bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiwavelength monitoring and reverberation mapping of NGC 2617 at deepest minimum with a sharp upward turn during 2021–2024
Authors: Oknyansky V L , Brotherton M S , Tsygankov S S , Dodin A V , Tatarnikov A M , Du P , Burlak M A , Ikonnikova N P , Metlov V G , Belinski A A , Shatsky N I , Wang J -M , Bao D -W , Fang F , Zhai S , Fu Y -X , Bai H -R , Zastrocky T E , Chelouche D , Figaredo C Sobrino , Kaspi S , Gaskell C M 
Published: December 2024

ABSTRACT
We present the results of a new X-ray to near-IR photometric and spectroscopic monitoring of the changing look active galactic nucleus NGC 2617 carried out from March 2022 to March 2024. We found significant variability at all wavelengths and in the intensities and profiles of the broad Balmer lines. Reverberation mapping was carried out for three observing seasons during 2021–2024. We obtained time delays of $\sim$4 d for the response of the H ${\beta }$ line to optical continuum variations. The X-ray variations correlate well with the UV and optical, with a few days lag for longer wavelengths. The K band lagged the B band by $\sim$ 15 d during the last three seasons, which is significantly shorter than the delays reported previously by the 2016 and 2017–2019 campaigns. Near-IR variability arises from two different emission regions: the outer part of the accretion disc and a more distant dust component. The $HK$-band variability is governed primarily by dust. The H ${\beta }$/H ${\alpha }$ ratio variations (for broad components only) correlate with the X-ray and UV fluxes. The spectral type changed from type 1.8 to type 1.9 during 2023 October–2024 January and then a more rapid change to type 1.5 occurred in 2024 February. We interpret these changes as a combination of two factors: changes in the accretion rate as a dominant cause but also the sublimation or recovery of dust along the line of sight.
Near-infrared spectroscopy of the LMC recurrent nova LMCN 1968-12a
Authors: Evans A , Banerjee D P K , Geballe T R , Polin A , Hsiao E Y , Page K L , Woodward C E , Starrfield S 
Published: December 2024

ABSTRACT
We have obtained near-infrared (0.80–2.45 $\, \mu$m) spectra of the recurrent nova LMCN 1968-12a on two occasions during its 2024 August eruption. This is the first near-infrared spectroscopy of an extragalactic nova. The initial spectrum, on day 8.48, caught the nova in the coronal phase, with the [Si x] 1.43 $\, \mu$m line being extremely strong. This line had a luminosity of $\sim 95$ $\rm L_\odot$, and is clearly a very powerful coolant. Its presence, together with the absence of [Si ix] 1.56$\, \mu$m, implies a coronal temperature $\gtrsim 3\times 10^6$ K, possibly amongst the highest recorded coronal temperature in a nova eruption. With the exception of the [Si x] line, the near-infrared spectra are remarkable for being devoid of metal lines. We suggest that this is due, in part, to the exceptionally high temperature of the coronal gas, causing ions, whose emission lines would normally appear in the near-infrared spectrum, to be collisionally ionized to higher stages.
Estimating photometric redshifts for galaxies from the DESI Legacy Imaging Surveys with Bayesian neural networks trained by DESI EDR
Authors: Zhou Xingchen , Li Nan , Zou Hu , Gong Yan , Deng Furen , Chen Xuelei , Yu Qian , He Zizhao , Ding Boyi 
Published: December 2024

ABSTRACT
We present a catalogue of photometric redshifts for galaxies from Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys, which includes $\sim 0.18$ billion sources covering 14 000 $\deg ^2$. The photometric redshifts, along with their uncertainties, are estimated through galaxy images in three optical bands (g, r, and z) from DESI and two near-infrared bands ($W1$ and $W2$) from Wide-field Infrared Survey Explorer (WISE) using a Bayesian neural network (BNN). The training of BNN is performed by above images and their corresponding spectroscopic redshifts given in DESI Early Data Release (EDR). Our results show that categorizing galaxies into individual groups based on their inherent characteristics and estimating their photo-zs within their group separately can effectively improve the performance. Specifically, the galaxies are categorized into four distinct groups based on DESI’s target selection criteria: bright galaxy sample (BGS), luminous red galaxies (LRG), emission-line galaxies (ELG), and a group comprising the remaining sources, referred to as NON. As measured by outliers of $|\Delta z| \gt 0.15 (1 + z_{\rm true})$, accuracy $\sigma _{\rm NMAD}$, and mean uncertainty $\overline{E}$ for BNN, we achieve low outlier percentage, high accuracy, and low uncertainty: 0.14  per cent, 0.018, and 0.0212 for BGS and 0.45  per cent, 0.026, and 0.0293 for LRG respectively, surpassing results without categorization. However, the photo-zs for ELG cannot be reliably estimated, showing result of $\gt 15~\,\mathrm{ per\,cent}$, $\sim 0.1$, and $\sim 0.1$ irrespective of training strategy. On the other hand, NON sources can reach 1.9  per cent, 0.039, and 0.0445 when a magnitude cut of $z\lt 21.3$ is applied. Our findings demonstrate that estimating photo-zs directly from galaxy images is significantly potential, and to achieve high-quality photo-z measurement for ongoing and future large-scale imaging survey, it is sensible to implement categorization of sources based on their characteristics.
TDP1 splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition
Authors: Goh Chen Gang , Bader Aldo S , Tran Tuan-Anh , Belotserkovskaya Rimma , D’Alessandro Giuseppina , Jackson Stephen P 
Published: December 2024

Abstract
HAP1 is a near-haploid human cell line commonly used for mutagenesis and genome editing studies due to its hemizygous nature. We noticed an unusual hypersensitivity of HAP1 to camptothecin, an antineoplastic drug that stabilizes topoisomerase I cleavage complexes (TOP1ccs). We have attributed this hypersensitivity to a deficiency of TDP1, a key phosphodiesterase involved in resolving abortive TOP1ccs. Through whole-exome sequencing and subsequent restoration of TDP1 protein via CRISPR-Cas9 endogenous genome editing, we demonstrate that TDP1 deficiency and camptothecin hypersensitivity in HAP1 cells are a result of a splice-site mutation (TDP1 c.660–1G &gt; A) that causes exon skipping and TDP1 loss of function. The lack of TDP1 in HAP1 cells should be considered when studying topoisomerase-associated DNA lesions and when generalizing mechanisms of DNA damage repair using HAP1 cells. Finally, we also report the generation of HAP1 STAR clones with restored TDP1 expression and function, which may be useful in further studies to probe cellular phenotypes relating to TOP1cc repair.
Long G4-rich enhancers target promoters via a G4 DNA-based mechanism
Authors: DeMeis Jeffrey D , Roberts Justin T , Delcher Haley A , Godang Noel L , Coley Alexander B , Brown Cana L , Shaw Michael H , Naaz Sayema , Dahal Ayush , Alqudah Shahem Y , Nguyen Kevin N , Nguyen Anita D , Paudel Sunita S , Shell John E , Patil Suhas S , Dang Hong , O’Neal Wanda K , Knowles Michael R , Houserova Dominika , Gillespie Mark N , Borchert Glen M 
Published: December 2024

Abstract
Several studies have now described instances where G-rich sequences in promoters and enhancers regulate gene expression through forming G-quadruplex (G4) structures. Relatedly, our group recently identified 301 long genomic stretches significantly enriched for minimal G4 motifs (LG4s) in humans and found the majority of these overlap annotated enhancers, and furthermore, that the promoters regulated by these LG4 enhancers are similarly enriched with G4-capable sequences. While the generally accepted model for enhancer:promoter specificity maintains that interactions are dictated by enhancer- and promoter-bound transcriptional activator proteins, the current study tested an alternative hypothesis: that LG4 enhancers interact with cognate promoters via a direct G4:G4 DNA-based mechanism. This work establishes the nuclear proximity of LG4 enhancer:promoter pairs, biochemically demonstrates the ability of individual LG4 single-stranded DNAs (ssDNAs) to directly interact target promoter ssDNAs, and confirms that these interactions, as well as the ability of LG4 enhancers to activate target promoters in culture, are mediated by G4 DNA.
Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics
Authors: Sundar Rajan Vinoth , Levin Sune , McCauley Micah J , Williams Mark C , Rouzina Ioulia , Wilhelmsson L Marcus , Westerlund Fredrik 
Published: December 2024

Abstract
It is widely appreciated that double stranded DNA (dsDNA) is subjected to strong and dynamic mechanical forces in cells. Under increasing tension B-DNA, the most stable double-stranded (ds) form of DNA, undergoes cooperative elongation into a mixture of S-DNA and single stranded DNA (ssDNA). Despite significant effort, the structure, energetics, kinetics and the biological role of S-DNA remains obscure. We here stretch 60 base pair (bp) dsDNA oligonucleotides with a variable number of tricyclic cytosine, tC, modifications using optical tweezers. We observe multiple fast cooperative and reversible two-state transitions between B-DNA and S-DNA. Notably, tC modifications increase the transition force, while reducing the transition extension and free energy due to progressively increasing fraying of the dsDNA ends. We quantify the average number of bps undergoing the B-to-S transition, as well as the free energies and rates. This allows us to reconstruct the B-to-S free energy profiles in absence of force. We conclude that S-DNA is an entirely force-induced state, and that the B-to-S transition is much faster than internal dsDNA melting. We hypothesize that S-DNA may have a role as a transient intermediate in, for example, molecular motor-induced local dsDNA strand separation.
GIN-TONIC: non-hierarchical full-text indexing for graph genomes
Authors: Öztürk Ünsal , Mattavelli Marco , Ribeca Paolo 
Published: December 2024

Abstract
This paper presents a new data structure, GIN-TONIC (Graph INdexing Through Optimal Near Interval Compaction), designed to index arbitrary string-labelled directed graphs representing, for instance, pangenomes or transcriptomes. GIN-TONIC provides several capabilities not offered by other graph-indexing methods based on the FM-Index. It is non-hierarchical, handling a graph as a monolithic object; it indexes at nucleotide resolution all possible walks in the graph without the need to explicitly store them; it supports exact substring queries in polynomial time and space for all possible walk roots in the graph, even if there are exponentially many walks corresponding to such roots. Specific ad-hoc optimizations, such as precomputed caches, allow GIN-TONIC to achieve excellent performance for input graphs of various topologies and sizes. Robust scalability capabilities and a querying performance close to that of a linear FM-Index are demonstrated for two real-world applications on the scale of human pangenomes and transcriptomes. Source code and associated benchmarks are available on GitHub.
Water-mediated ribonucleotide–amino acid pairs and higher-order structures at the RNA–protein interface: analysis of the crystal structure database and a topological classification
Authors: Jangra Raman , Trant John F , Sharma Purshotam 
Published: December 2024

Abstract
Water is essential for the formation, stability and function of RNA–protein complexes. To delineate the structural role of water molecules in shaping the interactions between RNA and proteins, we comprehensively analyzed a dataset of 329 crystal structures of these complexes to identify water-mediated hydrogen-bonded contacts at RNA–protein interface. Our survey identified a total of 4963 water bridges. We then employed a graph theory-based approach to present a robust classification scheme, encompassing triplets, quartets and quintet bridging topologies, each further delineated into sub-topologies. The frequency of water bridges within each topology decreases with the increasing degree of water node, with simple triplet water bridges outnumbering the higher-order topologies. Overall, this analysis demonstrates the variety of water-mediated interactions and highlights the importance of water as not only the medium but also the organizing principle underlying biomolecular interactions. Further, our study emphasizes the functional significance of water-mediated interactions in RNA–protein complexes, and paving the way for exploring how these interactions operate in complex biological environments. Altogether, this understanding not only enhances insights into biomolecular dynamics but also informs the rational design of RNA–protein complexes, providing a framework for potential applications in biotechnology and therapeutics. All the scripts, and data are available at https://github.com/PSCPU/waterbridges.
Human introns contain conserved tissue-specific cryptic poison exons
Authors: Margasyuk Sergey , Kuznetsova Antonina , Zavileyskiy Lev , Vlasenok Maria , Skvortsov Dmitry , Pervouchine Dmitri D 
Published: December 2024

Abstract
Eukaryotic cells express a large number of transcripts from a single gene due to alternative splicing. Despite hundreds of thousands of splice isoforms being annotated in databases, it has been reported that the current exon catalogs remain incomplete. At the same time, introns of human protein-coding (PC) genes contain a large number of evolutionarily conserved elements with unknown function. Here, we explore the possibility that some of them represent cryptic exons that are expressed in rare conditions. We identified a group of cryptic exons that are similar to the annotated exons in terms of evolutionary conservation and RNA-seq read coverage in the Genotype-Tissue Expression dataset. Most of them were poison, i.e. generated an nonsense-mediated decay (NMD) isoform upon inclusion, and many showed signs of tissue-specific and cancer-specific expression and regulation. We performed RNA-seq in A549 cell line treated with cycloheximide to inactivate NMD and confirmed using quantitative polymerase chain reaction that seven of eight exons tested are, indeed, expressed. This study shows that introns of human PC genes contain cryptic poison exons, which reside in conserved intronic regions and remain not fully annotated due to insufficient representation in RNA-seq libraries.
A phase Ib study evaluating the c-MET inhibitor INC280 (capmatinib) in combination with bevacizumab in patients with high-grade glioma
Authors: Falchook Gerald S , Battiste James D , Kalra Amandeep , Shastry Mythili , Finney Lindsey , Hoekstra Susan J , Shih Meredith G , Shih Kent C 
Published: December 2024

Abstract

Background
To improve survival in patients with high-grade glioma, INC280 (capmatinib) a highly selective and potent oral inhibitor of the MET receptor with robust central nervous system (CNS) penetration, was evaluated in combination with bevacizumab (BEV).

Methods
There were 2 phases, dose-escalation (3+3 design) and dose-expansion, which included patients (1) who progressed during or after first-line therapy (no prior BEV), (2) who progressed during or after second-line therapy with BEV, and (3) who had unresectable high-grade glioma (no prior BEV).

Results
Sixty-four patients with high-grade glioma were treated; 18 in escalation cohorts and 46 in expansion Cohorts A (21), B (15), and C (10). The maximum-tolerated dose (MTD) was not reached and the RP2D was 400 mg capmatinib PO BID (800 mg daily). Treatment continued for a median of 14 weeks and up to ~6 years in one patient. Common treatment-related adverse events (65% ≤ Grade 2) included fatigue, peripheral edema, nausea, diarrhea, ALT increased, and constipation. Headaches and seizures occurred in 11 patients; Grade 3+ events included Grade 3 headache (1) and Grade 3 seizures (4). There were no treatment-related deaths. The 12 responders to treatment (2 CRs [1 pt in escalation and 1 pt in Cohort A] and 10 PRs [2 pts in escalation and A = 6, B = 1, and C = 1]) had a median duration of response of 9.2 months. Two patients with durable responses (CR &gt;5 years, PR &gt;1 year) did not harbor baseline c-MET alterations.

Conclusion
Capmatinib + BEV was well-tolerated but had no clear signal of activity in c-MET non-activated high-grade glioma.
Can We Predict Who Will Experience Adverse Events While Using Smoking Cessation Pharmacotherapy? A Secondary Analysis of the EAGLES Clinical Trial
Authors: Wolf Bethany J , Gray Kevin M , Dahne Jennifer R , Hashemi Daniel , Tomko Rachel L 
Published: December 2024

Abstract

Introduction
Concerns about potential side effects remain a barrier to uptake of Food and Drug Administration-approved smoking cessation pharmacotherapy (ie, varenicline, bupropion, nicotine replacement therapy [NRT]). However, use of pharmacotherapy can double the odds of successful quitting. Knowledge of an individual’s likelihood of side effects while taking smoking cessation pharmacotherapy could influence treatment planning discussions and monitoring.

Methods
We conducted a secondary, post hoc analysis to predict an individual’s likelihood of adverse events (AEs) using the Evaluating Adverse Events in a Global Smoking Cessation Study data from 4209 adults in the United States who smoked. Participants were randomized to receive 12 weeks of treatment with varenicline, bupropion, NRT patch, or placebo. Our models predicted the likelihood of moderate to severe psychiatric and nonpsychiatric AEs during treatment.

Results
Using pretreatment demographic and clinical data, multivariable logistic regression models yielded acceptable areas under the receiver operating characteristic curve for an individual’s likelihood of moderate to severe (1) psychiatric AEs for bupropion and NRT and (2) nonpsychiatric AEs for varenicline and bupropion. Once we adjusted for demographic and baseline characteristics, medication was not associated with psychiatric AEs. Varenicline differed from placebo with regards to nonpsychiatric AEs.

Conclusions
It is possible to predict person-specific likelihood of moderate to severe psychiatric and nonpsychiatric AEs during smoking cessation treatment, though the probability of psychiatric AEs did not differ by medication. Future work should consider factors related to implementation in clinical settings, including determining whether lower burden assessment protocols can be equally accurate for AE prediction.

Implications
Using data from a large dataset people who smoke in the United States, it is possible to predict an individual’s likelihood of psychiatric and nonpsychiatric AEs during smoking cessation treatment prior to initiating treatment. These predictive models provide a starting point for future work addressing how best to modify and integrate such clinical decision support algorithms into treatment for smoking cessation.
Improving recruitment to occupational health professions through highlighting intrinsic rewards
Authors: Semkina A , Norrie C , Elaswarapu R , Kessler I , Moriarty J , Boaz A , Manthorpe J , Knight A 
Published: December 2024

Abstract

Background
There are currently 2.5 million people economically inactive in the UK due to sickness. The government is considering a range of new initiatives to bring them back into the workforce; however, a lack of occupational health (OH) professionals, who play an important part in the recovery of physical and mental conditions that would otherwise inhibit employees from working, is hindering these efforts.

Aims
To identify factors that make OH attractive as a source of employment with the aim of assisting those undertaking recruitment to the specialism.

Methods
We conducted a qualitative study comparing the views of 13 OH nurses and doctors (‘insiders’) and 45 students and professionals from other medical and nursing fields (‘outsiders’) across the UK. Both groups provided their perceptions about what makes OH an attractive career. Data collection involved a mix of interviews and focus groups conducted from March to July 2023. Transcripts were thematically analysed using NVivo 14 to manage the data.

Results
Both groups highly valued the work-life balance offered by OH work, which represents a positive point of attraction to employment. In addition, people working in OH talked extensively about more intrinsic rewards—the opportunity to be impactful, to enjoy job variety and to practise preventative approaches.

Conclusions
The intrinsic rewards that OH work brings need to be advertised more widely to attract potential recruits who are ‘a good fit’ to OH and will be committed to the field.
Dengue pancreatitis with ketoacidosis—a rare manifestation in Endemicity
Authors: Das Kalyan Kumar , Basu Rajdeep 
Published: December 2024

Abstract
Dengue may begin as a straightforward fever episode with or without rash also it may affect some organs and cause serious symptoms. Although it is uncommon, severe abdominal discomfort has been a concerning indicator of acute pancreatitis. We report on a male patient, age 26, who first presented with fever, vomiting, and stomach pain. Later, he developed severe pancreatitis. When an acute viral infection causes pancreatitis, ketoacidosis can occur without hyperglycemia. We emphasize that in dengue patients reporting stomach pain, it is important to rule out acute pancreatitis (AP), an uncommon but serious impediment in the course of treatment.
Linezolid induced acute toxic leukoencephalopathy and severe thrombocytopenia presenting as stroke mimic—a case report
Authors: Ahmed S , Hayman G , Moin S , Ubaide H , Sivakumar R , Padayatty J 
Published: December 2024

Abstract
A 67-year-old lady was admitted with, right sided weakness and right arm shaking. She had recently completed a course of Linezolid for a diabetic foot infection and osteomyelitis. Prior to this she had prodromal symptoms including lethargy and loss of appetite. Clinical features prompting presentation included global weakness, verbal dysfluency and visual disturbance. MRI brain showed bilateral alteration of signal in the deep white matter of the posterior frontal and parietal lobes, sparing the superficial cortical areas. These areas showed diffusion restriction, suggestive of, but not limited to, ischaemic stroke. During admission she had a decline in consciousness and was hypertensive. An acute drop in haemoglobin and platelets occurred prompting consideration of Thrombotic Microangiopathy and other drug related/malignant/infective aetiologies. A diagnosis of Linezolid induced Acute Toxic Leukoencephalopathy and thrombocytopenia was made based on clinico-radiographic features and exclusion of other causes.