bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dark Energy Survey Year 3 results: redshift calibration of the MagLim lens sample from the combination of SOMPZ and clustering and its impact on cosmology
Authors: Giannini G , Alarcon A , Gatti M , Porredon A , Crocce M , Bernstein G M , Cawthon R , Sánchez C , Doux C , Elvin-Poole J , Raveri M , Myles J , Lin H , Amon A , Allam S , Alves O , Andrade-Oliveira F , Baxter E , Bechtol K , Becker M R , Blazek J , Camacho H , Campos A , Rosell A Carnero , Kind M Carrasco , Choi A , Cordero J , De Vicente J , DeRose J , Diehl H T , Dodelson S , Drlica-Wagner A , Eckert K , Fang X , Farahi A , Fosalba P , Friedrich O , Gruen D , Gruendl R A , Gschwend J , Harrison I , Hartley W G , Huff E M , Jarvis M , Krause E , Kuropatkin N , Lemos P , MacCrann N , McCullough J , Muir J , Pandey S , Prat J , Rodriguez-Monroy M , Ross A J , Rykoff E S , Samuroff S , Secco L F , Sevilla-Noarbe I , Sheldon E , Troxel M A , Tucker D L , Weaverdyck N , Yanny B , Yin B , Zhang Y , Abbott T M C , Aguena M , Bacon D , Bertin E , Bocquet S , Brooks D , Burke D L , Carretero J , Castander F J , Costanzi M , da Costa L N , Pereira M E S , Desai S , Doel P , Ferrero I , Flaugher B , Friedel D , Frieman J , García-Bellido J , Gerdes D W , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Kent S , Kuehn K , Lahav O , Lidman C , Lima M , Melchior P , Mena-Fernández J , Menanteau F , Miquel R , Ogando R L C , Paterno M , Paz-Chinchón F , Pieres A , Malagón A A Plazas , Roodman A , Sanchez E , Scarpine V , Smith M , Suchyta E , Swanson M E C , Tarle G , Thomas D , To C , Vincenzi M ,   (DES Collaboration)
Published: October 2023

ABSTRACT
We present an alternative calibration of the MagLim lens sample redshift distributions from the Dark Energy Survey (DES) first 3 yr of data (Y3). The new calibration is based on a combination of a self-organizing-map-based scheme and clustering redshifts to estimate redshift distributions and inherent uncertainties, which is expected to be more accurate than the original DES Y3 redshift calibration of the lens sample. We describe in detail the methodology, and validate it on simulations and discuss the main effects dominating our error budget. The new calibration is in fair agreement with the fiducial DES Y3 n(z) calibration, with only mild differences (&lt;3σ) in the means and widths of the distributions. We study the impact of this new calibration on cosmological constraints, analysing DES Y3 galaxy clustering and galaxy–galaxy lensing measurements, assuming a Lambda cold dark matter cosmology. We obtain Ωm = 0.30 ± 0.04, σ8 = 0.81 ± 0.07, and S8 = 0.81 ± 0.04, which implies a ∼0.4σ shift in the Ω − S8 plane compared to the fiducial DES Y3 results, highlighting the importance of the redshift calibration of the lens sample in multiprobe cosmological analyses.
Response of gravitationally coupled gaseous and stellar components to asymmetric warp in disc galaxies
Authors: Goyary Sagar S , Singh H Shanjit 
Published: October 2023

ABSTRACT
The outer disc region of most spiral galaxies (approximately 50 per cent of all disc galaxies) shows warping above the galactic mid-plane and is primarily asymmetric by nature. In this work, we explore analytically the effect of the gas component on asymmetric warps in a realistic self-gravitating collision-less disc residing in a cold oblate dark matter halo’s potential field. We consider the disc to be composed of gravitationally coupled stars and gas components. The quadratic eigenvalue equation describing the shape and frequency of the bending mode is formulated and solved numerically. Two stable ground-state bending modes m = 0 and m = 1, representing the U-shape and the mostly observed S-shaped warp in the galactic disc are superimposed linearly to generate and examine the asymmetric warps in the disc. The resulting asymmetry in warp is measured by asymmetric index (Aasym) by varying physical parameters such as the mass of the gas components and the halo flattening parameter. It is shown that the gas fraction in the disc has a negligible contribution to the generation of asymmetric warp in the disc. The disc residing in a spherical dark matter halo is found to be more asymmetry than that in the counterpart oblate halo.
GMRT observations of the radio trail from CXOU J163802.6−471358
Authors: Green D A , Roy S 
Published: October 2023

ABSTRACT
The X-ray source CXOU J163802.6−471358 is thought to be a pulsar wind nebula (PWN), as it shows an extended, ≈40 arcsec trail from a compact source. Here, we present Giant Metrewave Radio Telescope observations of this source at 330 and 1390 MHz, which reveal a remarkable linear radio trail ≈90 arcsec in extent. Although the radio trail points back to the supernova remnant (SNR) G338.1+0.4, ≈50 arcmin from CXOU J163802.6−471358, associating it with this remnant would require a very large velocity for the pulsar. There are no known Galactic SNRs close to the PWN and radio trail. No pulsar has yet been identified in CXOU J163802.6−471358, but if one could be found, this would allow more quantitative studies of the PWN and radio trail to be made.
An information theory approach to identifying signs of life on transiting planets
Authors: Vannah Sara , Gleiser Marcelo , Kaltenegger Lisa 
Published: October 2023

ABSTRACT
Can information theory provide insights into whether exoplanets are habitable? Here, we apply information theory to a range of simulated exoplanet transmission spectra as a diagnostic tool to search for potential signatures of life on Earth-analogue planets. We test the algorithms on three epochs of evolution for Earth-like planets orbiting a range of host stars. The JWST and upcoming ground- and space-based missions promise to achieve sufficient high-resolution data that information theory can be applied to assess habitability. This approach provides a framework and a tool for observers to assess whether an exoplanet shows signs of habitability.
Hypoxia stabilizes SETDB1 to maintain genome stability
Authors: Park Sungryul , Cho Jin Hwa , Kim Jong-Hwan , Park Mijin , Park Seulki , Kim Seon-Young , Kim Seon-Kyu , Kim Kidae , Park Sung Goo , Park Byoung Chul , Moon Jeong Hee , Lee Gaseul , Kim Sunhong , Kim Jung-Ae , Kim Jeong-Hoon 
Published: October 2023

Abstract
Von Hippel–Lindau (VHL) is a tumor suppressor that functions as the substrate recognition subunit of the CRL2VHL E3 complex. While substrates of VHL have been identified, its tumor suppressive role remains to be fully understood. For further determination of VHL substrates, we analyzed the physical interactome of VHL and identified the histone H3K9 methyltransferase SETBD1 as a novel target. SETDB1 undergoes oxygen-dependent hydroxylation by prolyl hydroxylase domain proteins and the CRL2VHL complex recognizes hydroxylated SETDB1 for ubiquitin-mediated degradation. Under hypoxic conditions, SETDB1 accumulates by escaping CRL2VHL activity. Loss of SETDB1 in hypoxia compared with that in normoxia escalates the production of transposable element-derived double-stranded RNAs, thereby hyperactivating the immune-inflammatory response. In addition, strong derepression of TEs in hypoxic cells lacking SETDB1 triggers DNA damage-induced death. Our collective results support a molecular mechanism of oxygen-dependent SETDB1 degradation by the CRL2VHL E3 complex and reveal a role of SETDB1 in genome stability under hypoxia.
Unprecedented reactivity of polyamines with aldehydic DNA modifications: structural determinants of reactivity, characterization and enzymatic stability of adducts
Authors: Gusti Ngurah Putu Eka Putra , Cattiaux Laurent , Lavergne Thomas , Pommier Yves , Bombard Sophie , Granzhan Anton 
Published: October 2023

Abstract
Apurinic/apyrimidinic (AP) sites, 5-formyluracil (fU) and 5-formylcytosine (fC) are abundant DNA modifications that share aldehyde-type reactivity. Here, we demonstrate that polyamines featuring at least one secondary 1,2-diamine fragment in combination with aromatic units form covalent DNA adducts upon reaction with AP sites (with concomitant cleavage of the AP strand), fU and, to a lesser extent, fC residues. Using small-molecule mimics of AP site and fU, we show that reaction of secondary 1,2-diamines with AP sites leads to the formation of unprecedented 3′-tetrahydrofuro[2,3,4-ef]-1,4-diazepane (‘ribodiazepane’) scaffold, whereas the reaction with fU produces cationic 2,3-dihydro-1,4-diazepinium adducts via uracil ring opening. The reactivity of polyamines towards AP sites versus fU and fC can be tuned by modulating their chemical structure and pH of the reaction medium, enabling up to 20-fold chemoselectivity for AP sites with respect to fU and fC. This reaction is efficient in near-physiological conditions at low-micromolar concentration of polyamines and tolerant to the presence of a large excess of unmodified DNA. Remarkably, 3′-ribodiazepane adducts are chemically stable and resistant to the action of apurinic/apyrimidinic endonuclease 1 (APE1) and tyrosyl-DNA phosphoesterase 1 (TDP1), two DNA repair enzymes known to cleanse a variety of 3′ end-blocking DNA lesions.
Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae
Authors: Schrott Simon , Osman Christof 
Published: October 2023

Abstract
The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals are critical for mtDNA maintenance and packaging and have been linked to mtDNA copy number control. Here, we discover the previously unrecognized mitochondrial HMG-box protein Cim1 (copy number influence on mtDNA) in Saccharomyces cerevisiae, which exhibits metabolic state dependent mtDNA association. Surprisingly, in contrast to Abf2’s supportive role in mtDNA maintenance, Cim1 negatively regulates mtDNA copy number. Cells lacking Cim1 display increased mtDNA levels and enhanced mitochondrial function, while Cim1 overexpression results in mtDNA loss. Intriguingly, Cim1 deletion alleviates mtDNA maintenance defects associated with loss of Abf2, while defects caused by Cim1 overexpression are mitigated by simultaneous overexpression of Abf2. Moreover, we find that the conserved LON protease Pim1 is essential to maintain low Cim1 levels, thereby preventing its accumulation and concomitant repressive effects on mtDNA. We propose a model in which the protein ratio of antagonistically acting Cim1 and Abf2 determines mtDNA copy number.
TheMarker: a comprehensive database of therapeutic biomarkers
Authors: Zhang Yintao , Zhou Ying , Zhou Yuan , Yu Xinyuan , Shen Xinyi , Hong Yanfeng , Zhang Yuxin , Wang Shanshan , Mou Minjie , Zhang Jinsong , Tao Lin , Gao Jianqing , Qiu Yunqing , Chen Yuzong , Zhu Feng 
Published: October 2023

Abstract
Distinct from the traditional diagnostic/prognostic biomarker (adopted as the indicator of disease state/process), the therapeutic biomarker (ThMAR) has emerged to be very crucial in the clinical development and clinical practice of all therapies. There are five types of ThMAR that have been found to play indispensable roles in various stages of drug discovery, such as: Pharmacodynamic Biomarker essential for guaranteeing the pharmacological effects of a therapy, Safety Biomarker critical for assessing the extent or likelihood of therapy-induced toxicity, Monitoring Biomarker indispensable for guiding clinical management by serially measuring patients’ status, Predictive Biomarker crucial for maximizing the clinical outcome of a therapy for specific individuals, and Surrogate Endpoint fundamental for accelerating the approval of a therapy. However, these data of ThMARs has not been comprehensively described by any of the existing databases. Herein, a database, named ‘TheMarker’, was therefore constructed to (a) systematically offer all five types of ThMAR used at different stages of drug development, (b) comprehensively describe ThMAR information for the largest number of drugs among available databases, (c) extensively cover the widest disease classes by not just focusing on anticancer therapies. These data in TheMarker are expected to have great implication and significant impact on drug discovery and clinical practice, and it is freely accessible without any login requirement at: https://idrblab.org/themarker.
scTEA-db: a comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes
Authors: Barquin Miguel , Kouzel Ian U , Ehrmann Beat , Basler Michael , Gruber Andreas J 
Published: October 2023

Abstract
The usage of alternative terminal exons results in messenger RNA (mRNA) isoforms that differ in their 3′ untranslated regions (3′ UTRs) and often also in their protein-coding sequences. Alternative 3′ UTRs contain different sets of cis-regulatory elements known to regulate mRNA stability, translation and localization, all of which are vital to cell identity and function. In previous work, we revealed that ∼25 percent of the experimentally observed RNA 3′ ends are located within regions currently annotated as intronic, indicating that many 3′ end isoforms remain to be uncovered. Also, the inclusion of not yet annotated terminal exons is more tissue specific compared to the already annotated ones. Here, we present the single cell-based Terminal Exon Annotation database (scTEA-db, www.scTEA-db.org) that provides the community with 12 063 so far not yet annotated terminal exons and associated transcript isoforms identified by analysing 53 069 publicly available single cell transcriptomes. Our scTEA-db web portal offers an array of features to find and explore novel terminal exons belonging to 5538 human genes, 110 of which are known cancer drivers. In summary, scTEA-db provides the foundation for studying the biological role of large numbers of so far not annotated terminal exon isoforms in cell identity and function.
The effect of B-vitamins on the prevention and treatment of cardiovascular diseases: a systematic review and meta-analysis
Authors: Miao Ya , Guo Yihan , Chen Yixin , Lin Yijia , Lu Yan , Guo Qihao 
Published: October 2023

Abstract

Context
Previous research evaluating the effects in B-vitamins on the prevention and treatment of cardiovascular disease (CVD) has substantial limitations and lacks recently published large prospective studies; hence, conducting an updated meta-analysis is needed.

Objective
We investigated the association between vitamin B status and human CVD development in order to provide more specific advice about vitamin B intake for those at risk of CVD.

Data Sources
Relevant articles were identified by JSTOR, PubMed, and ProQuest databases.

Data Extraction
Key words used to identify the studies included the different combinations of B-vitamins, folate, folic acid, vitamin B6, vitamin B12, homocysteine, cardiovascular disease, stroke, coronary disease, myocardial infarction, and cerebrovascular and transient ischemic attack. The database search was supplemented by hand-searching of reference lists of selected articles.

Data Analysis
Pooled estimates were calculated from the mean differences using a random-effects model.

Results
Supplementation with folic acid was reported to have a clinical benefit of significantly reducing carotid intima-media thickness. Higher intakes of folic acid, vitamin B6, and vitamin B12 were generally associated with a lower risk of CVD in the general population, except in those without normal renal function and those with unstable angina or past non–ST-elevation myocardial infarction.

Conclusion
Vitamin B supplementation resulted in the greatest cardiovascular benefit in those with normal renal function and without unstable angina or non–ST-elevation myocardial infarction recently. Factors such as age, gender, and genetic polymorphisms contribute to varying effects.
Sex differences in patch-leaving foraging decisions in rats
Authors: Garcia Marissa , Gupta Sukriti , Wikenheiser Andrew M 
Published: October 2023

Abstract
The ubiquity, importance, and sophistication of foraging behavior makes it an ideal platform for studying naturalistic decision making in animals. We developed a spatial patch-foraging task for rats, in which subjects chose how long to remain in one foraging patch as the rate of food earnings steadily decreased. The cost of seeking out a new location was varied across sessions. The behavioral task was designed to mimic the structure of natural foraging problems, where distinct spatial locations are associated with different reward statistics, and decisions require navigation and movement through space. Male and female Long-Evans rats generally followed the predictions of theoretical models of foraging, albeit with a consistent tendency to persist with patches for too long compared to behavioral strategies that maximize food intake rate. The tendency to choose overly-long patch residence times was stronger in male rats. We also observed sex differences in locomotion as rats performed the task, but these differences in movement only partially accounted for the differences in patch residence durations observed between male and female rats. Together, these results suggest a nuanced relationship between movement, sex, and foraging decisions.
The role of high serum bilirubin as a predictor of complicated appendicitis: a retrospective cohort study
Authors: Bhandari Suyog , Baral Akriti , Tiwari Ashish , Shrestha Suman K. 
Published: October 2023

Introduction:
An appendectomy is one of the most common emergency surgeries. The delay in diagnosis and treatment of appendicitis can lead to complicated appendicitis. The definitive predictive factor that can diagnose complicated appendicitis is still lacking. The authors aim to assess the role of high serum bilirubin level as a predictor of complicated appendicitis.

Methods:
A retrospective cohort study was conducted among patients with acute appendicitis (AA) between March 2017 and March 2018. Appendicitis cases diagnosed with the help of the Alvarado score undergoing surgery were taken in study and based on the histopathological report, the cases were classified into two groups: uncomplicated and complicated. Preoperatively, biochemical parameters like increased white blood cell count (>11000/cubic millimeter), and level of serum bilirubin >1.4 mg/dl were studied. Informed written consent for the study was taken from the patients with AA. A χ
2 test was applied for the association between categorical variables. Statistical analysis was done with a statistical package for the social sciences (SPSS) version 20; P-value less than 0.05 was considered statistically significant.

Results:
A total of 100 patients were enrolled in the study with a mean age of 31.2±18.3 years, and 60% were male. Seventy-four (74%) had uncomplicated appendicitis and 26 (26%) had complicated appendicitis. Mean bilirubin was 1.2±0.8 mg/dl in uncomplicated and 1.8±0.8 mg/dl in complicated groups (P <0.05). The sensitivity and specificity of hyperbilirubinemia as a predictor of complicated appendicitis were 50 and 78.38%, respectively.

Conclusion:
The study revealed that patients with AA and a higher serum bilirubin level have a higher risk of having complicated appendicitis. Serum bilirubin level helps to predict complicated appendicitis and thus plan for timely and appropriate management. Thus, the study concludes that bilirubin should be used together with clinical examination and other laboratory investigations in the assessment of patients with suspected AA.
Anatomic Analysis of Masseteric-to-zygomatic Nerve Transfer in Rat and Pig Models
Authors: Millesi Elena , Suchyta Marissa , Wang Huan , Mardini Samir 
Published: October 2023

Background:
Nerve transfer from the masseteric branch of the trigeminal nerve is a widely performed procedure for facial reanimation. Despite achieving powerful muscle force, clinical and aesthetic results leave room for improvement. Preclinical animal models are invaluable to establishing new therapeutic approaches. This anatomical study aimed to establish a masseteric-to-zygomatic nerve transfer model in rats and pigs.

Methods:
The masseteric branch of the trigeminal nerve and the zygomatic branch of the facial nerve were dissected in 30 swine and 40 rat hemifaces. Both nerves were mobilized and approximated to achieve an overlap between the nerve ends. Over the course of dissecting both nerves, their anatomy, length, and branching pattern were documented. At the coaptation point, diameters of both nerves were measured, and samples were taken for neuromorphometric analysis.

Results:
Anatomic details and landmarks were described. Tension-free coaptation was possible in all rat and pig dissections. In rats, the masseteric branch had an average diameter of 0.36 mm (±0.06), and the zygomatic branch average diameter was 0.46 mm (±0.13). In pigs, the masseteric branch measured 0.52 (±0.16) mm and the zygomatic branch, 0.59 (±0.16) mm. No significant differences were found between the diameters and axon counts of both nerves in pigs. In rats, however, their diameters, axon counts, and fascicular areas were significantly different.

Conclusion:
Our study demonstrated the feasibility of direct masseteric-to-zygomatic nerve transfer in rats and pigs and provided general anatomic knowledge of both nerves.