Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county.

SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.

Paracrine Wnt signaling is necessary for prostate epithelial proliferation.

INTRODUCTION: The Wnt proteins play key roles in the development, homeostasis, and disease progression of many organs including the prostate. However, the spatiotemporal expression patterns of Wnt proteins in prostate cell lineages at different developmental stages and in prostate cancer remain inadequately characterized. METHODS: We isolated the epithelial and stromal cells in the developing and mature mouse prostate by flow cytometry and determined the expression levels of Wnt ligands. We used Visium spatial gene expression analysis to determine the spatial distribution of Wnt ligands in the mouse prostatic glands. Using laser-capture microscopy in combination with gene expression analysis, we also determined the expression patterns of Wnt signaling components in stromal and cancer cells in advanced human prostate cancer specimens. To investigate how the stroma-derived Wnt ligands affect prostate development and homeostasis, we used a Col1a2-CreERT2 mouse model to disrupt the Wnt transporter Wntless specifically in prostate stromal cells. RESULTS: We showed that the prostate stromal cells are a major source of several Wnt ligands. Visium spatial gene expression analysis revealed a distinct spatial distribution of Wnt ligands in the prostatic glands. We also showed that Wnt signaling components are highly expressed in the stromal compartment of primary and advanced human prostate cancer. Blocking stromal Wnt secretion attenuated prostate epithelial proliferation and regeneration but did not affect cell survival and lineage maintenance. DISCUSSION: Our study demonstrates a critical role of stroma-derived Wnt ligands in prostate development and homeostasis.

Visits to Registered Nurses: An Opportunity to Increase Contraceptive Access in California.

BACKGROUND: In 2013, California passed Assembly Bill (A.B.) 2348, approving registered nurses (RNs) to dispense patient self-administered hormonal contraceptives and administer injections of hormonal contraceptives. The Family Planning, Access, Care and Treatment (Family PACT) program, which came into effect in 1997 to expand low-income, uninsured California resident access to contraceptives at no cost, is one program in which qualified RNs can dispense and administer contraceptives. AIMS: The aims of this study were to (a) describe utilization of RN visits within California's Family PACT program and (b) evaluate the impact of RN visits on client birth control acquisition during the first 18 months after implementation of A.B. 2348 (January 1, 2013 to June 30, 2014). METHODS: A descriptive observational design using administrative databases was used. Family PACT claims were retrieved for RN visits and contraception. Paid claims for contraceptive dispensing and/or administration visits by physicians, nurse practitioners, certified nurse midwives, and physician assistants were compared before and after the implementation of A.B. 2348 at practice sites where RN visits were and were not utilized. Contraceptive methods and administration procedures were identified using Healthcare Common Procedure Coding System codes, National Drug Codes, and Common Procedural Terminology codes. Claims data for healthcare facilities were abstracted by site location based on a unique combination of National Provider Identifier (NPI), NPI Owner, and NPI location number. RESULTS: RN visits were found mainly in Northern California and the Central Valley (73%). Sixty-eight percent of RN visits resulted in same-day dispensing and/or administration of hormonal (and/or barrier) methods. Since benefit implementation, RN visits resulted in a 10% increase in access to birth control dispensing and/or administration visits. RN visits were also associated with future birth control acquisition and other healthcare utilization within the subsequent 30 days. DISCUSSION: RN visits, though underutilized across the state, have resulted in increased access to contraception in some communities, an effect that may continue to grow with time and can serve as a model for other states.

A high-throughput, polymerase-targeted RT-PCR for broad detection of mammalian filoviruses.

Filoviruses are some of the most lethal viruses in the modern world, and increasing numbers of filovirus species and genera have been discovered in recent years. Despite the potential severity of filovirus outbreaks in the human population, comparably few sensitive pan-filovirus RT-PCR assays have been described that might facilitate early detection and prevention. Here, we present a new pan-filovirus RT-PCR assay targeting the L polymerase gene for detection of all known mammalian filoviruses. We demonstrate the detection of 10 synthetic filovirus RNA templates with analytical sensitivity ranging from 178 to 3,354 copies/mL, without cross-reactivity on 10 non-filoviral human viral species. We verified assay performance on 10 inactivated filovirus isolates, yielding initial sensitivities of 0.012-44.17 TCID50/mL. We coupled this broadly reactive RT-PCR with a deep sequencing workflow that is amenable to high-throughput pooling to maximize detection and discovery potential. In summary, this pan-filovirus RT-PCR assay targets the most conserved filovirus gene, offers the widest breadth of coverage to date, and may help in the detection and discovery of novel filoviruses.IMPORTANCEFiloviruses remain some of the most mysterious viruses known to the world, with extremely high lethality rates and significant pandemic potential. Yet comparably few filovirus species and genera have been discovered to date and questions surround the definitive host species for zoonotic infections. Here, we describe a novel broadly reactive RT-PCR assay targeting the conserved L polymerase gene for high-throughput screening for filoviruses in a variety of clinical and environmental specimens. We demonstrate the assay can detect all known mammalian filoviruses and determine the sensitivity and specificity of the assay on synthetic RNA sequences, inactivated filovirus isolates, and non-filoviral species.

Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences.

Pathogen genomics can provide insights into disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets. Genetically proximal viruses indicate epidemiological linkage and are informative about transmission events. Here, we leverage pairs of identical sequences using 114,298 SARS-CoV-2 genomes collected via sentinel surveillance from March 2021 to December 2022 in Washington State, USA, with linked age and residence information to characterize fine-scale transmission. The location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postal codes with male prisons, consistent with transmission between prison facilities. Transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. This work improves our ability to characterize transmission from large pathogen genome datasets.

Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county.

SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.

Finite Element Model of a Deformable American Football Helmet Under Impact.

Despite the use of helmets in American football, brain injuries are still prevalent. To reduce the burden of these injuries, novel impact mitigation systems are needed. The Vicis Zero1 (VZ1) American football helmet is unique in its use of multi-directional buckling structures sandwiched between a deformable outer shell and a stiff inner shell. The objective of this study was to develop a model of the VZ1 and to assess this unique characteristic for its role in mitigating head kinematics. The VZ1 model was developed using a bottom-up framework that emphasized material testing, constitutive model calibration, and component-level validation. Over 50 experimental tests were simulated to validate the VZ1 model. CORrelation and Analysis (CORA) was used to quantify the similarity between experimental and model head kinematics, neck forces, and impactor accelerations and forces. The VZ1 model demonstrated good correlation with an overall mean CORA score of 0.86. A parametric analysis on helmet compliance revealed that the outer shell and column stiffness influenced translational head kinematics more than rotational. For the material parameters investigated, head linear acceleration ranged from 80 to 220 g, whereas angular velocity ranged from 37 to 40 rad/s. This helmet model is open-source and serves as an in silico design platform for helmet innovation.

Development of Open-Source Dummy and Impactor Models for the Assessment of American Football Helmet Finite Element Models.

The objective of this study was to develop and validate a set of Hybrid-III head and neck (HIII-HN) and impactor models that can be used to assess American football design modifications with established dummy-based injury metrics. The model was validated in two bare-head impact test configurations used by the National Football League and research groups to rank and assess helmet performance. The first configuration was a rigid pendulum impact to three locations on the HIII head (front, rear, side) at 3 m/s. The second configuration was a set of eight 5.5 m/s impacts to the HIII head at different locations using a linear impactor with a compliant end cap. The ISO/TS 18571 objective rating metric was used to quantify the correlation between the experimental and model head kinematics (linear and rotational velocity and acceleration) and neck kinetics (neck force and moment). The HIII-HN model demonstrated good correlation with overall mean ISO scores of 0.69-0.78 in the pendulum impacts and 0.65-0.81 in the linear impacts. These publically available models will serve as an in silico design platform that will be useful for investigating novel football helmet designs and studying human head impact biomechanics, in general.

Docetaxel and vinorelbine plus GM-CSF in malignant melanoma.

Patients having locoregional or metastatic melanoma have a poor prognosis, with 50% to 100% of patients dying from the disease within 5 years. Current chemotherapy regimens offer limited benefits to these patients, and more effective and less toxic treatments are needed. We therefore piloted a study of docetaxel (Taxotere), vinorelbine (Navelbine), granulocyte-macrophage colony-stimulating factor (GM-CSF, sargramostim [Leukine]), or the DVS regimen, in patients with stage IV melanoma. Eight patients were treated after previous biochemotherapy and two patients were given the regimen as an initial treatment. The DVS regimen consisted of docetaxel at 40 mg/m2 i.v. over 1 hour, vinorelbine at 30 mg/m2 i.v. over 6 to 10 minutes every 14 days, and GM-CSF at 250 mg/m2 SC on days 2 to 12. No grade 3 or 4 toxicities were encountered. Of the 10 patients evaluable for response, 5 were partial responders (50% response rate). Time to progression for the 10 cases ranged from 2 to 26+ months (median: 8 months). The DVS regimen was active against advanced melanoma in both previously treated and untreated patients. A larger study to confirm the activity of the DVS regimen for stage IV melanoma is currently under way.

Phase II clinical trial evaluating docetaxel, vinorelbine and GM-CSF in stage IV melanoma.

PURPOSE: Metastatic melanoma patients have a poor prognosis. No chemotherapy regimen has improved overall survival. More effective treatments are needed. Docetaxel has clinical activity in melanoma and may be more active when combined with vinorelbine. Granulocyte-macrophage colony-stimulating factor (GM-CSF) has shown activity as an adjuvant melanoma therapy. We carried out a phase II study of these agents in patients with stage IV melanoma. METHODS: Patients had documented stage IV melanoma and may have had prior immuno or chemotherapy. Previously treated brain metastases were allowed. Docetaxel (40 mg/m(2) IV) and vinorelbine (30 mg/m(2) IV) were administered every 14 days, followed by GM-CSF (250 mg/m2 SC on days 2 to 12). The primary endpoint of the study was 1-year overall survival (OS). Secondary objectives were median overall survival, response rate (per RECIST criteria), and the toxicity profiles. RESULTS: Fifty-two patients were enrolled; 80% had stage M1c disease. Brain metastases were present in 21%. Fifty-two percent of patients had received prior chemotherapy, including 35% who received prior biochemotherapy. Toxicity was manageable. Grade III/IV toxicities included neutropenia (31%), anemia (14%), febrile neutropenia (11.5%), and thrombocytopenia (9%). DVS chemotherapy demonstrated clinical activity, with a partial response in 15%, and disease stabilization in 37%. Six-month PFS was 37%. Median OS was 11.4 months and 1-year OS rate was 48.1%. CONCLUSIONS: The DVS regimen was active in patients with advanced, previously treated melanoma, with manageable toxicity. The favorable 1-year overall survival and median survival rates suggest that further evaluation of the DVS regimen is warranted.

Delayed oxaliplatin-associated neurotoxicity following adjuvant chemotherapy for stage III colon cancer.

Oxaliplatin-containing chemotherapy regimens are utilized commonly for metastatic colorectal cancer and increasingly in the adjuvant setting following surgical resection. The dose-limiting toxicity is neurotoxicity. Acute neurotoxicity is cold induced and transient. Chronic neurotoxicity usually has a predictable clinical course. It is manifested by paresthesias and dysesthesias of gradually prolonged duration that occur between treatment cycles, and increase in intensity and duration with the cumulative dose. We report here a case of a patient who developed significant grade 3 chronic neuropathy following completion of 6 months of adjuvant oxaliplatin-containing chemotherapy for stage III colon cancer. The neurotoxicity was not preceded by any transient symptoms characteristic of chronic oxaliplatin neuropathy and its onset was unpredictable. Delayed neurotoxicity is a complication which must be considered for patients receiving adjuvant therapy and attempts to utilize the minimum effective cumulative dose of oxaliplatin are warranted.

Multiple joint effusions associated with high-dose imatinib therapy in a patient with chronic myelogenous leukaemia.

Imatinib mesylate is a small molecule tyrosine kinase inhibitor that has significant efficacy in the treatment of chronic myelogenous leukaemia (CML). However, it is likely that patients with CML will require prolonged and perhaps life-long therapy. In general, the side-effects of imatinib therapy have been mild to moderate, with the large majority of patients tolerating prolonged periods of therapy. However, a minority of patients are completely intolerant of therapy, while others are able to remain on therapy despite significant side-effects. Here, we describe a novel form of fluid retention presenting as multiple joint effusions in a patient with advanced phase CML on high-dose imatinib, as well as successful measures that were undertaken to control this adverse event. Although fluid retention, including periorbital oedema, pleural and pericardial effusions, as well as life-threatening cerebral oedema have been previously described and attributed to imatinib, this is the first case of imatinib-associated polyarticular effusions that we are aware of. Further work will be required to confirm a casual relationship between imatinib therapy and this novel side-effect, as well as to determine the underlying pathophysiologic mechanisms.

Combined topoisomerase I inhibition for the treatment of metastatic colon cancer.

The objective of this study was to define the maximally tolerated dose (MTD) and response rate of a combination of two topoisomerase I inhibitors, topotecan and irinotecan, in patients with metastatic colon cancer. Eleven patients, the majority with previously progressive disease on 5-fluorouracil-based regimens, were enrolled onto a phase I/II dose escalation trial utilizing continuous infusion topotecan for 2 weeks and weekly irinotecan x 3 with cycles repeated every 28 days. Dosages of topotecan utilized included 0.2 and 0.25mg/m2/day. Irinotecan was administered at a dose of 62 mg/m2 by i.v. bolus. Patients were followed for toxicity and response. The MTD of the combination of agents was found to be 0.25mg/m2/day for topotecan and 62 mg/m2 for irinotecan. The most common serious toxicities were diarrhea and nausea/vomiting. Only one patient experienced grade III neutropenia. There were no complete or partial responses. However, four patients had prolonged disease stabilization (SD) of up to 324 days and this group remained on protocol therapy for an average of 227 days (p=0.0005 versus patients not achieving SD). We concluded that the MTD for this combination of topoisomerase I inhibitors, given on this particular schedule, has been defined. This combination cannot be recommended as a first- or second-line therapy for patients with metastatic colon cancer based on the responses observed. However, approximately one-third of patients achieved prolonged disease stabilization. Topotecan with irinotecan may be useful as a palliative regimen for a subgroup of colon cancer patients.

Stevens-Johnson syndrome/toxic epidermal necrolysis in a patient receiving concurrent radiation and gemcitabine.

A patient with stage IV malignant melanoma treated with daily radiotherapy and low-dose (100 mg/m2) daily gemcitabine developed a blistering skin eruption, fever and neutropenia consistent with overlap Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN). The diagnosis was confirmed by skin biopsy of an affected area. The case history is described, and the literature relating to the development of SJS/TEN in association with chemotherapy and radiotherapy administration is reviewed. This report describes a serious potential complication of concurrent gemcitabine and radiotherapy.