bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rotational excitation and de-excitation of interstellar chloronium cation in collisions with helium atoms
Authors: Mehnen Bilel , Hendaoui Hamza , Ajili Yosra , Al-Mogren Muneerah Mogren , Żuchowski Piotr , Hochlaf Majdi 
Published: March 2024

Abstract
Chloronium, H2Cl+, is detected in astrophysical media. It is key chemical intermediate for understanding of the physical chemistry of chlorine species there. At present, we compute the collision rates for the rotational excitation and de-excitation of ortho- and para-H2Cl+ colliding with He for T ≤ 150 K, relevant for the interstellar medium (ISM) conditions. Prior to that, we generated the 3D interaction potential of the weakly bound H2Cl+-He complex along the Jacobi coordinates. For electronic structure computations, we used a post-Hartree-Fock explicitly correlated method at the CCSD(T)-F12/aug-cc-pVTZ level. The analytical expansion of this potential was incorporated into close coupling computations of the cross-sections for the rotational excitation and de-excitation of ortho- and para-H2Cl+ colliding with He and for collision kinetic energies Ek ≤ 1000 cm−1. The rates were obtained after averaging these cross-sections over a Maxwell–Boltzmann distribution of kinetic energies. Our data show that the ∆j=∆ka=∆kc=−1 de-excitation transitions exhibit the largest values, in particular those used to identify this cation in the surveys. Besides, our results should help for determining more accurate abundances of H2Cl+ in the ISM and thus better modelling the chlorine chemistry there.
Formation of super-Mercuries via giant impacts
Authors: Dou Jingyao , Carter Philip J , Leinhardt Zoë M 
Published: March 2024

ABSTRACT
During the final stage of planetary formation, different formation pathways of planetary embryos could significantly influence the observed variations in planetary densities. Of the approximately 5000 exoplanets identified to date, a notable subset exhibits core fractions reminiscent of Mercury, potentially a consequence of high-velocity giant impacts. In order to better understand the influence of such collisions on planetary formation and compositional evolution, we conducted an extensive set of smoothed particle hydrodynamics giant impact simulations between two-layered rocky bodies. These simulations spanned a broad range of impact velocities from 1 to 11 times the mutual escape velocity. We derived novel scaling laws that estimate the mass and core mass fraction of the largest post-collision remnants. Our findings indicate that the extent of core vaporization markedly influences mantle stripping efficiency at low impact angles. We delineate the distinct roles played by two mechanisms – kinetic momentum transfer and vaporization-induced ejection – in mantle stripping. Our research suggests that collisional outcomes for multilayered planets are more complex than those for undifferentiated planetesimal impacts. Thus, a single universal law may not encompass all collision processes. We found a significant decrease in the mantle stripping efficiency as the impact angle increases. To form a 5 M⊕ super-Mercury at 45°, an impact velocity over 200 km s−1 is required. This poses a challenge to the formation of super-Mercuries through a single giant impact, implying that their formation would favour either relatively low-angle single impacts or multiple collisions.
PAPipe: A Pipeline for Comprehensive Population Genetic Analysis
Authors: Park Nayoung , Kim Hyeonji , Oh Jeongmin , Kim Jinseok , Heo Charyeong , Kim Jaebum 
Published: March 2024

Abstract
Advancements in next-generation sequencing (NGS) technologies have led to a substantial increase in the availability of population genetic variant data, thus prompting the development of various population analysis tools to enhance our understanding of population structure and evolution. The tools that are currently used to analyze population genetic variant data generally require different environments, parameters, and formats of the input data, which can act as a barrier preventing the wide-spread usage of such tools by general researchers who may not be familiar with bioinformatics. To address this problem, we have developed an automated and comprehensive pipeline called PAPipe to perform nine widely used population genetic analyses using population NGS data. PAPipe seamlessly interconnects and serializes multiple steps, such as read trimming and mapping, genetic variant calling, data filtering, and format converting, along with nine population genetic analyses such as principal component analysis, phylogenetic analysis, population tree analysis, population structure analysis, linkage disequilibrium decay analysis, selective sweep analysis, population admixture analysis, sequentially Markovian coalescent analysis, and fixation index analysis. PAPipe also provides an easy-to-use web interface that allows for the parameters to be set and the analysis results to be browsed in intuitive manner. PAPipe can be used to generate extensive results that provide insights that can help enhance user convenience and data usability. PAPipe is freely available at https://github.com/jkimlab/PAPipe.
Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs
Authors: Kramárek Michal , Souček Přemysl , Réblová Kamila , Grodecká Lucie Kajan , Freiberger Tomáš 
Published: March 2024

Abstract
Tandem donor splice sites (5′ss) are unique regions with at least two GU dinucleotides serving as splicing cleavage sites. The Δ3 tandem 5′ss are a specific subclass of 5′ss separated by 3 nucleotides which can affect protein function by inserting/deleting a single amino acid. One 5′ss is typically preferred, yet factors governing particular 5′ss choice are not fully understood. A highly conserved exon 21 of the STAT3 gene was chosen as a model to study Δ3 tandem 5′ss splicing mechanisms. Based on multiple lines of experimental evidence, endogenous U1 snRNA most likely binds only to the upstream 5′ss. However, the downstream 5′ss is used preferentially, and the splice site choice is not dependent on the exact U1 snRNA binding position. Downstream 5′ss usage was sensitive to exact nucleotide composition and dependent on the presence of downstream regulatory region. The downstream 5′ss usage could be best explained by two novel interactions with endogenous U6 snRNA. U6 snRNA enables the downstream 5′ss usage in STAT3 exon 21 by two mechanisms: (i) binding in a novel non-canonical register and (ii) establishing extended Watson–Crick base pairing with the downstream regulatory region. This study suggests that U6:5′ss interaction is more flexible than previously thought.
A comparison of the epidemiology of kidney replacement therapy between Europe and the United States: 2021 data of the ERA Registry and the USRDS
Authors: Stel Vianda S , Boenink Rianne , Astley Megan E , Boerstra Brittany A , Radunovic Danilo , Skrunes Rannveig , Ruiz San Millán Juan C , Slon Roblero Maria F , Bell Samira , Ucio Mingo Pablo , ten Dam Marc A G J , Ambühl Patrice M , Resic Halima , Rodríguez Arévalo Olga Lucia , Aresté-Fosalba Nuria , Tort i Bardolet Jaume , Lassalle Mathilde , Trujillo-Alemán Sara , Indridason Olafur S , Artamendi Marta , Finne Patrik , Rodríguez Camblor Marta , Nitsch Dorothea , Hommel Kristine , Moustakas George , Kerschbaum Julia , Lausevic Mirjana , Jager Kitty J , Ortiz Alberto , Kramer Anneke 
Published: March 2024

ABSTRACT

Background
This paper compares the most recent data on the incidence and prevalence of kidney replacement therapy (KRT), kidney transplantation rates, and mortality on KRT from Europe to those from the United States (US), including comparisons of treatment modalities (haemodialysis (HD), peritoneal dialysis (PD), and kidney transplantation (KTx)).

Methods
Data were derived from the annual reports of the European Renal Association (ERA) Registry and the United States Renal Data System (USRDS). The European data include information from national and regional renal registries providing the ERA Registry with individual patient data. Additional analyses were performed to present results for all participating European countries together.

Results
In 2021, the KRT incidence in the US (409.7 per million population (pmp)) was almost 3-fold higher than in Europe (144.4 pmp). Despite the substantial difference in KRT incidence, approximately the same proportion of patients initiated HD (Europe: 82%, US: 84%), PD (14%; 13%, respectively), or underwent pre-emptive KTx (4%; 3%, respectively). The KRT prevalence in the US (2436.1 pmp) was 2-fold higher than in Europe (1187.8 pmp). Within Europe, approximately half of all prevalent patients were living with a functioning graft (47%), while in the US, this was one third (32%). The number of kidney transplantations performed was almost twice as high in the US (77.0 pmp) compared to Europe (41.6 pmp). The mortality of patients receiving KRT was 1.6-fold higher in the US (157.3 per 1000 patient years) compared to Europe (98.7 per 1000 patient years).

Conclusions
The US had a much higher KRT incidence, prevalence, and mortality compared to Europe, and despite a higher kidney transplantation rate, a lower proportion of prevalent patients with a functioning graft.
How can inhibition of glucose and sodium transport in the early proximal tubule protect the cardiorenal system?
Authors: Vallon Volker 
Published: March 2024

ABSTRACT
What mechanisms can link the inhibition of sodium-glucose cotransporter 2 (SGLT2) in the early proximal tubule to kidney and heart protection in patients with and without type 2 diabetes? Due to physical and functional coupling of SGLT2 to other sodium and metabolite transporters in the early proximal tubule (including NHE3, URAT1), inhibitors of SGLT2 (SGLT2i) reduce reabsorption not only of glucose, inducing osmotic diuresis, but of other metabolites plus of a larger amount of sodium than expected based on SGLT2 inhibition alone, thereby reducing volume retention, hypertension and hyperuricemia. Metabolic adaptations to SGLT2i include a fasting-like response, with enhanced lipolysis and formation of ketone bodies that serve as additional fuel for kidneys and heart. Making use of the physiology of tubulo-glomerular communication, SGLT2i functionally lower glomerular capillary pressure and filtration rate, thereby reducing physical stress on the glomerular filtration barrier, tubular exposure to albumin and nephrotoxic compounds, and the oxygen demand for reabsorbing the filtered load. Together with reduced gluco-toxicity in the early proximal tubule and better distribution of transport work along the nephron, SGLT2i can preserve tubular integrity and transport function and, thereby, glomerular filtration rate in the long-term. By shifting transport downstream, SGLT2i may simulate systemic hypoxia at the oxygen sensors in the deep cortex/outer medulla, which stimulates erythropoiesis and, together with osmotic diuresis, enhances hematocrit and thereby improves oxygen delivery to all organs. The described SGLT2-dependent effects may be complemented by off-target effects of SGLT2i on the heart itself and on the microbiome formation of cardiovascular-effective uremic toxins.
Global health status and fatigue score in isocitrate dehydrogenase-mutant diffuse glioma grades 2 and 3: A longitudinal population-based study from surgery to 12-month follow-up
Authors: Gómez Vecchio Tomás , Rydén Isabelle , Ozanne Anneli , Blomstrand Malin , Carstam Louise , Smits Anja , Jakola Asgeir Store 
Published: March 2024

Abstract

Background
At the group level, health-related quality of life (HRQoL) in patients with IDH-mutant diffuse glioma grades 2 and 3 seems to remain stable over time. However, clinical experience indicates that there are patients with unfavorable outcomes on key HRQoL subdomains. The aim of this longitudinal population-based study, following patients over a period of 12 months from surgery, was to describe individual-level data on global health status and fatigue score and explore possible predictors of deterioration.

Methods
All patients undergoing surgery for presumed glioma grades 2 or 3 at the Sahlgrenska University Hospital during 2017–2022, were screened for the study. Patients were invited to complete the European Organization of Research and Treatment of Cancer core questionnaires and brain module at baseline, 3 and 12 months postoperatively. Data is reported with respect to minimal clinical important difference (MCID).

Results
We included 51 patients with IDH-mutant diffuse glioma grades 2 or 3. There was no difference in group-level data of either global health status or fatigue score from baseline to the 12-month follow-up (P-value &gt; .05). Unfavorable individual changes (beyond MCID) in global health status and fatigue score were observed in 12 and in 17 patients, respectively (23.5% and 33.3%). A lower proportion of proton radiotherapy was found in patients with unfavorable changes in fatigue (10/15, 66.7%) compared to all other patients undergoing radiotherapy (22/23, 95.7%, P-value .03).

Conclusions
Deterioration beyond MCID was seen in approximately one-third of patients. Changes in global health status could not be predicted, but changes in fatigue may be influenced by tumor-targeted and symptomatic treatment.
Incidence of Diabetes Mellitus and Associated Factors in the Era of Antiretroviral Drugs With a Low Metabolic Toxicity Profile
Authors: Montes Maria Luisa , Busca Carmen , Espinosa Nuria , Bernardino José Ignacio , Ibarra-Ugarte Sofia , Martín-Carbonero Luz , Moreno Cristina , Macias Juan , Rivero Antonio , Cervero-Jiménez Miguel , González-García Juan 
Published: March 2024

Abstract

Objective
The incidence of type 2 diabetes mellitus (T2DM) has risen dramatically. Among people living with HIV (PLHIV), chronic disease (now &gt;15 cases/1000 in the general population worldwide) and long-term exposure to antiretroviral therapy (ART) can alter metabolic processes early, favoring insulin resistance and T2DM. We retrospectively studied the incidence of T2DM and associated factors in the Cohort of the Spanish AIDS Research Network, a prospective cohort of PLHIV enrolled at diagnosis and before initiation of ART.

Methods
PLHIV were aged &gt;18 years and ART naive at inclusion. The incidence of new diagnoses of T2DM after initiation of ART (per 1000 person-years) was calculated. Predictors of a diagnosis of T2DM were identified by a Cox proportional hazards model adjusted for statistically significant and clinically relevant variables.

Results
Cumulative incidence was 5.9 (95% CI, 5.1–6.7) per 1000 person-years, increasing significantly in persons aged &gt;50 years to 14.4 (95% CI, 10.4–19.3). Median time to diagnosis of T2DM was 27 months. Only age and higher education were significant. Interestingly, higher education was associated with a 33% reduction in the incidence of T2DM. Having received tenofovir disoproxil fumarate + (lamivudine or emtricitabine) + rilpivirine was almost significant as a protective factor (hazard ratio, 0.49; 95% CI, .24–1.01; P = .05).

Conclusions
The incidence of T2DM in PLHIV in Spain was high, especially in persons aged &gt;50 years. Age was the factor most closely associated with onset, and educational level was the factor most associated with reduced risk. We highlight the lack of association between HIV-related factors and T2DM and show that, within nonnucleoside reverse transcriptase inhibitors, rilpivirine could prove more benign for metabolic comorbidities.
Serial Bronchoalveolar Lavage Fluid Aspergillus Galactomannan and Treatment Response in Invasive Pulmonary Aspergillosis
Authors: Friedman Daniel Z P , Theel Elitza S , Walker Randall C , Vikram Holenarasipur R , Razonable Raymund R , Vergidis Paschalis 
Published: March 2024

Abstract
We studied patients diagnosed with aspergillosis based on positive bronchoalveolar lavage (BAL) Aspergillus galactomannan (GM) who had follow-up BAL sampling within 180 days. GM trend and clinical outcome were concordant in only 60% (30/50). While useful for the initial diagnosis, BAL GM trending does not always correlate with treatment response.
Esophageal Candidiasis–Associated Hospitalizations: Declining Rates and Changes in Underlying Conditions, United States, 2010–2020
Authors: Gold Jeremy A W , Benedict Kaitlin 
Published: March 2024

Abstract
In a nationally representative hospital discharge database, esophageal candidiasis–associated hospitalization rates per 100 000 population steadily declined from 17.0 (n = 52 698, 2010) to 12.9 (n = 42 355, 2020). During this period, a decreasing percentage of EC-associated hospitalizations involved HIV and an increasing percentage involved gastroesophageal reflux disease, diabetes, and long-term steroid use.
Protracted and Progressive Crustal Melting during Continental Collision in the Pamir and Plateau Growth
Authors: Tang Gong-Jian , Wyman Derek A , Dan Wei , Wang Qiang , Liu Xi-Jun , Yang Ya-Nan , Gadoev Mustafo , Oimahmadov Ilhomjon 
Published: March 2024

AbstractDetermining crustal melting in parallel with geodynamic evolution provides critical information on plateau crustal thickening and uplift. Here we investigate the timing and duration of crustal melting through in situ analysis of zircon U–Pb ages, trace elements and Hf–O isotopes, and whole-rock elements and Sr–Nd–Hf isotopes for the granites and high-grade metamorphic rocks from the Pamir Plateau. Zircon dates record protracted crustal melting for both Central Pamir (43–33 and 22–12 Ma) and South Pamir (28–10 Ma). The Pamir Cenozoic granites are characterized by significant elemental and isotopic heterogeneity. The elemental variability within the Pamir Cenozoic granites is dominantly attributed to fractional crystallization of K-feldspar and plagioclase with subordinate biotite from a variably fractionated melt, and the accumulation of early crystallized feldspar during magma ascent. Peritectic mineral entrainment and accessory mineral crystallization had some influence on the geochemical characteristics of the garnet-bearing leucogranite dikes. Zircon Hf isotopes and whole-rock Sr–Nd–Hf isotopes show secular variations for both Central and South Pamir granites. The Central Pamir granites show a mild decrease in whole-rock ƐNd(t) values from Eocene (−4.3 to −4.9) to Miocene (−6.2 to −7.7), and the zircon ƐHf(t) values decrease from c. 40 Ma (+2 to −5) to c. 10 Ma (−4 to −8). In contrast, the South Pamir granites have highly variable whole-rock Sr–Nd–Hf (87Sr/86Sr(i) = 0.7053 to 0.7830; ƐNd(t) = −31.5 to +0.2; ƐHf(t) = −40.0 to +8.2) and zircon Hf isotopes (ƐHf(t) = −31.7 to +7.5) and display a strong decrease in ƐNd(t) and ƐHf(t) values from c. 25 Ma to c. 13 Ma. Geochemical and isotopic data indicate that both the Central and South Pamir experienced crustal melting from juvenile lower crust to ancient lower-middle crustal materials, and Indian crustal materials were incorporated into the melt region of the South Pamir leucogranites from c. 20 Ma. Our study highlights a causal link between a chain of events that includes magma underplating induced by lithosphere thinning and slab breakoff, lithosphere delamination and underthrusting of Indian lithosphere, and formation of the Cenozoic granites in Pamir. This series of processes are incorporated here into a comprehensive model for the geodynamic evolution of the Pamir during the India–Asia collision.
Transcription factor NtNAC56 regulates jasmonic acid-induced leaf senescence in tobacco
Authors: Chang Wei , Zhao Huina , Chen Hongqiao , Jiao Guixiang , Yu Jing , Wang Bing , Xia Haiqian , Meng Boyu , Li Xiaodong , Yu Mengna , Li Shengting , Qian Mingchao , Fan Yonghai , Zhang Kai , Lei Bo , Lu Kun 
Published: March 2024

Abstract
Leaf senescence is a vital aspect of plant physiology and stress responses and is induced by endogenous factors and environmental cues. The plant-specific NAC (NAM, ATAF1/2, CUC2) transcription factor family influences growth, development, and stress responses in Arabidopsis (Arabidopsis thaliana) and other species. However, the roles of NACs in tobacco (Nicotiana tabacum) leaf senescence are still unclear. Here, we report that NtNAC56 regulates leaf senescence in tobacco. Transgenic plants overexpressing NtNAC56 (NtNAC56-OE) showed induction of senescence-related genes and exhibited early senescence and lower chlorophyll content compared to wild-type (WT) plants and the Ntnac56-19 mutant. In addition, root development and seed germination were inhibited in the NtNAC56-OE lines. Transmission electron microscopy observations accompanied by physiological and biochemical assays revealed that NtNAC56 overexpression triggers chloroplast degradation and reactive oxygen species accumulation in tobacco leaves. Transcriptome analysis demonstrated that NtNAC56 activates leaf senescence-related genes and jasmonic acid (JA) biosynthesis pathway genes. In addition, the JA content of NtNAC56-OE plants was higher than in WT plants, and JA treatment induced NtNAC56 expression. We performed DNA affinity purification sequencing to identify direct targets of NtNAC56, among which we focused on LIPOXYGENASE 5 (NtLOX5), a key gene in JA biosynthesis. A dual-luciferase reporter assay and a yeast one-hybrid assay confirmed that NtNAC56 directly binds to the TTTCTT motif in the NtLOX5 promoter. Our results reveal a mechanism whereby NtNAC56 regulates JA-induced leaf senescence in tobacco and provide a strategy for genetically manipulating leaf senescence and plant growth.
A small molecule MST1/2 inhibitor accelerates murine liver regeneration with improved survival in models of steatohepatitis
Authors: Watkins Ryan , Gamo Ana , Choi Seung Hyuk , Kumar Manoj , Buckarma EeeLN , McCabe Chantal , Tomlinson Jennifer , Pereya David , Lupse Blaz , Geravandi Shirin , Werneburg Nathan W , Wang Chen , Starlinger Patrick , Zhu Siying , Li Sijia , Yu Shan , Surakattula Murali , Baguley Tyler , Ardestani Amin , Maedler Kathrin , Roland Jason , Nguyen-Tran Van , Joseph Sean , Petrassi Mike , Rogers Nikki , Gores Gregory , Chatterjee Arnab , Tremblay Matthew , Shen Weijun , Smoot Rory 
Published: March 2024

Abstract
Dysfunctional liver regeneration following surgical resection remains a major cause of postoperative mortality and has no therapeutic options. Without targeted therapies, the current treatment paradigm relies on supportive therapy until homeostasis can be achieved. Pharmacologic acceleration of regeneration represents an alternative therapeutic avenue. Therefore, we aimed to generate a small molecule inhibitor that could accelerate liver regeneration with an emphasis on diseased models, which represent a significant portion of patients who require surgical resection and are often not studied. Utilizing a clinically approved small molecule inhibitor as a parent compound, standard medicinal chemistry approaches were utilized to generate a small molecule inhibitor targeting serine/threonine kinase 4/3 (MST1/2) with reduced off-target effects. This compound, mCLC846, was then applied to preclinical models of murine partial hepatectomy, which included models of diet-induced metabolic dysfunction-associated steatohepatitis (MASH). mCLC846 demonstrated on target inhibition of MST1/2 and reduced epidermal growth factor receptor inhibition. The inhibitory effects resulted in restored pancreatic beta-cell function and survival under diabetogenic conditions. Liver-specific cell-line exposure resulted in Yes-associated protein activation. Oral delivery of mCLC846 perioperatively resulted in accelerated murine liver regeneration and improved survival in diet-induced MASH models. Bulk transcriptional analysis of regenerating liver remnants suggested that mCLC846 enhanced the normal regenerative pathways and induced them following liver resection. Overall, pharmacological acceleration of liver regeneration with mCLC846 was feasible, had an acceptable therapeutic index, and provided a survival benefit in models of diet-induced MASH.