bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nowcasting of a Warm‐Sector Rainfall Event in Southern China With the TRAMS Model: Sensitivity to Different Radar Reflectivity Retrieval Methods and Incremental Updating Strategies
Authors: Lin Xiaoxia , Feng Yerong , Jian Yuntao , Xu Daosheng , Huang Jincan , Chen Haowei , Zhang Banglin 
Published: January 2025

AbstractTo improve the radar data assimilation scheme for the high‐resolution Tropical Regional Atmospheric Model System (TRAMS) model, this study investigates the sensitivity of simulating a warm‐sector rainfall event in southern China to different radar reflectivity retrieval methods and incremental updating strategies. The findings indicate that the ice cloud retrieval (ICR) method yields more reasonable cloud hydrometeors. However, the impact of different retrieval methods is minimal without corresponding adjustments to the dynamic field. Further assimilation of the wind field effectively reduced the overestimated south winds and successfully simulated the observed low‐level convergence in northern Guangdong, significantly improving precipitation forecasts. Both incremental analysis update (IAU) and Nudging methods were able to adjust the forecast to better match the observations, with IAU performing slightly better. These findings are beneficial for further improving the forecast accuracy of precipitation intensity. Extending the IAU relaxation time from 4 to 10 min has almost no impact on the actual forecasting. However, prioritizing the adjustment of the wind field through time‐dependent IAU weighting factors, the impact of cloud particle adjustments on the dynamical field can be avoided (e.g., the drag caused by the sinking of cloud particles may offset the upward motion induced by dynamical convergence adjustments). This allows for more realistic low‐level wind convergence and precipitation forecasts to be obtained. Overall, the ICR method for retrieving cloud hydrometeors, combined with the IAU method using time‐dependent distribution weighting factors appears to be a more suitable option for the radar data assimilation scheme in TRAMS model.
Air Pollution and Cognitive Impairment Among the Chinese Elderly Population: An Analysis of the Chinese Longitudinal Healthy Longevity Survey (CLHLS)
Authors: Zhu Qingyang , Lyu Yuebin , Huang Keyong , Zhou Jinhui , Wang Wenhao , Steenland Kyle , Chang Howard H. , Ebelt Stefanie , Shi Xiaoming , Liu Yang 
Published: January 2025

AbstractCognitive impairment and dementia have long been recognized as growing public health threats. Studies have found that air pollution is a potential risk factor for dementia, but the literature remains inconclusive. This study aimed to evaluate the association between three major air pollutants (i.e., PM2.5, O3, and NO2) and cognitive impairment among the Chinese elderly population. Study participants were selected from the Chinese Longitudinal Health Longevity Survey (CLHLS) after 2005. We define cognitive impairment as a Chinese Mini‐Mental‐State Exam (CMMSE) score <24. The associations of air pollution with cognitive impairment and CMMSE score were evaluated with a logistic regression model and a linear mixed‐effect model with random intercepts, respectively. A total of 3,887 participants were enrolled in this study. Of the 2,882 participants who completed at least one follow‐up visit, 931 eventually developed cognitive impairment. In single‐pollutant models, we found that yearly average PM2.5 and NO2 as well as warm season O3, were positively associated with cognitive impairment. NO2 remained positively associated with cognitive impairment in the multi‐pollutant model. The linear mixed‐effect models revealed that warm season O3 and yearly average NO2 were significantly associated with decreased CMMSE scores. Our research has established a positive association between cognitive impairment and air pollution in China. These findings underscore the imperative for the next iteration of China's Air Pollution Prevention and Control Action Plan to broaden its focus to encompass gaseous air pollutants since mitigating single air pollutant is insufficient to protect the aging population.
Plausible Last Interglacial Antarctic Ice Sheet Changes Do Not Fully Explain Antarctic Ice Core Water Isotope Records
Authors: Zou Huiling , Sime Louise C. , Bertler Nancy A. N. , Keller Elizabeth D. , Wolff Eric W. 
Published: January 2025

AbstractAntarctic ice cores can help determine ice mass loss from the Antarctic Ice Sheet (AIS) during past warm periods. We compile Last Interglacial (LIG) measurements from eight Antarctic cores and compare these to new isotope‐enabled LIG simulations, which explore three plausible LIG AIS elevation and extent scenarios. We find that these simulations capture less than 10% of East Antarctic core‐mean changes. Although our simulations do not fully explain the changes, they capture some inter‐core geographical variations. Some LIG AIS configurations show higher skill than PI AIS configurations in simulating the inter‐core differences. The remaining discrepancies between the simulated and observed core‐mean water isotope changes suggest that LIG simulations also need to include the influences of reduced Antarctic sea ice, a warmer Southern Ocean, and resultant shifts in vapor source regions to produce a more satisfactory match to observed at ice core sites.
The Process‐Oriented Understanding on the Reduced Double‐ITCZ Bias in the High‐Resolution CESM1
Authors: Dong Enze , Song Fengfei , Wu Lixin , Dong Lu , Wang Shengpeng , Liu Fukai , Wang Hong 
Published: January 2025

AbstractThe double‐Intertropical Convergence Zone (ITCZ) bias is a common model bias, which has puzzled the climate model community for several decades. Here, by comparing a high‐ and low‐resolution state‐of‐the‐art model CESM1, it is found that the double‐ITCZ bias is largely reduced in the high‐resolution CESM1. The key reason is the realistic colder sea surface temperature (SST) over the southeast Pacific (SEP) in the high‐resolution model. This realistic SEP SST is mainly due to a spuriously deeper mixed layer with a more realistic wind, as the sensitivity of mixed layer depth to wind is overestimated in both versions of CESM1. The better representation of terrain, such as Andes Mountains, elevates warm advection from inland to the coastal region, which maintains the inversion structure favorable for low cloud. The resultant increased coastal cloud in the high‐resolution CESM1 causes the colder coastal SST, thus improving the wind and deepening the mixed layer.
Seismic Wavefield Modeling of Enceladus: Challenges and Opportunities Presented by a 3D Ice Shell
Authors: Dapré K. , Irving J. C. E. 
Published: January 2025

AbstractUnderstanding the interior structures of icy moons will be crucial in untangling narratives of formation and evolution, both within our solar system and beyond it. Seismology is a proven and unparalleled methodology for investigating the deep interiors of planetary bodies but has never been deployed on an icy moon. To improve future mission design, we conduct seismic simulations for Saturn's icy moon Enceladus which account for the unique seismic responses of icy ocean worlds. We discover that even with high surface temperatures at the south pole and 3D ice thickness models, seismic amplitudes are two orders of magnitude higher than the self‐noise of mission‐candidate instrumentation. We compare the effects of a 2D and 3D ice shell to determine the detail of seismic inversion for ice shell properties and how this varies with source and receiver location. We also compare the travel time differences caused by ice shell variation with potential effects from the uncertain core structure and discover that these two sources of travel time perturbation have similar magnitudes but could be distinguished through careful inversion strategy. We investigate varied source types to represent focal mechanisms likely to be present at the south pole of Enceladus. We finally make recommendations supporting landing sites between 20 and 30 from the south pole that should enable observation of a wide range of seismic phases, including core‐transmitted phases that could constrain core velocities.
Hot or Not? An Evaluation of Methods for Identifying Hot Moments of Nitrous Oxide Emissions From Soils
Authors: Stuchiner Emily R. , Xu Jiacheng , Eddy William C. , DeLucia Evan H. , Yang Wendy H. 
Published: January 2025

AbstractEffectively quantifying hot moments of nitrous oxide (N2O) emissions from agricultural soils is critical for managing this potent greenhouse gas. However, we are challenged by a lack of standard approaches for identifying hot moments, including (a) determining thresholds above which emissions are considered hot moments, and (b) considering seasonal variation in the magnitude and frequency distribution of net N2O fluxes. We used one year of hourly N2O flux measurements from 16 autochambers that varied in flux magnitude and frequency distribution in a conventionally tilled maize field in central Illinois, USA, to compare three approaches to identify hot moment thresholds: standard deviations (SD) above the mean, 1.5x the interquartile range (IQR), and isolation forest (IF) identification of anomalous values. We also compared these approaches on seasonally subdivided data (early, late, and non‐growing seasons) versus the whole year. Our analyses revealed that 1.5x IQR method best identified N2O hot moments. In contrast, using 2 or 4 SD both yielded hot moment threshold values too high, and IF yielded threshold values too low, leading to missed N2O hot moments or low net N2O fluxes mischaracterized as hot moments, respectively. Furthermore, seasonally subdividing the data set not only facilitated identification of smaller hot moments in the late‐ and non‐growing seasons when N2O hot moments were generally smaller but it also increased hot moment threshold values in the early growing season when N2O hot moments were larger. Consequently, of the methods evaluated here, we recommend using the 1.5x IQR method on whole year data sets to identify N2O hot moments.
Activation of glutamine synthetase (GS) as a new strategy for the treatment of major depressive disorder and other GS-related diseases
Authors: Kang Jae Soon , Kim Hwajin , Baek Ji Hyeong , Song Miyoung , Park Hyeongchan , Jeong Wonjune , Chung Hye Jin , Yoo Dae Young , Lee Dong Kun , Park Sang Won , Kim Hyun Joon 
Published: January 2025

AbstractGlutamine synthetase (GS) plays a crucial role in the homeostasis of the glutamate–glutamine cycle in the brain. Hypoactive GS causes depressive behaviors. Under chronic stress, GS has no change in expression, but its activity is decreased due to nitration of tyrosine (Tyr). Thus, we speculate that agents that prevent nitration or facilitate denitration of GS would be candidates for new antidepressants. Using human recombinant GS and mouse lysate from the medial prefrontal cortex, we demonstrated that Tyr (0.0313−0.5 µM) dose-dependently protected GS activity against peroxynitrite-induced Tyr-nitration of GS. Diet supplementation with Tyr exerted significant antidepressant effects in a chronic immobilization stress depression mouse model. We further found that dipeptides, such as tyrosyl-glutamine (YQ), that had appropriate chemical properties for medication also increased GS activity both in vitro and in vivo and exerted antidepressant effects. Because reduced GS activity also occurs in epilepsy and hyperammonemia, we evaluated whether Tyr and YQ had therapeutic effects. Interestingly, Tyr or YQ administration significantly attenuated kainic acid-induced seizures in mice and reduced blood ammonia levels in azoxymethane- or bile duct ligation-induced hyperammonemia mouse models, which was accompanied by an increment in GS activity. The activation of GS was accomplished by a decrement in Tyr-nitration, so-called Tyr-denitration. Therefore, this study demonstrates that the activation of GS could be a new strategy to treat depression and other GS-related diseases.
Double trouble: a comprehensive study into unrelated genetic comorbidities in adult patients with Facioscapulohumeral Muscular Dystrophy Type I
Authors: Puma Angela , Tammam Giulia , Ezaru Andra , Slioui Abderhmane , Torchia Eleonora , Tasca Giorgio , Villa Luisa , Cavalli Michele , Salviati Leonardo , van der Vliet Patrick J. , Lemmers Richard JLF , Pini Jonathan , van der Maarel Silvère M. , Sacconi Sabrina 
Published: January 2025

AbstractFacioscapulohumeral dystrophy type 1 (FSHD1) displays prominent intra- and interfamilial variability, which complicates the phenotype-genotype correlation. In this retrospective study, we investigated FSHD1 patients classified as category D according to the Comprehensive Clinical Evaluation Form (CCEF), a category defined by FSHD patients showing uncommon clinical features, to identify genetic causes explaining these uncommon phenotypes. Demographics, clinical data and clinical scales of FSHD1 patients were retrospectively evaluated. Patients were divided into four CCEF categories, and comparisons between groups were performed. In category D, when uncommon features suggested the presence of an unrelated genetic disease, a more extensive collection of data was performed. 157 FSHD1 patients were included in the study (82 males, 75 females) with mean age of 52.1 ± 13.5 years at the time of the study. D4Z4 repeat sizes ranged between 2 and 10 RU. According to the CCEF, 114 patients were classified into category A, 8 into category B and C each, and 27 into category D. In category D, 9 patients presented uncommon features related to commonly acquired comorbidities, whereas in the remaining 18 patients, all but two with upper-sized FSHD1 D4Z4 repeats (7–10 RU), we suspected an unrelated genetic neurological disease based on clinical phenotype. In 14/18 patients, we identified FSHD-unrelated genetic causes, most often unrelated repeat expansion disorders. This emphasizes the need of careful clinical and genetic work-up to avoid confusion between FSHD-intrinsic clinical variability and clinical features unrelated to the disease.
Are metal-based antibacterial gels a potential alternative for disinfection in contemporary endodontics?
Authors: Murchie Bryan D. , Edwards David 
Published: January 2025

Abstract
Aims
This study aimed to assess the effectiveness of a novel antimicrobial gel, containing copper and silver nanoparticles, for use in root canal disinfection.

Methods
Copper and silver-based gels were created in-house, using a support network of biocompatible polymers, including polyvinyl alcohol (PVA), polyvinyl pyrrolidone (PVP), and polyethylene glycol (PEG). Six experimental groups were created, three containing silver ions and three copper ions, where the PVA, PVP and PEG ratios were also adjusted in each group to test the gel’s physical state. One control contained no metal nanoparticles. The gels surface characteristics, roughness, mechanical properties, and flowability, were characterised using a combination of atomic force microscopy, scanning electron microscopy, transmission electron microscopy and Rheometery. Further biological testing measured the gels cytotoxicity levels, using human periodontal ligament cells, and the anti-microbial effects against E. Faecalis and a multi-species bacteria biofilm.

Results
Each gel demonstrated high levels of viscosity, which was lowered in gels containing a reduced PVA concentration. The overall antimicrobial properties of the gels increased in those with a higher dissolution, lower porosity, and reduced surface roughness. Copper nanoparticles were shown to be significantly more effective against E. Faecalis, compared with silver. Gels containing higher PVA levels, and silver nanoparticles, had greater toxicity levels against human cells, however, testing was not possible for most experimental groups as the gels dissolved before measurements took place. The antimicrobial properties of all gel formulations were significantly less effective than sodium hypochlorite (after 1 h), but a similar outcome was detected in comparison with calcium hydroxide (after 7 days).

Conclusions
Developing an antimicrobial gel is highly dependent upon numerous compositional factors, where development is still at the early stages. The use of copper nanoparticles appeared to be more appropriate for use in canal disinfection, compared with silver that also had higher levels of human cell toxicity. The ratios selected for the biocompatible polymers had a critical impact on the physical state, antimicrobial, and toxicity levels. At present, antimicrobial gels are not as effective as sodium hypochlorite.
The burden of X-linked retinitis pigmentosa (XLRP) on patient experience and patient-reported outcomes (PROs): findings from the EXPLORE XLRP-2 study
Authors: Parmeggiani Francesco , Weber Michel , Bremond-Gignac Dominique , Daly Avril , Denee Tom , Lahaye Marjolein , Lotery Andrew , Paudel Nabin , Ritter Markus , Rodríguez de la Rúa Enrique , Rotenstreich Ygal , Sankila Eeva-Marja , Stingl Katarina , Van Denderen Jacqueline , Pungor Katalin 
Published: January 2025

Abstract

Background/aims
X-linked retinitis pigmentosa (XLRP) is considered one of the most severe forms of retinitis pigmentosa (RP), accounting for 5–15% of all RP cases and primarily affecting males. However, the real-world humanistic impacts of this disease on patients are poorly investigated, especially with respect to burdens faced by patients with varying disease severities.

Methods
EXPLORE XLRP-2 was an exploratory, multicentre, non-interventional study. A retrospective chart review was conducted to collect clinical/demographic data, including XLRP clinical stage (mild, moderate or severe). Cross-sectional surveys were used to gather experiences directly from patients by validated and modified patient-reported outcomes.

Results
176 patients with XLRP caused by retinitis pigmentosa GTPase regulator (RPGR) gene mutation were enrolled, of whom 169 were included in analyses. 81% of patients were male, mean (SD) age was 39.3 (17.61) years, and 20 adolescents were included. Mean age (SD) at genetic confirmation was 33.4 years (17.98), and the mean duration (SD) from initial symptoms to genetic diagnosis was 16.4 (15.66) years. Compared with patients with mild disease, patients with severe XLRP are more likely to experience difficulties with functioning in low luminance, depression, unemployment, productivity issues, mobility and daily activities.

Conclusion
This is the first real-world study to collect data directly from patients on the burden of XLRP and to correlate that burden with disease stage. As a result, several areas of significant burden, especially for patients with severe disease, have been identified that should provide focus for future public policies and therapeutic prospects.
Safety and efficacy of supraciliary dexamethasone implantation for macular oedema: a preliminary comparative study
Authors: Doganay Selim , Ucan Gunduz Gamze , Kiristioglu Mehmet Omer , Demirel Elif , Yalcinbayir Ozgur 
Published: January 2025

Abstract

Purpose
To evaluate the efficacy and safety of dexamethasone implantation in the supraciliary (SC) space, a novel and potential effective implantation site, compared to intravitreal (IV) application.

Methods
This prospective study included 39 eyes of 38 patients with macular oedema (ME) who underwent SC and IV dexamethasone implantation (SC-DEX and IV-DEX). Patients were randomly assigned to treatment groups and followed for 3 months. Preoperative and postoperative assessments included maximum retinal thickness (MRT), change in central retinal thickness between consecutive visits (ΔCRT), intraocular pressure (IOP), and best corrected visual acuity (BCVA).

Results
Both SC-DEX and IV-DEX groups showed significant MRT reductions during at follow-up. In the SC group, MRT significantly decreased at 1st and 3rd months (p = 0.0002 for both), but not at 1st week (p = 0.2517). In the IV-DEX group, significant reductions in MRT were observed at all postoperative visits: 1st week (p = 0.0002), 1st month (p = 0.0004), and 3rd month (p = 0.0003). There were no significant differences in the change in ΔCRT between the SC-DEX and IV-DEX groups at any visit (p > 0.05). IOP did not show significant changes (p > 0.05). BCVA improved significantly in the SC group compared to the IV-DEX group during the first week (p = 0.014). No other perioperative or postoperative sight-threatening complications were noted in either group, including hypotony or endophthalmitis.

Conclusion
SC-DEX shows promise as an alternative for managing ME, offering similar effectiveness to IV-DEX with safe profile. Further studies are needed to confirm its long-term safety and efficacy.
UnidecNMR: automatic peak detection for NMR spectra in 1-4 dimensions
Authors: Buchanan Charles , Karunanithy Gogulan , Tkachenko Olga , Barber Michael , Marty Michael T. , Nott Timothy J. , Redfield Christina , Baldwin Andrew J. 
Published: January 2025

AbstractTo extract information from NMR experiments, users need to identify the number of resonances in the spectrum, together with characteristic features such as chemical shifts and intensities. In many applications, particularly those involving biomolecules, this procedure is typically a manual and laborious process. While many algorithms are available to tackle this problem, their performance tends to be inferior to that of an experienced user. Here, we introduce UnidecNMR, which identifies resonances in NMR spectra using deconvolution. We demonstrate its favourable performance on 1 and 2D simulated spectra, strongly overlapped 1D spectra of oligosaccharides and 2D HSQC, 3D HNCO, 3D HNCA and 3/4D methyl-methyl NOE experimental spectra from a range of proteins. UnidecNMR outperforms a number of freely available algorithms and provides results comparable to those generated manually. Introducing additional restraints, such as a 2D peak list when analysing 3 and 4D data and incorporating reflection symmetry in NOE analysis further improves the results. UnidecNMR outputs a back-calculated spectrum and a peak list, both of which can be easily examined using the supplied GUI. The software allows interactive processing using nmrPipe, allowing users to go directly from raw data to processed spectra with picked peak lists.
Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data
Authors: Lee Brian , Quadeer Ahmed Abdul , Sohail Muhammad Saqib , Finney Elizabeth , Ahmed Syed Faraz , McKay Matthew R. , Barton John P. 
Published: January 2025

AbstractNew and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could improve our understanding of viral biology and highlight new variants that warrant further study. Here we develop a generic, analytical epidemiological model to infer the transmission effects of mutations from genomic surveillance data. Applying our model to SARS-CoV-2 data across many regions, we find multiple mutations that substantially affect the transmission rate, both within and outside the Spike protein. The mutations that we infer to have the largest effects on transmission are strongly supported by experimental evidence from prior studies. Importantly, our model detects lineages with increased transmission even at low frequencies. As an example, we infer significant transmission advantages for the Alpha, Delta, and Omicron variants shortly after their appearances in regional data, when they comprised only around 1-2% of sample sequences. Our model thus facilitates the rapid identification of variants and mutations that affect transmission from genomic surveillance data.