The NEID precision radial velocity spectrometer: Commissioning of the Port Adapter

In October 2019, the NEID instrument (PI Suvrath Mahadevan, PSU) was delivered to the WIYN 3.5 m Telescope at Kitt Peak National Observatory. Commissioning began shortly after delivery, but was paused due to a COVID-19 imposed observatory shutdown in March 2020. The observatory has recently reopened and NEID commissioning has resumed. NEID is an optical (380-930 nm), fiber-fed, precision Doppler radial velocity system developed as part of the NN-EXPLORE partnership. While the spectrometer and calibration system are maintained in a highly controlled environment on the basement level of the WIYN, the NEID Port Adapter mounts directly to a bent-Cassegrain port on the telescope and is responsible for precisely and stably placing target light on the science fibers. Here we present a brief overview of the as-built Port Adapter and its sub-components. We then discuss preliminary on-sky performance compared to requirements as well as next steps as we complete commissioning

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Decreased Risk of Coronavirus Disease 2019-Related Hospitalization Associated With the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2.

Among 134 223 patients with coronavirus disease 2019 (COVID-19), we assessed how risk of hospitalization changed at different intervals in the pandemic, controlling for prior COVID-19 immunity. In multivariable analysis, outpatients with COVID-19 during the Omicron-predominant time period had significantly lower odds of hospitalization compared to pre-Delta (adjusted odds ratio, 0.26 [95% confidence interval, .22-.32])

Rates of COVID-19 among Unvaccinated Adults with Prior COVID-19

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Long-term intrahost evolution of methicillin resistant Staphylococcus aureus among cystic fibrosis patients with respiratory carriage

Staphylococcus aureus is the most commonly identified airway colonizer of cystic fibrosis (CF) patients, and infections with methicillin-resistant S. aureus (MRSA) are associated with poor outcomes. Yet, little is known about the intrahost evolution of S. aureus among CF patients. We investigated convergent evolution and adaptation of MRSA among four CF patients with long-term respiratory carriage. For each patient, we performed whole-genome sequencing on an average of 21 isolates (range: 19-23) carried for a mean of 1,403 days (range: 903-1,679), including 25 pairs of isolates collected on the same day. We assessed intrahost diversity, population structure, evolutionary history, evidence of switched intergenic regions (IGRs), and signatures of adaptation in the context of patient age, antibiotic treatment, and co-colonizing microbes. Phylogenetic analysis delineated distinct multilocus sequence type ST5 (n = 3) and ST72 (n = 1) clonal populations in addition to sporadic, non-clonal isolates, and uncovered a putative transmission event. Variation in antibiotic resistance was observed within clonal populations, even among isolates collected on the same day. Rates of molecular evolution ranged from 2.21 to 8.64 nucleotide polymorphisms per year, and lineage ages were consistent with acquisition of colonization in early childhood followed by subsequent persistence of multiple sub-populations. Selection analysis of 1,622 core genes present in all four clonal populations (n = 79) found 11 genes variable in three subjects - most notably, ATP-dependent protease clpX, 2-oxoglutarate dehydrogenase odhA, fmtC, and transcription-repair coupling factor mfd. Only one gene, staphylococcal protein A (spa), was found to have evidence of gene-wide diversifying selection. We identified three instances of intrahost IGR switching events, two of which flanked genes related to quorum sensing. The complex microbial ecology of the CF airway poses challenges for management. We illustrate appreciable intrahost diversity as well as persistence of a dominant lineage. We also show that intrahost adaptation is a continual process, despite purifying selective pressure, and provide targets that should be investigated further for their function in CF adaptation

Rates of COVID-19 Among Unvaccinated Adults With Prior COVID-19.

This cohort study compares rates of COVID-19 between unvaccinated adults who did and did not previously test positive for SARS-CoV-2

Documenting Penicillin Allergy: The Impact of Inconsistency

Background: Allergy documentation is frequently inconsistent and incomplete. The impact of this variability on subsequent treatment is not well described. Objective: To determine how allergy documentation affects subsequent antibiotic choice. Design: Retrospective, cohort study. Participants: 232,616 adult patients seen by 199 primary care providers (PCPs) between January 1, 2009 and January 1, 2014 at an academic medical system. Main Measures: Inter-physician variation in beta-lactam allergy documentation; antibiotic treatment following beta-lactam allergy documentation. Key Results: 15.6% of patients had a reported beta-lactam allergy. Of those patients, 39.8% had a specific allergen identified and 22.7% had allergic reaction characteristics documented. Variation between PCPs was greater than would be expected by chance (all p Conclusions: Provider documentation of beta-lactam allergy is highly variable, and details of the allergy are infrequently documented. Classification of a patient as beta-lactam allergic and incomplete documentation regarding the details of the allergy lead to beta-lactam avoidance and use of other antimicrobial agents, behaviors that may adversely impact care quality and cost.</p

SARS-CoV-2 percent positivity and risk factors among people with HIV at an urban academic medical center

Since the onset of the COVID-19 pandemic, it has been unclear how vulnerable people with HIV (PwH) are to SARS-CoV-2 infection. We sought to determine if PwH are more likely to test positive for SARS-CoV-2 than people without HIV, and to identify risk factors associated with SARS-CoV-2 positivity among PwH. We conducted a cross-sectional study in which we collected electronic medical record data for all patients who underwent SARS-CoV-2 PCR testing at an academic medical center. Presence of HIV and other chronic diseases were based on the presence of ICD-10 diagnosis codes. We calculated the percent positivity for SARS-CoV-2 among PwH and among people without HIV. Among PwH, we compared demographic factors, comorbidities, HIV viral load, CD4 T-cell count, and antiretroviral therapy (ART) regimens between those who tested positive for SARS-CoV-2 and those who tested negative. Comparisons were made using chi squared tests or Wilcoxon rank sum tests. Multivariate models were created using logistic regression. Among 69,763 people tested for SARS-CoV-2, 0.6% (431) were PwH. PwH were not significantly more likely to test positive for SARS-CoV-2 than people without HIV (7.2% (31/431) vs 8.4% (5820/69763), p = 0.35), but were more likely to be younger, Black, and male (p-values < .0001). There were no significant differences in HIV clinical factors, chronic diseases, or ART regimens among PwH testing positive for SARS-CoV-2 versus those testing negative. In our sample, PwH were not more likely to contract SARS-CoV-2, despite being more likely to be members of demographic groups known to be at higher risk for infection. Differences between PwH who tested positive for SARS-CoV-2 and those who tested negative were only seen in Hispanic/Latino ethnicity (non-Hispanic or Latino vs unknown Hispanic or Latino ethnicity (OR 0.2 95% CI (0.6, 0.9)) and site of testing(inpatient vs outpatient OR 3.1 95% CI (1.3, 7.4)).</p