bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate analytic mass–scale relations for dark matter haloes of all masses and redshifts
Authors: Salvador-Solé Eduard , Manrique Alberto , Canales David , Botella Ignacio 
Published: March 2023

ABSTRACTCUSP is a powerful formalism that recovers, from first principles and with no free parameter, all the macroscopic properties of dark matter haloes found in cosmological N-body simulations and unveils the origin of their characteristic features. Since it is not restricted by the limitations of simulations, it covers the whole mass and redshift ranges. In the present Paper we use CUSP to calculate the mass–scale relations holding for halo density profiles fitted to the usual NFW and Einasto functions in the most relevant cosmologies and for the most usual mass definitions. We clarify the origin of these relations and provide accurate analytic expressions holding for all masses and redshifts. The performance of those expressions is compared to that of previous models and to the mass–concentration relation spanning more than 20 orders of magnitude in mass at z = 0 obtained in recent simulations of a 100 GeV WIMP universe.
Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor
Authors: Hasanova Zdenka , Klapstova Veronika , Porrua Odil , Stefl Richard , Sebesta Marek 
Published: March 2023

AbstractProlonged pausing of the transcription machinery may lead to the formation of three-stranded nucleic acid structures, called R-loops, typically resulting from the annealing of the nascent RNA with the template DNA. Unscheduled persistence of R-loops and RNA polymerases may interfere with transcription itself and other essential processes such as DNA replication and repair. Senataxin (SETX) is a putative helicase, mutated in two neurodegenerative disorders, which has been implicated in the control of R-loop accumulation and in transcription termination. However, understanding the precise role of SETX in these processes has been precluded by the absence of a direct characterisation of SETX biochemical activities. Here, we purify and characterise the helicase domain of SETX in parallel with its yeast orthologue, Sen1. Importantly, we show that SETX is a bona fide helicase with the ability to resolve R-loops. Furthermore, SETX has retained the transcription termination activity of Sen1 but functions in a species-specific manner. Finally, subsequent characterisation of two SETX variants harbouring disease-associated mutations shed light into the effect of such mutations on SETX folding and biochemical properties. Altogether, these results broaden our understanding of SETX function in gene expression and the maintenance of genome integrity and provide clues to elucidate the molecular basis of SETX-associated neurodegenerative diseases.
HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription
Authors: Tian Rui , Huang Zheying , Li Lifang , Yuan Jingping , Zhang Qinghua , Meng Lirong , Lang Bin , Hong Yongfeng , Zhong Chaoyue , Tian Xun , Cui Zifeng , Jin Zhuang , Liu Jiashuo , Huang Zhaoyue , Wang Yuyan , Chen Ye , Hu Zheng 
Published: March 2023

Abstract
Human papillomavirus (HPV) integration is a critical step in cervical cancer development; however, the oncogenic mechanism at the genome-wide transcriptional level is still poorly understood. In this study, we employed integrative analysis on multi-omics data of six HPV-positive and three HPV-negative cell lines. Through HPV integration detection, super-enhancer (SE) identification, SE-associated gene expression and extrachromosomal DNA (ecDNA) investigation, we aimed to explore the genome-wide transcriptional influence of HPV integration. We identified seven high-ranking cellular SEs generated by HPV integration in total (the HPV breakpoint-induced cellular SEs, BP-cSEs), leading to intra-chromosomal and inter-chromosomal regulation of chromosomal genes. The pathway analysis revealed that the dysregulated chromosomal genes were correlated to cancer-related pathways. Importantly, we demonstrated that BP-cSEs existed in the HPV–human hybrid ecDNAs, explaining the above transcriptional alterations. Our results suggest that HPV integration generates cellular SEs that function as ecDNA to regulate unconstrained transcription, expanding the tumorigenic mechanism of HPV integration and providing insights for developing new diagnostic and therapeutic strategies.
Structural polymorphism driven by a register shift in a CGAG-rich region found in the promoter of the neurodevelopmental regulatorAUTS2gene
Authors: Novotný Aleš , Plavec Janez , Kocman Vojč 
Published: March 2023

AbstractThe AUTS2 gene has been shown to influence brain development by controlling the number of neurons, promoting the growth of axons and dendrites and regulating neuronal migration. The expression of two isoforms of AUTS2 protein is precisely regulated and misregulation of their expression has been correlated with neurodevelopmental delay and autism spectrum disorder. A CGAG-rich region, which includes a putative protein binding site (PPBS), d(AGCGAAAGCACGAA), was found in the promoter region of AUTS2 gene. We show that oligonucleotides from this region adopt thermally stable non-canonical hairpin structures stabilized by G:C and sheared G:A base pairs arranged in a repeating structural motif we termed CGAG block. These motifs are formed consecutively, in a way that exploits a shift in register throughout the whole CGAG repeat to maximize the number of consecutive G:C and G:A base pairs. The differences in CGAG repeat shifting affect the structure of the loop region, where PPBS residues are predominantly located, specifically the loop length, types of base pairs and the pattern of base-base stacking. Finally, we propose a previously unexplored mechanism, by which different folds in the CGAG-rich region could cause a switch in expression between the full-length and C-terminal isoforms of AUTS2.
RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling
Authors: Li Jun , Chen Shi-Jie 
Published: March 2023

Abstract
RNA 3D structures are critical for understanding their functions. However, only a limited number of RNA structures have been experimentally solved, so computational prediction methods are highly desirable. Nevertheless, accurate prediction of RNA 3D structures, especially those containing multiway junctions, remains a significant challenge, mainly due to the complicated non-canonical base pairing and stacking interactions in the junction loops and the possible long-range interactions between loop structures. Here we present RNAJP (‘RNA Junction Prediction’), a nucleotide- and helix-level coarse-grained model for the prediction of RNA 3D structures, particularly junction structures, from a given 2D structure. Through global sampling of the 3D arrangements of the helices in junctions using molecular dynamics simulations and in explicit consideration of non-canonical base pairing and base stacking interactions as well as long-range loop–loop interactions, the model can provide significantly improved predictions for multibranched junction structures than existing methods. Moreover, integrated with additional restraints from experiments, such as junction topology and long-range interactions, the model may serve as a useful structure generator for various applications.
A virus-borne DNA damage signaling pathway controls the lysogeny-induction switch in a group of temperate pleolipoviruses
Authors: Chen Zhao , Liu Ying , Wang Yixuan , Du Xincheng , Deng Xiaoyuan , Xiang Jialin , Wang Yangyang , Wang Jiao , Krupovic Mart , Du Shishen , Chen Xiangdong 
Published: March 2023

Abstract
Many prokaryotic viruses are temperate and their reactivation is tightly regulated. However, except for a few bacterial model systems, the regulatory circuits underlying the exit from lysogeny are poorly understood, especially in archaea. Here, we report a three-gene module which regulates the switch between lysogeny and replicative cycle in a haloarchaeal virus SNJ2 (family Pleolipoviridae). The SNJ2 orf4 encodes a winged helix-turn-helix DNA binding protein which maintains lysogeny through repressing the expression of the viral integrase gene intSNJ2. To switch to the induced state, two other SNJ2-encoded proteins, Orf7 and Orf8, are required. Orf8 is a homolog of cellular AAA+ ATPase Orc1/Cdc6, which is activated upon mitomycin C-induced DNA damage, possibly through posttranslational modification. Activated Orf8 initiates the expression of Orf7 which, in turn, antagonizes the function of Orf4, leading to the transcription of intSNJ2, thereby switching SNJ2 to the induced state. Comparative genomics analysis revealed that the SNJ2-like Orc1/Cdc6-centered three-gene module is common in haloarchaeal genomes, always present in the context of integrated proviruses. Collectively, our results uncover the first DNA damage signaling pathway encoded by a temperate archaeal virus and reveal an unexpected role of the widely distributed virus-encoded Orc1/Cdc6 homologs.
YbiB: a novel interactor of the GTPase ObgE
Authors: Deckers Babette , Vercauteren Silke , De Kock Veerke , Martin Charlotte , Lazar Tamas , Herpels Pauline , Dewachter Liselot , Verstraeten Natalie , Peeters Eveline , Ballet Steven , Michiels Jan , Galicia Christian , Versées Wim 
Published: March 2023

Abstract
Obg is a widely conserved and essential GTPase in bacteria, which plays a central role in a large range of important cellular processes, such as ribosome biogenesis, DNA replication, cell division and bacterial persistence. Nevertheless, the exact function of Obg in these processes and the interactions it makes within the associated pathways remain largely unknown. Here, we identify the DNA-binding TrpD2 protein YbiB as an interactor of the Escherichia coli Obg (ObgE). We show that both proteins interact with high affinity in a peculiar biphasic fashion, and pinpoint the intrinsically disordered and highly negatively charged C-terminal domain of ObgE as a main driver for this interaction. Molecular docking and X-ray crystallography, together with site-directed mutagenesis, are used to map the binding site of this ObgE C-terminal domain within a highly positively charged groove on the surface of the YbiB homodimer. Correspondingly, ObgE efficiently inhibits the binding of DNA to YbiB, indicating that ObgE competes with DNA for binding in the positive clefts of YbiB. This study thus forms an important step for the further elucidation of the interactome and cellular role of the essential bacterial protein Obg.
Atypical neurofibromas reveal distinct epigenetic features with proximity to benign peripheral nerve sheath tumor entities
Authors: Kresbach Catena , Dottermusch Matthias , Eckhardt Alicia , Ristow Inka , Paplomatas Petros , Altendorf Lea , Wefers Annika K , Bockmayr Michael , Belakhoua Sarra , Tran Ivy , Pohl Lara , Neyazi Sina , Bode Helena , Farschtschi Said , Well Lennart , Friedrich Reinhard E , Reuss David , Snuderl Matija , Hagel Christian , Mautner Victor-Felix , Schüller Ulrich 
Published: March 2023

Abstract

Background
Plexiform neurofibromas can transform into atypical neurofibromas (ANF) and then further progress to aggressive malignant peripheral nerve sheath tumors (MPNST). ANF have been described to harbor distinct histological features and frequent loss of CDKN2A/B. However, histological evaluation may be rater-dependent, and detailed knowledge about the molecular mechanisms of malignant transformation is scarce. In general, malignant transformation can be accompanied by significant epigenetic changes, and global DNA methylation profiling is able to differentiate relevant tumor subgroups. Therefore, epigenetic profiling might provide a valuable tool to distinguish and characterize ANF with differing extent of histopathological atypia from neurofibromas and MPNST.

Methods
We investigated 40 tumors histologically diagnosed as ANF and compared their global methylation profile to other peripheral nerve sheath tumors.

Results
Unsupervised class discovery and t-SNE analysis indicated that 36/40 ANF cluster with benign peripheral nerve sheath tumors with clear separation from MPNST. 21 ANF formed a molecularly distinct cluster in proximity to schwannomas. Tumors in this cluster had a frequent heterozygous or homozygous loss of CDKN2A/B and significantly more lymphocyte infiltration than MPNST, schwannomas, and NF. Few ANF clustered closely with neurofibromas, schwannomas, or MPNST, raising the question, whether diagnosis based on histological features alone might pose a risk to both over- and underestimate the aggressiveness of these lesions.

Conclusions
Our data suggest that ANF with varying histological morphology show distinct epigenetic similarities and cluster in proximity to benign peripheral nerve sheath tumor entities. Future investigations should pay special respect to correlating this methylation pattern to clinical outcomes.
Characterization and Management of Adverse Reactions From the CLEAR Study in Advanced Renal Cell Carcinoma Treated With Lenvatinib Plus Pembrolizumab
Authors: Motzer Robert , George Saby , Merchan Jaime R , Hutson Thomas E , Song Xun , Perini Rodolfo F , Xie Ran , Bapat Urmi , Puente Javier 
Published: March 2023

Abstract

Background
Lenvatinib plus pembrolizumab showed significantly improved progression-free and overall survival outcomes compared with sunitinib in patients with advanced renal cell carcinoma in the CLEAR study (NCT02811861). Here, we used CLEAR data to characterize common adverse reactions (ARs; adverse-event preferred terms grouped in accordance with regulatory authority review) associated with lenvatinib plus pembrolizumab and review management strategies for select ARs.

Materials and Methods
Safety data from the 352 patients who received lenvatinib plus pembrolizumab in the CLEAR study were analyzed. Key ARs were chosen based on frequency of occurrence (≥30%). Time to first onset and management strategies for key ARs were detailed.

Results
The most frequent ARs were fatigue (63.1%), diarrhea (61.9%), musculoskeletal pain (58.0%), hypothyroidism (56.8%), and hypertension (56.3%); grade ≥3 severity ARs that occurred in ≥5% of patients were hypertension (28.7%), diarrhea (9.9%), fatigue (9.4%), weight decreased (8.0%), and proteinuria (7.7%). Median times to first onset of all key ARs were within approximately 5 months (approximately 20 weeks) of starting treatment. Strategies for effectively managing ARs included baseline monitoring, drug–dose modifications, and/or concomitant medications.

Conclusion
The safety profile of lenvatinib plus pembrolizumab was consistent with the known profile of each monotherapy; ARs were considered manageable with strategies including monitoring, dose modifications, and supportive medications. Proactive and prompt identification and management of ARs are important for patient safety and to support continued treatment.

Clinicaltrials.gov ID
NCT02811861
The influence of traffic stop policy changes on assaults against officers: A quasi-experimental approach
Authors: Boehme Hunter M 
Published: March 2023

AbstractThis study investigates whether the Fayetteville (NC) Police Department’s (FPD) prioritization of safety traffic stops and de-prioritization of investigatory stops from 2013 to 2016 impacted assaults on the police officers. Time series models found a statistically significant decrease in assaults on officers within the FPD following their traffic stop policy changes. The comparison police departments did not experience a significant effect of assaults on police officers during the same timeframe. Although the FPD increased the aggregate number of traffic stops from 2013 to 2016, their prioritization of safety stops, and subsequent de-prioritization of investigatory traffic stops resulted in a reduction in assaults on police officers. Since investigatory traffic stops are agued to be more confrontational and have relatively low ‘hit rates,’ de-prioritizing (yet not completely withdrawing from) such type of stops may impact assaults on officers in the aggregate. Several policy implications are discussed.
An observational study of domestic violence in Greece during COVID-19 through police records: The profile of heinous crimes between nuclear and extended family relationships
Authors: Chatzisymeonidis Stavros , Kioskli Kitty 
Published: March 2023

AbstractIn Greece, the frequency of serious crimes within families has been alarmingly high during COVID-19; nonetheless, no study has systematically investigated this subject at a national level. The current study aims to estimate the crime rates of family violence across the country and explore the profile of perpetrators and victims based on their sociodemographic characteristics and relationship status. Out of 372 crime cases reported to the Hellenic Police during 2020–2021, the highest crime rate is observed in the geographical area of the Ionian Sea with 13.45 per 100,000 population. Overall, there were 372 perpetrators with 89.5% of them being males and 386 victims with 83.6% of them being females. The majority of both groups (perpetrators and victims) were Greek, whereas the prevalent age group for perpetrators was 46–60 (31.2%), and for victims was 36–45 (28.5%). Nuclear relatives outnumbered the extended ones regarding all groups of family violence crimes; however, there were no statistically significant differences. Lastly, our multivariate regression model indicated that the likelihood for Greeks to commit sexual abuse instead of rape was 3.27 times greater than immigrants. Younger perpetrators were 0.30 times less likely than elders to murder a relative rather than rape them, whereas they were 10,833,846.63 times more likely than elders to severely injure a victim as opposed to rape them.
Controllable electron self-injection in laser wakefield acceleration with asymmetric gas-jet nozzle
Authors: Lei Zhenzhe , Jin Zhan , Zhidkov Alexei , Pathak Naveen , Mizuta Yoshio , Huang Kai , Nakanii Nobuhiki , Daito Izuru , Kando Masaki , Hosokai Tomonao 
Published: March 2023

AbstractBeam charge control in the staging of laser wakefield acceleration (LWFA) is a crucial technique for developing full-optical jitter-free high-energy electron accelerators. Precise control of total charge in pre-accelerated electron bunches is necessary to achieve practical electron beam characteristics in the final acceleration stage(s). In contrast to the well-known cathode techniques in conventional accelerators, in LWFA the electron injection results from non-linear processes originating from plasma wave breaking. Therefore, the development of charge control requires a deep understanding of the electron self-injection processes and applications of non-trivial tools. The use of asymmetric gas-jet nozzles seems to be a promising way in developing charge control via tuning the target parameters such as plasma density, density slope, and acceleration length. Here, we demonstrate and characterize controllable electron self-injection, owing to a parametric resonance in slantwise density gas jets irradiated by 50 TW femtosecond laser pulses. The measured characteristics of the electron bunches, in which charge and energy distribution depend on the gas density and gas density gradient, agree well with those obtained by multidimensional particle-in-cell simulation and confirm the possibility of charge control.
A Systematic Appraisal of Conflicts of Interest and Researcher Allegiance in Clinical Studies of Dry Needling for Musculoskeletal Pain Disorders
Authors: Ware John W , Venere Kenny , Miller Stephanie A , Freeman Heather , Scalzitti David A , Hoogeboom Thomas 
Published: March 2023

Abstract

Objective
The purpose of this study was to determine the frequency and methods of conflicts of interest (COI) reporting in published dry needling (DN) studies and to determine the frequency of researcher allegiance (RA).

Methods
A pragmatic systematic search was undertaken to identify DN studies that were included in systematic reviews. Information regarding COI and RA were extracted from the full text of the published DN reports, and study authors were sent a survey inquiring about the presence of RA. A secondary analysis also was undertaken based on study quality/risk of bias scores that were extracted from the corresponding systematic reviews and study funding extracted from each DN study.

Results
Sixteen systematic reviews were identified, containing 60 studies of DN for musculoskeletal pain disorders, 58 of which were randomized controlled trials. Of the DN studies, 53% had a COI statement. None of these studies disclosed a COI. Nineteen (32%) authors of DN studies responded to the survey. According to the RA survey, 100% of DN studies included at least 1 RA criterion. According to the data extraction, 1 RA criterion was met in 45% of the DN studies. The magnitude of RA per study was 7 times higher according to the surveys than in the published reports.

Conclusion
These results suggest that COI and RA might be underreported in studies of DN. In addition, authors of DN studies might be unaware of the potential influence of RA on study results and conclusions.

Impact
Improved reporting of COI/RA might improve credibility of results and help identify the various factors involved in complex interventions provided by physical therapists. Doing so could help optimize treatments for musculoskeletal pain disorders provided by physical therapists.
Secret and Overt Information Acquisition in Financial Markets
Authors: Xiong Yan , Yang Liyan 
Published: March 2023

Abstract
We study the observability of investors’ information-acquisition activities in financial markets. Improving observability leads to two strategic effects on information acquisition: (1) the pricing effect, which arises from interactions between investors and the market maker and can encourage or discourage information acquisition, and (2) the competition effect, which concerns interactions among investors and always encourages information acquisition. We apply our theory to study voluntary and mandatory disclosures of corporate site visits. When the competition effect dominates, investors voluntarily disclose their visits. When the pricing effect dominates, mandatory disclosure is effective. Our analysis sheds novel light on Regulation Fair Disclosure.
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.