bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased transcriptional elongation and RNA stability of GPCR ligand binding genes unveiled via RNA polymerase II degradation
Authors: Bao Lijun , Zhu Junyi , Shi Tingxin , Jiang Yongpeng , Li Boyuan , Huang Jie , Ji Xiong 
Published: June 2024

Abstract
RNA polymerase II drives mRNA gene expression, yet our understanding of Pol II degradation is limited. Using auxin-inducible degron, we degraded Pol II’s RPB1 subunit, resulting in global repression. Surprisingly, certain genes exhibited increased RNA levels post-degradation. These genes are associated with GPCR ligand binding and are characterized by being less paused and comprising polycomb-bound short genes. RPB1 degradation globally increased KDM6B binding, which was insufficient to explain specific gene activation. In contrast, RPB2 degradation repressed nearly all genes, accompanied by decreased H3K9me3 and SUV39H1 occupancy. We observed a specific increase in serine 2 phosphorylated Pol II and RNA stability for RPB1 degradation-upregulated genes. Additionally, α-amanitin or UV treatment resulted in RPB1 degradation and global gene repression, unveiling subsets of upregulated genes. Our findings highlight the activated transcription elongation and increased RNA stability of signaling genes as potential mechanisms for mammalian cells to counter RPB1 degradation during stress.
PLASMODESMATA-LOCATED PROTEIN 6 regulates plasmodesmal function in Arabidopsis vasculature
Authors: Li Zhongpeng , Liu Su-Ling , Montes-Serey Christian , Walley Justin W , Aung Kyaw 
Published: June 2024

Abstract
Plasmodesmata connect adjoining plant cells, allowing molecules to move between the connected cells for communication and sharing resources. It has been well established that the plant polysaccharide callose is deposited at plasmodesmata, regulating their aperture and function. Among proteins involved in maintaining callose homeostasis, PLASMODESMATA-LOCATED PROTEINSs (PDLPs) promote callose deposition at plasmodesmata. This study explored the function of PDLP5 and PDLP6 in different cell types. We discovered that PDLP5 and PDLP6 are expressed in nonoverlapping cell types in Arabidopsis (Arabidopsis thaliana). The overexpression of PDLP5 and PDLP6 results in the overaccumulation of plasmodesmal callose at different cell interfaces, indicating that PDLP5 and PDLP6 are active in different cell types. We also observed 2 distinct patterns of starch accumulation in mature leaves of PDLP5 and PDLP6 overexpressors. An enzyme-catalyzed proximity labeling approach was used to identify putative functional partners of the PDLPs. We identified SUCROSE SYNTHASE 6 (SUS6) as a functional partner of PDLP6 in the vasculature. We further demonstrated that PDLP6 physically and genetically interacts with SUS6. In addition, CALLOSE SYNTHASE 7 (CALS7) physically interacts with SUS6 and PDLP6. Genetic interaction studies showed that CALS7 is required for PDLP6 function. We propose that PDLP6 functions with SUS6 and CALS7 in the vasculature to regulate plasmodesmal function.
Phosphorylated transcription factor PuHB40 mediates ROS-dependent anthocyanin biosynthesis in pear exposed to high light
Authors: Zhang Lu , Wang Lu , Fang Yongchen , Gao Yuhao , Yang Shulin , Su Jun , Ni Junbei , Teng Yuanwen , Bai Songling 
Published: June 2024

Abstract
Plants are increasingly vulnerable to environmental stresses because of global warming and climate change. Stress-induced reactive oxygen species (ROS) accumulation results in plant cell damage, even cell death. Anthocyanins are important antioxidants that scavenge ROS to maintain ROS homeostasis. However, the mechanism underlying ROS-induced anthocyanin accumulation is unclear. In this study, we determined that the HD-Zip I family member transcription factor PuHB40 mediates ROS-dependent anthocyanin biosynthesis under high-light stress in pear (Pyrus ussuriensis). Specifically, PuHB40 induces the PuMYB123-like–PubHLH3 transcription factor complex for anthocyanin biosynthesis. The PuHB40-mediated transcriptional activation depends on its phosphorylation level, which is regulated by protein phosphatase PP2A. Elevated ROS content maintains high PuHB40 phosphorylation levels while also enhancing the PuHB40-induced PuMYB123-like transcription by decreasing the PuPP2AA2 expression, ultimately leading to increased anthocyanin biosynthesis. Our study reveals a pathway regulating the ROS-induced anthocyanin biosynthesis in pears, further clarifying the mechanism underlying the abiotic stress-induced anthocyanin biosynthesis, which may have implications for improving plant stress tolerance.
Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid
Authors: Dorrell Richard G , Zhang Youjun , Liang Yue , Gueguen Nolwenn , Nonoyama Tomomi , Croteau Dany , Penot-Raquin Mathias , Adiba Sandrine , Bailleul Benjamin , Gros Valérie , Pierella Karlusich Juan José , Zweig Nathanaël , Fernie Alisdair R , Jouhet Juliette , Maréchal Eric , Bowler Chris 
Published: June 2024

Abstract
Organic carbon fixed in chloroplasts through the Calvin–Benson–Bassham Cycle can be diverted toward different metabolic fates, including cytoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis–gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis–gluconeogenesis, Enolase and bis-phosphoglycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative ‘omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high-latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic, and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway.
Watching the Grand Ethiopian Renaissance Dam from a distance: Implications for sustainable water management of the Nile water
Authors: Abdelmohsen Karem , Sultan Mohamed , Yan Eugene , Abotalib Abotalib Z , Save Himanshu , Emil Mustafa , Elhaddad Hesham , Abdelmalik Karim 
Published: June 2024

Abstract
Increased demands for sustainable water and energy resources in densely populated basins have led to the construction of dams, which impound waters in artificial reservoirs. In many cases, scarce field data led to the development of models that underestimated the seepage losses from reservoirs and ignored the role of extensive fault networks as preferred pathways for groundwater flow. We adopt an integrated approach (remote sensing, hydrologic modeling, and field observations) to assess the magnitude and nature of seepage from such systems using the Grand Ethiopian Renaissance Dam (GERD), Africa's largest hydropower project, as a test site. The dam was constructed on the Blue Nile within steep, highly fractured, and weathered terrain in the western Ethiopian Highlands. The GERD Gravity Recovery and Climate Experiment Terrestrial Water Storage (GRACETWS), seasonal peak difference product, reveals significant mass accumulation (43 ± 5 BCM) in the reservoir and seepage in its surroundings with progressive south-southwest mass migration along mapped structures between 2019 and 2022. Seepage, but not a decrease in inflow or increase in outflow, could explain, at least in part, the observed drop in the reservoir's water level and volume following each of the three fillings. Using mass balance calculations and GRACETWS observations, we estimate significant seepage (19.8 ± 6 BCM) comparable to the reservoir's impounded waters (19.9 ± 1.2 BCM). Investigating and addressing the seepage from the GERD will ensure sustainable development and promote regional cooperation; overlooking the seepage would compromise hydrological modeling efforts on the Nile Basin and misinform ongoing negotiations on the Nile water management.
Two-sample Mendelian randomization analysis of the relationship between periodontitis and risk of upper gastrointestinal cancers
Authors: Mi Shuyi , Cai Shangwen , Lou Guochun , Xue Meng 
Published: June 2024

Abstract

Purpose
The aim of the present study is to explore the possible association between periodontitis and upper gastrointestinal (UGI) cancers, including esophageal and gastric cancers, utilizing the Mendelian randomization method.

Methods
In this research, we utilized the Mendelian randomization method to examine the causal association between periodontitis and UGI cancers. Genome-wide association studies data for periodontitis were obtained from the Gene-Lifestyle Interactions in Dental Endpoints consortium, while UGI cancers’ data were accessed from FinnGen’s Biobank. After rigorously screening instrumental variables for periodontitis, we analyzed them with UGI cancers primarily using the inverse variance weighted. Finally, to identify outliers, the results were subjected to a leave-one-out sensitivity analysis.

Results
Inverse variance weighted (fixed effect) results revealed that periodontitis is a risk factor for gastric cancer (OR = 1.7735, 95% CI: 1.1576 to 2.7170, P = 0.0085). As for esophageal cancer, no statistically significant correlation was observed. Furthermore, no outliers were detected in any of the results.

Conclusion
Our two-sample Mendelian randomization study obviously demonstrates a significant positive association between periodontitis and gastric cancer, while no statistically significant correlation was found for esophageal cancer.
Protectors and guardians: observations from Australia
Authors: Barnett Katy 
Published: June 2024

Abstract
The role of protectors, guardians and other third-party officers is not well-explored in Australian case law. This article seeks to provide guidance for Australian practitioners, with reference to overseas case law, as cases involving these roles will become increasingly prominent in future years. The article discusses the definition of “protector”, the nature of different powers, the fiduciary aspects of the role and the possibility that a court may find a trust to be illusory, or “look through” the trust. The advantages and disadvantages of protectors are canvassed along with tips for drafters of trust deeds.
The way towards ethical anesthesia care: no aim – no game – no fame or blame?
Authors: Meco Basak Ceyda , Guclu Cigdem Yildirim , Berger-Estilita Joana , Radtke Finn M. 
Published: June 2024

Purpose of reviewThis review explores the intricacies of ethical anesthesia, exploring the necessity for precision anesthesia and its impact on patient-reported outcomes. The primary objective is to advocate for a defined aim, promoting the implementation of rules and feedback systems. The ultimate goal is to enhance precision anesthesia care, ensuring patient safety through the implementation of a teamwork and the integration of feedback mechanisms.Recent findingsRecent strategies in the field of anesthesia have evolved from intraoperative monitorization to a wider perioperative patient-centered precision care. Nonetheless, implementing this approach encounters significant obstacles. The article explores the evidence supporting the need for a defined aim and applicable rules for precision anesthesia's effectiveness. The implementation of the safety culture is underlined. The review delves into the teamwork description with structured feedback systems.SummaryAnesthesia is a multifaceted discipline that involves various stakeholders. The primary focus is delivering personalized precision care. This review underscores the importance of establishing clear aims, defined rules, and fostering effective and well tolerated teamwork with accurate feedback for improving patient-reported outcomes. The Safe Brain Initiative approach, emphasizing algorithmic monitoring and systematic follow-up, is crucial in implementing a fundamental and standardized reporting approach within patient-centered anesthesia care practice.
The drug titration paradox: a control engineering perspective
Authors: Sarraf Elie 
Published: June 2024

Purpose of review
The drug titration paradox describes that, from a population standpoint, drug doses appear to have a negative correlation with its clinical effect. This paradox is a relatively modern discovery in anesthetic pharmacology derived from large clinical data sets. This review will interpret the paradox using a control engineering perspective.

Recent findings
Drug titration is a challenging endeavor, and the medication delivery systems used in everyday clinical practice, including infusion pumps and vaporizers, typically do not allow for rapid or robust titration of medication being delivered. In addition, clinicians may be reluctant to deviate from a predetermined plan or may be content to manage patients within fixed goal boundaries.

Summary
This drug titration paradox describes the constraints of how the average clinician will dose a patient with an unknown clinical response. While our understanding of the paradox is still in its infancy, it remains unclear how alternative dosing schemes, such as through automation, may exceed the boundaries of the paradox and potentially affect its conclusions.
Utilization and Surgical Outcomes of Sentinel Lymph Node Biopsy for Endometrial Intraepithelial Neoplasia
Authors: Levin Gabriel , Wright Jason D. , Burke Yechiel Z. , Hamilton Kacey M. , Meyer Raanan 
Published: June 2024

OBJECTIVE:
To describe the rate and surgical outcomes of sentinel lymph node (SLN) biopsy in patients with endometrial intraepithelial neoplasia (EIN).

METHODS:
We conducted a cohort study that used the prospective American College of Surgeons National Surgical Quality Improvement Program database. Women with EIN on postoperative pathology who underwent minimally invasive hysterectomy from 2012 to 2020 were included. The cohort was dichotomized based on the performance of SLN biopsy. Patients' characteristics, perioperative morbidity, and mortality were compared between patients who underwent SLN biopsy and those who did not. Postoperative complications were defined using the Clavien-Dindo classification system.

RESULTS:
Overall, 4,447 patients were included; of those, 586 (13.2%) underwent SLN biopsy. The proportion of SLN biopsy has increased steadily from 0.6% in 2012 to 26.1% in 2020 (P<.001), with a rate of 16% increase per year. In a multivariable regression that included age, body mass index (BMI), and year of surgery, a more recent year of surgery was independently associated with an increased adjusted odds ratio of undergoing SLN biopsy (1.51, 95% CI, 1.43–1.59). The mean total operative time was longer in the SLN biopsy group (139.50±50.34 minutes vs 131.64±55.95 minutes, P=.001). The rate of any complication was 5.9% compared with 6.7%, the rate of major complications was 2.3% compared with 2.4%, and the rate of minor complications was 4.1% compared with 4.9% for no SLN biopsy and SLN biopsy, respectively. In a single complications analysis, the rate of venous thromboembolism was higher in the SLN biopsy group (four [0.7%] vs four [0.1%], P=.013). In a multivariable regression analysis adjusted for age, BMI, American Society of Anesthesiologists classification, uterus weight, and preoperative hematocrit, the performance of SLN biopsy was not associated with any complications, major complications, or minor complications.

CONCLUSION:
The performance of SLN biopsy in EIN is increasing. Sentinel lymph node biopsy for EIN is associated with an increased risk of venous thromboembolism and a negligible increased surgical time.
JournalADE: Creation and validation of a novel program for automated data extraction (ADE) to assess authorship gender representation
Authors: Larson Emily L. , Pandya Shivani , Stewart Sara , Schmerler Jessica , Jabori Sinan Kallo , Xun Helen , Jain Kriti , LaPorte Dawn , Aiyer Amiethab 
Published: June 2024

Background:
Analyses of gender in academic authorship are key to characterizing representation in surgical fields, but current methods of manual data collection are time-consuming and error prone. The purpose of this study was to design a program to automatically extract publication data and verify the accuracy of this program in comparison to manually-collected data in a pilot study of three orthopaedic surgery journals.

Methods:
Publications from three orthopaedic subspecialty journals between January 2019 and June 2021 were identified via PubMed search. For each publication, online publication date, journal issue month, first author name, and senior author name were collected from PubMed listings by hand and programmatically in a Python script (JournalADE). Gender was determined using Gender API.

Results:
The percent of publications for which manually- and program-collected online publication dates were within 14 days of each other was above 95% for all journals. There was 98.3% (95% CI=97.84-98.76%) agreement for online publication date, with a mean difference of 6.43 (SD 0.87) days. Journal issue month agreement was 99.6% (95% CI=99.37-99.83%). Agreement for first author gender was 97.33% (95% CI=96.75-97.91%) and for senior author gender was 96.77% (95% CI=96.14-97.4%). Estimated labor time for manual collection was 100 hr, compared to 15 min for JournalADE.

Conclusions:
When comparing the JournalADE- and manually-collected data, rates of agreement were high at a fraction of the time. This supports the efficacy of JournalADE and sets the stage for its use in future studies of gender in authorship.
Temporal Shape Changes of Pedicle Screw-rod Constructs After Lumbar Interbody Fusion
Authors: Ikezawa Munenari , Tanioka Satoru , Nishikawa Hirofumi , Aydin Orhun Utku , Hilbert Adam , Miyazaki Takahiro , Fujimoto Masashi , Ishida Fujimaro , Kamei Yusuke , Suzuki Hidenori , Mizuno Masaki , Frey Dietmar 
Published: June 2024

Study Design.
Retrospective multicenter study.

Objective.
To examine the shape change of screw-rod constructs over time after short-segment lumbar interbody fusion and to clarify its relationship to clinical characteristics.

Summary of Background Data.
No study has focused on the shape change of screw-rod constructs after short-segment fusion and its clinical implications.

Methods.
One hundred eight patients who had single-level lumbar interbody fusion with pedicle screws and cages were enrolled. Three-dimensional (3D) images of screw-rod constructs were generated from baseline CT on the day after surgery and follow-up CT and were superposed on the right and left side, respectively, using the iterative closest point algorithm. The shape change was quantitatively assessed by computing the median distance between the 3D images, which was defined as the shape change value. Among the 5 time-course categories of follow-up CT (≤1, 2–3, 4–6, 7–12, and ≥13 months), the shape change values were compared. The relationships between the shape change values and clinical characteristics, such as age, CT-derived vertebral bone mineral density, screw and rod materials, and postoperative interbody fusion status, cage subsidence, and screw loosening, were evaluated.

Results.
A total of 237 follow-up CTs were included (≤1 [34 scans], 2–3 [33 scans], 4–6 [80 scans], 7–12 [48 scans], and ≥13 months [42 scans]) because many patients underwent multiple follow-up CTs. There were significant differences in shape change values among the time-course categories (P<0.001 in Kruskal-Wallis test). Most shape changes occurred within 6 months postoperatively, with no significant changes observed at 7 months or more. There were no significant relationships between the shape change values and each clinical characteristic.

Conclusions.
The temporal shape changes of screw-rod constructs following short-segment lumbar interbody fusion progressed up to 6 months after surgery but not significantly thereafter.
BTLA deficiency promotes HSC activation and protects against hepatic ischemia-reperfusion injury
Authors: Shen Xiaoyun , Mai Rongyun , Han Xiao , Wang Qi , Wang Yifan , Ji Tong , Tong Yifan , Chen Ping , Zhao Jia , He Xiaoyan , Wen Tong , Liang Rong , Lin Yan , Luo Xiaoling , Cai Xiujun 
Published: June 2024

Background and Aims:
Hepatic ischemia-reperfusion injury (IRI) is unavoidable even despite the development of more effective surgical approaches. During hepatic IRI, activated HSC (aHSC) are involved in liver injury and recovery.

Approach and Result:
A proportion of aHSC increased significantly both in the mouse liver tissues with IRI and in the primary mouse HSCs and LX-2 cells during hypoxia-reoxygenation. “Loss-of-function” experiments revealed that depleting aHSC with gliotoxin exacerbated liver damage in IRI mice. Subsequently, we found that the transcription of mRNA and the expression of B and T lymphocyte attenuator (BTLA) protein were lower in aHSC compared with quiescent HSCs. Interestingly, overexpression or knockdown of BTLA resulted in opposite changes in the activation of specific markers for HSCs such as collagen type I alpha 1, α-smooth muscle actin, and Vimentin. Moreover, the upregulation of these markers was also observed in the liver tissues of global BLTA-deficient (BTLA−/−) mice and was higher after hepatic IRI. Compared with wild-type mice, aHSC were higher, and liver injury was lower in BTLA−/− mice following IRI. However, the depletion of aHSC reversed these effects. In addition, the depletion of aHSC significantly exacerbated liver damage in BTLA−/− mice with hepatic IRI. Furthermore, the TGF-β1 signaling pathway was identified as a potential mechanism for BTLA to negatively regulate the activation of HSCs in vivo and in vitro.

Conclusions:
These novel findings revealed a critical role of BTLA. Particularly, the receptor inhibits HSC-activated signaling in acute IRI, implying that it is a potential immunotherapeutic target for decreasing the IRI risk.
How to cultivate sustainable physical health and wellness in transplant recipients: the emerging and enduring role of exercise scientists
Authors: Sakkas Giorgos K. , Giannaki Christoforos D. , Wilund Kenneth R. , Karatzaferi Christina 
Published: June 2024

Purpose of review
The aim of the current review is to highlight the importance of exercise training as an important section of transplant recipient rehabilitation process and explain the role of the exercise scientist in the development, implementation, and assessment of the exercise regime.

Recent findings
Transplant patients face a unique set of challenges in their recovery and rehabilitation process, often requiring a multifaceted approach to address the physical, emotional, and psychological aspects of their condition. Exercise training has emerged as a crucial component in the care of these patients, providing a means to improve functional capacity, enhance quality of life, and mitigate the adverse effects of transplant-related complications. Exercise scientists who are trained to assess patient's physical limitations, develop and deliver personalized exercise programs, and monitor their progress are uniquely positioned to play a crucial role in the treatment of patients with chronic conditions that require exercise training as a mean of improving and maintaining health and quality of life.

Summary
Exercise scientists are the appropriate professionals for providing transplant recipients with the recommended exercise training for maintaining and improving their health status as part of the overall plan of long-term care and support.