bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA threading with secondary structure and sequence profile
Authors: Du Zongyang , Peng Zhenling , Yang Jianyi 
Published: February 2024

Abstract

Motivation
RNA threading aims to identify remote homologies for template-based modeling of RNA 3D structure. Existing RNA alignment methods primarily rely on secondary structure alignment. They are often time- and memory-consuming, limiting large-scale applications. In addition, the accuracy is far from satisfactory.

Results
Using RNA secondary structure and sequence profile, we developed a novel RNA threading algorithm, named RNAthreader. To enhance the alignment process and minimize memory usage, a novel approach has been introduced to simplify RNA secondary structures into compact diagrams. RNAthreader employs a two-step methodology. Initially, integer programming and dynamic programming are combined to create an initial alignment for the simplified diagram. Subsequently, the final alignment is obtained using dynamic programming, taking into account the initial alignment derived from the previous step. The benchmark test on 80 RNAs illustrates that RNAthreader generates more accurate alignments than other methods, especially for RNAs with pseudoknots. Another benchmark, involving 30 RNAs from the RNA-Puzzles experiments, exhibits that the models constructed using RNAthreader templates have a lower average RMSD than those created by alternative methods. Remarkably, RNAthreader takes less than two hours to complete alignments with ∼5000 RNAs, which is 3–40 times faster than other methods. These compelling results suggest that RNAthreader is a promising algorithm for RNA template detection.

Availability and implementation
https://yanglab.qd.sdu.edu.cn/RNAthreader
Doubly robust estimation under covariate-induced dependent left truncation
Authors: Wang Yuyao , Ying Andrew , Xu Ronghui 
Published: February 2024

Summary
In prevalent cohort studies with follow-up, the time-to-event outcome is subject to left truncation leading to selection bias. For estimation of the distribution of the time to event, conventional methods adjusting for left truncation tend to rely on the quasi-independence assumption that the truncation time and the event time are independent on the observed region. This assumption is violated when there is dependence between the truncation time and the event time, possibly induced by measured covariates. Inverse probability of truncation weighting can be used in this case, but it is sensitive to misspecification of the truncation model. In this work, we apply semiparametric theory to find the efficient influence curve of the expectation of an arbitrarily transformed survival time in the presence of covariate-induced dependent left truncation. We then use it to construct estimators that are shown to enjoy double-robustness properties. Our work represents the first attempt to construct doubly robust estimators in the presence of left truncation, which does not fall under the established framework of coarsened data where doubly robust approaches were developed. We provide technical conditions for the asymptotic properties that appear to not have been carefully examined in the literature for time-to-event data, and study the estimators via extensive simulation. We apply the estimators to two datasets from practice, with different right-censoring patterns.
Impact of elevated lipoprotein(a) on coronary artery disease phenotype and severity
Authors: Leistner David M , Laguna-Fernandez Andres , Haghikia Arash , Abdelwahed Youssef S , Schatz Anne-Sophie , Erbay Aslihan , Roehle Robert , Fonseca Ana F , Ferber Philippe , Landmesser Ulf 
Published: February 2024

AbstractAimsA thorough characterization of the relationship between elevated lipoprotein(a) [Lp(a)] and coronary artery disease (CAD) is lacking. This study aimed to quantitatively assess the association of increasing Lp(a) levels and CAD severity in a real-world population.Methods and resultsThis non-interventional, cross-sectional, LipidCardio study included patients aged ≥21 years undergoing angiography (October 2016−March 2018) at a tertiary cardiology centre, who have at least one Lp(a) measurement. The association between Lp(a) and CAD severity was determined by synergy between PCI with taxus and cardiac surgery (SYNTAX)-I and Gensini scores and angiographic characteristics. Overall, 975 patients (mean age: 69.5 years) were included; 70.1% were male, 97.5% had Caucasian ancestry, and 33.2% had a family history of premature atherosclerotic cardiovascular disease. Median baseline Lp(a) level was 19.3 nmol/L. Patients were stratified by baseline Lp(a): 72.9% had &lt; 65 nmol/L, 21.0% had ≥100 nmol/L, 17.2% had ≥125 nmol/L, and 12.9% had ≥150 nmol/L. Compared with the normal (Lp(a) &lt; 65 nmol/L) group, elevated Lp(a) groups (e.g. ≥ 150 nmol/L) had a higher proportion of patients with prior CAD (48.4% vs. 62.7%; P &lt; 0.01), prior coronary revascularization (39.1% vs. 51.6%; P = 0.01), prior coronary artery bypass graft (6.0% vs. 15.1%; P &lt; 0.01), vessel(s) with lesions (68.5% vs. 81.3%; P = 0.03), diffusely narrowed vessels (10.9% vs. 16.5%; P = 0.01) or chronic total occlusion lesions (14.3% vs. 25.2%; P &lt; 0.01), and higher median SYNTAX-I (3.0 vs. 5.5; P = 0.01) and Gensini (10.0 vs. 16.0; P &lt; 0.01) scores.ConclusionElevated Lp(a) was associated with a more severe presentation of CAD. Awareness of Lp(a) levels in patients with CAD may have implications in their clinical management.
State scope of practice restrictions and nurse practitioner practice in nursing homes: 2012–2019
Authors: Ryskina Kira L , Liang Junning , Ritter Ashley Z , Spetz Joanne , Barnes Hilary 
Published: February 2024

Abstract
Increased engagement of nurse practitioners (NPs) has been recommended as a way to address care delivery challenges in settings that struggle to attract physicians, such as primary care and rural areas. Nursing homes also face such physician shortages. We evaluated the role of state scope of practice regulations on NP practice in nursing homes in 2012–2019. Using linear probability models, we estimated the proportion of NP-delivered visits to patients in nursing homes as a function of state scope of practice regulations. Control variables included county demographic, socioeconomic, and health care workforce characteristics; state fixed effects; and year indicators. The proportion of nursing home visits conducted by NPs increased from 24% in 2012 to 42% in 2019. Expanded scope of practice regulation was associated with a greater proportion and total volume of nursing home visits conducted by NPs in counties with at least 1 NP visit. These relationships were concentrated among short-stay patients in urban counties. Removing scope of practice restrictions on NPs may address clinician shortages in nursing homes in urban areas where NPs already practice in nursing homes. However, improving access to advanced clinician care for long-term care residents and for patients in rural locations may require additional interventions and resources.
Young people’s views about the use of celebrities and social media influencers in gambling marketing
Authors: Pitt Hannah , McCarthy Simone , Randle Melanie , Daube Mike , Thomas Samantha L 
Published: February 2024

Abstract
Young people’s exposure to gambling marketing has had a clear impact on their gambling attitudes, risk perceptions and consumption intentions. Celebrities and social media influencers (SMIs) are increasingly used by the gambling industry in a wide range of promotions. While there is evidence that these types of promotions are influential in shaping young people’s attitudes towards other harmful products, there is limited evidence in relation to gambling. Qualitative focus groups (n = 22) with n = 64, 12–17 year olds were conducted in Australia. These investigated young people’s exposure to celebrity and SMI marketing for gambling and the influence they perceived this marketing had on young people’s gambling attitudes. Reflexive thematic analysis was used to construct four themes from the data. First, young people perceived that celebrities and SMIs created additional appeal and recall of gambling advertisements because they were attention grabbing and familiar. Second, young people thought that celebrities and SMIs increased the trust, legitimacy and social acceptance of gambling. Third, the use of celebrities and SMIs lowered the perceptions of risk associated with gambling. Lastly, there were suggestions to reduce the impact of celebrity and SMI gambling promotions on young people, such as bans and restrictions. This study highlights the importance of a comprehensive approach to preventing young people’s exposure to gambling marketing, that not only considers imposing stronger regulations to restrict the way the gambling industry is allowed to promote its products, but also aims to counter the novel ways the gambling industry attempts to appeal to children and young people.
Heat inactivation of aqueous viable norovirus and MS2 bacteriophage
Authors: Shaffer Marlee , Huynh Kimberly , Costantini Verónica , Vinjé Jan , Bibby Kyle 
Published: February 2024

Abstract

Aims
This study aimed to compare the heat inactivation kinetics of viable human norovirus with the surrogate, MS2 bacteriophage as well as assess the decay of the RNA signal.

Methods and results
Human intestinal enteroids were used to analyze the heat inactivation kinetics of viable human norovirus compared to the surrogate MS2 bacteriophage, which was cultured using a plaque assay. Norovirus decay rates were 0.22 min−1, 0.68 min−1, and 1.11 min−1 for 50°C, 60°C, and 70°C, respectively, and MS2 bacteriophage decay rates were 0.0065 min−1, 0.045 min−1, and 0.16 min−1 for 50°C, 60°C, and 70°C, respectively. Norovirus had significantly higher decay rates than MS2 bacteriophage at all tested temperatures (P = .002–.007). No decrease of RNA titers as measured by reverse transcription-PCR for both human norovirus and MS2 bacteriophage over time was observed, indicating molecular methods do not accurately depict viable human norovirus after heat inactivation and treatment efficiency is underestimated.

Conclusions
Overall, our data demonstrate that MS2 bacteriophage is a conservative surrogate to measure heat inactivation and potentially overestimates the infectious risk of norovirus. Furthermore, this study corroborates that measuring viral RNA titers, as evaluated by PCR methods, does not correlate with the persistence of viable norovirus under heat inactivation.
Unintended Consequences of the Global Derivatives Market Reform
Authors: Gandré Pauline , Mariathasan Mike , Merrouche Ouarda , Ongena Steven 
Published: February 2024

Abstract
Following the early implementation of the global over-the-counter (OTC) derivatives market reform in the USA and the associated increase in trading costs, US banks shifted up to 60% of their OTC derivatives activity abroad, particularly toward less regulated jurisdictions. Consistent with a cost saving incentive of regulatory arbitrage, we find that this flight abroad is driven by costlier blocks of the reform and subsequently causes a narrowing of swap spreads. We further show that this regulatory arbitrage causes an increase in financial risk as more activity is shifted to more lenient jurisdictions.
“I Can’t Think of Anything More Fulfilling”: An Interpretative Phenomenological Analysis of Eight Female-Identifying Music Therapists’ Career Longevity
Authors: Silverman Michael J , Segall Lorna E 
Published: February 2024

Abstract
Although there is literature exploring burnout and music therapists who have left the profession, there is a lack of research exploring the lived experience of music therapists who have remained in the profession for their careers. Therefore, the purpose of this study was to understand the lived experience of music therapy clinicians in the United States who remained in the profession for their careers. We individually interviewed eight female-identifying music therapy clinicians who had been in the profession between 25 and 48 (M = 40.63; SD = 8.53) years. We used interpretive phenomenological analysis to analyze the data. Participants reviewed their transcripts and the results to provide credibility to the themes. We identified nine themes that described career longevity: centering service users; other professional opportunities and responsibilities; building a sustainable and thriving program; humility, professional agency, and growth; professional service to support peers and service users; training and supervising music therapists; connecting with the professional community; coping with work-related stressors; and music as a resource for resiliency. On the basis of these results, we developed a model depicting professional resiliency in music therapy that centered and revolved around the service users. In addition to their clinical expertise, there is considerable knowledge to be gained from music therapists regarding professional resiliency and career longevity. Additional scholarship in music therapy career longevity is necessary to grow the profession and increase access to services. Implications, limitations, and suggestions for future research are provided.
Characterization of pediatric non-hematopoietic tumor metastases to the central nervous system: A single institution review
Authors: Newman John , Leelatian Nalin , Liang Jiancong 
Published: February 2024

Abstract
Central nervous system (CNS) metastases represent a small portion of pediatric CNS neoplasms and data surrounding this condition with high morbidity is scarce. Single institutional archival institutional pathology records between 1999 and 2022 were searched for patients over 21 years old and younger with CNS, dura, cranial nerve, CSF, or leptomeningeal metastases; 41 cases were identified. We documented primary tumor types and locations, metastasis locations, types of invasion (direct extension vs distant metastasis), times from imaging or pathologic diagnosis to CNS involvement, and outcomes. Distant metastasis was the most common mechanism of metastasis (n = 32, 78%). Interval times to CNS metastasis varied by both tumor type and primary tumor location. In this cohort, osteosarcoma portended the shortest survival following CNS metastasis. This study highlights the diverse mechanisms and locations of CNS involvement in pediatric CNS metastases and illuminates a need for varied monitoring strategies when considering primary tumor type and anatomic location.
A Century of Change in a Mature Urban Forest: the Thain Family Forest of the New York Botanical Garden, Bronx, New York
Authors: Nagele Eliot , Ashton Mark S , Harris Thomas B , Forrest Todd A , DeLuca Erica A , Martello Maria E , Duguid Marlyse C 
Published: February 2024

Abstract
Urban forests have long been understudied, resulting in a scarcity of long-term data to guide future management. The New York Botanical Garden in New York City has been stewarding the 20 ha Thain Family Forest since 1895. Using inventory data between 1937 and 2021, we document how structure, diversity, and composition of the forest have changed over the past century. Our results show an increase in the proportion and diversity of hardwood species, including oaks, hickories, red maple, black cherry, and American beech, following the loss of a dominant species, eastern hemlock. Despite changes in composition, we find no significant differences in the mean basal area, density, and tree diameter of canopy trees (diameter at breast height [DBH] ≥ 15 cm) from 1937 to 2021. Assessments of small diameter stems (DBH ≥ 2.54 cm) show increasing density, decreasing diameter, and increasing richness from 1985 to 2021, suggesting a period of understory recruitment/regeneration. During this time, native species have been dominant in both overstory and understory strata. These observations mirror trends recorded in hemlock–hardwood and oak–hickory forests region-wide, indicating that, with continued conservation and active management, urban and rural forests may develop in similar patterns and encouraging regional approaches to forest management.
Study Implications: Urban forests have long been understudied, resulting in a scarcity of long-term data to guide future management. Over the past century, the 20 ha Thain Family Forest in New York City has experienced a significant change in species composition, with an increase in the proportion and diversity of hardwood species following the loss of eastern hemlock. Despite these changes, forest canopy structure has remained stable. These observations mirror those observed in hemlock–hardwood and oak–hickory forests regionwide, suggesting that with continued conservation and active management, urban and rural forests may develop in similar patterns. The results of this study support continued investment in the research and management of urban forests as a comprehensive part of regional forest management efforts.
Migration of low-mass planets in inviscid discs: the effect of radiation transport on the dynamical corotation torque
Authors: Ziampras Alexandros , Nelson Richard P , Paardekooper Sijme-Jan 
Published: February 2024

ABSTRACT
Low-mass planets migrate in the type-I regime. In the inviscid limit, the contrast between the vortensity trapped inside the planet’s corotating region and the background disc vortensity leads to a dynamical corotation torque, which is thought to slow down inward migration. We investigate the effect of radiative cooling on low-mass planet migration using inviscid 2D hydrodynamical simulations. We find that cooling induces a baroclinic forcing on material U-turning near the planet, resulting in vortensity growth in the corotating region, which in turn weakens the dynamical corotation torque and leads to 2–3× faster inward migration. This mechanism is most efficient when cooling acts on a time-scale similar to the U-turn time of material inside the corotating region, but is none the less relevant for a substantial radial range in a typical disc (R ∼ 5–50 au). As the planet migrates inwards, the contrast between the vortensity inside and outside the corotating region increases and partially regulates the effect of baroclinic forcing. As a secondary effect, we show that radiative damping can further weaken the vortensity barrier created by the planet’s spiral shocks, supporting inward migration. Finally, we highlight that a self-consistent treatment of radiative diffusion as opposed to local cooling is critical in order to avoid overestimating the vortensity growth and the resulting migration rate.
Exploring the faintest end of mid-infrared luminosity functions up to z ≃ 5 with the JWST CEERS survey
Authors: Ling Chih-Teng , Goto Tomotsugu , Kim Seong Jin , Wu Cossas K -W , Hashimoto Tetsuya , Chien Tom C -C , Lin Yu-Wei , Ho Simon C -C , Kilerci Ece 
Published: February 2024

ABSTRACT
Mid-infrared (MIR) light from galaxies is sensitive to dust-obscured star formation activities because it traces the characteristic emission of dust heated by young, massive stars. By constructing the MIR luminosity functions (LFs), we are able to quantify the overall dusty star formation history and the evolution of galaxies over cosmic time. In this work, we report the first rest-frame MIR LFs at 7.7, 10, 12.8, 15, 18, and 21 μm as well as the total IR LF from the JWST Cosmic Evolution Early Release Science (CEERS) survey. We identify 506 galaxies at z = 0–5.1 in the CEERS survey that also have optical photometry from the Hubble Space Telescope. With the unprecedented sensitivity of the JWST, we probe the faintest end of the LFs at z = 0–1 down to L* ∼ 107L⊙, ∼2 orders of magnitude fainter than those from the previous generation of IR space telescopes. Our findings connect well with and continue the faint end of the MIR LFs from the deepest observations in past works. As a proxy of star formation history, we present the MIR-based luminosity density up to z ≃ 4.0, marking the first probe of the early Universe by JWST Mid-Infrared Instrument.
Effects of heterogeneous data sets and time-lag measurement techniques on cosmological parameter constraints from Mg ii and C iv reverberation-mapped quasar data
Authors: Cao Shulei , Zajaček Michal , Czerny Bożena , Panda Swayamtrupta , Ratra Bharat 
Published: February 2024

ABSTRACT
Previously, we demonstrated that Mg ii and C iv reverberation-mapped quasars (RM QSOs) are standardizable and that the cosmological parameters inferred using the broad-line region radius–luminosity (R–L) relation are consistent with those determined from better-established cosmological probes. With more data expected from ongoing and future spectroscopic and photometric surveys, it is imperative to examine how new QSO data sets of varied quality, with their own specific luminosity and time-delay distributions, can be best used to determine more restrictive cosmological parameter constraints. In this study, we test the effect of adding 25 OzDES Mg ii RM QSOs as well as 25 lower quality SDSS RM C iv QSOs, which increases the previous sample of RM QSOs by $\sim 36{{\ \rm per\ cent}}$. Although cosmological parameter constraints become tighter for some cosmological models after adding these new QSOs, the new combined data sets have increased differences between R–L parameter values obtained in different cosmological models and thus a lower standardizability for the larger Mg ii + C iv compilation. Different time-delay methodologies, particularly the ICCF and CREAM methods used for inferring time delays of SDSS RM QSOs, slightly affect cosmological and R–L relation parameter values, however, the effect is negligible for (smaller) compilations of robust time-delay detections. Our analysis indicates that increasing the sample size is not sufficient for tightening cosmological constraints and a quality cut is necessary to obtain a standardizable RM QSO sample.
RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria
Authors: Vaňková Hausnerová Viola , Shoman Mahmoud , Kumar Dilip , Schwarz Marek , Modrák Martin , Jirát Matějčková Jitka , Mikesková Eliška , Neva Silvia , Herrmannová Anna , Šiková Michaela , Halada Petr , Novotná Iva , Pajer Petr , Valášek Leoš Shivaya , Převorovský Martin , Krásný Libor , Hnilicová Jarmila 
Published: February 2024

Abstract
Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them have been known so far—6S RNA and Ms1 RNA but it is unclear if any other types of RNAs binding to RNAP exist in bacteria. To identify all RNAs interacting with RNAP and the primary σ factors, we have established and performed native RIP-seq in Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis and the pathogenic Mycobacterium tuberculosis. Besides known 6S RNAs in B. subtilis and Ms1 in M. smegmatis, we detected MTS2823, a homologue of Ms1, on RNAP in M. tuberculosis. In C. glutamicum, we discovered novel types of structured RNAs that associate with RNAP. Furthermore, we identified other species-specific RNAs including full-length mRNAs, revealing a previously unknown landscape of RNAs interacting with the bacterial transcription machinery.
Spinal cord hemangioblastomas in von Hippel–Lindau disease
Authors: Kreatsoulas Daniel C , Lonser Russell R 
Published: February 2024

Abstract

Background
von Hippel-Lindau disease (VHL) is an autosomal dominant familial neoplasia syndrome. The most common manifestation of VHL is central nervous system hemangioblastomas. VHL patients will often develop multiple hemangioblastomas along their craniospinal axis over their lifetime. Spinal cord hemangioblastomas account for nearly half of all nervous system hemangioblastomas in VHL.

Methods
The authors conducted a literature review and summation of available articles on spinal cord hemangioblastomas associated with VHL.

Results
The embryological origins, epidemiology, natural history, surgical outcomes, nonsurgical treatments, and future directions in spinal cord hemangioblastomas are discussed.

Conclusions
Hemangioblastomas in VHL are optimally managed with a multidisciplinary approach that includes surgical resection of symptomatic lesions. Novel treatments are gaining traction, but must be studied further for efficacy and safety.