bluuebunny/crossref_metadata_2025_split huggingface dataset:
The MPI + CUDA Gaia AVU–GSR Parallel Solver Toward Next-generation Exascale Infrastructures
Authors: Cesare Valentina , Becciani Ugo , Vecchiato Alberto , Lattanzi Mario Gilberto , Pitari Fabio , Aldinucci Marco , Bucciarelli Beatrice 
Published: August 2023

Abstract
We ported to the GPU with CUDA the Astrometric Verification Unit–Global Sphere Reconstruction (AVU–GSR) Parallel Solver developed for the ESA Gaia mission, by optimizing a previous OpenACC porting of this application. The code aims to find, with a [10, 100] μarcsec precision, the astrometric parameters of ∼108 stars, the attitude and instrumental settings of the Gaia satellite, and the global parameter γ of the parametrized Post-Newtonian formalism, by solving a system of linear equations, A ×
x
=
b
, with the LSQR iterative algorithm. The coefficient matrix A of the final Gaia data set is large, with ∼1011 × 108 elements, and sparse, reaching a size of ∼10–100 TB, typical for the Big Data analysis, which requires an efficient parallelization to obtain scientific results in reasonable timescales. The speedup of the CUDA code over the original AVU–GSR solver, parallelized on the CPU with MPI + OpenMP, increases with the system size and the number of resources, reaching a maximum of ∼14×, >9× over the OpenACC application. This result is obtained by comparing the two codes on the CINECA cluster Marconi100, with 4 V100 GPUs per node. After verifying the agreement between the solutions of a set of systems with different sizes computed with the CUDA and the OpenMP codes and that the solutions showed the required precision, the CUDA code was put in production on Marconi100, essential for an optimal AVU–GSR pipeline and the successive Gaia Data Releases. This analysis represents a first step to understand the (pre-)Exascale behavior of a class of applications that follow the same structure of this code. In the next months, we plan to run this code on the pre-Exascale platform Leonardo of CINECA, with 4 next-generation A200 GPUs per node, toward a porting on this infrastructure, where we expect to obtain even higher performances.
Satellite NO2 trends reveal pervasive impacts of wildfire and soil emissions across California landscapes
Authors: Wang Yurun , Faloona Ian C , Houlton Benjamin Z 
Published: August 2023

Abstract
Nitrogen dioxide (NO2) plays a pivotal role in the production of secondary pollutants, most importantly ozone (O3) and particulate matter. Regulatory controls have greatly reduced NO2 in cities, where most of the surface monitoring occurs, but the change in rural environments is less certain. Here, we present summertime (June–September) spatio-temporal patterns of NO2 concentrations using satellite and ground observations across California from 2009–2020, quantifying the differences in NO2 trends for five distinct land cover classes: urban, forests, croplands, scrublands (shrublands, savannas, and grasslands), and barren (minimally vegetated) lands. Over urban environments, NO2 columns exhibited continued but weakening downward trends (−3.7 ± 0.3%a−1), which agree fairly well with contemporaneous trends estimated from the surface air quality network (−4.5 ± 0.5%a−1). In rural (i.e., non-urban) parts of the state, however, secular trends are insignificant (0.0–0.4 ± 0.4%a−1) or in the case of remote forests are rapidly on the rise (+4.2 ± 1.2%a−1). Sorting the NO2 columns by air temperature and soil moisture reveals relationships that are commensurate with extant parameterizations but do indicate a stronger temperature dependence. We further find that rapidly rising temperatures and, to a lesser extent, decreasing precipitation in response to climate change are acting to increase soil NO
x
emissions, explaining about one-third of the observed NO2 rise in non-urban regions across California. Finally, we show that these trends, or their absence, can be attributed predominantly to the dramatic rise in wildfire frequency, especially since the turn of the 21st century.
Low flow sensitivity to water withdrawals in Central and Southwestern Europe under 2 K global warming
Authors: Greve Peter , Burek Peter , Guillaumot Luca , van Meijgaard Erik , Aalbers Emma , Smilovic Mikhail M , Sperna-Weiland Frederiek , Kahil Taher , Wada Yoshihide 
Published: August 2023

Abstract
A sufficient freshwater supply is vital for humans, ecosystems, and economies, but anticipated climate and socio-economic change are expected to substantially alter water availability. Across Europe, about two-third of the abstracted freshwater comes from rivers and streams. Various hydrological studies address the resulting need for projections on changes in river discharge. However, those assessments rarely specifically account for the impact of various water withdrawal scenarios during low flow periods. We present here a novel, high-resolution hydrological modeling experiment using pseudo-global warming climate data to investigate the effects of changing water withdrawals under 2 K global warming. Especially in Western and Central Europe the projected impacts on low flows highly depend on the chosen water withdrawal assumption and can severely decrease under the worst case assumptions. Our results highlight the importance of accounting for future water withdrawals in low flow projections, showing that climate-focused impact assessments in near-natural catchments provide only one piece of the anticipated response and do not necessarily reflect changes in heavily managed river basins.
Fire, frost, and drought constrain the structural diversity of wood within southern African Erica (Ericaceae)
Authors: Akinlabi F M , Pirie M D , Oskolski A A 
Published: August 2023

Abstract
Erica comprises ~860 species of evergreen shrubs and trees ranged from Europe to southern Africa and Madagascar. Wood structure of the around 20 European species is well studied, but despite its relevance to adaptation across the wider geographic range, it has not yet been explored across the much greater diversity, particularly of southern African lineages. In this study, we examine wood structure of 28 Erica species from southern Africa. In the African Erica clade, loss of scalariform perforation plates could be driven by increased aridity and seasonality in the mid-Miocene, and its re-gain can represent an adaptation to freezing in the high elevation species E. nubigena. As vessels in Erica are mostly solitary, imperforate tracheary elements probably form a subsidiary conduit network instead of vessel groups. Increase of ray frequency in habitats with a prominent dry and hot season probably facilitates refilling of vessels after embolism caused by water stress. Wider rays are ancestral for the lineage comprising African Erica and the Mediterranean E. australis. The negative correlation between ray width and expression of summer drought is consistent with Ojeda’s model explaining the diversification of seeders and resprouters among southern African Erica.
Gender-specific resting-state rDMPFC-centric functional connectivity underpinnings of intertemporal choice
Authors: Lv Chenyu , Xiao Zhibing , Sun Yachen , Zhang Rong , Feng Tingyong , Turel Ofir , He Qinghua 
Published: August 2023

Abstract
Although studies have observed gender differences in intertemporal choice, the neural bases of these differences require further research. The current study used resting state functional connectivity (rsFC) to explore the gender-specific neural basis of intertemporal choice in three independent samples (n1 = 86, n2 = 297, n3 = 172). Behaviorally, three samples (S1, S2, and S3) consistently demonstrated that men had larger delay discounting rate (log k) than women. Then, whole-brain functional connectivity analyses were performed for different genders in S2 and S3 using the right dorsomedial prefrontal cortex (rDMPFC) as a region of interest. By subtracting the common rsFC patterns of different genders, we identified gender-specific log k-related rsFC patterns with significant gender differences in S2. This was verified in an independent sample (S3). Specifically, in women, log k was found to be positively correlated with the rsFC between rDMPFC and anterior cingulate cortex/right orbitofrontal cortex. In contrast, in men, log k was negatively correlated with rsFC between rDMPFC and left orbitofrontal cortex/right precuneus. These gender differences were confirmed by slope tests. The findings highlight how gender may differ when engaging in intertemporal choice. They improve the understanding of gender differences in decision impulsivity and its underlying neural bases.
Neural retrieval processes occur more rapidly for visual mental images that were previously encoded with high-vividness
Authors: Gjorgieva Eva , Morales-Torres Ricardo , Cabeza Roberto , Woldorff Marty G 
Published: August 2023

Abstract
Visual mental imagery refers to our ability to experience visual images in the absence of sensory stimulation. Studies have shown that visual mental imagery can improve episodic memory. However, we have limited understanding of the neural mechanisms underlying this improvement. Using electroencephalography, we examined the neural processes associated with the retrieval of previously generated visual mental images, focusing on how the vividness at generation can modulate retrieval processes. Participants viewed word stimuli referring to common objects, forming a visual mental image of each word and rating the vividness of the mental image. This was followed by a surprise old/new recognition task. We compared retrieval performance for items rated as high- versus low-vividness at encoding. High-vividness items were retrieved with faster reaction times and higher confidence ratings in the memory judgment. While controlling for confidence, neural measures indicated that high-vividness items produced an earlier decrease in alpha-band activity at retrieval compared with low-vividness items, suggesting an earlier memory reinstatement. Even when low-vividness items were remembered with high confidence, they were not retrieved as quickly as high-vividness items. These results indicate that when highly vivid mental images are encoded, the speed of their retrieval occurs more rapidly, relative to low-vivid items.
Personalized and Population-Based Reference Intervals for 48 Common Clinical Chemistry and Hematology Measurands: A Comparative Study
Authors: Coşkun Abdurrahman , Sandberg Sverre , Unsal Ibrahim , Cavusoglu Coskun , Serteser Mustafa , Kilercik Meltem , Aarsand Aasne K 
Published: August 2023

Abstract

Background
Personalized reference intervals (prRIs) have the potential to improve individual patient follow-up as compared to population-based reference intervals (popRI). In this study, we estimated popRI and prRIs for 48 clinical chemistry and hematology measurands using samples from the same reference individuals and explored the effect of using group-based and individually based biological variation (BV) estimates to derive prRIs.

Methods
143 individuals (median age 28 years) were included in the study and had fasting blood samples collected once. From this population, 41 randomly selected subjects had samples collected weekly for 5 weeks. PopRIs were estimated according to Clinical Laboratory Standards Institute EP28 and within-subject BV (CVI) were estimated by CV-ANOVA. Data were assessed for trends and outliers prior to calculation of individual prRIs, based on estimates of (a) within-person BV (CVP), (b) CVI derived in this study, and (c) publically available CVI estimates.

Results
For most measurands, the individual prRI ranges were smaller than the popRI range, but overall about half the study participants had a prRI wider than the popRI for 5 or more out of 48 measurands. The dispersion of prRIs based on CVP was wider than that of prRIs based on CVI.

Conclusion
The prRIs derived in our study varied significantly between different individuals, especially if based on CVP. Our results highlight the limitations of popRIs in interpreting test results of individual patients. If sufficient data from a steady-state situation are available, using prRI based on CVP estimates will provide a RI most specific for an individual patient.
Long-term neurodevelopmental outcome and serial cerebral magnetic resonance imaging assessment in Fontan patients at school age
Authors: Reich Bettina , Schwan Sabrina , Heye Kristina , Logeswaran Thushiha , Hahn Andreas , Götschi Andrea , Held Ulrike , Wetterling Kristina , Steger Celine , Kottke Raimund , Latal Beatrice , Knirsch Walter 
Published: August 2023

Abstract

OBJECTIVES
Children with univentricular congenital heart disease undergoing staged surgical palliation are at risk for impaired neurodevelopmental (ND) outcome. Little is known about the long-term effects on brain growth until school age.

METHODS
In a prospective two-centre study, consecutive patients undergoing stage I (Hybrid or Norwood) to stage III (Fontan procedure) were evaluated by 2 serial cerebral magnetic resonance imaging examinations, somatic growth and ND testing before Fontan procedure at 2 years of age (Bayley-III) and after Fontan at 6–8 years of age (Wechsler Intelligence Scale for Children-third edition). Magnetic resonance imaging findings were compared with 8 healthy controls. Medical and sociodemographic characteristics were documented and related to cerebral and ND findings.

RESULTS
We examined 33 children (16 female) at a mean age of 2.3 (0.35) and 6.8 (± 0.7) years. The mean Bayley-III cognitive scales were 99.1 (9.9), language scales 98.4 (11.9) and motor scales 98.5 (13.8) at the first examination. Follow-up at school age showed a mean total IQ of 86.7 (13.6). The rate of structural brain lesions increased from 39% at 2 years to 58% at school age. Bayley-III language scale (P = 0.021) and mean Wechsler Intelligence Scale for Children-third edition (P = 0.019) were lower in children with pathological MR findings. Total brain volume (P &lt; 0.001), total grey matter volume (P = 0.002), deep grey matter volume (P = 0.001) and white matter volume (P &lt; 0.001) were smaller in patients compared to age- and gender-matched healthy controls.

CONCLUSIONS
Smaller brain volumes and structural brain lesions in complex congenital heart defect patients at school age are associated with impaired ND outcome. For the evaluation of predictive surgical or clinical factors, larger multicentre studies are needed.
Sex differences in cause-specific mortality: regional trends in seven European countries, 1996–2019
Authors: Sauerberg Markus , Klüsener Sebastian , Mühlichen Michael , Grigoriev Pavel 
Published: July 2023

Abstract

Background
Male excess mortality is mostly related to non-biological factors, and is thus of high social- and health-policy concern. Previous research has mainly focused on national patterns, while subnational disparities have been less in the focus. This study takes a spatial perspective on subnational patterns, covering seven European countries at the crossroad between Eastern and Western Europe.

Methods
We analyze a newly gathered spatially detailed data resource comprising 228 regions with well-established demographic methods to assess the contribution of specific causes of death to the evolution of sex mortality differentials (SMDs) since the mid-1990s.

Results
Our results show that declines in SMDs were mostly driven by a reduction of male excess mortality from cardiovascular diseases and neoplasms (about 50–60% and 20–30%, respectively). In Western Europe, trends in deaths from neoplasms contributed more to the reduction of SMDs, while among regions located in Eastern-Central Europe narrowing SMDs were mostly driven by changes in cardiovascular disease-related deaths. Moreover, men show up to three times higher mortality levels from external causes as compared to women in several analyzed regions. But in absolute terms, external deaths play only a minor role in explaining SMDs due to their small contribution to overall mortality.

Conclusions
We conclude that examining the regional development of SMDs is useful for introducing targeted social and health policies in order to reduce and prevent mortality inequalities between women and men.
Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages
Authors: Gangwal Aakriti , Kumar Nishant , Sangwan Nitika , Dhasmana Neha , Dhawan Uma , Sajid Andaleeb , Arora Gunjan , Singh Yogendra 
Published: August 2023

Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein–protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
Zuo1, a ribosome-associated J protein, is involved in glucose repression in Saccharomyces cerevisiae
Authors: Yamada Yoichi , Shiroma Atsuki , Hirai Suguru , Iwasaki Jun 
Published: August 2023

Abstract
In Saccharomyces cerevisiae, the J-protein Zuo1 and the nonconventional Hsp70 homologue Ssz1 stimulate the ATPase activity of the chaperone proteins Ssb1 and Ssb2 (Ssb1/2), which are associated with the ribosomes. The dephosphorylation of sucrose nonfermenting 1 (Snf1) on Thr210 is required for glucose repression. The Ssb1/2 and 14–3-3 proteins Bmh1 and Bmh2 appear to be responsible for the dephosphorylation of Snf1 on Thr210 and glucose repression. Here, we investigated the role of Zuo1 in glucose repression. The zuo1∆ strain as well as the ssb1∆ssb2∆ strain exhibited a glucose-specific growth defect during logarithmic growth on glucose. Many of the respiratory chain genes examined were statistically significantly upregulated, but less than 2-fold, in the zuo1∆ strain as well as in the ssb1∆ssb2∆ strain on glucose. In addition, excessive phosphorylation of Snf1 on Thr210 was observed in the zuo1∆ strain as well as in the ssb1∆ssb2∆ strain in the presence of glucose. The mRNA levels of SSB1/2 and BMH1 were statistically significantly reduced by approximately 0.5- to 0.8-fold relative to the wild-type level in the zuo1∆ strain on glucose. These results suggest that Zuo1 is responsible for glucose repression, possibly by increasing the mRNA levels of SSB1/2 and BMH1 during growth on glucose.
Routine nasogastric tube placement in patients with small esophageal perforation after endoscopic foreign body removal may be unnecessary: a propensity score matching analysis
Authors: Liao Foqiang , Yang Qinyu , Zhan Zhenyi , Zhu Zhenhua , Pan Xiaolin , Wang Chong , Li Bimin , Zhu Yin , Chen Youxiang , Shu Xu 
Published: July 2023

Abstract

Background
Nasogastric tube (NGT) placement is part of the post-operative management of upper gastrointestinal perforation, but its routine use in esophageal perforation (EP) caused by foreign bodies remains unclear. The purpose of this research was to investigate the necessity for routine NGT placement in patients with EP after endoscopic foreign body removal.

Methods
A total of 323 patients diagnosed with EP caused by foreign bodies at the First Affiliated Hospital of Nanchang University between January 2012 and December 2021 were included in this retrospective study. Patients were divided into the NGT group and the non-NGT group according to whether or not NGT placement was performed. The perforation healing rate, post-operative adverse events, hospital stay, and death rate were analysed using a 1:1 propensity score matching model.

Results
Before matching, there were 263 patients in the NGT group and 60 patients in the non-NGT group. There were significant differences in the time to treatment, infection, albumin, and types of endoscopy between the two groups, while the length of hospital stay in the NGT group was significantly longer than that in the non-NGT group. After 1:1 propensity score matching, 48 pairs of patients were matched between the two groups. The perforation healing rate, post-operative adverse events, length of hospital stay, and death rate did not show significant differences between the two groups.

Conclusions
For patients with small EP caused by foreign bodies, routine NGT placement after endoscopic foreign body removal may be unnecessary.
Influence of partial saturation on bulk modulus and attenuation: the experiment and the theoretical model
Authors: He Lingyi , Ding Pinbo , Di Bangrang , Zhang Feng 
Published: July 2023

SUMMARY
Modelling the dispersion and attenuation of seismic waves in partially saturated rocks is important for quantitative interpretation of seismic data. To observe the partial saturation effects on modulus and attenuation, three sandstone samples with different porosities were used in the laboratory experiment. The samples were measured by ultrasonic testing system under different water saturation using drainage process. The experimental results show that the bulk modulus more rapidly increased at higher saturations (&gt;80 per cent), and attenuation peaks could be observed. Then we develop a new partial saturation model based on Chapman’s theory and poroelastic theory. The new model is consistent with the Gassmann equation when the water saturation is 0 or 100 per cent. By analysing the characteristic frequency, the new model can be concluded in the form of a standard linear solid model. A comparison of the new model with the White model and the measured data is conducted. The results show that the model performed well at predicting the effective bulk modulus and attenuation of the rock with different water saturation. Finally, we discussed the impact of frequency, fluids and pore structures on the new model. The results reveal that the new model will be helpful in discussing partial saturation in rocks.
The Gaussian wave packet transform via quadrature rules
Authors: Bergold Paul , Lasser Caroline 
Published: July 2023

Abstract
We analyse the Gaussian wave packet transform. Based on the Fourier inversion formula and a partition of unity, which is formed by a collection of Gaussian basis functions, a new representation of square-integrable functions is presented. Including a rigorous error analysis, the variants of the wave packet transform are then derived by a discretization of the Fourier integral via different quadrature rules. Based on Gauss–Hermite quadrature, we introduce a new representation of Gaussian wave packets in which the number of basis functions is significantly reduced. Numerical experiments in 1D illustrate the theoretical results.
A matrix algebra approach to approximate Hessians
Authors: Hare Warren , Jarry-Bolduc Gabriel , Planiden Chayne 
Published: July 2023

Abstract
This work presents a novel matrix-based method for constructing an approximation Hessian using only function evaluations. The method requires less computational power than interpolation-based methods and is easy to implement in matrix-based programming languages such as MATLAB. As only function evaluations are required, the method is suitable for use in derivative-free algorithms. For reasonably structured sample sets, the method is proven to create an order-$1$ accurate approximation of the full Hessian. Under more specialized structures, the method is proved to yield order-$2$ accuracy. The underdetermined case, where the number of sample points is fewer than required for full interpolation, is studied and error bounds are developed for the resulting partial Hessians.