Polyphonia: detecting inter-sample contamination in viral genomic sequencing data.

Summary: In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, and detection of superinfections and recombination events. While sample barcoding methods exist to track inter-sample contamination, they are not always used and can only detect contamination in the experimental pipeline from the point they are added. The underlying genomic information in a sample, however, carries information about inter-sample contamination occurring at any stage.

Cobain, Hemingway, Sinatra and me.

A postdoc explains how being medicated for bipolar changed her life and the way she conducts research.

Inferring Viral Transmission Pathways from Within-Host Variation.

Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop a robust evolutionary model for transmission reconstruction that tracks the genetic composition of within-host viral populations over time and the lineages transmitted between hosts. We confirm that our model reliably describes within-host variant frequencies in a dataset of 134,682 SARS-CoV-2 deep-sequenced genomes from Massachusetts, USA.

Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants.

The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting.

Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak.

An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event.

Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts.

Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), in July 2021 contributed to an outbreak of over one thousand COVID-19 cases among residents and visitors. Most cases were fully vaccinated, many of whom were also symptomatic, prompting a comprehensive public health response, motivating changes to national masking recommendations, and raising questions about infection and transmission among vaccinated individuals. To characterize the outbreak and the viral population underlying it, we combined genomic and epidemiological data from 467 individuals, including 40% of known outbreak-associated cases.

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.

Analysis of 772 complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from early in the Boston-area epidemic revealed numerous introductions of the virus, a small number of which led to most cases. The data revealed two superspreading events. One, in a skilled nursing facility, led to rapid transmission and significant mortality in this vulnerable population but little broader spread, whereas other introductions into the facility had little effect.

Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.

SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe.

Combining genomics and epidemiology to track mumps virus transmission in the United States.

Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health investigations with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing on Massachusetts university communities. Our analysis suggests continuous, undetected circulation of mumps locally and nationally, including multiple independent introductions into Massachusetts and into individual communities.

Towards the indium nitride laser: obtaining infrared stimulated emission from planar monocrystalline InN structures.

The observation of a stimulated emission at interband transitions in monocrystalline n-InN layers under optical pumping is reported. The spectral position of the stimulated emission changes over a range of 1.64 to 1.

Comparative efficacy evaluation of catheter intraperitoneal chemotherapy, normothermic and hyperthermic chemoperfusion in a rat model of ascitic ovarian cancer.

Objectives: The choice of an optimal administration route for intraperitoneal (IP) chemotherapy and a suitable chemotherapeutic regime in the treatment of ovarian cancer remains a controversy. We investigated survival outcomes according to catheter intraperitoneal chemotherapy (CIPC), normothermic and hyperthermic chemoperfusion (NIPEC and HIPEC) with cytostatic drugs dioxadet and cisplatin in rats with transplantable ascitic ovarian cancer.

Methods: Ascitic liquid containing 1 × 10 tumour cells was inoculated to female Wistar rats and 48 hours after rats received dioxadet and cisplatin at the maximum tolerated doses.

[Intraperitoneal chemotherapy--a method of improving treatment effectiveness in ovarian cancer].

The study or antitumor effects of dioxadet, cisplatin, melphalan, paclitaxel, mitomycin C, cyclophosphamide and gemcitabine at intraperitoneal (i.p.) and intravenous (i.

[An evaluation of effectiveness of cytological method in diagnostics of breast tumors].

This paper presents an analysis of the results of cytological diagnostics of breast tumors in 3415 patients who underwent tests in the Laboratory of Cytology for 2009-2013. In 1434 patients there were performed cytohistological correlations. Sensitivity of cytology was 99.

[Comparison of results of elastography with hormonal and metabolic status in patients with the diagnosis of thyroid neoplasms].

In order to assess the effectiveness of compression elastography of the thyroid gland as a method for differential diagnosis to studies conducted in the pre-operative period, there were involved 34 patients with a mean age 46.6 +/- 2.7 years.

[Evaluation of coronary bed function by positron emission tomography using 13N-ammonium during cold stimulation].

The purpose of the present investigation was to study the time course of changes in myocardial blood flow (MBF) in response to cold stimulation. Thirty-eight patients having risk factors of cardiovascular complications were examined. The time course of MBF changes was estimated by positron emission tomography (PET) using 13N-ammonium at rest and during a cold test (CT).

[Direct results of endovascular prosthetics of aneurysms of the infrarenal part of the aorta in patients with a severe concomitant pathology].

From May 2007 to March 2009 under observation there were 58 patients aged from 52 to 79 years (mean age 68) with the diagnosis of abdominal aortic aneurysm (AAA). Selection of patients for endoprosthesis was performed by the data of spiral computed aortography. The endovascular exclusion ofAAA from blood flow was performed in 15 patients.

[Modern diagnostic technologies in determination of the strategy of treatment of patients with obliterating atherosclerosis of the lower artery vessels].

The authors analyzed results of surgical treatment of 332 patients in whom 410 reconstructive operations were performed on the lower extremity arteries. During 12 months after operation on the aorto-femoral segment with high peripheral vascular resistance reocclusions were noted in 61% of the cases, with normal resistance--in 11.8%, after operation on the femoro-popliteal segment--in 77.

[Evaluation of coronary bed function by positron emission tomography using 13N-ammonium during cold stimulation].

The present investigation was to study the time course of changes in myocardial blood flow (MBF) in response to cold stimulation. Thirty-eight patients having risk factors of cardiovascular complications were examined. The time course of MBF changes was estimated by positron emission tomography (PET) using 13N-ammonium at rest and during a cold test (CT).

[Cytological diagnosis and prognosis in Ewing's sarcoma in children].

143 cytological studies of the material obtained from 98 children aged from 2 to 18 years with tentative diagnosis of Ewing's sarcoma were made. Histocytological correlations showed 96.2% cases to be of informative value, 87% of them with precise cytological diagnosis of the above sarcoma.

[Correlation of cytologic and DNA ploidy evidence and prognosis in childhood Wilm's tumor].

A retrospective evaluation of the clinical features, cytological, biological (DNA) and histological data on 29 children with Wilms' tumor. Two prognosis-related groups were identified: (1) good outcome (17)--all children, aged 4-15, had survived by end of follow-up; (2) bad outcome (12)--all children died within 4 months--4 years. Cytological examination by fine-needle biopsy of smears was carried out prior to preoperative neoadjuvant therapy in all 29 patients; in addition, print smears from resected tumor were taken from 21.

[Ultrasound diagnosis of angiopathy in antitumor therapy].

The ultrasound characteristics of arterial walls were assessed in 78 young and middle-aged male (42) and female (36) cancer patients (mean age 36 +/- 0.9) receiving radiation and/or polychemotherapy. The study was specifically concerned with quantitative and qualitative changes in the "intima-media" complex and the vasoactive dysfunction of the endothelium.

[The results of cytologic diagnosis of bone tumors].

The results of bone tumor cytological diagnosis in 968 patients examined and treated at the Institute Clinic (1988-1997) were analyzed. Histological examinations were performed in 479 cases. The share of cytologically inconclusive findings was significantly higher with benign lesions (17.

[Cytologic diagnosis of retroperitoneal tumors in children].

Cytological diagnosis of retroperitoneal tumors in 173 children (1985-1996) has been evaluated, using aspiration biopsy (165), imprint smears (84) and cytohistological examination (128). Fine-needle biopsy data were confirmed in 99%; histological examination--97.3%.