bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel Queuovirinae lineage of Pseudomonas aeruginosa phages encode dPreQ0 DNA modifications with a single GA motif that provide restriction and CRISPR Cas9 protection in vitro
Authors: Olsen Nikoline S , Nielsen Tue K , Cui Liang , Dedon Peter , Neve Horst , Hansen Lars H , Kot Witold 
Published: July 2023

Abstract
Deazaguanine DNA modifications are widespread in phages, particularly in those with pathogenic hosts. Pseudomonas phage iggy substitutes ∼16.5% of its genomic 2′-deoxyguanosine (G) with dPreQ0, and the iggy deazaguanine transglycosylase (DpdA) is unique in having a strict GA target motif, not observed previously. The iggy PreQ0 modification is shown to provide protection against both restriction endonucleases and Cas9 (when present in PAM), thus expanding our understanding of the deazaguanine modification system, its potential, and diversity. Phage iggy represents a new genus of Pseudomonas phages within the Queuovirinae subfamily; which have very little in common with other published phage genomes in terms of nucleotide similarity (&lt;10%) and common proteins (&lt;2%). Interestingly, shared similarity is concentrated in dpdA and preQ0 biosynthesis genes. TEM imaging confirmed a siphovirus morphology with a prolate icosahedral head and a non-contractile flexible tail with one long central tail spike. The observed protective effect of the deazaguanine modification on the iggy DNA may contribute to its broad within-species host range. Phage iggy was isolated on Pseudomonas aeruginosa PAO1, but also infects PDO300, PAK, PA14, as well as 10 of 27 tested environmental isolates and 13 of 20 tested clinical isolates of P. aeruginosa from patients with cystic fibrosis.
Examining Cigar Pack Quantity Purchases by Cigar Type in the United States Between 2014 and 2017
Authors: King Jensen Jessica L , Cornacchione Ross Jennifer , Rebentisch Kayla , Delnevo Cristine D , Azagba Sunday 
Published: July 2023

Abstract

Introduction
We examined whether the proportion of cigar pack quantity usually purchased differed between 2014 and 2017 in the United States.

Methods
Data are from waves 1 and 4 of the Population Assessment of Tobacco and Health Study. The proportions of pack quantity purchases between waves for premium cigars, large cigars, cigarillos, and filtered cigars for 10-pack quantities (singles, 2-packs, 3-packs, 4-packs, 5-packs, 6–9-packs, 10-packs, 11–-19-packs, 20-packs, ≥21 packs) were compared using Z-tests. We used multivariable linear regressions to examine factors associated with pack quantity.

Results
For premium cigars, most adults purchased singles, with 84.4% in 2014 and 88.7% in 2017. For large cigars, single purchases increased from 46.2% to 62.7% (p &lt; .00001). Two-packs also increased, 3.1% to 10.2% (p &lt; .00001), while 5-packs, 6–9 packs, 10–19-packs, and 20-packs decreased. For cigarillos, singles purchases increased from 51.9% to 57.5% (p = .0002). Two-packs also increased, 8.8% to 19.6% (p &lt; .00001), while 3-packs, 4-packs, 5-packs, and 20-packs decreased. For filtered cigars, the most prevalent pack quantity shifted from 20-packs in 2014 (62.6%) to singles in 2017 (36.7%). Singles, 2-packs, 3–4-packs, and 5-packs increased while 11–19-packs, 20-packs, and ≥21 packs decreased. Days used were positively associated with pack quantity purchase for all cigar types in 2017, while the price was positively associated with premium cigar purchase.

Conclusions
Between 2014 and 2017, the proportion of consumers who purchased singles remained at over 80% for premium cigars and increased for other cigars. Continued monitoring of use behaviors, including pack quantities by cigar type, is needed as the market and policy landscapes continue shifting.

Implications
Single cigar purchases are prominent across cigar types. Five-packs and 20-packs were the second most common pack quantities across cigar types, with relatively low proportions for other pack quantities. These findings suggest adults consuming premium cigars consistently prefer singles, a pattern that was found across cigar types. However, when considering purchases made online, premium cigars are widely purchased in larger pack quantities. Age and race were associated with purchase for some cigar types at some years, days used were associated with the purchase quantity in 2017 for all cigar types, and price was positively associated across time periods for only premium cigar purchases. Thus, the factors associated with cigar pack quantity purchase remain unclear. As the cigar policy landscape shifts, continued monitoring of the purchase behaviors by cigar type will be important to better inform future cigar policies.
Estimating Prevalence of Premium or Traditional Cigar &#x2028;Use and User Characteristics Based on Varying Definitions of Use
Authors: Ganz Ollie , Villanti Andrea C , Young William J , Mays Darren , Bover Manderski Michelle T , Delnevo Cristine D 
Published: July 2023

Abstract

Background
Premium cigar use is infrequent compared with the use of other tobacco products, including other cigar types (eg, cigarillos), though current measurement methods for premium cigar use have limitations. Accordingly, prevalence estimates from existing surveillance studies likely underestimate the true prevalence of premium cigar use.

Aims and Methods
Using an online convenience sample of adults (ages 18–45 years) surveyed in February 2022, we examined premium or traditional cigar prevalence and characterized users based on four definitions of use: (1) past-year use, (2) past 30-day use, (3) use every day or some days, and (4) use every day, some days, or rarely, using a novel, one-item measure. We examined demographics, cigar use behaviors, and other tobacco product use for each definition and conducted sensitivity analyses using cigar brands.

Results
Prevalence estimates ranged from 1.8% using Definition 3 to 11.6% using Definition 1. Regardless of definition, premium or traditional cigar users were largely male, white, and aged 25–45 years. A large proportion of users based on Definition 3 were aged 25–34 years, had a regular premium cigar brand, smoked cigars on more than one day in the past month, used cannabis in the past month, and reported perceiving premium cigars as less harmful compared with cigarettes.

Discussion
Prevalence estimates of premium or traditional cigar use varied by more than fivefold based on the definition of use and user characteristics varied by definition. Existing national surveys are likely underestimating the prevalence and patterns of premium cigar use.

Implications
Given that the negative health effects of premium cigars vary based on how the cigars are used (eg, frequency or duration), as well as co-use with other tobacco products and substances (eg, alcohol and cannabis), accurate measurement of these products is important for understanding patterns of use and their impact on public health.
Exploring the Presence and Type of Premium Cigar Retailers With Neighborhood Sociodemographic Correlates in the United States, 2019–2021
Authors: Kong Amanda Y , Ganz Ollie , Villanti Andrea C 
Published: July 2023

Abstract

Introduction
Little is known about the location and store type of premium cigar retailers in the United States. Different store types may expose people to secondhand smoke (eg, cigar bar or lounge) and may also have age restrictions (eg, tobacco shops) that could reduce youth exposure to products and marketing.

Aims and Methods
We obtained a national retailer dataset from the Premium Cigar Association (PCA) from 2019 to 2021. We coded store type using nine categories and used generalized estimating equations to examine associations between census tract sociodemographic characteristics and PCA store type.

Results
Of the 1279 PCA retailers, the majority were cigar stores (39%), followed by tobacco shops (26%), cigar bars or lounges (20%), and beer, wine, or liquor stores (15%). Overall, there were no statistically significant associations between tract-level sociodemographic characteristics and the odds that a retailer was a specific store type versus another store type. However, PCA retailers located in tracts with a higher percentage of non-Hispanic Black residents were associated with 1.12 times the odds of being a cigar bar or lounge versus another type (95% CI, 1.02 to 1.22).

Conclusions
The majority of PCA retailers are specialty cigar stores or cigar bars or lounges, and few are more traditional tobacco retailers, such as convenience stores. We document a higher odds of a store being a cigar bar or lounge for retailers located in neighborhoods with a higher proportion of Black residents, which may contribute to inequities in tobacco-related disease and disability because of potentially greater secondhand smoke exposure.

Implications
Specialized retailers account for most premium cigar stores. One in five PCA retailers was a cigar bar or lounge, which raises public health concerns around exposure to secondhand smoke for patrons and employees. Local jurisdictions should examine zoning ordinances in tandem with sociodemographic characteristics to ensure inequities in the location of cigar bars or lounges are not produced or sustained given the potential harms associated with secondhand smoke exposure.
Oritavancin vs Standard of Care for Treatment of Nonendovascular Gram-Positive Bloodstream Infections
Authors: Moenster Ryan P , Wallace-Lacey Ashleigh , Western Hannah , Tiefenaur Seth , Abdulbasir Anosha , Alberts Justin , Doty Jonathan , Abner Hartley , Skouby Danielle , Lorenz Michael , Fong Rebecca , Arora Jyoti , Linneman Travis W 
Published: July 2023

Abstract

Background
Data is limited comparing oritavancin (ORT) to the standard-of-care (SOC) for the treatment gram-positive blood stream infections (BSI).

Methods
This was a retrospective study of all patients in the Veteran's Affairs Health Care System treated with at least 1 dose of oritavancin or at least 5 days of vancomycin, daptomycin, ceftaroline, ampicillin, ampicillin-sulbactam, nafcillin, oxacillin, or cefazolin for a documented gram-positive BSI from 1 January 2015 to 30 June 2021. Patients with polymicrobial blood cultures or positive cultures from other sites were included if the organisms were sensitive to the incident antimicrobial; no concomitant antimicrobials could be used once the incident agent was started. Individuals were also excluded if they were diagnosed with endocarditis, had a neutrophil count 96-hours of treatment before the incident antimicrobial was started.
The primary composite outcome was clinical failure, defined as all-cause mortality within 30-days from the end of therapy, or blood cultures positive for the incident organisms ≥72 hours after administration of the first dose and ≤30 days after the administration of the final dose of the study antimicrobial, or any drug or line-related readmissions within 30-days of hospital discharge.

Results
Two hundred-forty patients were identified for screening with 96 meeting criteria (27 in ORT and 69 in SOC groups). Baseline characteristics were generally balanced between groups except more patients in the ORT group received &gt;96-hours of treatment before the incident antimicrobial was started (70.3% (19/27) vs 13.04% 9/69); P &lt; .001). The pathogen most prevalent was methicillin susceptible Staphylococcus aureus (MSSA) (ORT 33.3% (9/27) vs SOC 46.4% (32/69)). Clinical failure occurred in 7.4% (2/27) in the ORT group and 17.4% (12/69) in SOC (P = .34). No components of the primary outcome were significantly different between groups, but AKI did occur more commonly in the SOC group (27.5% (19/69) vs 3.7% (1/27); P = .01).

Conclusions
ORT appears to be a safe and effective option when directly compared to the SOC for non-endocarditis BSIs.
Insights into the protonation state and spin structure for the g = 2 multiline electron paramagnetic resonance signal of the oxygen-evolving complex
Authors: Saito Keisuke , Nishio Shunya , Asada Mizue , Mino Hiroyuki , Ishikita Hiroshi 
Published: July 2023

Abstract
In photosystem II (PSII), one-electron oxidation of the most stable oxidation state of the Mn4CaO5 cluster (S1) leads to formation of two distinct states, the open-cubane S2 conformation [Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV)] with low spin and the closed-cubane S2 conformation [Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III)] with high spin. In electron paramagnetic resonance (EPR) spectroscopy, the open-cubane S2 conformation exhibits a g = 2 multiline signal. However, its protonation state remains unclear. Here, we investigated the protonation state of the open-cubane S2 conformation by calculating exchange couplings in the presence of the PSII protein environment and simulating the pulsed electron–electron double resonance (PELDOR). When a ligand water molecule, which forms an H-bond with D1-Asp61 (W1), is deprotonated at dangling Mn4(IV), the first-exited energy (34 cm−1) in manifold spin excited states aligns with the observed value in temperature-dependent pulsed EPR analyses, and the PELDOR signal is best reproduced. Consequently, the g = 2 multiline signal observed in EPR corresponds to the open-cubane S2 conformation with the deprotonated W1 (OH−).
ARTop: an open-source tool for measuring active region topology at the solar photosphere
Authors: Alielden K , MacTaggart D , Ming Q , Prior C , Raphaldini B 
Published: July 2023

ABSTRACT
The importance of measuring topological quantities, such as magnetic helicity, in solar observations has long been recognized. In particular, topological quantities play an important role in both understanding and predicting solar eruptions. In this paper, we present ARTop (Active Region Topology), an open-source and end-to-end software tool that allows researchers to calculate the fluxes of topological quantities based on solar magnetograms. In addition to this, ARTop also allows for the efficient analysis of these quantities in both 2D maps and time series. ARTop calculates the fluxes of magnetic helicity and magnetic winding, together with particular decompositions of these quantities. To perform these calculations, SHARP magnetograms are downloaded and velocity maps are created using the DAVE4VM method. Visualization tools, written in Python, are provided to aid in the selection of appropriate output variables and for the straightforward creation of maps and time series. Additionally, other analysis functions are included to facilitate and aid solar flare investigations. This software offers researchers a powerful tool for investigating the behaviour of active regions and the origins of space weather.
Natural radioactivity and radiological hazard analysis of construction stones from various quarries in Machakos County-Kenya
Authors: Mutua John O , Linturi James M , Maweu Onesmus M , Kebwaro Jeremiah M , Matsitsi Stanley M 
Published: July 2023

Abstract
The radioactivity levels of rocks sampled from the quarries of Kyasioni, Mavoloni and Kathaana located in the lower Eastern County of Machakos in Kenya were determined. Forty-two samples were collected using stratified random sampling and analysed using NaI(TI) detector with a specially designed lead shield. The parametric values of activity concentration, absorbed dose, annual dose rate and hazard indices were estimated using activity–dose relations suggested in UNSCEAR and ICRP reports. The mean activity concentration for the entire work for 238U (226Ra), 232Th and 40K were 68.33 ± 3.11, 101.10 ± 1.83 and 1084.02 ± 30.28 Bq/kg, respectively. Kyasioni quarry presented the highest activity concentration of 74.75 ± 3.15, 118.48 ± 1.91 and 1120.35 ± 30.07 Bq/kg for 226Ra, 232Th and 40K, respectively. The average annual effective dose was estimated as 0.58 ± 0.01, 0.47 ± 0.01 and 0.52 ± 0.01 mSv/y for Kyasioni, Kathaana and Mavoloni quarries, respectively. Other radiological parameters estimated from the corresponding activities were within the recommended limits hence guaranteeing safety to the users.
Effects of multiple vitamin E levels and two fat sources in diets for swine fed to heavy slaughter weight of 150 kg: I. Growth performance, lean growth, organ size, carcass characteristics, primal cuts, and pork quality
Authors: Wang Ding , Jang Young Dal , Kelley Marlee , Rentfrow Gregg K , Azain Michael J , Lindemann Merlin D 
Published: July 2023

Abstract
The study objective was to evaluate the effect of two fat source and graded levels of vitamin E (VE) supplementation on growth performance, carcass characteristics, and meat quality of pigs at heavy slaughter weight (150 kg). A total of 48 individually-fed pigs (24 barrows, 24 gilts; 28.44  ± 2.69 kg) were blocked by sex and weight and randomly assigned to eight dietary treatments in a 2 × 4 factorial arrangement. Fat treatments were 5% tallow (TW) and distiller’s corn-oil (DCO) in the diets. The VE treatments included four levels of α-tocopheryl-acetate (11, 40, 100, and 200 ppm). Growth performance, carcass traits, organ weight, primal cuts, and pork quality were measured. Increasing dietary VE supplementation levels linearly increased overall Average daily gain (ADG) and average daily feed intake (P &lt; 0.05), with an interaction between fat sources and VE supplementation levels on cumulative ADG (P &lt; 0.05) during phases 1 and 3 (28 to 100 kg) and 1 to 4 (28 to125 kg) wherein ADG in the pigs fed the DCO diet, but not the TW diet, increased with increasing dietary VE supplementation level. A similar interaction was observed in 24 h pH and picnic shoulder (P &lt; 0.05). No notable effect of fat source was observed in growth performance. With increasing dietary VE supplementation levels, there were quadratic responses in pork pH at 45 min and 24 h postmortem with the highest value in 40 and 100 ppm of VE levels while TBARS values on day 7 postmortem decreased linearly (P &lt; 0.05). Compared with the TW diet, the DCO diet resulted in greater TBARS values during 7 postmortem (P &lt; 0.05; day 5, P = 0.09). These results demonstrated that increasing dietary VE supplementation level could enhance growth rate and feed intake and reduce lipid peroxidation of pork whereas the diet containing DCO as a fat source could negatively affect pork shelf-life and carcass characteristics and that increasing VE supplementation level had no notable interaction with fat sources for carcass characteristics.
3Digital Humanities
Authors: Roy Dibyadyuti , Deshbandhu Aditya 
Published: July 2023

Abstract
The absence of an entry on digital humanities in the last volume of The Year’s Work in Critical and Cultural Theory due to the Covid-19 pandemic as well as the exacerbation of academic precarity (that was acknowledged in the editorial preface of the last volume) predicates that this chapter develop a narrative bibliography of notable scholarship in the digital humanities from both 2021 and 2022. Therefore the unprecedented circumstances that have extended the scope of scholarly review for this chapter beyond a single chronological year also provide the unique opportunity to not only ‘trace and expand upon currents in critical and cultural theory, and to engage in [the] areas’ key debates’ (Quinn and Ghosh, ‘Preface’ to YWCCT 2022) but also (and more importantly, one might argue) understand some of the radical thematic transformations brought about and anticipated by the legacies, presents, and futures of digital humanities within the supposedly ‘new normal’ of a post-Covid world.
Through consolidating diverse conversations from varied contexts that are shaping contemporary digital humanities and in anticipating the futures of the discipline, this chapter locates scholarship in the digital humanities and related fields from the years 2021 and 2022 within the interconnected themes of resistive ontologies, organizations, and new directions in the digital humanities. While the focus remains on the scholarship produced within the aforesaid chronological period, our methodological attempt in this intervention has been to acknowledge and put into dialogue relevant contributions related to the three primary themes of analysis that may fall beyond the ambit of a specific period.
Inferring the behaviour of predatory gastropods and their ostracod prey across the Cretaceous–Palaeogene boundary
Authors: Villegas-Martín Jorge , Ceolin Daiane , Klompmaker Adiël A , Fauth Gerson , Koutsoukos Eduardo A M 
Published: July 2023

Abstract
Predator–prey dynamics involving ostracod prey across the Cretaceous–Palaeogene (K–Pg) extinction event have not been evaluated rigorously. We studied 3146 Maastrichtian and Danian ostracod specimens from a section in eastern Brazil across the K–Pg boundary. The Maastrichtian assemblage level predation intensity (2.7%) is lower than in the Danian (4.7%). However, the drilling intensity in assemblages immediately above the K–Pg boundary is 0%, perhaps due to abrupt palaeoecological and palaeoenvironmental changes resulting from the K–Pg event. For the Maastrichtian, the dorsal and posterior regions are preferentially drilled, whereas the dorsal and median regions are primarily drilled during the Danian. Variation in Maastrichtian and Danian predation intensities between species (0.0–50.0%) and null model analyses suggest significant prey preference and avoidance, particularly in the Danian, unrelated to prey abundance. Drilling intensities for smooth specimens are significantly greater than for ornamented specimens for the Maastrichtian and the Danian. Finally, Danian drill-hole diameters and predator–prey size ratios are statistically larger than in the Maastrichtian, suggesting predatory gastropods were larger after the boundary, also relative to their prey. We conclude that predator–prey dynamics were affected by the K–Pg extinction event.
Update on autoantibodies and related biomarkers in autoimmune inflammatory myopathies
Authors: Choi May Y. , Satoh Minoru , Fritzler Marvin J. 
Published: July 2023

Purpose of reviewThis manuscript reviews recently published advances in the identification of autoimmune inflammatory myopathies (AIM)-specific and AIM-related autoantibodies considered of value in the workup of patients suspected of having AIM. Newer autoantibodies, developments, and advances in the methodology of testing, the gaps and pitfalls in using these assays as diagnostic biomarkers, and the importance of considering overlap diseases and unique clinical AIM phenotypes are discussed.Recent findingsSummaryThe spectrum of autoantibodies and related biomarkers in AIM continues to expand. Many of these have clear clinical implications in regard to subsets and overlap conditions of AIM, associated malignancy and pathological findings.