bluuebunny/crossref_metadata_2025_split huggingface dataset:
The East China Sea Kuroshio Current Intensifies Deep Convective Precipitation: A Case Study
Authors: Xu Peidong , Liu Jing‐Wu 
Published: August 2024

AbstractDeep atmospheric convection is often observed over the Kuroshio in the East China Sea (ECSK). However, the mechanisms by which warm oceanic currents fuel transient deep convection are not fully understood. This study investigates an atmospheric cold front that brought heavy precipitation as it traversed the ECSK in April 2004. The southwesterlies ahead of the cold front advected moist and warm air, creating a zone with high convective available potential energy (CAPE) values. As the cold front approached the ECSK, the pre‐frontal high CAPE values coalesced with those over the warm current that substantially strengthened the deep convection, with precipitation rate increasing from 3 mm hr−1 to 10 mm hr−1. A numerical model well simulated the marked increase in precipitation over the ECSK, permitting the isolation of the ECSK's influence by contrasting the control (CTRL) run with an experiment with smoothed sea surface temperatures (SMTH run). Results show the ECSK contributed to 46% of the precipitation over the warm current. The ECSK was found to amplify ascending motion and elevate neutral buoyancy levels, extending its effect up to the tropopause. Furthermore, the strengthened deep convection significantly lowered the sea level pressure (SLP) over the ECSK and impressed upon the time‐mean SLP field. An additional experiment with lowered SST underscored the high SST's critical role in deep convection. This case study suggests a novel pathway by which the effects of warm oceanic currents influence the upper troposphere under extreme conditions with strong baroclinic instability.
Pharmacogenomic scores in psychiatry: systematic review of current evidence
Authors: Sharew Nigussie T. , Clark Scott R. , Schubert K. Oliver , Amare Azmeraw T. 
Published: August 2024

AbstractIn the past two decades, significant progress has been made in the development of polygenic scores (PGSs). One specific application of PGSs is the development and potential use of pharmacogenomic- scores (PGx-scores) to identify patients who can benefit from a specific medication or are likely to experience side effects. This systematic review comprehensively evaluates published PGx-score studies in psychiatry and provides insights into their potential clinical use and avenues for future development. A systematic literature search was conducted across PubMed, EMBASE, and Web of Science databases until 22 August 2023. This review included fifty-three primary studies, of which the majority (69.8%) were conducted using samples of European ancestry. We found that over 90% of PGx-scores in psychiatry have been developed based on psychiatric and medical diagnoses or trait variants, rather than pharmacogenomic variants. Among these PGx-scores, the polygenic score for schizophrenia (PGSSCZ) has been most extensively studied in relation to its impact on treatment outcomes (32 publications). Twenty (62.5%) of these studies suggest that individuals with higher PGSSCZ have negative outcomes from psychotropic treatment — poorer treatment response, higher rates of treatment resistance, more antipsychotic-induced side effects, or more psychiatric hospitalizations, while the remaining studies did not find significant associations. Although PGx-scores alone accounted for at best 5.6% of the variance in treatment outcomes (in schizophrenia treatment resistance), together with clinical variables they explained up to 13.7% (in bipolar lithium response), suggesting that clinical translation might be achieved by including PGx-scores in multivariable models. In conclusion, our literature review found that there are still very few studies developing PGx-scores using pharmacogenomic variants. Research with larger and diverse populations is required to develop clinically relevant PGx-scores, using biology-informed and multi-phenotypic polygenic scoring approaches, as well as by integrating clinical variables with these scores to facilitate their translation to psychiatric practice.
DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression
Authors: Shao Lan , Yu Haoran , Wang Mengyun , Chen Lu , Ji Boshu , Wu Tong , Teng Xiangqi , Su Mu , Han Xiao , Shi Weikai , Hu Xin , Wang Ziwen , He Hongjuan , Han Guiping , Zhang Yan , Wu Qiong 
Published: August 2024

AbstractSuper-enhancers are a class of DNA cis-regulatory elements that can regulate cell identity, cell fate, stem cell pluripotency, and even tumorigenesis. Increasing evidence shows that epigenetic modifications play an important role in the pathogenesis of various types of cancer. However, the current research is far from enough to reveal the complex mechanism behind it. This study found a super-enhancer enriched with abnormally active histone modifications in pancreatic ductal adenocarcinoma (PDAC), called DKK1-super-enhancer (DKK1-SE). The major active component of DKK1-SE is component enhancer e1. Mechanistically, AP1 induces chromatin remodeling in component enhancer e1 and activates the transcriptional activity of DKK1. Moreover, DKK1 was closely related to the malignant clinical features of PDAC. Deletion or knockdown of DKK1-SE significantly inhibited the proliferation, colony formation, motility, migration, and invasion of PDAC cells in vitro, and these phenomena were partly mitigated upon rescuing DKK1 expression. In vivo, DKK1-SE deficiency not only inhibited tumor proliferation but also reduced the complexity of the tumor microenvironment. This study identifies that DKK1-SE drives DKK1 expression by recruiting AP1 transcription factors, exerting oncogenic effects in PDAC, and enhancing the complexity of the tumor microenvironment.
A Euclidean transformer for fast and stable machine learned force fields
Authors: Frank J. Thorben , Unke Oliver T. , Müller Klaus-Robert , Chmiela Stefan 
Published: August 2024

AbstractRecent years have seen vast progress in the development of machine learned force fields (MLFFs) based on ab-initio reference calculations. Despite achieving low test errors, the reliability of MLFFs in molecular dynamics (MD) simulations is facing growing scrutiny due to concerns about instability over extended simulation timescales. Our findings suggest a potential connection between robustness to cumulative inaccuracies and the use of equivariant representations in MLFFs, but the computational cost associated with these representations can limit this advantage in practice. To address this, we propose a transformer architecture called SO3krates that combines sparse equivariant representations (Euclidean variables) with a self-attention mechanism that separates invariant and equivariant information, eliminating the need for expensive tensor products. SO3krates achieves a unique combination of accuracy, stability, and speed that enables insightful analysis of quantum properties of matter on extended time and system size scales. To showcase this capability, we generate stable MD trajectories for flexible peptides and supra-molecular structures with hundreds of atoms. Furthermore, we investigate the PES topology for medium-sized chainlike molecules (e.g., small peptides) by exploring thousands of minima. Remarkably, SO3krates demonstrates the ability to strike a balance between the conflicting demands of stability and the emergence of new minimum-energy conformations beyond the training data, which is crucial for realistic exploration tasks in the field of biochemistry.
Early evolution of small body size in Homo floresiensis
Authors: Kaifu Yousuke , Kurniawan Iwan , Mizushima Soichiro , Sawada Junmei , Lague Michael , Setiawan Ruly , Sutisna Indra , Wibowo Unggul P. , Suwa Gen , Kono Reiko T. , Sasaki Tomohiko , Brumm Adam , van den Bergh Gerrit D. 
Published: August 2024

AbstractRecent discoveries of Homo floresiensis and H. luzonensis raise questions regarding how extreme body size reduction occurred in some extinct Homo species in insular environments. Previous investigations at Mata Menge, Flores Island, Indonesia, suggested that the early Middle Pleistocene ancestors of H. floresiensis had even smaller jaws and teeth. Here, we report additional hominin fossils from the same deposits at Mata Menge. An adult humerus is estimated to be 9 − 16% shorter and thinner than the type specimen of H. floresiensis dated to ~60,000 years ago, and is smaller than any other Plio-Pleistocene adult hominin humeri hitherto reported. The newly recovered teeth are both exceptionally small; one of them bears closer morphological similarities to early Javanese H. erectus. The H. floresiensis lineage most likely evolved from early Asian H. erectus and was a long-lasting lineage on Flores with markedly diminutive body size since at least ~700,000 years ago.
Impacts of large-scale deployment of vertical bifacial photovoltaics on European electricity market dynamics
Authors: Szabo Laszlo , Moner- Girona Magda , Jäger-Waldau Arnulf , Kougias Ioannis , Mezosi Andras , Fahl Fernando , Szabo Sandor 
Published: August 2024

AbstractSelf-sufficiency, climate change and increasing geopolitical risks have driven energy policies to make renewable energy sources dominant in the power production portfolios. The initial boom in the mid-2000s of global photovoltaic installations demonstrated the feasibility of the ambitious renewable energy targets. However, this rapid scale-up has introduced challenges, including price volatility and system integration issues. This communication calls the attention to these emerging challenges and offers quantitative insights on how rapid adoption of a more diversified photovoltaics deployment strategies can mitigate price volatilities, reduce fossil fuel dependence and steer Europe towards a forward-thinking sustainable energy pathway. The analysis reveals that as innovative bifacial photovoltaic systems are incorporated on a large-scale disruptive scenario, four main patterns emerge: economic value of solar production increases, base-load electricity price decreases, sun-rich countries expand their solar contributions, whereas nations with ample grid interconnections enhance their energy imports from neighbouring countries. It also underscores the importance of maintaining photovoltaics an attractive option for energy investors and traders in the future. Establishing this groundwork is critical since a successful integration of large-scale solar systems contributing to decrease price volatilities in Europe and US will carry significant repercussions for global energy policy formulation.
Heterogeneously deacetylated chitosans possess an unexpected regular pattern favoring acetylation at every third position
Authors: Hellmann Margareta J. , Gillet Dominique , Trombotto Stéphane , Raetz Sonja , Moerschbacher Bruno M. , Cord-Landwehr Stefan 
Published: August 2024

AbstractChitosans are promising biopolymers for diverse applications, with material properties and bioactivities depending i.a. on their pattern of acetylation (PA). Commercial chitosans are typically produced by heterogeneous deacetylation of chitin, but whether this process yields chitosans with a random or block-wise PA has been debated for decades. Using a combination of recently developed in vitro assays and in silico modeling surprisingly revealed that both hypotheses are wrong; instead, we found a more regular PA in heterogeneously deacetylated chitosans, with acetylated units overrepresented at every third position in the polymer chain. Compared to random-PA chitosans produced by homogeneous deacetylation of chitin or chemical N-acetylation of polyglucosamine, this regular PA increases the elicitation activity in plants, and generates different product profiles and distributions after enzymatic and chemical cleavage. A regular PA may be beneficial for some applications but detrimental for others, stressing the relevance of the production process for product development.
Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase
Authors: Bulvas Ondřej , Knejzlík Zdeněk , Sýs Jakub , Filimoněnko Anatolij , Čížková Monika , Clarová Kamila , Rejman Dominik , Kouba Tomáš , Pichová Iva 
Published: August 2024

AbstractAllosteric regulation of inosine 5′-monophosphate dehydrogenase (IMPDH), an essential enzyme of purine metabolism, contributes to the homeostasis of adenine and guanine nucleotides. However, the precise molecular mechanism of IMPDH regulation in bacteria remains unclear. Using biochemical and cryo-EM approaches, we reveal the intricate molecular mechanism of the IMPDH allosteric regulation in mycobacteria. The enzyme is inhibited by both GTP and (p)ppGpp, which bind to the regulatory CBS domains and, via interactions with basic residues in hinge regions, lock the catalytic core domains in a compressed conformation. This results in occlusion of inosine monophosphate (IMP) substrate binding to the active site and, ultimately, inhibition of the enzyme. The GTP and (p)ppGpp allosteric effectors bind to their dedicated sites but stabilize the compressed octamer by a common mechanism. Inhibition is relieved by the competitive displacement of GTP or (p)ppGpp by ATP allowing IMP-induced enzyme expansion. The structural knowledge and mechanistic understanding presented here open up new possibilities for the development of allosteric inhibitors with antibacterial potential.
Microstructural brain assessment in late-life depression and apathy using diffusion MRI multi-compartments models and tractometry
Authors: Hédouin Renaud , Roy Jean-Charles , Desmidt Thomas , Robert Gabriel , Coloigner Julie 
Published: August 2024

AbstractLate-life depression (LLD) is both common and disabling and doubles the risk of dementia onset. Apathy might constitute an additional risk of cognitive decline but clear understanding of its pathophysiology is lacking. While white matter (WM) alterations have been assessed using diffusion tensor imaging (DTI), this model cannot accurately represent WM microstructure. We hypothesized that a more complex multi-compartment model would provide new biomarkers of LLD and apathy. Fifty-six individuals (LLD n = 35, 26 females, 75.2 ± 6.4 years, apathy evaluation scale scores (41.8 ± 8.7) and Healthy controls, n = 21, 16 females, 74.7 ± 5.2 years) were included. In this article, a tract-based approach was conducted to investigate novel diffusion model biomarkers of LLD and apathy by interpolating microstructural metrics directly along the fiber bundle. We performed multivariate statistical analysis, combined with principal component analysis for dimensional data reduction. We then tested the utility of our framework by demonstrating classically reported from the literature modifications in LDD while reporting new results of biological-basis of apathy in LLD. Finally, we aimed to investigate the relationship between apathy and microstructure in different fiber bundles. Our study suggests that new fiber bundles, such as the striato-premotor tracts, may be involved in LLD and apathy, which bring new light of apathy mechanisms in major depression. We also identified statistical changes in diffusion MRI metrics in 5 different tracts, previously reported in major cognitive disorders dementia, suggesting that these alterations among these tracts are both involved in motivation and cognition and might explain how apathy is a prodromal phase of degenerative disorders.
Early monitoring of inlay wear after total knee arthroplasty on plain radiographs using model-based wear measurement
Authors: Emonde Crystal Kayaro , Hurschler Christof , Breuer André , Eggers Max-Enno , Wichmann Marcel , Ettinger Max , Denkena Berend 
Published: August 2024

AbstractWear of the ultra-high molecular-weight polyethylene (UHMWPE) component in total knee arthroplasty contributes to implant failure. It is often detected late, when patients experience pain or instability. Early monitoring could enable timely intervention, preventing implant failure and joint degeneration. This study investigates the accuracy and precision (repeatability) of model-based wear measurement (MBWM), a novel technique that can estimate inlay thickness and wear radiographically. Six inlays were milled from non-crosslinked UHMWPE and imaged via X-ray in anteroposterior view at flexion angles 0°, 30°, and 60° on a phantom knee model. MBWM measurements were compared with reference values from a coordinate measurement machine. Three inlays were subjected to accelerated wear generation and similarly evaluated. MBWM estimated inlay thickness with medial and lateral accuracies of 0.13 ± 0.09 and 0.14 ± 0.09 mm, respectively, and linear wear with an accuracy of 0.07 ± 0.06 mm. Thickness measurements revealed significant lateral differences at 0° and 30° (0.22 ± 0.08 mm vs. 0.06 ± 0.06 mm, respectively; t-test, p = 0.0002). Precision was high, with average medial and lateral differences of − 0.01 ± 0.04 mm between double experiments. MBWM using plain radiographs presents a practical and promising approach for the clinical detection of implant wear.
Timber trade in 17th-century Europe: different wood sources for artworks of Flemish painters
Authors: Seim Andrea , Edvardsson Johannes , Daly Aoife , Fraiture Pascale , Tyers Ian , Tegel Willy , Pukienė Rūtilė , Wazny Tomasz , de Celis Maite Jover , Auwera Joost Vander , Davies Justin 
Published: August 2024

AbstractThe former Spanish Netherlands experienced a period of social, cultural and economic prosperity in the seventeenth century, with Antwerp as its most important commercial and artistic centre. The era’s vibrant art scene, once pivotal culturally, economically, and diplomatically, now offers invaluable insights for scientific studies on art, trade, and craftsmanship. In a study on 294 panel paintings by or related to two famous Flemish artists, Jacques Jordaens (1593–1678) and Anthony van Dyck (1599–1641), we applied classical art historical techniques, archival research, dendrochronology, and the study of panel maker’s and guild marks on the painting’s reverse to gain insights into the precise time of tree felling, the geographical provenance of the wood, and the panel makers patronised by the painters. The majority of the paintings (~ 80%), which were subjected to a dendrochronological analysis, could be dated and the results accorded well with the concomitant art historical assessment on authorship. Besides an active and well-known Baltic timber trade which provided over 71% of all the planks examined, straight-grained oak trees were also sourced from western Central Europe (20%). Interestingly, planks from the Baltic and the Ardennes region (France/Belgium) were used together in three different paintings, likely cut apart from larger panels. Employing a multidisciplinary approach to a comprehensive painting collection by individual painters provides not only a new tool to determine a painting’s date and authorship but also allows for a better understanding of the contemporary timber trade and associated craftsmanship.
Impact of intrapartum antibiotic prophylaxis on the oral and fecal bacteriomes of children in the first week of life
Authors: Pivrncova Eliska , Buresova Lucie , Kotaskova Iva , Videnska Petra , Andryskova Lenka , Piler Pavel , Janku Petr , Borek Ivo , Bohm Jan , Klanova Jana , Budinska Eva , Borilova Linhartova Petra 
Published: August 2024

AbstractIntrapartum antibiotic prophylaxis (IAP) is commonly used during C-section delivery and in Group B Streptococcus-positive women before vaginal delivery. Here, we primarily aimed to investigate the effect of IAP on the neonatal oral and fecal bacteriomes in the first week of life. In this preliminary study, maternal and neonatal oral swabs and neonatal fecal (meconium and transitional stool) swabs were selected from a pool of samples from healthy mother-neonate pairs participating in the pilot phase of CELSPAC: TNG during their hospital stay. The DNA was extracted and bacteriome profiles were determined by 16S rRNA amplicon sequencing (Illumina). In the final dataset, 33 mother-neonate pairs were exposed to antibiotics during C-section or vaginal delivery (cases; +IAP) and the vaginal delivery without IAP (controls, -IAP) took place in 33 mother-neonate pairs. Differences in alpha diversity (Shannon index, p=0.01) and bacterial composition (PERMANOVA, p<0.05) between the +IAP and -IAP groups were detected only in neonatal oral samples collected ≤48 h after birth. No significant differences between meconium bacteriomes of the +IAP and -IAP groups were observed (p>0.05). However, the IAP was associated with decreased alpha diversity (number of amplicon sequence variants, p<0.001), decreased relative abundances of the genera Bacteroides and Bifidobacterium, and increased relative abundances of genera Enterococcus and Rothia (q<0.01 for all of them) in transitional stool samples. The findings of this study suggest that exposure to IAP may significantly influence the early development of the neonatal oral and gut microbiomes. IAP affected the neonatal oral bacteriome in the first two days after birth as well as the neonatal fecal bacteriome in transitional stool samples. In addition, it highlights the necessity for further investigation into the potential long-term health impacts on children.
Distinct effect of calorie restriction between congenic mating types of Cryptococcus neoformans
Authors: Oliveira Natalia Kronbauer , Yoo Kyungyoon , Bhattacharya Somanon , Gambhir Rina , Kirgizbaeva Nigina , García Pilar Arcones , Prados Ignacio Pompa , Fernandes Caroline Mota , Del Poeta Maurizio , Fries Bettina C. 
Published: August 2024

AbstractCryptococcus neoformans (Cn) is an opportunistic yeast that causes meningoencephalitis in immunocompromised individuals. Calorie restriction (CR) prolongs Cn replicative lifespan (RLS) and mimics low-glucose environments in which Cn resides during infection. The effects of CR-mediated stress can differ among strains and have only been studied in MATα cells. Cn replicates sexually, generating two mating types, MATα and MATa. MATα strains are more dominant in clinical and environmental isolates. We sought to compare the effects of CR stress and longevity regulation between congenic MATα and MATa. Although MATα and MATa cells extended their RLS in response to CR, they engaged different pathways. The sirtuins were upregulated in MATα cells under CR, but not in MATa cells. RLS extension was SIR2-dependent in KN99α, but not in KN99a. The TOR nutrient-sensing pathway was downregulated in MATa strains under CR, while MATα strains demonstrated no difference. Lower oxidative stress and higher ATP production were observed in KN99α cells, possibly due to higher SOD expression. SIR2 was important for mitochondrial morphology and function in both mating types. Increased ATP production during CR powered the upregulated ABC transporters, increasing efflux in MATα cells. This led to enhanced fluconazole tolerance, while MATa cells remained sensitive to fluconazole. Our investigation highlights differences in the response of the mating types to CR.