bluuebunny/crossref_metadata_2025_split huggingface dataset:
Operative strategies and outcomes for patients with severe pulmonary artery hypertension and intestinal obstruction: case series from single institution—sharing lessons to improve surgical outcomes
Authors: Ghazali Khairunnisa Che , Mat Ann Dasimakamalia , Yaacob Huzairi , Hamdan Muhammad Urfi Omar , Sidek Ahmad Shanwani Mohamed 
Published: November 2024

Abstract
Pulmonary hypertension is a known perioperative risk factor that carries a high morbidity and mortality rate. Severe pulmonary hypertension is related to high morbidity after general anaesthesia. We are reporting three patients with underlying severe pulmonary hypertension, who presented with intestinal obstruction managed with different perioperative approaches. In case 1, a 38-year-old man with Eisenmenger syndrome and severe pulmonary hypertension underwent exploratory laparotomy, right hemicolectomy, and double barrel stoma for obstructed right-sided colonic tumour. He passed away on Day 6 post-operation. In case 2, a 52-year-old man with Eisenmenger syndrome and severe pulmonary hypertension presented with obstructed rectosigmoid tumour and jejunojejunal intussusception and underwent exploratory laparotomy and Hartmann’s procedure. He succumbed after 33 days of fighting with cardiovascular and respiratory complications. In case 3, a 65-year-old woman, with strangulated paraumbilical hernia, underwent mini laparotomy, small bowel resection, primary anastomosis, and paraumbilical hernia repair under monitored sedation and local anaesthesia. She was discharged home after 7 days of hospitalization.
Utilizing a surgical sabermetrics framework to assess the impact of trainer behavior on trainee cognitive load during vascular surgery simulation
Authors: Norton Joel , Boyle Connor , Kerray Fiona , Tambyraja Andrew , Yule Steven 
Published: November 2024

Abstract
Surgical training programs lack data-driven, objective feedback of resident surgeon technical performance, non-technical skill and intraoperative cognitive load (CogL). Cognitive load is the working memory resource required to perform a task. When capacity is exceeded, cognitive overload occurs, which can negatively affect fine motor and communication skills. Surgical sabermetrics is an emerging field, which focuses on advanced analytics of data derived from audiovisual recordings of operations and non-invasive physiological sensors measuring surgeon CogL. Incivility is prevalent across surgical specialties and has been shown to negatively influence morale, teamwork and performance. Little is known about the impact of CogL on trainee surgeon development, and a gap in knowledge is the impact of intraoperative trainer teaching style and behavior on trainee CogL. Simulation models provide an opportunity to instigate a sabermetrics framework to assess whether trainer behavior objectively impacts trainee CogL and surgical performance, with no risk to patient safety. In this randomized trial, vascular surgery residents will be allocated to one of two groups: supportive trainer or critical trainer. All participants will be tasked with completing a standardized, simulated vascular anastomosis using a femoral artery model, during which they will be exposed to one of these trainer behaviors. A sabermetrics framework will be utilized to collate objective data about participant technical performance, non-technical skills and CogL. Full ethical approval has been obtained for this study. Dissemination of the results will be through conferences and publications in peer reviewed journals.
Investigating biological nitrogen fixation via single-cell transcriptomics
Authors: Pereira Wendell J , Conde Daniel , Perron Noé , Schmidt Henry W , Dervinis Christopher , Venado Rafael E , Ané Jean-Michel , Kirst Matias 
Published: November 2024

Abstract
The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: (i) single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species; (ii) characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations; (iii) single-cell transcriptomics data have enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization; and (iv) trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.
Parent comets of IAU MDC meteoroid streams unaltered by dynamical evolution
Authors: Ďurišová S , Neslušan L , Hajduková M , Rudawska R , Jopek T J 
Published: November 2024

ABSTRACT
Meteoroids that are members of a meteoroid stream move around the Sun in the mutually similar orbits, and their mean orbit is also similar to the orbit of the parent body, at least in the first stage of their dynamical evolution. This similarity enables the identification of the parent body of the stream. We evaluated the similarity of the meteoroid streams’ mean orbits from the IAU Meteor Data Center data base and all-known orbits of comets in course to find further, not-yet-known associations between meteor showers and their parent comets. We found 81 new associations and confirmed 84 associations that were discovered by other authors in the past.
The relation between the ADF and the ionized nebular mass in PNe
Authors: Peña Miriam , Ruiz-Escobedo Francisco , Juárez Torres Brenda N 
Published: November 2024

ABSTRACT
In this work, we analyse the proposed relation between abundance discrepancy factors (ADFs) and ionized masses in planetary nebulae (PNe). For this, we have collected from the literature the ADFs and other parameters such as heliocentric distances, H $\beta$ luminosities, logarithmic reddening correction at H $\beta$, c(H $\beta$), electron densities, and others and we calculated the ionized mass for a sample of 132 PNe, 27 of which possess a binary central star (14 are close binaries). In addition, the distribution of these objects in our Galaxy is analysed. The ionized masses were calculated considering two different electron densities, the one provided by the [S ii] density sensitive lines ratio and the one provided by the [Cl iii] lines ratio. No relation was found between ionized masses and ADFs for this sample, although it is confirmed than the PNe with the largest ADFs correspond in general to objects with a close binary central star, although it is important to say that about 20 per cent of these objects have an ADF larger than 5 but smaller than 10. Therefore, a PN having a close binary central star does not necessarily exhibit an extremely large ADF. We also have searched for possible relations between the ADFs and the stellar atmospheres, divided in H-rich and H-poor stars. No particular relation was found. Interestingly, several PNe with a [WR] H-poor CSPN present an ADF larger than 10, but so far they have not been reported as having a binary central star.
NGTS-33b: a young super-Jupiter hosted by a fast-rotating massive hot star
Authors: Alves Douglas R , Jenkins James S , Vines Jose I , Battley Matthew P , Lendl Monika , Bouchy François , Nielsen Louise D , Gill Samuel , Moyano Maximiliano , Anderson D R , Burleigh Matthew R , Casewell Sarah L , Goad Michael R , Hawthorn Faith , Kendall Alicia , McCormac James , Osborn Ares , Smith Alexis M S , Udry Stéphane , Wheatley Peter J , Saha Suman , Parc Léna , Nigioni Arianna , Apergis Ioannis , Ramsay Gavin 
Published: November 2024

ABSTRACT
In the last few decades, planet search surveys have been focusing on solar-type stars, and only recently the high-mass regimes. This is mostly due to challenges arising from the lack of instrumental precision, and more importantly, the inherent active nature of fast-rotating massive stars. Here, we report NGTS-33b (TOI-6442b), a super-Jupiter planet with mass, radius, and orbital period of 3.6 $\pm$ 0.3 M$_{\rm J}$, 1.64 $\pm$ 0.07 R$_{\rm J}$, and $2.827\,972 \pm 0.000\,001$ d, respectively. The host is a fast-rotating ($0.6654 \pm 0.0006$ d) and hot (T$_{\rm eff}$ = 7437 $\pm$ 72 K) A9V type star, with a mass and radius of 1.60 $\pm$ 0.11 M$_{\odot }$ and 1.47 $\pm$ 0.06 R$_{\odot }$, respectively. Planet structure and gyrochronology models show that NGTS-33 is also very young with age limits of 10–50 Myr. In addition, membership analysis points towards the star being part of the Vela OB2 association, which has an age of $\sim$ 20–35 Myr, thus providing further evidence about the young nature of NGTS-33. Its low bulk density of 0.19$\pm$0.03 g cm$^{-3}$ is 13 per cent smaller than expected when compared to transiting hot Jupiters (HJs) with similar masses. Such cannot be solely explained by its age, where an up to 15 per cent inflated atmosphere is expected from planet structure models. Finally, we found that its emission spectroscopy metric is similar to JWST community targets, making the planet an interesting target for atmospheric follow-up. Therefore, NGTS-33b’s discovery will not only add to the scarce population of young, massive and HJs, but will also help place further strong constraints on current formation and evolution models for such planetary systems.
The impact of baryons on the internal structure of dark matter haloes from dwarf galaxies to superclusters in the redshift range 0 &lt; z &lt; 7
Authors: Sorini Daniele , Bose Sownak , Pakmor Rüdiger , Hernquist Lars , Springel Volker , Hadzhiyska Boryana , Hernández-Aguayo César , Kannan Rahul 
Published: November 2024

ABSTRACT
We investigate the redshift evolution of the concentration–mass relationship of dark matter haloes in state-of-the-art cosmological hydrodynamic simulations and their dark-matter-only (DMO) counterparts. By combining the IllustrisTNG suite and the novel MillenniumTNG simulation, our analysis encompasses a wide range of box size ($50{-}740 \: \rm cMpc$) and mass resolution ($8.5 \times 10^4 {-} 3.1 \times 10^7 \: \rm {\rm M}_{\odot }$ per baryonic mass element). This enables us to study the impact of baryons on the concentration–mass relationship in the redshift interval $0\lt z\lt 7$ over an unprecedented halo mass range, extending from dwarf galaxies to superclusters ($\sim 10^{9.5}{-}10^{15.5} \, \rm {\rm M}_{\odot }$). We find that the presence of baryons increases the steepness of the concentration–mass relationship at higher redshift, and demonstrate that this is driven by adiabatic contraction of the profile, due to gas accretion at early times, which promotes star formation in the inner regions of haloes. At lower redshift, when the effects of feedback start to become important, baryons decrease the concentration of haloes below the mass scale $\sim 10^{11.5} \, \rm {\rm M}_{\odot }$. Through a rigorous information criterion test, we show that broken power-law models accurately represent the redshift evolution of the concentration–mass relationship, and of the relative difference in the total mass of haloes induced by the presence of baryons. We provide the best-fitting parameters of our empirical formulae, enabling their application to models that mimic baryonic effects in DMO simulations over six decades in halo mass in the redshift range $0\lt z\lt 7$.
Effectiveness and safety of low-energy shock wave therapy for digital ulcers associated with systemic sclerosis: A Phase 3 pivotal clinical trial
Authors: Ishii Tomonori , Kawaguchi Yasushi , Ishikawa Osamu , Takemori Hiromitsu , Takasawa Naruhiko , Kobayashi Hitoshi , Takahashi Yuichi , Yasuoka Hidekata , Kodera Takao , Takai Osamu , Nakaya Izaya , Sato Yukio , Izumiyama Tomomasa , Fujii Hiroshi , Kamogawa Yukiko , Shirota Yuko , Shirai Tsuyoshi , Fujita Yoko , Saito Shinichiro , Chiu Shih-Wei , Yamaguchi Takuhiro , Shimokawa Hiroaki , Harigae Hideo 
Published: November 2024

ABSTRACT

Objectives
Systemic sclerosis (SSc) is characterised by ischaemic skin ulcers on the fingertips, and low-energy shock wave therapy is suggested as a novel treatment for ischaemic lesions with angiogenic effects. We aimed to investigate the efficacy and safety of shock wave therapy for skin ulcers in patients with SSc.

Methods
In this Phase 3 pivotal study, we analysed 60 SSc patients with digital ulcers that did not disappear after &gt;4 weeks of existing treatment: 30 patients were treated with extracorporeal shock wave therapy and 30 with conventional treatment. The ulcer count reduction observed after an 8-week treatment period was compared between the shock wave therapy and conventional treatment groups.

Results
After an 8-week treatment period, the mean reduction in the number of ulcers was 0.83 (SD 2.79) in the conventional treatment group compared to a more pronounced reduction of 4.47 (SD 2.65) in the shock wave therapy group.

Conclusions
The study findings indicate the efficacy of extracorporeal shock wave therapy for refractory digital ulcers associated with SSc, which has limited therapeutic options. This therapy is non-invasive and safe and can be used without restriction in combination with other therapies, thus serving as a novel therapeutic method.
sc2GWAS: a comprehensive platform linking single cell and GWAS traits of human
Authors: Yin Mingxue , Feng Chenchen , Yu Zhengmin , Zhang Yuexin , Li Ye , Wang Xuan , Song Chao , Guo Maozu , Li Chunquan 
Published: November 2024

Abstract
Identifying cell populations associated with risk variants is essential for uncovering cell-specific mechanisms that drive disease development and progression. Integrating genome-wide association studies (GWAS) with single-cell RNA sequencing (scRNA-seq) has become an effective strategy for detecting trait–cell relationships. The accumulation of trait-related single cell data has led to an urgent need for its comprehensively processing. To address this, we developed sc2GWAS (https://bio.liclab.net/sc2GWAS/), which aims to document large-scale GWAS trait–cell regulatory pairs at single-cell resolution and provide comprehensive annotations and enrichment analyses for these related pairs. The current version of sc2GWAS curates a total of 15 078 310 candidate trait–cell pairs from &gt; 6 300 000 individual cells, offering a valuable resource for exploring complex regulatory relationships between traits and cells. We applied strict quality control measures on both scRNA-seq data and GWAS data, ensuring the reliability and accuracy of the datasets for the identification of trait-relevant cells and genes. In addition, sc2GWAS provides ranked lists of trait-relevant genes and extensive (epi) genetic annotations, making it a valuable resource for downstream analyses. We demonstrate the utility of the platform by investigating Alzheimer’s disease, where we identified significant associations between the disease and microglial cells, with the APOE gene emerging as particularly significant. This platform facilitates detailed research into complex trait–cell and trait–gene interactions, we anticipate that sc2GWAS will become a comprehensive and valuable platform for exploring GWAS trait–cell regulatory mechanisms.
A systematic quantitative approach comprehensively defines domain-specific functional pathways linked to Schizosaccharomyces pombe heterochromatin regulation
Authors: Muhammad Abubakar , Sarkadi Zsuzsa , Mazumder Agnisrota , Ait Saada Anissia , van Emden Thomas , Capella Matias , Fekete Gergely , Suma Sreechakram Vishnu N , Al-Sady Bassem , Lambert Sarah A E , Papp Balázs , Barrales Ramón Ramos , Braun Sigurd 
Published: November 2024

Abstract
Heterochromatin plays a critical role in regulating gene expression and maintaining genome integrity. While structural and enzymatic components have been linked to heterochromatin establishment, a comprehensive view of the underlying pathways at diverse heterochromatin domains remains elusive. Here, we developed a systematic approach to identify factors involved in heterochromatin silencing at pericentromeres, subtelomeres and the silent mating type locus in Schizosaccharomyces pombe. Using quantitative measures, iterative genetic screening and domain-specific heterochromatin reporters, we identified 369 mutants with different degrees of reduced or enhanced silencing. As expected, mutations in the core heterochromatin machinery globally decreased silencing. However, most other mutants exhibited distinct qualitative and quantitative profiles that indicate heterochromatin domain-specific functions, as seen for example for metabolic pathways affecting primarily subtelomere silencing. Moreover, similar phenotypic profiles revealed shared functions for subunits within complexes. We further discovered that the uncharacterized protein Dhm2 plays a crucial role in heterochromatin maintenance, affecting the inheritance of H3K9 methylation and the clonal propagation of the repressed state. Additionally, Dhm2 loss resulted in delayed S-phase progression and replication stress. Collectively, our systematic approach unveiled a landscape of domain-specific heterochromatin regulators controlling distinct states and identified Dhm2 as a previously unknown factor linked to heterochromatin inheritance and replication fidelity.
Glucose binds and activates NSUN2 to promote translation and epidermal differentiation
Authors: Miao Weili , Porter Douglas F , Li Ya , Meservey Lindsey M , Yang Yen-Yu , Ma Chengjie , Ferguson Ian D , Tien Vivian B , Jack Timothy M , Ducoli Luca , Lopez-Pajares Vanessa , Tao Shiying , Savage Paul B , Wang Yinsheng , Khavari Paul A 
Published: November 2024

Abstract
Elevations in intracellular glucose concentrations are essential for epithelial cell differentiation by mechanisms that are not fully understood. Glucose has recently been found to directly bind several proteins to alter their functions to enhance differentiation. Among the newly identified glucose-binding proteins is NSUN2, an RNA-binding protein that we identified as indispensable for epidermal differentiation. Glucose was found to bind conserved sequences within NSUN2, enhancing its binding to S-adenosyl-L-methionine and boosting its enzymatic activity. Additionally, glucose enhanced NSUN2’s proximity to proteins involved in mRNA translation, with NSUN2 modulating global messenger RNA (mRNA) translation, particularly that of key pro-differentiation mRNAs containing m5C modifications, such as GRHL3. Glucose thus engages diverse molecular mechanisms beyond its energetic roles to facilitate cellular differentiation processes.
PGxDB: an interactive web-platform for pharmacogenomics research
Authors: Duong Nguyen Trinh Trung , Tanoli Ziaurrehman , Hassan Saad , Özcan Umut Onur , Caroli Jimmy , Kooistra Albert J , Gloriam David E , Hauser Alexander S 
Published: November 2024

Abstract
Pharmacogenomics, the study of how an individual's genetic makeup influences their response to medications, is a rapidly evolving field with significant implications for personalized medicine. As researchers and healthcare professionals face challenges in exploring the intricate relationships between genetic profiles and therapeutic outcomes, the demand for effective and user-friendly tools to access and analyze genetic data related to drug responses continues to grow. To address these challenges, we have developed PGxDB, an interactive, web-based platform specifically designed for comprehensive pharmacogenomics research. PGxDB enables the analysis across a wide range of genetic and drug response data types - informing cell-based validations and translational treatment strategies. We developed a pipeline that uniquely combines the relationship between medications indexed with Anatomical Therapeutic Chemical (ATC) codes with molecular target profiles with their genetic variability and predicted variant effects. This enables scientists from diverse backgrounds - including molecular scientists and clinicians - to link genetic variability to curated drug response variability and investigate indication or treatment associations in a single resource. With PGxDB, we aim to catalyze innovations in pharmacogenomics research, empower drug discovery, support clinical decision-making, and pave the way for more effective treatment regimens. PGxDB is a freely accessible database available at https://pgx-db.org/
Protein moonlighting by a target gene dominates phenotypic divergence of the Sef1 transcriptional regulatory network in yeasts
Authors: Hsu Po-Chen , Lu Tzu-Chiao , Hung Po-Hsiang , Leu Jun-Yi 
Published: November 2024

Abstract
Transcriptional rewiring generates phenotypic novelty, acting as an important mechanism contributing to evolutionary development, speciation, and adaptation in all organisms. The phenotypic outcomes (functions) of transcription factor (TF) activity are determined by the combined effects of all target genes in the TF’s regulatory network. Plastic rewiring of target genes accumulates during species divergence and ultimately alters phenotypes, indicating a TF functional switch. We define this phenomenon as ‘disruptive rewiring’, where the rewiring process disrupts the link between a TF and its original target genes that determine phenotypes. Here, we investigate if ‘complete’ disruptive rewiring is a prerequisite for a TF functional switch by employing chromatin immunoprecipitation sequencing, RNA expression, and phenotypic assays across yeast species. In yeasts where Sef1 targets TCA (tricarboxylic acid) cycle genes, we demonstrate that Sef1 orthologs can promote and inhibit respiratory growth by modulating the moonlighting function of their conserved target, NDE1. This modulation occurs without changing the overall association of Sef1 with TCA cycle genes. We propose that phenotypic masking by NDE1 promotes ‘deceptive’ disruptive rewiring of the Sef1 regulatory network in Saccharomyces cerevisiae, thereby potentially constraining future evolutionary trajectories.
Molecular modification enables CO2 electroreduction to methane on platinum surface in acidic media
Authors: Yang Hengpan , Cai Huizhu , Li Deliang , Kong Yan , Feng Shangzhao , Jiang Xingxing , Hu Qi , He Chuanxin 
Published: November 2024

ABSTRACT
Cu-based materials can produce hydrocarbons in CO2 electroreduction (CO2RR), but their stability still needs to be enhanced particularly in acidic media. Metallic Pt is highly stable in both acidic and alkaline media, yet rarely utilized in CO2RR, due to the competitive activity in hydrogen evolution reaction (HER). In this research, abundant thionine (Th) molecules are stably confined within Pt nanocrystals via a molecular doping strategy. The Pt surface is successfully modulated by these Th molecules, and thereby the dominant HER activity is converted to CO2RR activity. CO2 could be electroreduced to CH4 using organic molecule-modified Pt-based catalysts for the first time. Specifically, this composite catalyst maintains more than 100-hour stability in strong acid conditions (pH 1), even comparable to those state-of-the-art CO2RR catalysts. In-situ spectroscopic analysis and theoretical calculations reveal that the molecular modification can decrease the energy barrier for *COOH formation, and guarantee the sufficient local *H near Pt surface. Additionally, the *H derived from H2O dissociation is favorable for the *CO hydrogenation pathway towards *CHO, eventually leading to the formation of CH4. This strategy might be easily applied to microenvironment and interface regulation in other electrocatalytic reactions.