bluuebunny/crossref_metadata_2025_split huggingface dataset:
A non-parametric panel model for climate data with seasonal and spatial variation
Authors: Gao Jiti , Linton Oliver , Peng Bin 
Published: August 2023

Abstract
We consider a panel data model that allows for heterogeneous time trends at different locations. The model is well suited to identifying trends in climate data recorded at multiple stations. We propose a new estimation method for the model and derive an asymptotic theory for the proposed estimation method. For inferential purposes, we develop a bootstrap method for the case where weak correlation presents in both dimensions of the error terms. We examine the finite-sample properties of the proposed model and estimation method through extensive simulated studies. Finally, we use the newly proposed model and method to investigate monthly rainfall, temperature, and sunshine data of the UK, respectively. Overall, we find spring and winter have changed significantly over the past 50 years. Changes vary with respect to locations for the other seasons.
The dynamic duo: how DNA methylation and gene transcription help diatoms thrive in modern oceans
Authors: Lin Xin , Tirichine Leila , Zhang Xu 
Published: August 2023

This article comments on:Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao J, Dai X, Xia J, Jin P. 2023. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. Journal of Experimental Botany74, 4259–4276.
Star cluster classification using deep transfer learning with PHANGS-HST
Authors: Hannon Stephen , Whitmore Bradley C , Lee Janice C , Thilker David A , Deger Sinan , Huerta E A , Wei Wei , Mobasher Bahram , Klessen Ralf , Boquien Médéric , Dale Daniel A , Chevance Mélanie , Grasha Kathryn , Sanchez-Blazquez Patricia , Williams Thomas , Scheuermann Fabian , Groves Brent , Kim Hwihyun , Kruijssen J M Diederik ,   the PHANGS-HST Team
Published: August 2023

ABSTRACT
Currently available star cluster catalogues from the Hubble Space Telescope (HST) imaging of nearby galaxies heavily rely on visual inspection and classification of candidate clusters. The time-consuming nature of this process has limited the production of reliable catalogues and thus also post-observation analysis. To address this problem, deep transfer learning has recently been used to create neural network models that accurately classify star cluster morphologies at production scale for nearby spiral galaxies (D ≲ 20 Mpc). Here, we use HST ultraviolet (UV)–optical imaging of over 20 000 sources in 23 galaxies from the Physics at High Angular resolution in Nearby GalaxieS (PHANGS) survey to train and evaluate two new sets of models: (i) distance-dependent models, based on cluster candidates binned by galaxy distance (9–12, 14–18, and 18–24 Mpc), and (ii) distance-independent models, based on the combined sample of candidates from all galaxies. We find that the overall accuracy of both sets of models is comparable to previous automated star cluster classification studies (∼60–80 per cent) and shows improvement by a factor of 2 in classifying asymmetric and multipeaked clusters from PHANGS-HST. Somewhat surprisingly, while we observe a weak negative correlation between model accuracy and galactic distance, we find that training separate models for the three distance bins does not significantly improve classification accuracy. We also evaluate model accuracy as a function of cluster properties such as brightness, colour, and spectral energy distribution (SED)-fit age. Based on the success of these experiments, our models will provide classifications for the full set of PHANGS-HST candidate clusters (N ∼ 200 000) for public release.
The unseen host galaxy and high dispersion measure of a precisely localized fast radio burst suggests a high-redshift origin
Authors: Marnoch Lachlan , Ryder Stuart D , James Clancy W , Gordon Alexa C , Sammons Mawson W , Prochaska J Xavier , Tejos Nicolas , Deller Adam T , Scott Danica R , Bhandari Shivani , Glowacki Marcin , Mahony Elizabeth K , McDermid Richard M , Sadler Elaine M , Shannon Ryan M , Qiu Hao 
Published: August 2023

ABSTRACT
FRB 20210912A is a fast radio burst (FRB), detected and localized to subarcsecond precision by the Australian Square Kilometre Array Pathfinder. No host galaxy has been identified for this burst despite the high precision of its localization and deep optical and infrared follow-up, to 5σ limits of R = 26.7 mag and Ks = 24.9 mag with the Very Large Telescope. The combination of precise radio localization and deep optical imaging has almost always resulted in the secure identification of a host galaxy, and this is the first case in which the line of sight is not obscured by the Galactic disc. The dispersion measure of this burst, DMFRB = 1233.696 ± 0.006 pc cm−3, allows for a large source redshift of z &gt; 1 according to the Macquart relation. It could thus be that the host galaxy is consistent with the known population of FRB hosts, but is too distant to detect in our observations (z &gt; 0.7 for a host like that of the first repeating FRB source, FRB 20121102A); that it is more nearby with a significant excess in DMhost, and thus dimmer than any known FRB host; or, least likely, that the FRB is truly hostless. We consider each possibility, making use of the population of known FRB hosts to frame each scenario. The fact of the missing host has ramifications for the FRB field: even with high-precision localization and deep follow-up, some FRB hosts may be difficult to detect, with more distant hosts being the less likely to be found. This has implications for FRB cosmology, in which high-redshift detections are valuable.
Mapping pediatric brain tumors to their origins in the developing cerebellum
Authors: Okonechnikov Konstantin , Joshi Piyush , Sepp Mari , Leiss Kevin , Sarropoulos Ioannis , Murat Florent , Sill Martin , Beck Pengbo , Chan Kenneth Chun-Ho , Korshunov Andrey , Sah Felix , Deng Maximilian Y , Sturm Dominik , DeSisto John , Donson Andrew M , Foreman Nicholas K , Green Adam L , Robinson Giles , Orr Brent A , Gao Qingsong , Darrow Emily , Hadley Jennifer L , Northcott Paul A , Gojo Johannes , Kawauchi Daisuke , Hovestadt Volker , Filbin Mariella G , von Deimling Andreas , Zuckermann Marc , Pajtler Kristian W , Kool Marcel , Jones David T W , Jäger Natalie , Kutscher Lena M , Kaessmann Henrik , Pfister Stefan M 
Published: August 2023

Abstract

Background
Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas.

Methods
We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques.

Results
We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study.

Conclusion
Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar “lineage of origin.”
LESION SIMULATING DISEASE 3 regulates disease resistance via fine-tuning histone acetylation in cassava
Authors: Zeng Hongqiu , Xu Haoran , Tan Mengting , Zhang Bowen , Shi Haitao 
Published: August 2023

Abstract
Bacterial blight seriously affects the growth and production of cassava (Manihot esculenta Crantz), but disease resistance genes and the underlying molecular mechanism remain unknown. In this study, we found that LESION SIMULATING DISEASE 3 (MeLSD3) is essential for disease resistance in cassava. MeLSD3 physically interacts with SIRTUIN 1 (MeSRT1), inhibiting MeSRT1-mediated deacetylation modification at the acetylation of histone 3 at K9 (H3K9Ac). This leads to increased H3K9Ac levels and transcriptional activation of SUPPRESSOR OF BIR1 (SOBIR1) and FLAGELLIN-SENSITIVE2 (FLS2) in pattern-triggered immunity, resulting in immune responses in cassava. When MeLSD3 was silenced, the release of MeSRT1 directly decreased H3K9Ac levels and inhibited the transcription of SOBIR1 and FLS2, leading to decreased disease resistance. Notably, DELLA protein GIBBERELLIC ACID INSENSITIVE 1 (MeGAI1) also interacted with MeLSD3, which enhanced the interaction between MeLSD3 and MeSRT1 and further strengthened the inhibition of MeSRT1-mediated deacetylation modification at H3K9Ac of defense genes. In summary, this study illustrates the mechanism by which MeLSD3 interacts with MeSRT1 and MeGAI1, thereby mediating the level of H3K9Ac and the transcription of defense genes and immune responses in cassava.
Development of a Tool to Determine Excellence in the Provision of Physical Therapist Clinical Education: A Modified Delphi Study
Authors: Timmerberg Jean Fitzpatrick , Pelletier Deborah , Harding Elizabeth , Recker-Hughes Carol , Wetherbee-McDevitt Ellen , Stolfi Angela 
Published: August 2023

Abstract

Objective
The purpose of this study was to create a Site of Excellence in Clinical Education (SECE-PT) tool with the essential criteria used to determine excellence in the provision of physical therapist clinical education at a clinical site using a consensus-building approach.

Methods
The development of the SECE-PT tool was divided into 2 parts. Part 1 involved the development of an initial set of proposed criteria, whereas part 2 employed a modified Delphi approach for consensus building. Purposive selection and snowball sampling techniques were used to recruit clinical instructors, recent graduates, site coordinators of clinical education, and directors of clinical education who met the inclusion criteria for the modified Delphi study. Three web-based survey rounds were used to achieve consensus, defined as a mean score of ≥7 on the 11-point Likert scale. The first round gathered demographic information on participants and collected information about clarity and redundancy in the criteria provided, the second gathered information once again about clarity and redundancy on the revised criteria provided, and the third asked participants to rate how essential it was for a site of excellence to demonstrate each of the final criteria.

Results
A total of 123 participants, equally representing clinical and academic perspectives, completed the demographic survey and round 1. Ninety-four participants completed round 2, and 80 participants completed the third and final round. Consensus revealed that 44 criteria were deemed essential for a SECE-PT to demonstrate.

Conclusion
This study provides a measure to evaluate clinical sites providing clinical education. The SECE-PT tool should be widely adopted to evaluate the quality of the clinical site providing the education to student physical therapists.

Impact
The SECE-PT tool can be used by clinical sites for self-assessment to examine aspects of their clinical education programs and determine whether parts of their program should be further developed. This can provide a framework for discussion and collaboration between clinical and academic partners, as well as regional consortia.
Kinetics of skeletal muscle regeneration after mild and severe muscle damage induced by electrically‐evoked lengthening contractions
Authors: Bernard Clara , Jomard Charline , Chazaud Bénédicte , Gondin Julien 
Published: August 2023

AbstractPost‐injury skeletal muscle regeneration requires interactions between myogenic and non‐myogenic cells. Our knowledge on the regeneration process is mainly based on models using toxic, chemical, or physical (e.g., based on either muscle freezing or crushing) injury. Strikingly, the time course and magnitude of changes in the number of cells involved in muscle regeneration have been poorly described in relation to mild and severe muscle damage induced by electrically‐evoked lengthening contractions. We investigated for the first time the kinetics and magnitude of changes in mononuclear cells in relation to the extent of muscle damage. Mild and severe injury were induced in vivo in the mouse gastrocnemius muscle by 1 and 30 electrically‐evoked lengthening contractions, respectively. Several days after muscle damage, functional analysis of maximal torque production and histological investigations were performed to assess the related cellular changes. Torque recovery was faster after mild injury than after severe muscle damage. More necrotic and regenerating myofibers were observed after severe muscle damage as compared with mild injury, illustrating an association between functional and histological alterations. The kinetics of changes in muscle stem cells (total, proliferating, and differentiating), endothelial cells, fibro‐adipogenic progenitors (FAPs), and macrophages in the regenerating muscle was similar in mild and severe models. However, the magnitude of changes in the number of differentiating muscle stem cells, hematopoietic cells, among which macrophages, and FAPs was higher in severe muscle damage. Collectively, our results show that the amount of myogenic and non‐myogenic cells varies according to the extent of skeletal muscle injury to ensure efficient skeletal muscle regeneration while the kinetics of changes is independent of muscle tissue alterations. The possibility to experimentally modulate the extent of muscle damage will be useful to further investigate the cellular and molecular events involved in muscle regeneration.
Neutrophil extracellular traps facilitate sympathetic hyperactivity by polarizing microglia toward M1 phenotype after traumatic brain injury
Authors: Qu Xiaolin , Hou Xiaoxiang , Zhu Kaixin , Chen Wen , Chen Kun , Sang Xianzheng , Wang Chenqing , Zhang Yelei , Xu Haoxiang , Wang Junyu , Hou Qibo , Lv Liquan , Hou Lijun , Zhang Danfeng 
Published: August 2023

AbstractTraumatic brain injury (TBI), particularly diffuse axonal injury (DAI), often results in sympathetic hyperactivity, which can exacerbate the prognosis of TBI patients. A key component of this process is the role of neutrophils in causing neuroinflammation after TBI by forming neutrophil extracellular traps (NETs), but the connection between NETs and sympathetic excitation following TBI remains unclear. Utilizing a DAI rat model, the current investigation examined the role of NETs and the HMGB1/JNK/AP1 signaling pathway in this process. The findings revealed that sympathetic excitability intensifies and peaks 3 days post‐injury, a pattern mirrored by the activation of microglia, and the escalated NETs and HMGB1 levels. Subsequent in vitro exploration validated that HMGB1 fosters microglial activation via the JNK/AP1 pathway. Moreover, in vivo experimentation revealed that the application of anti‐HMGB1 and AP1 inhibitors can mitigate microglial M1 polarization post‐DAI, effectively curtailing sympathetic hyperactivity. Therefore, this research elucidates that post‐TBI, NETs within the PVN may precipitate sympathetic hyperactivity by stimulating M1 microglial polarization through the HMGB1/JNK/AP1 pathway.
Perinatal Mortality Despite Prenatal Diagnosis of Vasa Previa
Authors: Heyborne Kent 
Published: August 2023

OBJECTIVE:
To determine the causes and potential preventability of perinatal deaths in prenatally identified cases of vasa previa.

DATA SOURCES:
Reports of prenatally identified cases of vasa previa published in the English language literature since 2000 were identified in Medline and ClinicalTrials.gov with the search terms “vasa previa,” “abnormal cord insertion,” “velamentous cord,” “marginal cord,” “bilobed placenta,” and “succenturiate lobe.”

METHODS OF STUDY SELECTION:
All cases from the above search with an antenatally diagnosed vasa previa present at delivery in singleton or twin gestations with perinatal mortality information were included.

TABULATION, INTEGRATION, AND RESULTS:
Cases meeting inclusion criteria were manually abstracted, and multiple antenatal, intrapartum, and outcome variables were recorded. Deaths and cases requiring neonatal transfusion were analyzed in relation to plurality, routine hospitalization, and cervical length monitoring. A total of 1,109 prenatally diagnosed cases (1,000 singletons, 109 twins) were identified with a perinatal mortality rate attributable to vasa previa of 1.1% (95% CI 0.6–1.9%). All perinatal deaths occurred with unscheduled deliveries. The perinatal mortality rate in twin pregnancies was markedly higher than that in singleton pregnancies (9.2% vs 0.2%, P<.001), accounting for 80% of overall mortality despite encompassing only 9.8% of births. Compared with individuals with singleton pregnancies, those with twin pregnancies are more likely to undergo unscheduled delivery (56.4% vs 35.1%, P=.01) despite delivering 2 weeks earlier (33.2 weeks vs 35.1 weeks, P=.006). An institutional policy of routine hospitalization is associated with a reduced need for neonatal transfusion (0.9% vs 6.0%, P<.001) and a reduction in the perinatal mortality rate in twin pregnancies (0% vs 25%, P=.002) but not in singleton pregnancies (0% vs 0.5%, P=.31).

CONCLUSION:
Routine hospitalization and earlier delivery of twins may result in a reduction in the perinatal mortality rate. A smaller benefit from routine admission of individuals with singleton pregnancies cannot be excluded. There is currently insufficient evidence to recommend the routine use of cervical length measurements to guide clinical management.
Association of Clinical Trial Participation With Improved Overall Survival for Recurrent, Platinum-Resistant Ovarian Cancer
Authors: Morton Molly , Yao Meng , Chalif Julia , Lampert Erika J. , Chau Danielle , Rose Peter G. , Debernardo Robert , Michener Chad M. , Vargas Roberto , Chambers Laura M. 
Published: August 2023

OBJECTIVE:
To investigate whether clinical trial participation is associated with overall survival in patients with platinum-resistant ovarian cancer.

METHODS:
An IRB-approved, retrospective, single-institution cohort study was performed in patients with platinum-resistant ovarian cancer from January 1, 2009, to December 31, 2017. Platinum resistance was defined as progression within 6 months after completion of platinum chemotherapy. Patients were divided into two cohorts: 1) clinical trial participants for platinum-resistant ovarian cancer or 2) standard of care. The association of trial participation with overall survival from the date of platinum resistance was assessed with univariate and multivariable models.

RESULTS:
Of 305 eligible patients with recurrent platinum-resistant ovarian cancer, 46 (15.1%) were clinical trial participants. There were no significant differences in age (61.2 years vs 63.3 years, P=.21), body mass index (27.5 vs 27.6, P=.90), race (P=.61), medical comorbidities (P>.05), or performance status (P=.07) for clinical trial participants compared with those receiving standard of care. The majority underwent primary cytoreduction (76.1% vs 69.1%, P=.34) with no differences in residual disease (P=.43) for clinical trial participants compared with those receiving standard of care. There was no difference in poly-ADP-ribose polymerase inhibitor (21.7% vs 15.1%, P=.26) or bevacizumab (22.2% vs 32.1%, P=.31) use for clinical trial participants compared with those receiving standard of care. On multivariable analysis controlling for comorbidities, stage, and germline mutational status, clinical trial participation was associated with significantly improved overall survival from the date of platinum resistance compared with standard of care (13.8 months vs 10.5 months, adjusted hazard ratio 1.46, 95% CI 1.04–2.05, P=.028).

CONCLUSIONS:
In this retrospective cohort of patients with platinum-resistant ovarian cancer, clinical trial participation was associated with improved overall survival compared with standard of care therapies. Availability and participation in clinical trials should be prioritized in patients with recurrent, platinum-resistant ovarian cancer.
Risks of Uterine Perforation and Expulsion Associated With Intrauterine Devices
Authors: Fassett Michael J. , Reed Susan D. , Rothman Kenneth J. , Pisa Federica , Schoendorf Juliane , Wahdan Yesmean , Peipert Jeffrey F. , Gatz Jennifer , Ritchey Mary E. , Armstrong Mary Anne , Raine-Bennett Tina , Postlethwaite Debbie , Getahun Darios , Shi Jiaxiao M. , Xie Fagen , Chiu Vicki Y. , Im Theresa M. , Takhar Harpreet S. , Wang Jinyi , Anthony Mary S. 
Published: August 2023

OBJECTIVE:
The APEX-IUD (Association of Perforation and Expulsion of Intrauterine Devices) study evaluated the association of postpartum timing of intrauterine device (IUD) insertion, breastfeeding, heavy menstrual bleeding, and IUD type (levonorgestrel-releasing vs copper) with risks of uterine perforation and IUD expulsion in usual clinical practice. We summarize the clinically important findings to inform counseling and shared decision making.

METHODS:
APEX-IUD was a real-world (using U.S. health care data) retrospective cohort study of individuals aged 50 years and younger with IUD insertions between 2001 and 2018 and with electronic health record data. Cumulative incidences of uterine perforation and IUD expulsion were calculated. Adjusted hazard ratios (aHRs) and 95% CIs were estimated from proportional hazards models with control of confounding.

RESULTS:
Among the study population of 326,658, absolute risk of uterine perforation was low overall (cumulative incidence, 0.21% [95% CI 0.19–0.23%] at 1 year and 0.61% [95% CI 0.56–0.66% at 5 years]) but was elevated for IUDs inserted during time intervals within 1 year postpartum, particularly among those between 4 days and 6 weeks postpartum (aHR 6.71, 95% CI 4.80–9.38), relative to nonpostpartum insertions. Among postpartum insertions, IUD expulsion risk was greatest for insertions in the immediate postpartum period (0–3 days after delivery) compared with nonpostpartum (aHR 5.34, 95% CI 4.47–6.39). Postpartum individuals who were breastfeeding had a slightly elevated risk of perforation and lowered risk of expulsion than those not breastfeeding. Among nonpostpartum individuals, those with a heavy menstrual bleeding diagnosis were at greater risk of expulsion than those without (aHR 2.84, 95% CI 2.66–3.03); heavy menstrual bleeding also was associated with a slightly elevated perforation risk. There was a slightly elevated perforation risk and slightly lower expulsion risk associated with levonorgestrel-releasing IUDs compared with copper IUDs.

CONCLUSION:
Absolute risk of adverse outcomes with IUD insertion is low. Clinicians should be aware of the differences in risks of uterine perforation and expulsion associated with IUD insertion during specific postpartum time periods and with a heavy menstrual bleeding diagnosis. This information should be incorporated into counseling and decision making for patients considering IUD insertion.

FUNDING SOURCE:
Bayer AG.

CLINICAL TRIAL REGISTRATION:
EU PAS register, EUPAS33461.