catalyst when combined with nutrient modulation of using sorbitol as a carbon source helped obtain high enantiomeric and chemical yield.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1036-2) contains supplementary material, which is available to authorized users.