bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Climate on the Variation in Abundance of Three Tick Species in Illinois
Authors: Bacon E A , Kopsco H , Gronemeyer P , Mateus-Pinilla N , Smith R L 
Published: December 2021

AbstractThe range of ticks in North America has been steadily increasing likely, in part, due to climate change. Along with it, there has been a rise in cases of tick-borne disease. Among those medically important tick species of particular concern are Ixodes scapularis Say (Acari: Ixodidae), Dermacentor variabilis Say (Acari: Ixodidae), and Amblyomma americanum Linneaus (Acari: Ixodidae). The aim of this study was to determine if climate factors explain existing differences in abundance of the three aforementioned tick species between two climatically different regions of Illinois (Central and Southern), and if climate variables impact each species differently. We used both zero-inflated regression approaches and Bayesian network analyses to assess relationships among environmental variables and tick abundance. Results suggested that the maximum average temperature and total precipitation are associated with differential impact on species abundance and that this difference varied by region. Results also reinforced a differential level of resistance to desiccation among these tick species. Our findings help to further define risk periods of tick exposure for the general public, and reinforce the importance of responding to each tick species differently.
The Rare Books of the Galway Poor Clares
Authors: Goodrich Jaime 
Published: December 2021

Abstract
The Poor Clares of Galway are the oldest surviving convent in Ireland, maintaining a small but important collection of rare books from the seventeenth and eighteenth centuries. This essay offers a bibliographical analysis of these rare books in order to sketch the role of reading within the convent from the seventeenth through the twentieth centuries. By analysing material evidence of reading and circulation practices—signatures, readers’ marks, marginalia, and bookmarks—broader patterns of book usage among the Galway Poor Clares are reconstructed for the first four centuries of existence. The essay concludes with a short bibliographical catalogue of the convent’s special collections.
The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II
Authors: Carnesecchi Julie , Boumpas Panagiotis , van Nierop y Sanchez Patrick , Domsch Katrin , Pinto Hugo Daniel , Borges Pinto Pedro , Lohmann Ingrid 
Published: December 2021

Abstract
Transcription factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. Our results demonstrate a new RNA-binding ability of Ubx. We find that the N51 amino acid of the DNA-binding Homeodomain is non-essential for RNA interaction in vitro, but is required for RNA interaction in vivo and Ubx splicing activity. Moreover, mutation of the N51 amino acid weakens the interaction between Ubx and active RNA Polymerase II (Pol II). Our results reveal that Ubx regulates elongation-coupled splicing, which could be coordinated by a dynamic interplay with active Pol II on chromatin. Overall, our work uncovered a novel role of the Hox TFs at the mRNA regulatory layer. This could be an essential function for other classes of TFs to control cell diversity.
Opioid prescribing practices in chronic kidney disease: a population-based cohort study
Authors: Molnar Amber O , Bota Sarah E , Naylor Kyla , Nash Danielle M , Smith Graham , Suri Rita S , Sood Manish M , Gomes Tara , Garg Amit X 
Published: December 2021

ABSTRACT

Background
Chronic pain is common, and its management is complex in patients with chronic kidney disease (CKD), but limited data are available on opioid prescribing. We examined opioid prescribing for non-cancer and non-end-of-life care in patients with CKD.

Methods
This was a population-based retrospective cohort study using administrative databases in Ontario, Canada which included adults with CKD defined by an estimated glomerular filtration rate (eGFR) &lt;60 mL/min/1.73 m2 from 1 November 2012 to 31 December 2018 and estimated the proportion of opioid prescriptions (type, duration, dose, potentially inappropriate prescribing, etc.) within 1 year of cohort entry. Prescriptions had to precede dialysis, kidney transplant or death.

Results
We included 680 445 adults with CKD, and 198 063 (29.1%) were prescribed opioids. Codeine (14.9%) and hydromorphone (7.2%) were the most common opioids. Among opioid users, 24.3% had repeated or long-term use, 26.1% were prescribed high doses and 56.8% were new users. Opioid users were more likely to be female, had cardiac disease or a mental health diagnosis, and had more healthcare visits. The proportions for potentially inappropriate prescribing indicators varied (e.g. 50.1% with eGFR &lt;30 were prescribed codeine, and 20.6% of opioid users were concurrently prescribed benzodiazepines, while 7.2% with eGFR &lt;30 mL/min/1.73 m2 were prescribed morphine, and 7.0% were received more than one opioid concurrently). Opioid prescriptions declined with time (2013 cohort: 31.1% versus 2018 cohort: 24.5%; p &lt;0.0001), as did indicators of potentially inappropriate prescribing.

Conclusions
Opioid use was common in patients with CKD. While opioid prescriptions and potentially inappropriate prescribing have declined in recent years, interventions to improve pain management without the use of opioids and education on safer prescribing practices are needed.
3. Stopping Hospital Infections with Environmental Services (SHINE): A Cluster-Randomized Trial of Intensive Monitoring Methods for Terminal Room Cleaning on Rates of Multidrug-Resistant Organisms (MDROs) in the Intensive Care Unit (ICU)
Authors: Ziegler Matthew J , Babcock Hilary , Babcock Hilary , Welbel Sharon F , Warren David K , Trick William , Reddy Sujan , Tolomeo Pam C , Omorogbe Jacqueline , Garcia Diana , Habrock-Bach Tracey , Donceras Onfofre T , Gaynes Steven M , Cressman Leigh , Burnham Jason P , Pegues David A , Lautenbach Ebbing , Han Jennifer 
Published: December 2021

Abstract

Background
MDROs frequently contaminate hospital environments. We performed a multicenter cluster-randomized, crossover trial of two methods for intensive monitoring of terminal cleaning effectiveness at reducing infection and colonization with MDROs within ICUs.

Methods
Six medical and surgical ICUs at three medical centers received both intensive monitoring interventions sequentially, in a randomized order. The intervention included surveying a minimum of 10 surfaces each in 5 rooms weekly, after terminal cleaning, with adenosine triphosphate (ATP) monitoring or an ultraviolet fluorescent marker (UV/F). Results were delivered to environmental services (EVS) staff in real-time, with failing surfaces recleaned. The primary study outcome was the monthly rate of infection or colonization with MDROs, including methicillin-resistant Staphylococcus aureus, Clostridioides difficile, vancomycin-resistant Enterococcus, and multidrug-resistant gram-negative bacilli (MDR-GNB), assessed during a 12-month baseline comparison period and sequential 6-month intervention periods, separated by a 2-month washout. Outcomes during each intervention period were compared to the combined baseline period plus the alternative intervention period using mixed-effects Poisson regression, with study hospital as a random effect.

Results
The primary outcome rate varied by hospital and ICU (Figure 1). The ATP method was associated with a relative reduction in the incidence rate of infection or colonization with MDROs (incidence rate ratio (IRR) 0.887, 95% confidence-interval (CI) 0.811–0.969, P=0.008) (Table 1), infection with MDROs (IRR 0.924, 95% CI 0.855–0.998, P=0.04), and infection or colonization limited to multidrug-resistant MDR-GNB (IRR 0.856, 95% CI 0.825–0.887, P&lt; 0.001). The UV/F intervention was not associated with a statistically significant impact on these outcomes. Room turn-around time was increased by a median of one minute with the ATP intervention and 4.5 minutes with the UV/F intervention compared to baseline.

Conclusion
Intensive monitoring of ICU terminal room cleaning with an ATP modality is associated with a relative reduction of infection and colonization with MDROs with a negligible impact on TAT.

Disclosures
Hilary Babcock, MD, MPH, FIDSA, FSHEA (nothing to disclose), David K. Warren, MD, MPH, Homburg & Partner (consultant), Ebbing Lautenbach, MD, MPH, MSCE (nothing to disclose), Jennifer Han, MD, MSCE, GlaxoSmithKline (employee, shareholder).
11. Electronic Surveillance Criteria for Non-Ventilator HAP: Empiric testing and Chart Review at Veterans Affairs Facilities
Authors: Stern Sarah , Christensen Matthew A , Nevers McKenna , Ying Jian , Smith Caroline , Jin Robert , Ochoa Aileen , Rhee Chanu , Samore Matthew H , Klompas Michael , Jones Barbara E 
Published: December 2021

Abstract

Background
Surveillance of Non-Ventilator Hospital-Acquired Pneumonia (NV-HAP) is limited by the ambiguity in diagnosing pneumonia. We implemented electronic surveillance criteria for NV-HAP across the VA healthcare system and tested for reliability, validity and meaning of the electronic criteria vs manual chart review.

Methods
We defined NV-HAP surveillance criteria as oxygen deterioration concurrent with fever or abnormal WBC count, ≥3 days of antibiotics, and orders for chest imaging. We applied these criteria to EHR data from all patients hospitalized ≥3 days at all VA acute care facilities from 1/1/2015-12/31/2020 and calculated NV-HAP incidence and inpatient mortality. Clinician reviewers used a consensus review guide to independently review and adjudicate 47 cases meeting NV-HAP surveillance criteria for 1) clinical deterioration, 2) CDC-NHSN pneumonia criteria, 3) treating clinicians’ assessment, and 4) reviewer’s diagnosis. All reviewers subsequently adjudicated all cases and conducted an error analysis to identify sources of discordance.

Results
Among 2.3M hospitalizations, 14,023 met NV-HAP surveillance criteria (0.6 per 100 admissions). Inpatient mortality was 26% (vs 2% for non-flagged hospitalizations). Among 47 hospitalizations flagged by surveillance criteria, 45 (97%) had a confirmed clinical deterioration, (the other 2 were immediate post-operative cases), 20 (43%) met CDC-NHSN pneumonia criteria, 21 (47%) had possible pneumonia per treating clinicians, and 25 (53%) had possible or probable NV-HAP per reviewers. Agreement among the 3 reviewers before adjudication was 51% (Fleiss’ κ 0.43) for CDC-NHSN and 58% (Fleiss’ κ 0.33) for NV-HAP. The most common source of discordance between reviewers was chest imaging classification (15/19 discordant cases).

Conclusion
NV-HAP electronic surveillance criteria demonstrated high precision for identifying clinical deterioration and moderate concordance with CDC-NHSN pneumonia criteria or reviewer diagnosis. Agreement between electronic surveillance criteria vs manual chart review was low but similar to agreement amongst manual reviewers applying NHSN criteria. Electronic surveillance may provide greater consistency than human review while facilitating wide-scale automated surveillance.

Disclosures
Chanu Rhee, MD, MPH, UpToDate (Other Financial or Material Support, Chapter Author) Michael Klompas, MD, MPH, UpToDate (Other Financial or Material Support, Chapter Author)
27. Co-infections and antimicrobial use in patients hospitalized with COVID-19
Authors: Prasad Prithiv , Zacharioudakis Ioannis , Poles Jordan , Dubrovskaya Yanina , Delpachitra Dinuli , Iturrate Eduardo , Munoz-Gomez Sigridh 
Published: December 2021

Abstract

Background
In-hospital antimicrobial use among COVID-19 patients is widespread due to perceived bacterial and fungal co-infections. We aim to describe the incidence of these co-infections and antimicrobial use in patients hospitalized with COVID-19 to elucidate data for guiding effective antimicrobial use in this population.

Methods
This retrospective study included all patients admitted with COVID-19 from January 1, 2020, to February 1, 2021 at any of the three teaching hospitals of the NYU Langone Health system. Variables of interest were extracted from the health system’s de-identified clinical database. The nadir of hospital admissions between the first and second peaks of hospital admissions in the dataset was used to delineate the First Wave and Late Pandemic periods of observation. A cut-off of 48 hours after admission was used to differentiate Co-infections and Secondary infections respectively among isolates of clinically relevant bacterial or fungal pathogens in blood or sputum samples. Population statistics are presented as median with interquartile range (IQR) or total numbers with percentages.

Results
663 of 7,213 (9.2%) inpatients were found to have a positive bacterial or fungal culture of the respiratory tract or blood during the entire course of their initial admission at our hospitals for COVID-19. Positive respiratory cultures were found in 437 (6.1%) patients, with 94 (1.3%) being collected within 48 hours of admission. Blood culture positivity occurred in 333 patients (4.6%), with 115 (1.6%) identified within 48 hours of admission. Infection-free survival decreased with duration of hospitalization, with rate of secondary infections steadily rising after the second week of hospitalization as seen in Figure 1. 70.2% of inpatients received antimicrobials for a median duration of 6 antimicrobial days (IQR 3.0 – 12.0) per patient. A higher proportion of patients received antimicrobials in the first wave than in the late pandemic period (82.6% vs. 51.8%).
Table 1.

Table 2

Figure 1

Infection free survival represented as duration of admission in days on the X-axis, and proportion of admitted patients remaining infection-free in the Y-axis. The blue line represents blood cultures and the orange line represents sputum cultures.

Conclusion
There was a very low incidence of co-infection with SARS-CoV-2 infection at admission. A longer duration of hospitalization was associated with an increased risk of secondary infections. Antimicrobial use far exceeded the true incidence and detection of co-infections in these patients.

Disclosures
All Authors: No reported disclosures
29. Sustained Recovery in Patients Admitted to Hospital With COVID-19
Authors: Moestrup Kasper S , Zucco Adrian G , Reekie Joanne , MacPherson Cameron , Otrowski Sisse R , Niemann Carsten Utoft , Lundgren Jens , Helleberg Marie 
Published: December 2021

Abstract

Background
Several interventional Coronavirus Disease 2019 (COVID-19) studies assess outcomes at day 28, but this follow-up time can be too short, since COVID-19 often cause protracted disease. Further, data on mortality and readmissions after discharge are scarse.

Methods
Patients aged 18-100 years and hospitalized with COVID-19 in Eastern Denmark between March 18th, 2020 and January 12th, 2021, were followed for 91 days after admission. Patients were stratified in a first and second wave, by admissions before or after June 15th, 2020, app. when remdesivir and dexamethasone were introduced as standard of care. Sustained recovery was defined as the first date, achieving 14 consecutive days after hospital discharge without an event of readmission or death. Cumulative incidences of sustained recovery were estimated in both waves and in subgroups based on the patient’s maximum level of respiratory support in the first 14 days of admission as a proxy for disease severity. Risk factors for poor outcomes were assessed in a multivariable cox proportional hazards model.

Results
Overall 3,386 patients were included in the study; 1,137 and 2,249 patients were admitted in the first and second wave, respectively (Table 1). The cumulative incidence of sustained recovery at day 91 was higher in the second (0.79, 95% CI: 0.77,0.81) than in the first wave (0.72, 95% CI: 0.70, 0.75) (Fig. 1A). In both waves, those with more severe disease recovered at a slower rate (Fig. 2B). There were no differences in cumulative incidences of readmissions or deaths at day 91 after discharge between the two waves, cumulative incidence (0.20, 95% CI: 0.19,0.21) and (0.11, 95% CI: 0.09,0.12), respectively (Fig 1C, Fig 1D). Male sex, high age, cardiovascular disease, diabetes, chronic pulmonary disease, renal disease, malignancies and neurological disease were associated with lower rates of sustained recovery (Table 2).

Conclusion
A follow-up period of 28 days in clinical trials for COVID-19 treatments is too short, especially for patients with severe disease. Rates of adverse outcomes after hospital discharge are non-neglible. In-hospital mortality was reduced with improvements in treatment, but post discharge mortality and readmissions rates did not change significantly.

Disclosures
Carsten Utoft Niemann, PhD MD, Abbvie (Grant/Research Support, Advisor or Review Panel member)Astra Zeneca (Grant/Research Support, Advisor or Review Panel member, teaching)CSL Behring (Consultant)Genmab (Grant/Research Support)Gilead (Grant/Research Support)Janssen (Grant/Research Support, teaching)Novo Nordisk Foundation (Grant/Research Support)Roche (Grant/Research Support)Sunesis (Grant/Research Support)
45. COVID-19 Vulnerability and Data Reporting in Africa: Reflections from Cameroon
Authors: Judson Seth D , Njabo Kevin , Torimiro Judith 
Published: December 2021

Abstract

Background
At the beginning of the COVID-19 pandemic there were many questions about vulnerability and data reporting among African countries. We previously found that policymakers in Cameroon value region-specific risk maps for emerging diseases. Therefore, we created regional vulnerability indices for COVID-19 in Cameroon. As the pandemic grew, we aimed to compare how these predictions related to reported COVID-19 cases in Cameroon and whether additional African countries had available data to assess vulnerability for COVID-19.

Methods
Using data from the Cameroon 2018 Demographic and Health Survey (DHS), we had constructed an epidemiological vulnerability index based on comorbidities potentially associated with COVID-19 severity. Similarly, we had created a healthcare access index. We then compared these indices with regional COVID-19 cases per population from weekly situation reports in Cameroon. Finally, we identified the availability of DHS data and COVID-19 reporting systems in other African countries.
Vulnerability Indices for COVID-19 in Cameroon

The epidemiological and healthcare access vulnerability indices constructed for Cameroon are shown along with COVID-19 cases per population.

Results
Adjusting for data reporting limitations, regions in Cameroon that scored higher on the epidemiological vulnerability index were associated with greater COVID-19 cases per population. We also identified regions with mismatches between high epidemiological vulnerability and low healthcare access. COVID-19 data reporting systems varied among African countries. 29/54 (53.7%) of African countries had recurrent situation reports or online dashboards with subnational COVID-19 data in 2020. Meanwhile, 36/54 (66.7%) of African countries had DHS data reported in the last decade.

Conclusion
We found that vulnerability indices could be a rapid way of identifying populations at risk for emerging diseases such as COVID-19. This method could be used in other countries that have both recent health surveys from programs such as the DHS and subnational reporting of COVID-19 cases. Indices could be useful for decision-making, but they will need to be refined with national expert input. National situation reports and online dashboards provided subnational COVID-19 data in approximately half of African countries. Therefore, increased baseline health surveys as well as expanded reporting of COVID-19 case data could inform future vulnerability assessments in other countries.

Disclosures
All Authors: No reported disclosures
47. Impact of COVID-19 Pandemic on an Emergency Department Opt-out HIV Screening Program: An Interrupted Time Series Analysis
Authors: Niu Jianli , Eckardt Paula 
Published: December 2021

Abstract

Background
The coronavirus disease 2019 (COVID-19) pandemic has posed tremendous challenges to health care systems, including emergency department (ED) priorities and visits. We describe the impact of COVID-19 pandemic on ED-based “Opt-out” HIV testing at a public healthcare system in South Florida.

Methods
The programmatic data of ED-based HIV testing from July 2018 to March 2021 at the Memorial Regional Hospital, Hollywood, Florida was retrospectively analyzed. Interrupted time series (ITS) analysis models were developed to evaluate the immediate and gradual effects of the pandemic on the monthly number of HIV tests over time, with an interruption point at March 2020.

Results
45,185 HIV tests were recorded between July 2018 and March 2021. A mean of 1,745 (SD, 266) HIV tests per month before the COVID-19 pandemic (July 2018 to Feb 2020) and a mean of 791 (SD, 187) HIV tests per month during the pandemic period (March 2020 to March 2021) was seen (p&lt; 0.0001). As shown in Table 1, there was a slight decline trend in the number of monthly HIV test before the pandemic (estimate -10.29, p=0.541). We estimated a significant decrease in monthly HIV tests (estimate -678.48, p = 0.008), whereas the slope change after the pandemic was non-significant (estimate 4.84, p = 0.891). The number of monthly HIV tests declined significantly during the early phase of the pandemic, particularly between March 2020 and September 2020 (all p&lt; 0.05), with an estimated 48.0% decrease in the March 2020 (estimate -678.48, p = 0.007), 43% in the April 2020 (estimate -673.65, p=0.007), and 50.7% in the May 2020 (estimate -668.83, p=0.009), compared with the same month of the pre-pandemic period (Figure 1). This decline in number of monthly HIV tests is consistent with the first wave of the COVID-19 pandemic in South Florida. Number of decreased monthly HIV tests from October 2020 through March 2021 was less pronounced (all p &gt;0.05) and returned to pre-pandemic levels.

Conclusion
The COVID-19 pandemic led to a significant and immediate decline in monthly number of ED-based HIV tests. Disruption of basic health services by the COVID-19 pandemic is a public health concern. Strategies to develop an infrastructure to meet the demands of HIV testing should be implemented to ensure the current HIV prevention during the COVID-19 period.

Disclosures
All Authors: No reported disclosures