bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population-Based Severe Acute Respiratory Syndrome Coronavirus 2 Whole-Genome Sequencing and Contact Tracing During the Coronavirus Disease 2019 Pandemic in Switzerland
Authors: Anderegg Nanina , Schwab Tiana , Borcard Loïc , Mugglin Catrina , Keune-Dübi Bettina , Ramette Alban , Fenner Lukas 
Published: March 2023

AbstractBackgroundTesting and contact tracing (CT) can interrupt transmission chains of SARS-CoV-2. Whole-genome sequencing (WGS) can potentially strengthen these investigations and provide insights on transmission.MethodsWe included all laboratory-confirmed COVID-19 cases diagnosed between 4 June and 26 July 2021, in a Swiss canton. We defined CT clusters based on epidemiological links reported in the CT data and genomic clusters as sequences with no single-nucleotide polymorphism (SNP) differences between any 2 pairs of sequences being compared. We assessed the agreement between CT clusters and genomic clusters.ResultsOf 359 COVID-19 cases, 213 were sequenced. Overall, agreement between CT and genomic clusters was low (Cohen's κ = 0.13). Of 24 CT clusters with ≥2 sequenced samples, 9 (37.5%) were also linked based on genomic sequencing but in 4 of these, WGS found additional cases in other CT clusters. Household was most often reported source of infection (n = 101 [28.1%]) and home addresses coincided well with CT clusters: In 44 of 54 CT clusters containing ≥2 cases (81.5%), all cases in the cluster had the same reported home address. However, only a quarter of household transmission was confirmed by WGS (6 of 26 genomic clusters [23.1%]). A sensitivity analysis using ≤1-SNP differences to define genomic clusters resulted in similar results.ConclusionsWGS data supplemented epidemiological CT data, supported the detection of potential additional clusters missed by CT, and identified misclassified transmissions and sources of infection. Household transmission was overestimated by CT.
Time alters urban singing strategies in a North American songbird
Authors: Sanchez Karina A , Fialko Kristina , Benedict Lauryn , Cicero Carla 
Published: March 2023

AbstractLocal habitats shape animal vocalizations through selection to improve transmission of signals to receivers. This process can be variable, however, when landscapes are changing continuously due to urbanization or other factors. Studies have shown that some birds alter the frequency, amplitude and structure of their songs in urban habitats. Because songbirds learn their songs from other individuals, this cultural transmission can result in substantial change over time. Urban bird populations may therefore show rapid shifts in song form and variation may result from the combined or interacting effects of time and anthropogenic habitat change. In this study, we used historic and recent song recordings to investigate changes in spotted towhee (Pipilo maculatus) songs over 45 years across an urban-to-rural gradient in northern California. We found that pre-trill and trilled song parts covaried differently with urban development at the two time-points, with more change occurring in trill phrases than pre-trills. Additionally, we found that birds in 1970 adjusted trills in urban areas by raising maximum frequencies and broadening bandwidths, while birds in 2015 narrowed song bandwidths by decreasing maximum frequencies in more urban areas. These results did not fit our prediction that urbanization would have a consistent effect on song at two time-points. We suggest that habitat, cultural evolution and cultural drift can act on song elements in complicated ways that vary over time.
Molecular origins of mutational spectra produced by the environmental carcinogen N-nitrosodimethylamine and SN1 chemotherapeutic agents
Authors: Armijo Amanda L , Thongararm Pennapa , Fedeles Bogdan I , Yau Judy , Kay Jennifer E , Corrigan Joshua J , Chancharoen Marisa , Chawanthayatham Supawadee , Samson Leona D , Carrasco Sebastian E , Engelward Bevin P , Fox James G , Croy Robert G , Essigmann John M 
Published: March 2023

Abstract
DNA-methylating environmental carcinogens such as N-nitrosodimethylamine (NDMA) and certain alkylators used in chemotherapy form O6-methylguanine (m6G) as a functionally critical intermediate. NDMA is a multi-organ carcinogen found in contaminated water, polluted air, preserved foods, tobacco products, and many pharmaceuticals. Only ten weeks after exposure to NDMA, neonatally-treated mice experienced elevated mutation frequencies in liver, lung and kidney of ∼35-fold, 4-fold and 2-fold, respectively. High-resolution mutational spectra (HRMS) of liver and lung revealed distinctive patterns dominated by GC→AT mutations in 5’-Pu-G-3’ contexts, very similar to human COSMIC mutational signature SBS11. Commonly associated with alkylation damage, SBS11 appears in cancers treated with the DNA alkylator temozolomide (TMZ). When cells derived from the mice were treated with TMZ, N-methyl-N-nitrosourea, and streptozotocin (two other therapeutic methylating agents), all displayed NDMA-like HRMS, indicating mechanistically convergent mutational processes. The role of m6G in shaping the mutational spectrum of NDMA was probed by removing MGMT, the main cellular defense against m6G. MGMT-deficient mice displayed a strikingly enhanced mutant frequency, but identical HRMS, indicating that the mutational properties of these alkylators is likely owed to sequence-specific DNA binding. In sum, the HRMS of m6G-forming agents constitute an early-onset biomarker of exposure to DNA methylating carcinogens and drugs.
CMV Infection After Letermovir Primary Prophylaxis Discontinuation in Allogeneic Hematopoietic Cell Transplant Recipients
Authors: Chavaz Lara , Royston Léna , Masouridi-Levrat Stavroula , Mamez Anne-Claire , Giannotti Federica , Morin Sarah , Van Delden Christian , Chalandon Yves , Neofytos Dionysios 
Published: March 2023

Abstract
In this single-center study of 61 allogeneic hematopoietic cell transplant (HCT) recipients receiving letermovir primary cytomegalovirus (CMV) prophylaxis for the first 100 days, we report 23% incidence of clinically significant CMV infection during the first 100 days after letermovir discontinuation, predominately in haploidentical HCT recipients, without any associations with CMV-DNAemia under letermovir.
A novel variant of Paganini-Miozzo syndrome: a case report
Authors: Sarmadian Roham , Gilani Abolfazl , Biglari Habibe Nejad 
Published: March 2023

ABSTRACTPaganini-Miozzo syndrome (MRXSPM) is a rare neurogenetic disorder that is transmitted by X-linked recessive inheritance. This is the third case reported of this disease in the world with a novel variant. A boy was referred due to the absence of neck holding and hand tremors. The examinations found facial anomalies. The brain magnetic resonance imaging (MRI) showed cerebral atrophy and diffused white matter, and irregularities were seen in his electroencephalogram (EEG). The echocardiography revealed a mid-muscular ventricular septal defect. A whole exome sequencing (WES) analysis revealed a novel variant (c.979C &gt; T; p.Pro327Ser) of uncertain significance in the HS6ST2 gene indicating Paganini-Miozzo syndrome. The current case provides additional evidence that MRXSPM can be associated with various neurological and cardiac complications. It is essential to rule out other causes, such as metabolic and infectious diseases. EEG, MRI and WES analyses can help to make a definitive diagnosis.
The Uprooting of Indigenous Women’s Horticultural Practices in Brazil, 1500–1650
Authors: O’Leary Jessica 
Published: March 2023

Abstract
In the land now known as Brazil, Indigenous women were responsible for cultivating and preparing a tuberous root called mandioca (cassava). Following the arrival of Europeans in 1500, mandioca replaced wheat bread to become the staple carbohydrate in settlers’ diets. Travellers’ accounts between 1500 and 1550 describe how Indigenous women taught settlers to prepare the tubers for consumption through the use of special tools and processes of soaking, drying and pulverizing. However, with the arrival of the Jesuits, European sources began to elide or problematize knowledge among Indigenous women that did not cohere with Christian normative values. By the mid seventeenth century, naturalists were no longer acknowledging the original female informants who had taught Europeans how to identify and cultivate the plant. In line with recent scholarship on the history of science and medicine in colonial contexts, a close reading of the sources reflects the importance of Indigenous knowledges to imperial expansion, on the one hand, and the interactive nature of cross-cultural knowledge sharing that became hidden by early modern European epistemological practices. Drawing on a broad body of colonial documentation, this article examines how European representations of the cultivation of mandioca identified, exploited, assimilated, suppressed and, finally, alienated Indigenous women’s knowledges from their original holders between 1500 and 1650.
Weaving It In: How Political Radio Reacts to Events
Authors: Vandeweerdt Clara 
Published: March 2023

Abstract
How do ideologically slanted media outlets react to politically relevant events? Previous research suggests that partisan media trumpet ideologically congenial events, such as opposing-party scandals, while ignoring bad news for their own side. Looking at reactions to newsworthy events on political radio—an often-partisan medium that reaches more Americans than Twitter—I find a different pattern. Based on recordings of hundreds of shows totaling two million broadcast hours, I demonstrate that regardless of their ideological leanings, political shows respond to events by dramatically increasing the attention they give to related policy issues. At the same time, liberal and conservative shows continue to frame those issues in very different ways. Instead of ignoring inconvenient events, partisan media “weave them in,” interpreting them in ways consistent with their ideological leanings. These media dynamics imply that nationally significant events can cause opinion polarization rather than convergence—becoming a divisive rather than a shared experience.
Why We Don’t Fight: A Review Article
Authors: Beehner Lionel 
Published: March 2023

Abstract
Wars are the exception, not the rule, as Christopher Blattman, a political scientist and development economist from the University of Chicago, reveals in his new book, Why We Fight: The Roots of War and the Paths to Peace. Blattman makes the case that both strategic and psychological factors explain most outbreaks of violence, whether they are gangland beefs over urban turf, asymmetric counterinsurgencies, or conventional wars like the current conflict in Ukraine. The book is a helpful compendium for scholars of international relations and comparative politics on the causes of conflict, drawing on lessons from game theory and the rational choice school to explain why nations and nonstate actors fight. Much of the analysis is drawn from Blattman’s own distinguished career as a development economist in Africa, and he helpfully intersperses the prose with first-person vignettes from some of the world’s most dangerous conflict zones, including Liberia, Uganda, Colombia, and inner-city Chicago.
How to Talk When a Machine Is Listening: Corporate Disclosure in the Age of AI
Authors: Cao Sean , Jiang Wei , Yang Baozhong , Zhang Alan L 
Published: March 2023

Abstract
Growing AI readership (proxied for by machine downloads and ownership by AI-equipped investors) motivates firms to prepare filings friendlier to machine processing and to mitigate linguistic tones that are unfavorably perceived by algorithms. Loughran and McDonald (2011) and BERT available since 2018 serve as event studies supporting attribution of the decrease in the measured negative sentiment to increased machine readership. This relationship is stronger among firms with higher benefits to (e.g., external financing needs) or lower cost (e.g., litigation risk) of sentiment management. This is the first study exploring the feedback effect on corporate disclosure in response to technology.
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host
Authors: Veith Talitha , Bleicker Tobias , Eschbach-Bludau Monika , Brünink Sebastian , Mühlemann Barbara , Schneider Julia , Beheim-Schwarzbach Jörn , Rakotondranary S Jacques , Ratovonamana Yedidya R , Tsagnangara Cedric , Ernest Refaly , Randriantafika Faly , Sommer Simone , Stetter Nadine , Jones Terry C , Drosten Christian , Ganzhorn Jörg U , Corman Victor M 
Published: March 2023

Abstract
Adenoviruses (AdVs) are important human and animal pathogens and are frequently used as vectors for gene therapy and vaccine delivery. Surprisingly, there are only scant data regarding primate AdV origin and evolution, especially in the most basal primate hosts. We detect and sequence AdVs from faeces of two Madagascan lemur species. Complete genome sequence analyses define a new AdV species with a particularly large gene encoding a protein of unknown function in the early gene region 3. Unexpectedly, the new AdV species is not most similar to human or other simian AdVs but to bat adenovirus C. Genome characterisation shows signals of virus–host codivergence in non-structural genes, which show lower diversity than structural genes. Outside a lemur species mixing zone, recombination less frequently separates structural genes, as in human adenovirus C. The evolutionary history of lemur AdVs likely involves both a host switch and codivergence with the lemur hosts.
Sustained Perturbation of Metabolism and Metabolic Subphenotypes Are Associated With Mortality and Protein Markers of the Host Response
Authors: Jennaro Theodore S. , Puskarich Michael A. , Evans Charles R. , Karnovsky Alla , Flott Thomas L. , McLellan Laura A. , Jones Alan E. , Stringer Kathleen A. 
Published: March 2023

OBJECTIVES:
Perturbed host metabolism is increasingly recognized as a pillar of sepsis pathogenesis, yet the dynamic alterations in metabolism and its relationship to other components of the host response remain incompletely understood. We sought to identify the early host-metabolic response in patients with septic shock and to explore biophysiological phenotyping and differences in clinical outcomes among metabolic subgroups.

DESIGN:
We measured serum metabolites and proteins reflective of the host-immune and endothelial response in patients with septic shock.

SETTING:
We considered patients from the placebo arm of a completed phase II, randomized controlled trial conducted at 16 U.S. medical centers. Serum was collected at baseline (within 24 hr of the identification of septic shock), 24-hour, and 48-hour postenrollment. Linear mixed models were built to assess the early trajectory of protein analytes and metabolites stratified by 28-day mortality status. Unsupervised clustering of baseline metabolomics data was conducted to identify subgroups of patients.

PATIENTS:
Patients with vasopressor-dependent septic shock and moderate organ dysfunction that were enrolled in the placebo arm of a clinical trial.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Fifty-one metabolites and 10 protein analytes were measured longitudinally in 72 patients with septic shock. In the 30 patients (41.7%) who died prior to 28 days, systemic concentrations of acylcarnitines and interleukin (IL)-8 were elevated at baseline and persisted at T24 and T48 throughout early resuscitation. Concentrations of pyruvate, IL-6, tumor necrosis factor-α, and angiopoietin-2 decreased at a slower rate in patients who died. Two groups emerged from clustering of baseline metabolites. Group 1 was characterized by higher levels of acylcarnitines, greater organ dysfunction at baseline and postresuscitation (p < 0.05), and greater mortality over 1 year (p < 0.001).

CONCLUSIONS:
Among patients with septic shock, nonsurvivors exhibited a more profound and persistent dysregulation in protein analytes attributable to neutrophil activation and disruption of mitochondrial-related metabolism than survivors.
The Effectiveness of the Interventions to Reduce Sound Levels in the ICU: A Systematic Review
Authors: Vreman Jeanette , Lemson Joris , Lanting Cris , van der Hoeven Johannes , van den Boogaard Mark 
Published: March 2023

OBJECTIVES:
Excessive noise is ubiquitous in the ICU, and there is growing evidence of the negative impact on work performance of caregivers. This study aims to determine the effectiveness of interventions to reduce noise in the ICU.

DATA SOURCES:
Databases of PubMed, EMBASE, PsychINFO, CINAHL, and Web of Science were systematically searched from inception to September 14, 2022.

STUDY SELECTION:
Two independent reviewers assessed titles and abstracts against study eligibility criteria. Noise mitigating ICU studies were included when having at least one quantitative acoustic outcome measure expressed in A-weighted sound pressure level with an experimental, quasi-experimental, or observational design. Discrepancies were resolved by consensus, and a third independent reviewer adjudicated as necessary.

DATA EXTRACTION:
After title, abstract, and full-text selection, two reviewers independently assessed the quality of each study using the Cochrane’s Risk Of Bias In Nonrandomized Studies of Interventions tool. Data were synthesized according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines, and interventions were summarized.

DATA SYNTHESIS:
After screening 12,652 articles, 25 articles were included, comprising either a mixed group of healthcare professionals (n = 17) or only nurses (n = 8) from adult or PICU settings. Overall, the methodological quality of the studies was low. Noise reduction interventions were categorized into education (n = 4), warning devices (n = 3), multicomponent programs (n = 15), and architectural redesign (n = 3). Education, a noise warning device, and an architectural redesign significantly decreased the sound pressure levels.

CONCLUSIONS:
Staff education and visual alert systems seem promising interventions to reduce noise with a short-term effect. The evidence of the studied multicomponent intervention studies, which may lead to the best results, is still low. Therefore, high-quality studies with a low risk of bias and a long-term follow-up are warranted. Embedding noise shielding within the ICU-redesign is supportive to reduce sound pressure levels.
Pulse Methylprednisolone Versus Dexamethasone in COVID-19: A Multicenter Cohort Study
Authors: Watanabe Atsuyuki , Inokuchi Ryota , Kuno Toshiki , Uda Kazuaki , Komiyama Jun , Adomi Motohiko , Ishisaka Yoshiko , Abe Toshikazu , Tamiya Nanako , Iwagami Masao 
Published: March 2023

IMPORTANCE:
Although pulse (high-dose) methylprednisolone therapy can hypothetically control immune system flare-ups effectively, the clinical benefit of pulse methylprednisolone compared with dexamethasone in COVID-19 remains inconclusive.

OBJECTIVES:
To compare pulse methylprednisolone to dexamethasone as a COVID-19 treatment.

DESIGN, SETTING, AND PARTICIPANTS:
Using a Japanese multicenter database, we identified adult patients admitted for COVID-19 and discharged between January 2020 and December 2021 treated with pulse methylprednisolone (250, 500, or 1,000 mg/d) or IV dexamethasone (≥ 6 mg/d) at admission day 0 or 1.

Main Outcomes and Measures:
The primary outcome was in-hospital mortality. Secondary outcomes were 30-day mortality, new ICU admission, insulin initiation, fungal infection, and readmission. Multivariable logistic regression was conducted to differentiate the dose of pulse methylprednisolone (250, 500, or 1,000 mg/d). Additionally, subgroup analyses by characteristics such as the need for invasive mechanical ventilation (IMV) were also conducted.

RESULTS:
A total of 7,519, 197, 399, and 1,046 patients received dexamethasone, 250, 500, and 1,000 mg/d of methylprednisolone, respectively. The crude in-hospital mortality was 9.3% (702/7,519), 8.6% (17/197), 17.0% (68/399), and 16.2% (169/1,046) for the different doses, respectively. The adjusted odds ratio (95% CI) was 1.26 (0.69–2.29), 1.48 (1.07–2.04), and 1.75 (1.40–2.19) in patients starting 250, 500, and 1,000 mg/d of methylprednisolone, respectively, compared with those starting dexamethasone. In subgroup analyses, the adjusted odds ratio of in-hospital mortality was 0.78 (0.25–2.47), 1.12 (0.55–2.27), and 1.04 (0.68–1.57) in 250, 500, and 1,000 mg/d of methylprednisolone, respectively, among patients with IMV, whereas the adjusted odds ratio was 1.54 (0.77–3.08), 1.62 (1.13–2.34), and 2.14 (1.64–2.80) among patients without IMV.

CONCLUSIONS AND RELEVANCE:
Higher doses of pulse methylprednisolone (500 or 1,000 mg/d) may be associated with worse COVID-19 outcomes when compared with dexamethasone, especially in patients not on IMV.
Intrapulmonary and Intracardiac Shunts in Adult COVID-19 Versus Non-COVID Acute Respiratory Distress Syndrome ICU Patients Using Echocardiography and Contrast Bubble Studies (COVID-Shunt Study): A Prospective, Observational Cohort Study
Authors: Lau Vincent I. , Mah Graham D. , Wang Xiaoming , Byker Leon , Robinson Andrea , Milovanovic Lazar , Alherbish Aws , Odenbach Jeffrey , Vadeanu Cristian , Lu David , Smyth Leo , Rohatensky Mitchell , Whiteside Brian , Gregoire Phillip , Luksun Warren , van Diepen Sean , Anderson Dustin , Verma Sanam , Slemko Jocelyn , Brindley Peter , Kustogiannis Demetrios J. , Jacka Michael , Shaw Andrew , Wheatley Matt , Windram Jonathan , Opgenorth Dawn , Baig Nadia , Rewa Oleksa G. , Bagshaw Sean M. , Buchanan Brian M. 
Published: March 2023

OBJECTIVES:
Studies have suggested intrapulmonary shunts may contribute to hypoxemia in COVID-19 acute respiratory distress syndrome (ARDS) with worse associated outcomes. We evaluated the presence of right-to-left (R-L) shunts in COVID-19 and non-COVID ARDS patients using a comprehensive hypoxemia workup for shunt etiology and associations with mortality.

DESIGN:
Prospective, observational cohort study.

SETTING:
Four tertiary hospitals in Edmonton, Alberta, Canada.

PATIENTS:
Adult critically ill, mechanically ventilated, ICU patients admitted with COVID-19 or non-COVID (November 16, 2020, to September 1, 2021).

INTERVENTIONS:
Agitated-saline bubble studies with transthoracic echocardiography/transcranial Doppler ± transesophageal echocardiography assessed for R-L shunts presence.

MEASUREMENTS AND MAIN RESULTS:
Primary outcomes were shunt frequency and association with hospital mortality. Logistic regression analysis was used for adjustment. The study enrolled 226 patients (182 COVID-19 vs 42 non-COVID). Median age was 58 years (interquartile range [IQR], 47–67 yr) and Acute Physiology and Chronic Health Evaluation II scores of 30 (IQR, 21–36). In COVID-19 patients, the frequency of R-L shunt was 31 of 182 COVID patients (17.0%) versus 10 of 44 non-COVID patients (22.7%), with no difference detected in shunt rates (risk difference [RD], –5.7%; 95% CI, –18.4 to 7.0; p = 0.38). In the COVID-19 group, hospital mortality was higher for those with R-L shunt compared with those without (54.8% vs 35.8%; RD, 19.0%; 95% CI, 0.1–37.9; p = 0.05). This did not persist at 90-day mortality nor after adjustment with regression.

CONCLUSIONS:
There was no evidence of increased R-L shunt rates in COVID-19 compared with non-COVID controls. R-L shunt was associated with increased in-hospital mortality for COVID-19 patients, but this did not persist at 90-day mortality or after adjusting using logistic regression.