bluuebunny/crossref_metadata_2025_split huggingface dataset:
Swift
: a modern highly parallel gravity and smoothed particle hydrodynamics solver for astrophysical and cosmological applications
Authors: Schaller Matthieu , Borrow Josh , Draper Peter W , Ivkovic Mladen , McAlpine Stuart , Vandenbroucke Bert , Bahé Yannick , Chaikin Evgenii , Chalk Aidan B G , Chan Tsang Keung , Correa Camila , van Daalen Marcel , Elbers Willem , Gonnet Pedro , Hausammann Loïc , Helly John , Huško Filip , Kegerreis Jacob A , Nobels Folkert S J , Ploeckinger Sylvia , Revaz Yves , Roper William J , Ruiz-Bonilla Sergio , Sandnes Thomas D , Uyttenhove Yolan , Willis James S , Xiang Zhen 
Published: March 2024

ABSTRACT
Numerical simulations have become one of the key tools used by theorists in all the fields of astrophysics and cosmology. The development of modern tools that target the largest existing computing systems and exploit state-of-the-art numerical methods and algorithms is thus crucial. In this paper, we introduce the fully open-source highly-parallel, versatile, and modular coupled hydrodynamics, gravity, cosmology, and galaxy-formation code Swift. The software package exploits hybrid shared- and distributed-memory task-based parallelism, asynchronous communications, and domain-decomposition algorithms based on balancing the workload, rather than the data, to efficiently exploit modern high-performance computing cluster architectures. Gravity is solved for using a fast-multipole-method, optionally coupled to a particle mesh solver in Fourier space to handle periodic volumes. For gas evolution, multiple modern flavours of Smoothed Particle Hydrodynamics are implemented. Swift also evolves neutrinos using a state-of-the-art particle-based method. Two complementary networks of sub-grid models for galaxy formation as well as extensions to simulate planetary physics are also released as part of the code. An extensive set of output options, including snapshots, light-cones, power spectra, and a coupling to structure finders are also included. We describe the overall code architecture, summarize the consistency and accuracy tests that were performed, and demonstrate the excellent weak-scaling performance of the code using a representative cosmological hydrodynamical problem with ≈300 billion particles. The code is released to the community alongside extensive documentation for both users and developers, a large selection of example test problems, and a suite of tools to aid in the analysis of large simulations run with Swift.
SIRT2 promotes base excision repair by transcriptionally activating OGG1 in an ATM/ATR-dependent manner
Authors: Geng Anke , Sun Jiahui , Tang Huanyin , Yu Yang , Wang Xiyue , Zhang Jingyuan , Wang Xiaona , Sun Xiaoxiang , Zhou Xiaofang , Gao Neng , Tan Rong , Xu Zhu , Jiang Ying , Mao Zhiyong 
Published: March 2024

Abstract
Sirtuin 2 (SIRT2) regulates the maintenance of genome integrity by targeting pathways of DNA damage response and homologous recombination repair. However, whether and how SIRT2 promotes base excision repair (BER) remain to be determined. Here, we found that independent of its catalytic activity SIRT2 interacted with the critical glycosylase OGG1 to promote OGG1 recruitment to its own promoter upon oxidative stress, thereby enhancing OGG1 promoter activity and increasing BER efficiency. Further studies revealed that SIRT2 was phosphorylated on S46 and S53 by ATM/ATR upon oxidative stress, and SIRT2 phosphorylation enhanced the SIRT2-OGG1 interaction and mediated the stimulatory effect of SIRT2 on OGG1 promoter activity. We also characterized 37 cancer-derived SIRT2 mutants and found that 5 exhibited the loss of the stimulatory effects on OGG1 transcription. Together, our data reveal that SIRT2 acts as a tumor suppressor by promoting OGG1 transcription and increasing BER efficiency in an ATM/ATR-dependent manner.
Critical steps in the assembly process of the bacterial 50S ribosomal subunit
Authors: Seffouh Amal , Nikolay Rainer , Ortega Joaquin 
Published: March 2024

Abstract
During assembly, ribosomal particles in bacteria fold according to energy landscapes comprised of multiple parallel pathways. Cryo-electron microscopy studies have identified a critical maturation step that occurs during the late assembly stages of the 50S subunit in Bacillus subtilis. This step acts as a point of convergency for all the parallel assembly pathways of the subunit, where an assembly intermediate accumulates in a ‘locked’ state, causing maturation to pause. Assembly factors then act on this critical step to ‘unlock’ the last maturation steps involving the functional sites. Without these factors, the 50S subunit fails to complete its assembly, causing cells to die due to a lack of functional ribosomes to synthesize proteins. In this review, we analyze these findings in B. subtilis and examine other cryo-EM studies that have visualized assembly intermediates in different bacterial species, to determine if convergency points in the ribosome assembly process are a common theme among bacteria. There are still gaps in our knowledge, as these methodologies have not yet been applied to diverse species. However, identifying and characterizing these convergency points can reveal how different bacterial species implement unique mechanisms to regulate critical steps in the ribosome assembly process.
Defective transfer of parental histone decreases frequency of homologous recombination by increasing free histone pools in budding yeast
Authors: Karri Srinivasu , Yang Yi , Zhou Jiaqi , Dickinson Quinn , Jia Jing , Huang Yuxin , Wang Zhiquan , Gan Haiyun , Yu Chuanhe 
Published: March 2024

Abstract
Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging strands, respectively. Single Dpb3 deletion (dpb3Δ) or Mcm2 mutation (mcm2-3A), which each disrupts one parental histone transfer pathway, leads to the other's predominance. However, the biological impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3–H4 tetramer transfer. We found that a dpb3Δ mcm2-3A double mutant did not exhibit the asymmetric parental histone patterns caused by a single dpb3Δ or mcm2-3A mutation, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3Δ, mcm2-3A and dpb3Δ mcm2-3A mutants, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones during DNA replication is essential for maintaining chromatin structure and that lower homologous recombination activity due to parental histone transfer defects is detrimental to cells.
SIX2 promotes cell plasticity via Wnt/β-catenin signalling in androgen receptor independent prostate cancer
Authors: Leppänen Noora , Kaljunen Heidi , Takala Eerika , Kaarijärvi Roosa , Mäkinen Petri I , Ylä-Herttuala Seppo , Paatero Ilkka , Paakinaho Ville , Ketola Kirsi 
Published: March 2024

Abstract
The use of androgen receptor (AR) inhibitors in prostate cancer gives rise to increased cellular lineage plasticity resulting in resistance to AR-targeted therapies. In this study, we examined the chromatin landscape of AR-positive prostate cancer cells post-exposure to the AR inhibitor enzalutamide. We identified a novel regulator of cell plasticity, the homeobox transcription factor SIX2, whose motif is enriched in accessible chromatin regions after treatment. Depletion of SIX2 in androgen-independent PC-3 prostate cancer cells induced a switch from a stem-like to an epithelial state, resulting in reduced cancer-related properties such as proliferation, colony formation, and metastasis both in vitro and in vivo. These effects were mediated through the downregulation of the Wnt/β-catenin signalling pathway and subsequent reduction of nuclear β-catenin. Collectively, our findings provide compelling evidence that the depletion of SIX2 may represent a promising strategy for overcoming the cell plasticity mechanisms driving antiandrogen resistance in prostate cancer.
A phage nucleus-associated RNA-binding protein is required for jumbo phage infection
Authors: Enustun Eray , Armbruster Emily G , Lee Jina , Zhang Sitao , Yee Brian A , Malukhina Kseniya , Gu Yajie , Deep Amar , Naritomi Jack T , Liang Qishan , Aigner Stefan , Adler Benjamin A , Cress Brady F , Doudna Jennifer A , Chaikeeratisak Vorrapon , Cleveland Don W , Ghassemian Majid , Bintu Bogdan , Yeo Gene W , Pogliano Joe , Corbett Kevin D 
Published: March 2024

Abstract
Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.
Low Level Viremia Is Associated With Serious non-AIDS Events in People With HIV
Authors: Ganesan Anuradha , Hsieh Hsing-Chuan , Chu Xiuping , Colombo Rhonda E , Berjohn Catherine , Lalani Tahaniyat , Yabes Joseph , Joya Christie A , Blaylock Jason , Agan Brian K 
Published: March 2024

Abstract

Background
The consequences of low-level viremia in people with HIV are unclear. We used data from the US Military HIV Natural History Study to examine the association of low-level viremia (LLV) and serious non-AIDS events (SNAEs).

Methods
Included participants initiated antiretroviral therapy after 1996 and had ≥3 viral loads (VLs) measured, using an assay with a lower limit of detection of &lt;50 copies/mL, ≥6 months after antiretroviral therapy initiation. VLs were categorized as lower levels of LLV (51–199 copies/mL), higher level of low-level viremia (HLLV; 200–999 copies/mL), and (VF; ≥200 copies/mL on 2 or more successive determinations or a single VL ≥1000 copies/mL), and virologic suppression (VS; ie, VL &lt;50 copies/mL). Viral blips (ie, VLs between 50 and 999 copies/mL that are preceded and succeeded by VL &lt;50 copies/mL) were analyzed in the VS category. Cox proportional hazards models were used to examine the association of LLV and SNAEs, adjusted hazard ratios and 95% confidence intervals are presented.

Results
A total of 439 (17.4%) SNAEs were recorded among the 2528 participants (93% male, 40% Caucasian, 43% African American) followed for a median of 11 years. In 8.5% and 4.6% of the participants, respectively, LLV and HLLV were the highest recorded viremia strata. Compared with VS, SNAEs were associated with LLV (1.3 [1.2–1.4]), HLLV (1.6 [1.5–1.7]), and virologic failure (1.7 [1.7–1.8]).

Conclusions
The results of this study suggest that LLV is associated with the occurrence of SNAEs and needs further study.
Influence of egg sacs on the swimming performance of freshwater cyclopoid copepods
Authors: Svetlichny Leonid , Obertegger Ulrike 
Published: March 2024

Abstract
Female cyclopoid copepods carry their embryos in egg sacs that impact swimming performance until nauplii hatch. We studied kinematic parameters and mechanical energy of small routine jumps and large escape jumps of non-egg-carrying (NEC) and egg-carrying (EC) females of Mesocyclops leuckarti and Macrocyclops albidus. The drag and body acceleration costs for EC females of M. leuckarti and M. albidus during routine jumps were 28 and 40%, respectively, higher than those for NEC females moving at the same speed. Maintaining position in the water column by small jumps was more costly for EC females, requiring 2.2–2.3 times more jumps and energy. Consequently, the persistence of EC females was limited in the open water. In M. leuckarti and M. albidus, the average speed and distances of jumps were 5–6 and 1.5–2.2 times higher, respectively, and the duration of jumps was 2.2–2.5 times shorter during escape than routine swimming. The maximum jumping speeds of NEC females, 40.6 and 50.5 cm s−1, respectively, were 12–14% higher than those of EC females, whereas their power and cost of transport were 16 and 23% lower, respectively. These results clearly indicated that egg sacs impair swimming and increase energetic costs of movement.
Dysfunction of striatal parvalbumin interneurons drives motor stereotypies in Cntnap2−/− mouse model of autism spectrum disorders
Authors: Thabault Mathieu , Fernandes-Gomes Cloé , Huot Anne-Lise , Francheteau Maureen , Balbous-Gautier Anaïs , Fernagut Pierre-Olivier , Galvan Laurie 
Published: March 2024

Abstract
The involvement of parvalbumin (PV) interneurons in autism spectrum disorders (ASD) pathophysiology has been widely described without clearly elucidating how their dysfunctions could lead to ASD symptoms. The Cntnap2−/− mice, an ASD mouse model deficient for a major ASD susceptibility gene, display core ASD symptoms including motor stereotypies, which are directly linked to striatal dysfunction. This study reveals that striatal PV interneurons display hyperexcitability and hyperactivity in Cntnap2−/− mice, along with a reduced response in medium spiny neurons. We also provide evidence for a crucial role of striatal PV interneurons in motor stereotypies by demonstrating that their selective inhibition rescued a wild type-like phenotype. Our study identifies how PV interneuron dysfunctions disrupt striatal circuitry and drive the motor stereotypies in ASD.
The Labor Market Effects of Loan Guarantee Programs
Authors: Barrot Jean-Noël , Martin Thorsten , Sauvagnat Julien , Vallée Boris 
Published: March 2024

Abstract
We investigate the labor market effects of a loan guarantee program targeting French SMEs during the financial crisis. Exploiting differences in regional treatment intensity in a border discontinuity design, we uncover a central trade-off for such interventions. While the program has a positive impact on workers’ employment and earnings trajectories that translates into positive aggregate employment effects, it dampens the worker reallocation toward more productive firms that happens following recessions, and particularly so for high-skill workers. This labor allocation effect is economically significant and translates into a reduction in aggregate productivity.
Performance evaluation of computed tomography scanners in Indonesia: recommendation from a nation-wide study
Authors: Lubis Lukmanda Evan , Rafika Rafika , Noerwasana Adi Dradjat , Suryanti Rini , Soejoko Djarwani Soeharso 
Published: March 2024

Abstract
In this study, an evaluation of the compliance test data from 684 computed tomography (CT)-scanners in Indonesia for the 2019–22 test period was carried out. The study was aimed to describe the performance profile of CT-scanners in Indonesia and evaluate the testing protocol. A total of 87.8% of the CT-scanners unconditionally passed the tests, 8.8% passed the tests with conditions and 3.4% failed the tests. Of the devices conditionally passed the tests, the top two causes were water CT number accuracy (45.2%) and laser position accuracy (41.9%). Meanwhile, 75.0% of the failed devices were due to failing to meet the patient dose test criteria. The failure of the test for the water CT number accuracy parameter was caused by variations in the type of phantom used in the test, where several types of phantoms did not use water as material of the homogeneity module. Failures in laser position accuracy test were caused by the passing criteria that adjust to the minimum slice thickness, so that modern CT-scanner with small detector sizes and collimations tend not to pass. On the other hand, the failure on dose aspects was due to the frequent unavailability of baseline values for comparison. Of these top three failure causes, two of them, namely the CT number and dose test parameters, have been accommodated in the latest regulation (BAPETEN Regulation No. 2/2022) with a change in the evaluation method, while for the laser position accuracy test it is recommended to alter the passing criteria to an absolute value, namely 1 mm.
Study on the Extrapolability of Current Tumorgenicity Test With Mice by Comparing the Syngeneic or Allogeneic Mouse Transplantation Model
Authors: Tamura Takashi , Tahara Tsuyoshi , Inoue Michiko , Nanjo Ryota , Onoe Hirotaka , Yamamoto Takako , Kawamata Shin 
Published: March 2024

Abstract
The extrapolability of the current tumorigenicity test performed by transplanting human cell product into immunodeficient (NOG) mice was investigated. For this purpose, the susceptibility to form teratomas of NOG mice was assessed by transplanting undifferentiated human-induced pluripotent stem cells (hiPSCs) as positive control cells via the liver, striatum, or tail vein and evaluating the TPD50 value (dose required to form teratomas in half of the transplanted mice). This was then compared to the TPD50 of syngeneic or allogeneic mouse models. The TPD50 of C57/BL/6(B6)-iPSC or 129/Ola(129)-embryonic stem cell (ESC) transplanted into the liver of syngeneic mice was 4.08 × 105 and 4.64 × 104 cells, respectively, while the TPD50 of hiPSC administered into the liver of NOG mice was 4.64 × 104 cells. The TPD50 of B6-miPSC-synergic, 129-mESC-synergic, or 129-cell/B6 allogeneic transplantation into the striatum was 5.09 × 102, 1.0 × 104, and 3.73 × 104 cells, respectively, while that of hiPSC/NOG mice was 1.0 × 103 cells. The TPD50 for B6-miPSC or 129-mESC syngeneic tail vein infusion was 3.16 × 106 or 5.62 × 106 cells, respectively, while no incidence was observed from 1 × 107 B6-miPSCs in 129 mice or hiPSCs in NOG mice infusion study. Although the number of data sets was limited, these data indicate that the teratoma formation from transplanted undifferentiated hiPSCs via the liver or striatum in NOG mice is comparable to that in syngeneic or allogeneic mouse transplantation model, suggesting that the result of the current tumorigenicity test in NOG mice would provide useful information to infer the incidence of teratoma from residual undifferentiated hPSCs in hPSC-derived products after transplantation.
Chitosan and Grifola Frondosa nanoparticles insulate liver dysfunction in EAC-bearing mice
Authors: Radwan Aliaa M , Gebreel Doaa T , Allam Sahar , El-Atrash Afaf , Tousson Ehab 
Published: March 2024

Abstract

Background
Ehrlich ascites carcinoma (EAC) is a rapidly growing and undifferentiated tumor that can prompt oxidative stress and liver toxicity, whereas chitosan and Grifola Frondosa have widely recognized biological qualities. Therefore, our study designed to assess the potential ameliorative ability of chitosan nanoparticles (CS NPs) and Grifola Frondosa nanoparticles (GF-loaded casein NPs) on EAC-induced hepatic injury in mice.

Methods
A total of 60 female albino mice were segregated into 6 groups (10 mice each), G1, control group; G2, CS NPs group; G3, GF-loaded casein NPs group; G4, EAC group; G5, EAC treated with CS NPs; G6, EAC treated with GF-loaded casein NPs.

Results
According to the findings, EAC considerably increased serum activities of ALT, AST, ALP as well as LDL, cholesterol, and triglycerides levels coincided with marked decrease in albumin and total protein content in liver tissue. At the same time, it drastically lowered GSH levels and catalase activity while significantly elevating MDA levels. In addition, EAC caused DNA damage and apoptosis by decreasing Bcl-2 while increasing p53 expressions. However, either CS NPs or GF-loaded casein NPs therapy improved liver architecture and functioning, increased antioxidant parameters, and prevented hepatocyte death in EAC mice.

Conclusions
Our findings concluded that CS NPs and GF-loaded casein NPs have insulating functions against EAC-induced hepatic damage in mice.
Further draining of Discocyrtus to expand Neopachylinae (Opiliones, Gonyleptidae): absorption of taxa and establishment of new genera and species
Authors: Carvalho Rafael N , Kury Adriano B 
Published: March 2024

Abstract
The gonyleptids are one of the most diverse groups of harvestmen, exhibiting a vast range of sizes, shapes and behaviors. However, its internal classification, earlier based on meristic characters, particularly in larger groups such as Pachylinae and Discocyrtus, has been called into question by new proposals that consider morphological and molecular synapomorphies. Here, we aspire to evaluate the transfer of seven species currently classified under Discocyrtus sensu lato and the monotypic genus Oliverius from Pachylinae to Neopachylinae. Additionally, we propose the inclusion of two new species in Neopachylinae. To test our hypothesis, we expand upon previous cladistic analyses using maximum parsimony and incorporate 40 terminals representing Gonyleptoidea, including all existing members of Neopachylinae, and 116 morphological characters. Our results confirm the hypothesis of monophyly of Neopachylinae after the inclusion of the new and transferred taxa. To provide a comprehensive assessment of the results, we update some diagnoses at the genus and species-level within Neopachylinae. Furthermore, to accommodate the taxonomic changes resulting from this study, we propose 1) the establishment of two new genera, 2) the reassignment of five taxa at the generic level, and 3) the establishment of two new junior subjective synonymies at the species level.