bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of red, star-forming galaxies (red misfits) in a ΛCDM universe
Authors: Manuwal Aditya 
Published: June 2024

ABSTRACT
We investigate the formation of red misfits (RM) using a cosmological, hydrodynamical simulation from the eagle project. Similar to observations, the RM possess less dust, higher stellar metallicities, and older stellar populations compared to blue, star-forming galaxies (BA) at the same $M_\star$. Lagrangian particle-tracking reveals that the older ages of RM have resulted from a combined effect of higher star formation efficiency (SFE), and the earlier onset and faster net depletion of their interstellar medium (ISM). For the centrals, the latter was partially due to higher efficiency of escape from ISM, driven by stronger stellar and/or active galactic nucleus feedback (depending on the mass). There was an additional contribution to this escape from gas stripping for satellite RM, as suggested by the higher group masses ($\gtrsim 0.5$ dex) and $\mathrm{H_2}/\mathrm{H}\, {\rm{\small I}}$ ratios ($\gtrsim 0.3$ dex). Moreover, accretion of circumgalactic gas (CGM) on to the galaxy has been less efficient for the satellites. On the metallicity front, the offsets are largely due to the disparity in SFE, causing varying degrees of enrichment through the mass transfers associated with stellar winds and supernovae. We ascribe this SFE disparity to the lower specific angular momentum (j) of freshly accreted CGM for RM, which ultimately manifested in the ISM kinematics due to interactions with cooling flows. The impact on $j_{\rm ism}$ was further intensified by poorer alignment with the flow’s $\vec{j}$, particularly for the satellites. Our results illuminate potential origins of RM, and motivate further exploration of this peculiar class through a synergy between observations and simulations.
Efficient activation of hundreds of LTR12C elements reveals cis-regulatory function determined by distinct epigenetic mechanisms
Authors: Ohtani Hitoshi , Liu Minmin , Liang Gangning , Jang H Josh , Jones Peter A 
Published: June 2024

Abstract
Long terminal repeats (LTRs), which often contain promoter and enhancer sequences of intact endogenous retroviruses (ERVs), are known to be co-opted as cis-regulatory elements for fine-tuning host-coding gene expression. Since LTRs are mainly silenced by the deposition of repressive epigenetic marks, substantial activation of LTRs has been found in human cells after treatment with epigenetic inhibitors. Although the LTR12C family makes up the majority of ERVs activated by epigenetic inhibitors, how these epigenetically and transcriptionally activated LTR12C elements can regulate the host-coding gene expression remains unclear due to genome-wide alteration of transcriptional changes after epigenetic inhibitor treatments. Here, we specifically transactivated &gt;600 LTR12C elements by using single guide RNA-based dCas9-SunTag-VP64, a site-specific targeting CRISPR activation (CRISPRa) system, with minimal off-target events. Interestingly, most of the transactivated LTR12C elements acquired the H3K27ac-marked enhancer feature, while only 20% were co-marked with promoter-associated H3K4me3 modifications. The enrichment of the H3K4me3 signal was intricately associated with downstream regions of LTR12C, such as internal regions of intact ERV9 or other types of retrotransposons. Here, we leverage an optimized CRISPRa system to identify two distinct epigenetic signatures that define LTR12C transcriptional activation, which modulate the expression of proximal protein-coding genes.
HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair
Authors: Di Giorgio Eros , Dalla Emiliano , Tolotto Vanessa , D’Este Francesca , Paluvai Harikrishnareddy , Ranzino Liliana , Brancolini Claudio 
Published: June 2024

Abstract
Access to DNA is the first level of control in regulating gene transcription, a control that is also critical for maintaining DNA integrity. Cellular senescence is characterized by profound transcriptional rearrangements and accumulation of DNA lesions. Here, we discovered an epigenetic complex between HDAC4 and HDAC1/HDAC2 that is involved in the erase of H2BK120 acetylation. The HDAC4/HDAC1/HDAC2 complex modulates the efficiency of DNA repair by homologous recombination, through dynamic deacetylation of H2BK120. Deficiency of HDAC4 leads to accumulation of H2BK120ac, impaired recruitment of BRCA1 and CtIP to the site of lesions, accumulation of damaged DNA and senescence. In senescent cells this complex is disassembled because of increased proteasomal degradation of HDAC4. Forced expression of HDAC4 during RAS-induced senescence reduces the genomic spread of γH2AX. It also affects H2BK120ac levels, which are increased in DNA-damaged regions that accumulate during RAS-induced senescence. In summary, degradation of HDAC4 during senescence causes the accumulation of damaged DNA and contributes to the activation of the transcriptional program controlled by super-enhancers that maintains senescence.
The impact of mRNA poly(A) tail length on eukaryotic translation stages
Authors: Biziaev Nikita , Shuvalov Alexey , Salman Ali , Egorova Tatiana , Shuvalova Ekaterina , Alkalaeva Elena 
Published: June 2024

Abstract
The poly(A) tail plays an important role in maintaining mRNA stability and influences translation efficiency via binding with PABP. However, the impact of poly(A) tail length on mRNA translation remains incompletely understood. This study explores the effects of poly(A) tail length on human translation. We determined the translation rates in cell lysates using mRNAs with different poly(A) tails. Cap-dependent translation was stimulated by the poly(A) tail, however, it was largely independent of poly(A) tail length, with an exception observed in the case of the 75 nt poly(A) tail. Conversely, cap-independent translation displayed a positive correlation with poly(A) tail length. Examination of translation stages uncovered the dependence of initiation and termination on the presence of the poly(A) tail, but the efficiency of initiation remained unaffected by poly(A) tail extension. Further study unveiled that increased binding of eRFs to the ribosome with the poly(A) tail extension induced more efficient hydrolysis of peptidyl-tRNA. Building upon these findings, we propose a crucial role for the 75 nt poly(A) tail in orchestrating the formation of a double closed-loop mRNA structure within human cells which couples the initiation and termination phases of translation.
Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability
Authors: Kim Jung-Hyun , Nagaraja Ramaiah , Ogurtsov Alexey Y , Noskov Vladimir N , Liskovykh Mikhail , Lee Hee-Sheung , Hori Yutaro , Kobayashi Takehiko , Hunter Kent , Schlessinger David , Kouprina Natalay , Shabalina Svetlana A , Larionov Vladimir 
Published: June 2024

Abstract
Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35 to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5′ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.
Oral phosphate binders and incident osteoporotic fracture in patients on dialysis
Authors: Kim Ji Eun , Park Jina , Jang Yunyoung , Kang Eunjeong , Kim Yong Chul , Kim Dong Ki , Joo Kwon Wook , Kim Yon Su , Lee Hajeong 
Published: June 2024

ABSTRACT

Background
End-stage kidney disease (ESKD) has an elevated risk of osteoporotic fractures in relation to mineral and bone disorder (MBD) as well as conventional risks of osteoporosis. We investigated the association between oral phosphate binders, the mainstay of MBD treatment, and osteoporotic fracture in dialysis patients.

Methods
We obtained data from the National Health Insurance database for incident dialysis patients without a history of osteoporotic fractures. Participants were categorized into four groups based on their initial 1-year prescription profiles: calcium-based phosphate binder (CBPB), non-calcium-based phosphate binder (NCBPB), both CBPB and NCBPB (mixed), and non-phosphate binder (non-user) groups. The primary outcome was the occurrence of new-onset osteoporotic fractures after 1 year of dialysis. Secondary outcomes included cardiovascular events and mortality.

Results
Out of 69 368 incident dialysis patients, 22 326, 5020, 2853 and 39 169 were included in the CBPB, NCBPB, mixed and non-user groups, respectively. The overall risk of osteoporotic fractures was lower in patients taking any phosphate binders compared with non-users. Specifically, only the CBPB group showed a reduced risk of vertebral [adjusted hazard ratio (aHR) 0.83 (0.76–0.92)], hip [aHR 0.81 (0.74–0.89)] and distal radius [aHR 0.88 (0.78–0.99)] fractures compared with non-users. This relationship presented in a time-dependent manner with fracture risk reduction in patients taking CBPB for 3–6 months [aHR 0.9 (0.83–0.99)] and ≥6 months [aHR 0.83 (0.78–0.89)], compared with those using CBPB for &lt;3 months. Additionally, only the CBPB group had a lower risk of MACE, cardiac arrest and ventricular arrhythmia than non-users. All phosphorus binder groups showed a reduced mortality risk compared with non-users.

Conclusions
Our findings indicate that the using phosphate binders in ESKD patients is lowers the risk of osteoporotic fractures. Notably, those taking CBPB had a reduced risk without increasing cardiovascular events or mortality compared with non-users.
NRG-BN002: Phase I study of ipilimumab, nivolumab, and the combination in patients with newly diagnosed glioblastoma
Authors: Sloan Andrew E , Winter Kathryn , Gilbert Mark R , Aldape Kenneth , Choi Serah , Wen Patrick Y , Butowski Nicholas , Iwamoto Fabio M , Raval Raju R , Voloschin Alfredo D , Kamiya-Matsuoka Carlos , Won Minhee , Mehta Minesh P 
Published: June 2024

Abstract

Background
Immune checkpoint inhibitors (ICIs) have efficacy in several solid tumors but limited efficacy in glioblastoma (GBM). This study evaluated the safety of anti-CTLA-4 and anti-PD-1 ICIs alone or in combination in newly diagnosed GBM after completion of standard radiochemotherapy with the subsequent intent to test combinatorial ICIs in this setting.

Methods
The primary endpoint was dose-limiting toxicity (DLT) for adults with unifocal, supratentorial newly diagnosed GBM after resection and chemoradiation. Ipilimumab and nivolumab were tested separately and in combination with a planned expansion cohort dependent upon DLT results.

Results
Thirty-two patients were enrolled at 9 institutions: 6 to each DLT assessment cohort and 14 to the expansion cohort. Median age: 55 years, 67.7% male, 83.9% White. Treatment was well tolerated with 16% Grade 4 events; the combination did not have unexpectedly increased toxicity, with no Grade 5 events. One DLT was seen in each single-agent treatment; none were observed in the combination, leading to expanded accrual of the combined treatment. The median follow-up was 19.6 months. For all patients receiving combination treatment, median overall survival (OS) and progression-free survival (PFS) were 20.7 and 16.1 months, respectively.

Conclusions
IPI and NIVO are safe and tolerable with toxicities similar to those noted with other cancers when given in combination with adjuvant temozolomide for newly diagnosed GBM. Combination IPI + NIVO is not substantially more toxic than single agents. These results support a subsequent efficacy trial to test the combination of ICIs in Phase II/III for patients with newly diagnosed GBM.

ClinicalTrials.gov Registration
NCT02311920
Polygenic and Socioeconomic Contributions to Nicotine Use and Cardiometabolic Health in Early Mid-Life
Authors: Lippert Adam M , Corsi Daniel J , Kim Rockli , Wedow Robbee , Kim Jinho , Taddess Beza , Subramanian S V 
Published: June 2024

Abstract

Introduction
Early mid-life is marked by accumulating risks for cardiometabolic illness linked to health-risk behaviors like nicotine use. Identifying polygenic indices (PGI) has enriched scientific understanding of the cumulative genetic contributions to behavioral and cardiometabolic health, though few studies have assessed these associations alongside socioeconomic (SES) and lifestyle factors.

Aims and Methods
Drawing on data from 2337 individuals from the United States participating in the National Longitudinal Study of Adolescent to Adult Health, the current study assesses the fraction of variance in five related outcomes—use of conventional and electronic cigarettes, body mass index (BMI), waist circumference, and glycosylated hemoglobin (A1c)—explained by PGI, SES, and lifestyle.

Results
Regression models on African ancestry (AA) and European ancestry (EA) subsamples reveal that the fraction of variance explained by PGI ranges across outcomes. While adjusting for sex and age, PGI explained 3.5%, 2.2%, and 0% in the AA subsample of variability in BMI, waist circumference, and A1c, respectively (in the EA subsample these figures were 7.7%, 9.4%, and 1.3%). The proportion of variance explained by PGI in nicotine-use outcomes is also variable. Results further indicate that PGI and SES are generally complementary, accounting for more variance in the outcomes when modeled together versus separately.

Conclusions
PGI are gaining attention in population health surveillance, but polygenic variability might not align clearly with health differences in populations or surpass SES as a fundamental cause of health disparities. We discuss future steps in integrating PGI and SES to refine population health prediction rules.

Implications
Study findings point to the complementary relationship of PGI and socioeconomic indicators in explaining population variance in nicotine outcomes and cardiometabolic wellness. Population health surveillance and prediction rules would benefit from the combination of information from both polygenic and socioeconomic risks. Additionally, the risk for electronic cigarette use among users of conventional cigarettes may have a genetic component tied to the cumulative genetic propensity for heavy smoking. Further research on PGI for vaping is needed.
Native Aortic Valve Endocarditis Caused by Scopulariopsis Species: Case Report, Considerations for Management, and Review of Literature
Authors: Imam Sabrina , Kaperak Christopher J , Hozain Ahmed E , Qin Hecong , Nguyen Cynthia T , Sudhindra Praveen , Jeevanandam Valluvan , Landon Emily 
Published: June 2024

Abstract
We present the first case of native aortic valve endocarditis caused by Scopulariopsis. Intraoperative images and videos from valve replacement surgery illustrate the severity of fungal endocarditis. This case demonstrates the aggressive presentation of left-sided fungal endocarditis, highlights challenges with treating highly resistant fungi, and considers the potential utility of olorofim.
Testing the TTG–Metabasite Connection in the Southern Superior Province: an Integrated Geochemical, Isotopic, and Petrogenetic Modelling Approach
Authors: Kendrick Jillian , Duguet Manuel , Kirkland Christopher L , Liebmann Janne , Moser Desmond E , Vervoort Jeffrey D , Yakymchuk Chris 
Published: June 2024

Abstract
Archean cratons are dominated by tonalite–trondhjemite–granodiorite (TTG) suites, the products of crustal differentiation that formed early continental crust. These rocks may have been primarily generated by partial melting of hydrated basaltic crust in a variety of settings including subduction zones or the deep lithosphere. Sources are mainly inferred from examination of TTGs alone, as potential source rocks are rarely exposed. In the southern Superior Province, Canada, the Kapuskasing Uplift exposes an important crustal cross-section with upper- to middle-crustal TTGs and lower-crustal metabasites, which show evidence of having produced trondhjemitic anatectic melt. Here, we test the hypothesis that these metabasites were the source of the Mesoarchean to Neoarchean TTGs in the Kapuskasing Uplift by combining phase equilibrium and melt trace element modelling with whole-rock and zircon Lu–Hf isotope analysis and geochronology (garnet Lu–Hf and zircon U–Pb) of metabasic samples. By comparison of the results with existing data from TTGs in the Kapuskasing Uplift, we determined that the metabasites are plausible source rocks for the TTGs. The Lu–Hf systematics of the metabasites and TTGs are the most robust evidence of a genetic connection. Modelling results support an increase in TTG source depth over time. New geochronological data constrain partial melting of metabasite and crystallization of anatectic melt between ca. 2685 Ma and ca. 2600 Ma, coeval with crystallization of only the youngest TTGs. Overall, these results indicate a complex history of intracrustal differentiation in the Kapuskasing Uplift, with partial melting of two isotopically distinct lower-crustal metabasic sources at different times and depths.
Cross-cultural adaptation and psychometric validation of the French version of the Defense and Veterans Pain Rating Scale for acute and chronic pain: a prospective clinical study
Authors: Safran Szilard Laszlo , Follonier David , Weber Eric , Vayne-Bossert Petra , Ahrendts Ulrike , Rehberg-Klug Benno 
Published: June 2024

Abstract

Background
Pain assessment and proper evaluation of pain are prerequisites for treatment of acute and chronic pain. Until now, most evaluations have used only resting pain intensity and a unidimensional scale, although multidimensional pain assessment and especially assessment of functional pain impact on activities are recommended. The Defense and Veterans Pain Rating Scale (DVPRS) permits this multidimensional assessment, but no validated French translation exists.

Objectives
To validate the French translation of the multidimensional DVPRS, called the Functional Pain Scale (FPS), in multiple settings of acute and chronic pain.

Study design
Prospective observational study.

Setting
Two large hospitals in the French-speaking region of Switzerland.

Methods
We recruited 232 patients from February 2022 to January 2023. Patients with acute or chronic pain in different settings received a paper questionnaire with both a numerical rating scale (NRS) and the FPS and a customized evaluation questionnaire. Correlation between the FPS and NRS, psychometric properties, and patient preferences were analyzed.

Results
Correlation between the FPS and NRS was high for the whole group of 232 patients, as well for all subgroups. The multi-item FPS scale showed excellent internal consistency. A large majority of patients, even those &gt;75 years of age, preferred the FPS over the NRS and stated that the FPS was easy to use.

Conclusions
The study confirms that the French translation of the DVPRS (the FPS) is a valid measurement instrument for acute and chronic pain evaluation in a wide range of patient groups and is easy for patients to use.

Trial registration
ClinicalTrials.gov ID: NCT05307380.
Containing the COVID-19 Pandemic Under an External Threat: A Case Study of Taiwan
Authors: Tsai Chia-hung , Lin Shane Hsuan-yu 
Published: June 2024

Abstract
Given the global reach of the COVID-19 pandemic, external factors play a critical role in containing its spread and prompt questions about how such threats affect a country's response. Taiwan has received recognition for its effective management of the early stages of the pandemic, but faced significant international obstruction, especially from China. This study examines the relationship between Taiwanese citizens' trust in China and their satisfaction with the government’s COVID-19 policies by analyzing data from six rounds of the Taiwan Election and Democratization Study (TEDS) conducted between 2020 and 2022. This research reveals that public opinion about China can significantly influence people’s satisfaction with domestic policies, particularly during crises like pandemics. Thus, factors beyond national borders can influence public satisfaction with public health policies. The findings contribute to existing literature on shaping public opinion under external threats and have broader implications for China's impact on Taiwan’s domestic politics.
Probing New Physics in Light of Recent Developments in b → c ℓ v Transitions
Authors: Yasmeen Tahira , Ahmed Ishtiaq , Shafaq Saba , Arslan Muhammad , Aslam Muhammad Jamil 
Published: June 2024

Abstract
Experimental studies of the observables associated with $b \rightarrow c$ transitions in semileptonic B-meson decays at BaBar, Belle, and LHCb have shown some deviations from the Standard Model predictions, consequently providing a handy tool to probe the possible new physics (NP). In this context, we first revisit the impact of recent measurements of $R({D^{(*)}})$ and $R(\Lambda _c)$ on the parametric space of the NP scenarios. In addition, we include the $R(J/\psi )$ data in the analysis and find that their influence on the best-fit point and the parametric space is mild. Using the recent HFLAV data, after validating the well established sum rule of $R(\Lambda _c)$, we derive a similar sum rule for $R(J/\psi )$. Furthermore, according to the updated data, we modify the correlation among the different observables, giving us their interesting interdependence. Finally, to discriminate the various NP scenarios, we plot the different angular observables and their ratios for $B \rightarrow D^{*} \tau \nu _\tau$ against the transfer momentum square $\left(q^2\right)$, using the $1\sigma$ and $2\sigma$ parametric space of considered NP scenarios. By implementing the collider bounds on NP Wilson coefficients (WCs), we find that the parametric space of some NP WCs is significantly restrained. To see the clear influence of NP on the amplitude of the angular observables, we also calculate their numerical values in different $q^2$ bins and show them through bar plots. We hope that their precise measurements will help to discriminate various NP scenarios.