Optimized infection control practices augment the robust protective effect of vaccination for ESRD patients during a hemodialysis facility SARS-CoV-2 outbreak.

BACKGROUND: While dialysis patients are at greater risk of serious SARS-CoV-2 complications, stringent infection prevention measures can help mitigate infection and transmission risks within dialysis facilities. We describe an outbreak of 14 cases diagnosed in a hospital-based outpatient ESRD facility over 13 days in the second quarter of 2021, and our coordinated use of epidemiology, viral genome sequencing, and infection control practices to quickly end the transmission cycle. METHODS: Symptomatic patients and staff members were diagnosed by RT-PCR. Facility-wide screening utilized SARS-CoV-2 antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic specimens. RESULTS: Of the 106 patients receiving dialysis in the facility, 10 were diagnosed with SARS-CoV-2 infection, as was 1 patient support person. Of 3 positive staff members, 2 were unvaccinated and had provided care for 6 and 4 of the affected patients, respectively. Sequencing demonstrated that all cases in the cluster shared an identical B.1.1.7./Alpha substrain. Attack rates were greatest among unvaccinated patients and staff. Vaccine effectiveness was 88% among patients. CONCLUSIONS: Prompt recognition of an infection cluster and rapid intervention efforts successfully ended the outbreak. Alongside consistent adherence to core infection prevention measures, vaccination was highly effective in reducing disease incidence and morbidity in this vulnerable population.

Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient.

The implementation of monoclonal antibody therapeutics during the COVID-19 pandemic altered the selective pressures encountered by SARS-CoV-2, raising the possibility of selection for resistant variants. Within-host viral evolution was reported in treated immunocompromised individuals but whether this signifies a real risk of onward transmission is unclear. We used a regional SARS-CoV-2 sequencing program to monitor lineages with clinically relevant variants in identified patients, which facilitated analysis of parameters potentially relevant to new variant emergence. Here we describe a newly acquired spike E484K mutation detected within the B.1.311 lineage. Multiple individuals in 2 households of the same extended family were infected. The timing and patterns of spread were consistent with de novo emergence of this E484K variant in the bamlanivimab-treated index patient. Our study suggests that the selective pressures introduced by the widespread administration of these antibodies may warrant increased genomic surveillance to identify and mitigate spread of therapy-induced variants.

Outbreak or pseudo-outbreak? Integrating SARS-CoV-2 sequencing to validate infection control practices in a dialysis facility.

BACKGROUND: The COVID-19 pandemic poses a particularly high risk for End Stage Renal Disease (ESRD) patients so rapid identification of case clusters in ESRD facilities is essential. Nevertheless, with high community prevalence, a series of ESRD patients may test positive contemporaneously for reasons unrelated to their shared ESRD facility. Here we describe a series of 5 cases detected within 11 days in November 2020 in a hospital-based 32-station ESRD facility in Southwest Wisconsin, the subsequent facility-wide testing, and the use of genetic sequence analysis to evaluate links between cases. METHODS: Four patient cases and one staff case were identified in symptomatic individuals by RT-PCR. Facility-wide screening was conducted using rapid SARS-CoV-2 antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic specimens. RESULTS: Facility-wide screening of 47 staff and 107 patients identified no additional cases. Residual specimens from 4 of 5 cases were available for genetic sequencing. Clear genetic differences proved that these contemporaneous cases were not linked. CONCLUSIONS: With high community prevalence, epidemiological data alone is insufficient to deem a case cluster an outbreak. Cluster evaluation with genomic data, when available with a short turn-around time, can play an important role in infection prevention and control response programs.

Syncope in pulmonary embolism: a retrospective cohort study.

OBJECTIVE: To determine the prevalence of syncope or collapse in pulmonary embolism (PE). METHODS: A retrospective cohort study was conducted. We examined the frequency with which syncope or collapse (presyncope) occurred alone or with other symptoms and signs in an unselected series of 224 patients presenting to a district general hospital with PE between September 2012 and March 2016. Confirmation of PE was by CT pulmonary angiogram in each case. RESULTS: Our cohort of 224 patients comprised 97 men and 127 women, average age 66 years with age range of 21-94 years. Syncope or collapse was one of several symptoms and signs that led to a diagnosis of PE in 22 patients (9.8%) but was never the sole presenting feature. In descending order, these other clinical features were hypoxaemia (17 patients), dyspnoea (12), chest pain (9), tachycardia (7) and tachypnoea (7). ECG abnormalities reported to occur more commonly in PE were found in 13/17 patients for whom ECGs were available. Patients with PE presenting with syncope or collapse were judged to have a large clot load in 15/22 (68%) cases. CONCLUSION: Syncope was a frequent presenting symptom in our study of 224 consecutive patients with PE but was never the sole clinical feature. It would be difficult to justify routine testing for PE in patients presenting only with syncope or collapse.

Acquisition of Cabozantinib-Sensitive MET D1228N Mutation During Progression on Crizotinib in MET-Amplified Triple-Negative Breast Cancer.

BACKGROUND: Targeting of somatic MET mutations using crizotinib has led to strong clinical responses, most frequently in patients with lung cancer, raising the possibility of adopting similar treatment strategies in patients with MET alterations in other cancer types. PATIENT AND METHODS: We describe a patient with advanced triple-negative breast cancer with a 30-fold amplification of MET. Next-generation sequencing of pre- and postprogression biopsies was performed to identify the resistance mechanism emerging after an initial exceptional response to crizotinib. The response of the resistance mutant to type I and II MET inhibitors was assessed in cultured cells. RESULTS: After progressing on crizotinib, a MET-D1228N mutation was detected, which is located in the crizotinib-binding region of the MET kinase domain. Experimental studies demonstrated that this mutation confers complete resistance to crizotinib yet retains cabozantinib sensitivity. Treatment of the patient with cabozantinib led to a subjective improvement in clinical symptoms, but the patient progressed after 7 weeks. CONCLUSION: Although MET mutations are rare in breast cancer, these patients may experience substantial clinical benefit from crizotinib treatment. Nevertheless, drug resistance owing to on-target MET mutations will likely be frequently encountered and comprehensive mechanistic studies to assess sensitivity of these mutants to a series of potential second-line therapies may help guide subsequent treatment for these patients.

Sequential treatment failures in response to BRAF/MEK and immune checkpoint inhibitors mediated by MAP2K2 and B2M mutations in melanoma.

Although the treatment of metastatic melanoma has been significantly improved by both anti-BRAF/MEK and checkpoint immunotherapies, resistance to these treatment modalities remains a substantial clinical problem. Multiple clinical studies are addressing the optimal sequencing of these agents in larger patient cohorts, but successful long-term individualized treatment will likely require the elucidation of resistance mechanisms from post-progression samples. Here, we describe a patient with BRAF-V600E-positive metastatic melanoma who was sequentially treated with BRAF/MEK inhibitors (dabrafenib/trametinib) and checkpoint inhibitor immunotherapy (nivolumab, followed by pembrolizumab). After the emergence of resistance, whole exome sequencing was performed, implicating MAP2K2 and B2M mutations in loss of response to anti-BRAF/MEK and anti-PD1 therapies, respectively.

Genomic case report of a low grade bladder tumor metastasis to lung.

BACKGROUND: We present a rare case where distant metastasis of a low grade bladder tumor was observed. We carried out detailed genomic analysis and cell based experiments on patient tumor samples to study tumor evolution, possible cause of disease and provide personalized treatment strategies. CASE PRESENTATION: A man with a smoking history was diagnosed with a low-grade urothelial carcinoma of the bladder and a concurrent high-grade upper urinary tract tumor. Seven years later he had a lung metastasis. We carried out exome sequencing on all the patient's tumors and peripheral blood (germline) to identify somatic variants. We constructed a phylogenetic tree to capture how the tumors are related and to identify somatic changes important for metastasis. Although distant metastasis of low-grade bladder tumor is rare, the somatic variants in the tumors and the phylogenetic tree showed that the metastasized tumor had a mutational profile most similar to the low grade urothelial carcinoma. The primary and the metastatic tumors shared several important mutations, including in the KMT2D and the RXRA genes. The metastatic tumor also had an activating MTOR mutation, which may be important for tumor metastasis. We developed a mutational signature to understand the biologic processes responsible for tumor development. The mutational signature suggests that the tumor mutations are associated with tobacco carcinogen exposure, which is concordant with the patient's smoking history. We cultured cells from the lung metastasis to examine proliferation and signaling mechanisms in response to treatment. The mTOR inhibitor Everolimus inhibited downstream mTOR signaling and induced cytotoxicity in the metastatic tumor cells. CONCLUSION: We used genomic analysis to examine a rare case of low grade bladder tumor metastasis to distant organ (lung). Our analysis also revealed exposure to carcinogens found is tobacco as a possible cause in tumor development. We further validated that the patient might benefit from mTOR inhibition as a potential salvage therapy in an adjuvant or recurrent disease setting.

Glycogen debranching enzyme (AGL) is a novel regulator of non-small cell lung cancer growth.

Glycogen debranching enzyme (AGL) and Glycogen phosphorylase (PYG) are responsible for glycogen breakdown. We have earlier shown that AGL is a regulator of bladder tumor growth. Here we investigate the role of AGL in non-small cell lung cancers (NSCLC). Short hairpin RNA (shRNA) driven knockdown of AGL resulted in increased anchorage independent and xenograft growth of NSCLC cells. We further establish that an increase in hyaluronic acid (HA) synthesis driven by Hyaluronic Acid Synthase 2 (HAS2) is critical for anchorage independent growth of NSCLC cells with AGL loss. Using gene knockdown approach against HAS2 and by using 4-methylumbelliferone (4MU), an inhibitor of HA synthesis, we show that HA synthesis is critical for growth of NSCLC cells that have lost AGL. We further show NSCLC cells without AGL expression are dependent on RHAMM for HA signaling and growth. Analysis of NSCLC patient datasets established that patients with low AGL/high HAS2 or low AGL/high RHAMM mRNA expression have poor overall survival compared to patients with high AGL/low HAS2 or high AGL/low RHAMM expression. We show for the first time that loss of AGL promotes anchorage independent growth of NSCLC cells. We further show that HAS2 driven HA synthesis and signaling via RHAMM is critical in regulating growth of these cancer cells with AGL loss. Further patients presenting with low AGL and HAS2 or RHAMM over expressing tumors might present the ideal cohort who would respond to inhibitors of HA synthesis and signaling.

Determining Biogenic Content of Biogas by Measuring Stable Isotopologues 12CH4, 13CH4, and CH3D with a Mid-Infrared Direct Absorption Laser Spectrometer.

A tunable laser absorption spectrometer (TLAS) was developed for the simultaneous measurement of δ13C and δD values of methane (CH4). A mid-infrared interband cascade laser (ICL) emitting around 3.27 µm was used to measure the absorption of the three most abundant isotopologues in CH4 with a single, mode-hop free current sweep. The instrument was validated against methane samples of fossil and biogenic origin with known isotopic composition. Three blended mixtures with varied biogenic content were prepared volumetrically, and their δ13C and δD values were determined. Analysis demonstrated that, provided the isotopic composition of the source materials was known, the δ13C and δD values alone were sufficient to determine the biogenic content of the blended samples to within 1.5%.

Ruthenium Water Oxidation Catalysts based on Pentapyridyl Ligands.

Ruthenium complexes containing the pentapyridyl ligand 6,6''-(methoxy(pyridin-2-yl)methylene)di-2,2'-bipyridine (L-OMe) of general formula trans-[RuII (X)(L-OMe-κ-N5 )]n+ (X=Cl, n=1, trans-1+ ; X=H2 O, n=2, trans-22+ ) have been isolated and characterized in solution (by NMR and UV/Vis spectroscopy) and in the solid state by XRD. Both complexes undergo a series of substitution reactions at oxidation state RuII and RuIII when dissolved in aqueous triflic acid-trifluoroethanol solutions as monitored by UV/Vis spectroscopy, and the corresponding rate constants were determined. In particular, aqueous solutions of the RuIII -Cl complex trans-[RuIII (Cl)(L-OMe-κ-N5 )]2+ (trans-12+ ) generates a family of Ru aquo complexes, namely trans-[RuIII (H2 O)(L-OMe-κ-N5 )]3+ (trans-23+ ), [RuIII (H2 O)2 (L-OMe-κ-N4 )]3+ (trans-33+ ), and [RuIII (Cl)(H2 O)(L-OMe-κ-N4 )]2+ (trans-42+ ). Although complex trans-42+ is a powerful water oxidation catalyst, complex trans-23+ has only a moderate activity and trans-33+ shows no activity. A parallel study with related complexes containing the methyl-substituted ligand 6,6''-(1-pyridin-2-yl)ethane-1,1-diyl)di-2,2'-bipyridine (L-Me) was carried out. The behavior of all of these catalysts has been rationalized based on substitution kinetics, oxygen evolution kinetics, electrochemical properties, and density functional theory calculations. The best catalyst, trans-42+ , reaches turnover frequencies of 0.71 s-1 using CeIV as a sacrificial oxidant, with oxidative efficiencies above 95 %.

Ruthenium water oxidation catalysts containing the non-planar tetradentate ligand, biisoquinoline dicarboxylic acid (biqaH2).

Two ruthenium complexes containing the tetradentate ligand [1,1'-biisoquinoline]-3,3'-dicarboxylic acid, and 4-picoline or 6-bromoisoquinoline as axial ligands have been prepared. The complexes have been fully characterised and initial studies on their potential to function as molecular water oxidation catalysts have been performed. Both complexes catalyse the oxidation of water in acidic media with CeIV as a stoichiometric chemical oxidant, although turnover numbers and turnover frequencies are modest when compared with the closely related Ru-bda and Ru-pda analogues. Barriers for the water nucleophilic attack and intermolecular coupling pathways were obtained from density functional theory calculations and the crucial influence of the ligand framework in determining the most favourable reaction pathway was elucidated from a combined analysis of the theoretical and experimental results.

Ru-bis(pyridine)pyrazolate (bpp)-Based Water-Oxidation Catalysts Anchored on TiO2: The Importance of the Nature and Position of the Anchoring Group.

Three distinct functionalisation strategies have been applied to the in,in-[{Ru(II)(trpy)}2(µ-bpp)(H2O)2](3+) (trpy=2,2':6',2''-terpyridine, bpp=bis(pyridine)pyrazolate) water-oxidation catalyst framework to form new derivatives that can adsorb onto titania substrates. Modifications included the addition of sulfonate, carboxylate, and phosphonate anchoring groups to the terpyridine and bis(pyridyl)pyrazolate ligands. The complexes were characterised in solution by using 1D NMR, 2D NMR, and UV/Vis spectroscopic analysis and electrochemical techniques. The complexes were then anchored on TiO2-coated fluorinated tin oxide (FTO) films, and the reactivity of these new materials as water-oxidation catalysts was tested electrochemically through controlled-potential electrolysis (CPE) with oxygen evolution detected by headspace analysis with a Clark electrode. The results obtained highlight the importance of the catalyst orientation with respect to the titania surface in regard to its capacity to catalytically oxidize water to dioxygen.

Supramolecular water oxidation with Ru-bda-based catalysts.

Extremely slow and extremely fast new water oxidation catalysts based on the Ru-bda (bda=2,2'-bipyridine-6,6'-dicarboxylate) systems are reported with turnover frequencies in the range of 1 and 900 cycles s(-1) , respectively. Detailed analyses of the main factors involved in the water oxidation reaction have been carried out and are based on a combination of reactivity tests, electrochemical experiments, and DFT calculations. These analyses give a convergent interpretation that generates a solid understanding of the main factors involved in the water oxidation reaction, which in turn allows the design of catalysts with very low energy barriers in all the steps involved in the water oxidation catalytic cycle. We show that for this type of system π-stacking interactions are the key factors that influence reactivity and by adequately controlling them we can generate exceptionally fast water oxidation catalysts.

Molecular artificial photosynthesis.

The replacement of fossil fuels by a clean and renewable energy source is one of the most urgent and challenging issues our society is facing today, which is why intense research has been devoted to this topic recently. Nature has been using sunlight as the primary energy input to oxidise water and generate carbohydrates (solar fuel) for over a billion years. Inspired, but not constrained, by nature, artificial systems can be designed to capture light and oxidise water and reduce protons or other organic compounds to generate useful chemical fuels. This tutorial review covers the primary topics that need to be understood and mastered in order to come up with practical solutions for the generation of solar fuels. These topics are: the fundamentals of light capturing and conversion, water oxidation catalysis, proton and CO2 reduction catalysis and the combination of all of these for the construction of complete cells for the generation of solar fuels.

A flow-system array for the discovery and scale up of inorganic clusters.

The batch synthesis of inorganic clusters can be both time consuming and limited by a lack of reproducibility. Flow-system approaches, now common in organic synthesis, have not been utilized widely for the synthesis of clusters. Herein we combine an automated flow process with multiple batch crystallizations for the screening and scale up of syntheses of polyoxometalates and manganese-based single-molecule magnets. Scale up of the synthesis of these architectures was achieved by programming a multiple-pump reactor system to vary reaction conditions sequentially, and thus explore a larger parameter space in a shorter time than conventionally possible. Also, the potential for using the array as a discovery tool is demonstrated. Successful conditions for product isolation were identified easily from the array of reactions, and a direct route to 'scale up' was then immediately available simply by continuous application of these flow conditions. In all cases, large quantities of phase-pure material were obtained and the time taken for the discovery, repetition and scale up decreased.

Spectroscopy and dynamics of the predissociated, quasi-linear S2 state of chlorocarbene.

In this work, we report on the spectroscopy and dynamics of the quasi-linear S(2) state of chlorocarbene, CHCl, and its deuterated isotopologue using optical-optical double resonance (OODR) spectroscopy through selected rovibronic levels of the S(1) state. This study, which represents the first observation of the S(2) state in CHCl, builds upon our recent examination of the corresponding state in CHF, where pronounced mode specificity was observed in the dynamics, with predissociation rates larger for levels containing bending excitation. In the present work, a total of 14 S(2) state vibrational levels with angular momentum l = 1 were observed for CHCl, and 34 levels for CDCl. The range of l in this case was restricted by the pronounced Renner-Teller effect in the low-lying S(1) levels, which severely reduces the fluorescence lifetime for levels with K(a) > 0. Nonetheless, by exploiting different intermediate S(1) levels, we observed progressions involving all three fundamental vibrations. For levels with long predissociation lifetimes, rotational constants were determined by measuring spectra through different intermediate J levels of the S(1) state. Plots of the predissociation linewidth (lifetime) vs. energy for various S(2) levels show an abrupt onset, which lies near the calculated threshold for elimination to form C((3)P) + HCl on the triplet surface. Our experimental results are compared with a series of high level ab initio calculations, which included the use of a dynamically weighted full-valence CASSCF procedure, focusing maximum weight on the state of interest (the singlet and triplet states were computed separately). This was used as the reference for subsequent Davidson-corrected MRCI(+Q) calculations. These calculations reveal the presence of multiple conical intersections in the singlet manifold.

Integrated 3D-printed reactionware for chemical synthesis and analysis.

Three-dimensional (3D) printing has the potential to transform science and technology by creating bespoke, low-cost appliances that previously required dedicated facilities to make. An attractive, but unexplored, application is to use a 3D printer to initiate chemical reactions by printing the reagents directly into a 3D reactionware matrix, and so put reactionware design, construction and operation under digital control. Here, using a low-cost 3D printer and open-source design software we produced reactionware for organic and inorganic synthesis, which included printed-in catalysts and other architectures with printed-in components for electrochemical and spectroscopic analysis. This enabled reactions to be monitored in situ so that different reactionware architectures could be screened for their efficacy for a given process, with a digital feedback mechanism for device optimization. Furthermore, solely by modifying reactionware architecture, reaction outcomes can be altered. Taken together, this approach constitutes a relatively cheap, automated and reconfigurable chemical discovery platform that makes techniques from chemical engineering accessible to typical synthetic laboratories.