bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes
Authors: Yoon Peter H , Skopintsev Petr , Shi Honglue , Chen LinXing , Adler Benjamin A , Al-Shimary Muntathar , Craig Rory J , Loi Kenneth J , DeTurk Evan C , Li Zheng , Amerasekera Jasmine , Trinidad Marena , Nisonoff Hunter , Chen Kai , Lahiri Arushi , Boger Ron , Jacobsen Steve , Banfield Jillian F , Doudna Jennifer A 
Published: November 2023

Abstract
RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and a TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12s. In eukaryotes, TnpB homologs occur as two distinct types, Fanzor1s and Fanzor2s. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, which revealed that both Fanzor1s and Fanzor2s stem from a single lineage of IS607 TnpBs with unusual active site arrangement. The widespread nature of Fanzors implies that the properties of this particular lineage of IS607 TnpBs were particularly suited to adaptation in eukaryotes. Biochemical analysis of an IS607 TnpB and Fanzor1s revealed common strategies employed by TnpBs and Fanzors to co-evolve with their cognate transposases. Collectively, our results provide a new model of sequential evolution from IS607 TnpBs to Fanzor2s, and Fanzor2s to Fanzor1s that details how genes of prokaryotic origin evolve to give rise to new protein families in eukaryotes.
PRIMPOL ensures robust handoff between on-the-fly and post-replicative DNA lesion bypass
Authors: Mellor Christopher , Nassar Joelle , Šviković Saša , Sale Julian E 
Published: November 2023

Abstract
The primase/polymerase PRIMPOL restarts DNA synthesis when replication is arrested by template impediments. However, we do not have a comprehensive view of how PRIMPOL-dependent repriming integrates with the main pathways of damage tolerance, REV1-dependent ‘on-the-fly’ lesion bypass at the fork and PCNA ubiquitination-dependent post-replicative gap filling. Guided by genome-wide CRISPR/Cas9 screens to survey the genetic interactions of PRIMPOL in a non-transformed and p53-proficient human cell line, we find that PRIMPOL is needed for cell survival following loss of the Y-family polymerases REV1 and POLη in a lesion-dependent manner, while it plays a broader role in promoting survival of cells lacking PCNA K164-dependent post-replicative gap filling. Thus, while REV1- and PCNA K164R-bypass provide two layers of protection to ensure effective damage tolerance, PRIMPOL is required to maximise the effectiveness of the interaction between them. We propose this is through the restriction of post-replicative gap length provided by PRIMPOL-dependent repriming.
Structural and biochemical analysis of the PARP1-homology region of PARP4/vault PARP
Authors: Frigon Léonie , Pascal John M 
Published: November 2023

Abstract
PARP4 is an ADP-ribosyltransferase that resides within the vault ribonucleoprotein organelle. Our knowledge of PARP4 structure and biochemistry is limited relative to other PARPs. PARP4 shares a region of homology with PARP1, an ADP-ribosyltransferase that produces poly(ADP-ribose) from NAD+ in response to binding DNA breaks. The PARP1-homology region of PARP4 includes a BRCT fold, a WGR domain, and the catalytic (CAT) domain. Here, we have determined X-ray structures of the PARP4 catalytic domain and performed biochemical analysis that together indicate an active site that is open to NAD+ interaction, in contrast to the closed conformation of the PARP1 catalytic domain that blocks access to substrate NAD+. We have also determined crystal structures of the minimal ADP-ribosyltransferase fold of PARP4 that illustrate active site alterations that restrict PARP4 to mono(ADP-ribose) rather than poly(ADP-ribose) modifications. We demonstrate that PARP4 interacts with vault RNA, and that the BRCT is primarily responsible for the interaction. However, the interaction does not lead to stimulation of mono(ADP-ribosylation) activity. The BRCT–WGR–CAT of PARP4 has lower activity than the CAT alone, suggesting that the BRCT and WGR domains regulate catalytic output. Our study provides first insights into PARP4 structure and regulation and expands understanding of PARP structural biochemistry.
Structural and biochemical insights into NEIL2’s preference for abasic sites
Authors: Eckenroth Brian E , Bumgarner Joshua D , Matsumoto-Elliott Olivia , David Sheila S , Doublié Sylvie 
Published: November 2023

Abstract
Cellular DNA is subject to damage from a multitude of sources and repair or bypass of sites of damage utilize an array of context or cell cycle dependent systems. The recognition and removal of oxidatively damaged bases is the task of DNA glycosylases from the base excision repair pathway utilizing two structural families that excise base lesions in a wide range of DNA contexts including duplex, single-stranded and bubble structures arising during transcription. The mammalian NEIL2 glycosylase of the Fpg/Nei family excises lesions from each of these DNA contexts favoring the latter two with a preference for oxidized cytosine products and abasic sites. We have determined the first liganded crystal structure of mammalian NEIL2 in complex with an abasic site analog containing DNA duplex at 2.08 Å resolution. Comparison to the unliganded structure revealed a large interdomain conformational shift upon binding the DNA substrate accompanied by local conformational changes in the C-terminal domain zinc finger and N-terminal domain void-filling loop necessary to position the enzyme on the DNA. The detailed biochemical analysis of NEIL2 with an array of oxidized base lesions indicates a significant preference for its lyase activity likely to be paramount when interpreting the biological consequences of variants.
Accumulation of Phosphorylated SnRK2 Substrate 1 Promotes Drought Escape in Arabidopsis
Authors: Katagiri Sotaro , Kamiyama Yoshiaki , Yamashita Kota , Iizumi Sara , Suzuki Risa , Aoi Yuki , Takahashi Fuminori , Kasahara Hiroyuki , Kinoshita Toshinori , Umezawa Taishi 
Published: November 2023

Abstract
Plants adopt optimal tolerance strategies depending on the intensity and duration of stress. Retaining water is a priority under short-term drought conditions, whereas maintaining growth and reproduction processes takes precedence over survival under conditions of prolonged drought. However, the mechanism underlying changes in the stress response depending on the degree of drought is unclear. Here, we report that SNF1-related protein kinase 2 (SnRK2) substrate 1 (SNS1) is involved in this growth regulation under conditions of drought stress. SNS1 is phosphorylated and stabilized by SnRK2 protein kinases reflecting drought conditions. It contributes to the maintenance of growth and promotion of flowering as drought escape by repressing stress-responsive genes and inducing FLOWERING LOCUS T (FT) expression, respectively. SNS1 interacts with the histone methylation reader proteins MORF-related gene 1 (MRG1) and MRG2, and the SNS1–MRG1/2 module cooperatively regulates abscisic acid response. Taken together, these observations suggest that the phosphorylation and accumulation of SNS1 in plants reflect the intensity and duration of stress and can serve as a molecular scale for maintaining growth and adopting optimal drought tolerance strategies under stress conditions.
Artificial intelligence and allergic rhinitis: does ChatGPT increase or impair the knowledge?
Authors: Høj Simon , Thomsen Simon F , Meteran Hanieh , Sigsgaard Torben , Meteran Howraman 
Published: November 2023

Abstract

Background
Optimal management of allergic rhinitis requires patient education with easy access to accurate information. However, previous online platforms have provided misleading information. The demand for online medical information continues to grow, especially with the introduction of advanced chatbots like ChatGPT.

Methods
This study aimed to evaluate the quality of information provided by ChatGPT regarding allergic rhinitis. A Likert scale was used to assess the accuracy of responses, ranging from 1 to 5. Four authors independently rated the responses from a healthcare professional’s perspective.

Results
A total of 20 questions covering various aspects of allergic rhinitis were asked. Among the answers, eight received a score of 5 (no inaccuracies), five received a score of 4 (minor non-harmful inaccuracies), six received a score of 3 (potentially misinterpretable inaccuracies) and one answer had a score of 2 (minor potentially harmful inaccuracies).

Conclusions
The variability in accuracy scores highlights the need for caution when relying solely on chatbots like ChatGPT for medical advice. Patients should consult qualified healthcare professionals and use online sources as a supplement. While ChatGPT has advantages in medical information delivery, its use should be approached with caution. ChatGPT can be useful for patient education but cannot replace healthcare professionals.
Parental Schooling, Educational Attainment, Skills, and Earnings: A Trend Analysis across Fifteen Countries
Authors: Pensiero Nicola , Barone Carlo 
Published: November 2023

Abstract
Using data on fifteen countries based on the harmonization of IALS and PIAC data, we provide a cross-national analysis of the evolution of the role of educational attainment and cognitive skills as mediators of intergenerational inequalities between 1994 and 2015. We find that the association between parents’ education and children’s earnings is large and highly stable over time in most countries, except for Scandinavian countries, where we detect a downward trend. Conversely, the United States stands out as the country displaying the largest earning differentials by parents’ education and as the only country where these differentials increased over time. We demonstrate that educational attainment and skills contributed in different ways to the persistence of these intergenerational inequalities. On the one hand, educational equalization was compensated by increasing earning returns to education in several countries. On the other hand, the association between parents’ education and cognitive skills, as well as the related earning returns, stayed largely unchanged across these two decades.
GPS-based noise mapping of Ahmedabad city
Authors: Vora Akshay Vinaychandra , Vasani Rupesh P 
Published: November 2023

ABSTRACT
Noise mapping is an effective tool to measure noise. By noise mapping one can represent noise graphically. Noise mapping was carried out for Ahmedabad city. Data was collected at 633 different locations across the city. Latitude, longitude and real-time noise levels were noted at each location. ArcGIS software was used for creating noise maps and colour noise maps. The percentage of the city covered by the respective value of contour of noise was also found using the software, as well as the number of people in the city suffering from the respective levels of noise. Considering all the results, a multi-linear regression model was developed to predict noise, using SPSS statistics software. The developed model was analysed using an R2 test as well as a paired t-test.
An Analysis of Negative One-star Patient Reviews and Complaints for Pediatric Orthopaedic Surgeons throughout the United States: A Retrospective Study
Authors: Hitchman Kyle J. , Baumann Anthony N. , Glasgow Wyatt R. , Rivera Karla G. , Anastasio Albert T. , Walley Kempland C. , Baldwin Keith D. 
Published: November 2023

Objective:
Patients commonly use physician review websites when choosing a surgeon for an elective procedure. Although data exist regarding other orthopaedic specialties, no study has investigated one-star reviews for pediatric orthopaedic surgeons. The goal of this retrospective study was to classify the factors contributing to one-star reviews of pediatric orthopaedic surgeons to identify which areas contribute to lower patient satisfaction.

Methods:
Patient ratings on a 5-star system and comments about pediatric orthopaedic surgeons were collected from the state with the most physicians registered in the “Pediatric Orthopaedic Society of North American” database for each of the 9 geographical regions of the United States as defined by the Association of American Medical Colleges. One-star reviews that included comments were classified as either surgical or nonsurgical. These comments were then further classified based on their content.

Results:
Three hundred fifty-four one-star reviews with 700 complaints were included in this study. Of these complaints, 481 (68.7%) were from nonsurgical patients and 219 (31.3%) were from surgical patients. Nonsurgical patients were significantly more likely to reference the amount of time spent with the physician (12.9% to 6.6%, P = 0.026), wait time (11.9% to 0.0%, P < 0.001), and bedside manner (41.2% to 22.8%, P < 0.001). Patients who said they had undergone a surgical procedure in their one-star review were significantly more likely to reference a disagreement with the physician’s decision or plan (35.3% to 17.5%, P < 0.001), and uncontrolled pain (21.6% to 5.2%, P < 0.001). There was no significant difference in the comments that referenced medical staff or institutional complaints between surgical and nonsurgical patients (13.8% to 11.4%, P = 0.424).

Conclusion:
Most one-star reviews of pediatric orthopaedic surgeons referenced interpersonal skills and other nonclinical aspects of a clinical encounter, with bedside manner being the most frequent complaint. Patients who had undergone surgical procedures were less likely to leave a one-star review, but if they did, their comment was usually about a disagreement with the physician’s plan.

Clinical Relevance:
Prognostic studies III.
The Surgical Algorithm for the AO Spine Sacral Injury Classification System
Authors: Lee Yunsoo , Lambrechts Mark , Narayanan Rajkishen , Bransford Richard , Benneker Lorin , Schnake Klaus , Öner Cumhur , Canseco Jose A. , Kepler Christopher K. , Schroeder Gregory D. , Vaccaro Alexander R. ,   AO Spine Sacral Classification Group Members
Published: November 2023

Study Design:
Global cross-sectional survey.

Objective:
To establish a surgical algorithm for sacral fractures based on the AO Spine Sacral Injury Classification System.

Summary of Background Data:
Although the AO Spine Sacral Injury Classification has been validated across an international audience of surgeons, a consensus on a surgical algorithm has yet to be developed for sacral fractures by using the Sacral AO Spine Injury Score (Sacral AOSIS).

Methods:
A survey was sent to general orthopedic surgeons, orthopedic spine surgeons, and neurosurgeons across the five AO Spine regions of the world. Descriptions of controversial sacral injuries based on different fracture subtypes were given and surgeons were asked whether the patient should undergo operative or non-operative management. The results of the survey were used to create a surgical algorithm based on each subtypes’ Sacral AOSIS.

Results:
International agreement of 70% was decided on by the AO Spine Knowledge Forum Trauma experts to indicate a recommendation of initial operative intervention. Using this, sacral fracture subtypes of AOSIS 5 or greater were considered operative while those with AOSIS 4 or less were generally non-operative. For subtypes with an AOSIS of 3 or 4, if the sacral fracture was associated with an anterior pelvic ring injury (M3 case-specific modifier), intervention should be left to the surgeons’ discretion.

Conclusion:
The AO Spine Sacral Injury Classification System offers a validated hierarchical system to approach sacral injuries. Through multi-specialty and global surgeon input, a surgical algorithm was developed to determine appropriate operative indications for sacral trauma. Further validation is required, but this algorithm provides surgeons across the world with the basis for discussion and the development of standard of care treatment.

Level of Evidence:
Level IV.
Cancer cachexia: Focus on cachexia factors and inter-organ communication
Authors: Wang Yongfei , Dong Zikai , An Ziyi , Jin Weilin 
Published: November 2023

Abstract
Cancer cachexia is a multi-organ syndrome and closely related to changes in signal communication between organs, which is mediated by cancer cachexia factors. Cancer cachexia factors, being the general name of inflammatory factors, circulating proteins, metabolites, and microRNA secreted by tumor or host cells, play a role in secretory or other organs and mediate complex signal communication between organs during cancer cachexia. Cancer cachexia factors are also a potential target for the diagnosis and treatment. The pathogenesis of cachexia is unclear and no clear effective treatment is available. Thus, the treatment of cancer cachexia from the perspective of the tumor ecosystem rather than from the perspective of a single molecule and a single organ is urgently needed. From the point of signal communication between organs mediated by cancer cachexia factors, finding a deeper understanding of the pathogenesis, diagnosis, and treatment of cancer cachexia is of great significance to improve the level of diagnosis and treatment. This review begins with cancer cachexia factors released during the interaction between tumor and host cells, and provides a comprehensive summary of the pathogenesis, diagnosis, and treatment for cancer cachexia, along with a particular sight on multi-organ signal communication mediated by cancer cachexia factors. This summary aims to deepen medical community's understanding of cancer cachexia and may conduce to the discovery of new diagnostic and therapeutic targets for cancer cachexia.
Diagnosis and management of blunt cardiac injury: What you need to know
Authors: Biffl Walter L. , Fawley Jason A. , Mohan Rajeev C. 
Published: November 2023

ABSTRACT
Blunt cardiac injury (BCI) encompasses a wide spectrum, from occult and inconsequential contusion to rapidly fatal cardiac rupture. A small percentage of patients present with abnormal electrocardiogram or shock, but most are initially asymptomatic. The potential for sudden dysrhythmia or cardiac pump failure mandates consideration of the presence of BCI, including appropriate monitoring and management. In this review, we will present what you need to know to diagnose and manage BCI.
Non-REM parasomnia experiences share EEG correlates with dreams
Authors: Cataldi Jacinthe , Stephan Aurélie M. , Haba-Rubio José , Siclari Francesca 
Published: November 2023

AbstractSleepwalking and related parasomnias result from sudden and incomplete awakenings out of slow wave sleep. Clinical observations suggest that behavioral episodes can occur without consciousness and recollection, or in relation to dream-like experiences. To understand what accounts for these differences in consciousness and amnesia, we recorded parasomnia episodes with high-density EEG and interviewed participants immediately afterwards. Compared to reports of unconsciousness (19%), reports of conscious experience (81%) were preceded, during prior sleep, by high-amplitude slow waves in anterior cortical regions and an activation of posterior cortical regions. Reduced posterior slow wave activity was also present during the episode when patients displayed elaborate behaviours in relation to dream-like scenarios. Amnesia for the experience (25%) was modulated by right medial temporal activation during prior sleep and fronto-parietal slow wave activity during the episode. Thus, the neural correlates of parasomnia experiences are similar to those previously reported for dreams and therefore likely reflect core physiological processes involved in sleep consciousness.
Temperature effects on the global patterns of photosynthetic quantum efficiency
Authors: Sandoval David , Flo Victor , Morfopoulos Catherine , Prentice Iain Colin 
Published: November 2023

AbstractThe photosynthetic quantum efficiency (φ0) is a key input parameter for modelling gross primary productivity in terrestrial biosphere models. Historically, these models assumedφ0to be constant, based on leaf measurements under unstressed conditions and within a narrow temperature range. However, increasing evidence suggests a temperature-dependentφ0on temperature, though it remains unclear whether this response is generalized or if it propagates to the ecosystem. Here, we derivedφ0(T) at the ecosystem level for sites distributed globally, using sub-daily eddy covariance measurements of CO2exchange and above/below-canopy measurements of photosynthetic flux density to derive the fraction of absorbed photosynthetically active radiation (fAPAR). We found thatφ0(T) shows a consistent bell-shaped response curve with temperature in all the sites we analysed. These patterns held when analysed with a larger global dataset using remotely sensed fAPAR. Furthermore, we observed that the values ofφ0(T) are not markedly different among biomes, instead, there is a gradual transition of the peakφ0(T) which decreases following an aridity gradient. Additionally, we noted varying sensitivity to temperature among the different sites, with sensitivity increasing as growth temperature decreases.
Operator model for evolutionary dynamics
Authors: Park Kangbien , Bae Yonghee 
Published: November 2023

AbstractDrift, selection, and mutation are integral evolutionary factors. In this article,operator modelis newly suggested to intuitively represent those evolutionary factors into mathematical operators, and to ultimately offer unconventional methodology for understanding evolutionary dynamics. To be specific, each of the drift, selection, and mutation was respectively interpreted as operator which in essence is a random matrix that acts upon the vector which contains population distribution information. The simulation results from the operator model coincided with the previous theoretical results for beneficial mutation accumulation rate in concurrent and successional regimes for asexually reproducing case. Furthermore, beneficial mutation accumulation in strong drift regime for asexually reproducing case was observed from the simulation while allowing the interactions of mutations with diverse selection coefficients. Lastly, methods to justify, reinforce, apply, and expand the operator model were discussed to scrutinize the implications of the model. With its unique characteristics, the operator model is expected to broaden perspective and to offer effective methodology for understanding the evolutionary process.