bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Nançay Radio Telescope study of the hyperactive repeating FRB 20220912A
Authors: Konijn David C , Hewitt Danté M , Hessels Jason W T , Cognard Ismaël , Huang Jeff , Ould-Boukattine Omar S , Chawla Pragya , Nimmo Kenzie , Snelders Mark P , Gopinath Akshatha , Manaswini Ninisha 
Published: October 2024

ABSTRACT
The repeating fast radio burst source FRB 20220912A was remarkably active in the weeks after its discovery. Here, we report 696 bursts detected with the Nançay Radio Telescope (NRT) as part of the Extragalactic Coherent Light from Astrophysical Transients (ÉCLAT) monitoring campaign. We present 68 observations, conducted from 2022 October to 2023 April, with a total duration of 61 h and an event rate peaking at $75^{+10}_{-9}$ bursts per hour above a fluence threshold of 0.59 Jy ms in the $1.2\!-\!1.7$ GHz band. Most bursts in the sample occur towards the bottom of the observing band. They follow a bimodal wait-time distribution, with peaks at 33.4 ms and 67.0 s. We find a roughly constant dispersion measure (DM) over time ($\delta$DM $\lesssim$ 2 pc cm$^{-3}$) when taking into account ‘sad-trombone’ drift, with a mean drift rate of $-8.8\,$ MHz ms$^{-1}$. None the less, we confirm small $\sim 0.3$ pc cm$^{-3}$ DM variations using microshot structure, while finding that microstructure is rare in our sample–despite the 16 $\mu$s time resolution of the data. The cumulative spectral energy distribution shows more high-energy bursts ($E_\nu \gtrsim 10^{31}$ erg Hz$^{-1}$) than would be expected from a simple power-law distribution. The burst rate per observation appears Poissonian, but the full set of observations is better modelled by a Weibull distribution, showing clustering. We discuss the various observational similarities that FRB 20220912A shares with other (hyper)active repeaters, which as a group are beginning to show a common set of phenomenological traits that provide multiple useful dimensions for their quantitative comparison and modelling.
Modelling stellar irradiances I: the transition regions of FGKM stars
Authors: Deliporanidou E , Del Zanna G 
Published: October 2024

ABSTRACT
We employed advanced ionization equilibrium models that we developed in Dufresne et al. (2024), which include charge transfer and density effects, to model UV stellar irradiances for a sample of stars. Our sample includes $\epsilon$ Eridani (K2 V), $\alpha$ Centauri A (G2 V), Procyon (F5 V), and Proxima Centauri (M5.5 Ve). We measured line fluxes from STIS data sets and used O iv and O v as density diagnostics to find the formation pressure of ions in the transition region (TR) and adopted a simple differential emission measure (DEM) modelling. Our findings indicate significant improvements in modelling spectral lines from anomalous ions such as Si iv, C iv, and N v of the Li- and Na-like sequences, which produce the strongest lines in the UV. For example, the Si iv lines were under-predicted by a factor of 5 and now are within 40 per cent the observed fluxes. The improved models allow us to obtain for the first time reliable estimates of some stellar chemical abundances in the TR. We compared our results with available photospheric abundances in the literature and found no evidence for the first ionization potential (FIP) effect in the TR of our stellar sample. Finally, we compared our results with the solar TR that can also be described by photospheric abundances.
PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization
Authors: Wei Zhiting , Si Duanmiao , Duan Bin , Gao Yicheng , Yu Qian , Zhang Zhenbo , Guo Ling , Liu Qi 
Published: October 2024

Abstract
Single-cell perturbation (scPerturbation) sequencing techniques, represented by single-cell genetic perturbation (e.g. Perturb-seq) and single-cell chemical perturbation (e.g. sci-Plex), result from the integration of single-cell toolkits with conventional bulk screening methods. These innovative sequencing techniques empower researchers to dissect perturbation effects in biological systems at an unprecedented resolution. Despite these advancements, a notable gap exists in the availability of a dedicated database for exploring scPerturbation data. To address this gap, we present PerturBase, the most comprehensive database designed for the analysis and visualization of scPerturbation data (http://www.perturbase.cn/). PerturBase curates 122 datasets from 46 publicly available studies, covering 115 single-modal and 7 multi-modal datasets that include 24 254 genetic and 230 chemical perturbations from approximately 5 million cells. The database, comprising the ‘Dataset’ and ‘Perturbation’ modules, provides insights into various results, encompassing quality control, denoising, differential gene expression analysis, functional analysis of perturbation effects and characterization of relationships between perturbations. All the datasets and results are presented on user-friendly, easy-to-browse web pages and can be visualized through intuitive and interactive plot and table formats. In summary, PerturBase stands as a pioneering, high-content database intended for searching, visualizing and analyzing scPerturbation datasets, contributing to a deeper understanding of perturbation effects.
Light-chain (AL) amyloidosis for nephrologists—treatment standard
Authors: Anand Shankara , O'Neill-Dee Maggie , Sanchorawala Vaishali , Verma Ashish 
Published: October 2024

ABSTRACT
Amyloidosis is a group of complex diseases caused by the misfolding and aggregation of proteins into amyloid fibrils. Light-chain (AL) amyloidosis is one of the most prevalent forms of amyloidosis, characterized by the gradual proliferation of light chains from plasma cell clones. A growing body of evidence has contributed to our understanding of its pathogenesis, presentation and clinical course. Increased recognition of its clinical sequelae has increased the prevalence of AL amyloidosis. Renal involvement, seen in up to 70% of cases, is particularly challenging due to its impact on quality of life and access to treatment options. Thus, early recognition of its unique sequelae, appropriate staging and a comprehensive understanding of treatment options balanced by their organ toxicities are crucial to managing this disease. We review the current treatment standards and discuss novel developments in the pathophysiology, diagnosis, outcome prediction and management of AL amyloidosis for the Nephrologist.
Molecular and clinical heterogeneity within MYC-family amplified medulloblastoma is associated with survival outcomes: A multicenter cohort study
Authors: Schwalbe Edward C , Lindsey Janet C , Danilenko Marina , Hill Rebecca M , Crosier Stephen , Ryan Sarra L , Williamson Daniel , Castle Jemma , Hicks Debbie , Kool Marcel , Milde Till , Korshunov Andrey , Pfister Stefan M , Bailey Simon , Clifford Steven C 
Published: October 2024

Abstract

Background
MYC/MYCN are the most frequent oncogene amplifications in medulloblastoma (MB) and its primary biomarkers of high-risk (HR) disease. However, while many patients’ MYC(N)-amplified tumors are treatment-refractory, some achieve long-term survival. We therefore investigated clinicobiological heterogeneity within MYC(N)-amplified MB and determined its relevance for improved disease management.

Methods
We characterized the clinical and molecular correlates of MYC- (MYC-MB; n = 64) and MYCN-amplified MBs (MYCN-MB; n = 95), drawn from &gt;1600 diagnostic cases.

Results
Most MYC-MBs were molecular group 3 (46/58; 79% assessable) and aged ≥3 years at diagnosis (44/64 [69%]). We identified a “canonical” very high-risk (VHR) MYC-amplified group (n = 51/62; 82%) with dismal survival irrespective of treatment (11% 5-year progression-free survival [PFS]), defined by co-occurrence with ≥1 additional established risk factor(s) (subtotal surgical-resection [STR], metastatic disease, LCA pathology), and commonly group 3/4 subgroup 2 with a high proportion of amplified cells. The majority of remaining noncanonical MYC-MBs survived (i.e. non-group 3/group 3 without other risk features; 11/62 (18%); 61% 5-year PFS). MYCN survival was primarily related to molecular group; MYCN-amplified SHH MB, and group 3/4 MB with additional risk factors, respectively defined VHR and HR groups (VHR, 39% [35/89]; 20% 5-year PFS/HR, 33% [29/89]; 46% 5-year PFS). Twenty-two out of 35 assessable MYCN-amplified SHH tumors harbored TP53 mutations; 9/12 (75%) with data were germline. MYCN-amplified group 3/4 MB with no other risk factors (28%; 25/89) had 70% 5-year PFS.

Conclusions
MYC(N)-amplified MB displays significant clinicobiological heterogeneity. Diagnostics incorporating molecular groups, subgroups, and clinical factors enable their risk assessment. VHR “canonical” MYC tumors are essentially incurable and SHH-MYCN-amplified MBs fare extremely poorly (20% survival at 5 years); both require urgent development of alternative treatment strategies. Conventional risk-adapted therapies are appropriate for more responsive groups, such as noncanonical MYC and non-SHH-MYCN MB.
Mapping the Evidence for Measuring Energy Expenditure and Indicating Hypermetabolism in Motor Neuron Disease: A Scoping Review
Authors: Roscoe Sarah A , Allen Scott P , McDermott Christopher J , Stavroulakis Theocharis 
Published: October 2024

Abstract

Objective
To map the international methods used to measure energy expenditure of adults living with motor neuron disease (MND) and to highlight discrepancies when indicating hypermetabolism in the MND literature.

Background
A decline in the nutritional status of patients is associated with exacerbated weight loss and shortened survival. Assessments of energy expenditure, using a variety of methods, are important to ensure an adequate energy intake to prevent malnutrition-associated weight loss. Assessments of energy expenditure are also commonly used to indicate hypermetabolism in MND, although these approaches may not be optimal.

Methods
A protocol based on the Preferred Reporting Items for Systematic Reviews and Meta-analyses extension for Scoping Reviews Guidelines was developed. Three electronic databases (Medline [Ovid], CINAHL [EBSCO], and Web of Science) were exhaustively searched. Identified publications were systematically screened according to predefined PICOS eligibility criteria. The primary outcome was the identification of methods used to measure energy expenditure in MND. The secondary outcome was the identification of applications of energy expenditure assessments to indicate hypermetabolism in MND.

Results
Thirty-two observational primary research publications were identified. Thirteen (40.6%) were longitudinal in design, with data on repeated measurements of energy expenditure presented in 3 (9.4%). Thirteen (40.6%) were case-control studies, of which 11 use a matched control group. Pulmonary function was used to assess eligibility in 10 publications. Energy expenditure was measured using indirect calorimetry (IC) in 31 studies. Discrepancies in the durations of fasted, measurement, and washout periods were observed. Of all included publications, 50% used assessments of resting energy expenditure to identify hypermetabolism. Bioelectrical impedance analysis was used to assess body composition alongside energy expenditure in 93.8% of publications.

Conclusions
Resting energy expenditure is most frequently measured using an open-circuit IC system. However, there is a lack of a standardized, validated protocol for the conduct and reporting of IC and metabolic status in patients with MND.
Beyond Human Babesiosis: Prevalence and Association of Babesia Coinfection with Mortality in the United States, 2015–2022: A Retrospective Cohort Study
Authors: Ssentongo Paddy , Venugopal Natasha , Zhang Yue , Chinchilli Vernon M , Ba Djibril M 
Published: October 2024

Abstract

Background
The prevalence of Babesia coinfecting tick-borne zoonoses and mortality outcomes are not fully elucidated. The objective of the present study was to determine babesiosis coinfection prevalence rates and estimate the association with severe disease and mortality.

Methods
We queried the TriNetX database between 2015 and 2022 for patients with babesiosis. The prevalence of Babesia coinfecting tick-borne zoonoses was estimated. The analysis focused on babesiosis coinfection with Borrelia burgdorferi, ehrlichiosis, and anaplasmosis. The exposure was coinfection, and the control group was the Babesia-only group. The primary outcome was 90-day mortality from the diagnosis of Babesia. Secondary outcomes were prevalence of coinfection, association of coinfection with acute respiratory distress syndrome, multiorgan failure, and disseminated intravascular coagulation. A multivariable logistic regression model was employed to estimate the disease severity and mortality risk associated with coinfections.

Results
Of the 3521 patients infected with Babesia, the mean age (SD) was 56 (18) years, 51% were male, and 78% were White. The frequency of overall malignancies, lymphomas, and asplenia was 19%, 2%, and 2%, respectively. Temporal distribution of coinfections followed the overall babesiosis pattern, peaking in the summer months. The prevalence of 1 or more coinfections was 42% (95% CI, 40%–43%). The rate of coinfection with Borrelia burgdorferi was the highest at 41% (95% CI, 39%–42%), followed by ehrlichiosis at 3.7% (95% CI, 3.1%–4.4%) and anaplasmosis at only 0.3% (95% CI, 0.2%–0.6%). Doxycycline was more likely to be prescribed in the coinfection group than the Babesia-only group (25% vs 18%; P &lt; .0001). Overall, 90-day mortality was 1.4% (95% CI, 1.0%–1.8%). After adjusting for potential confounding factors, compared with the babesiosis-only group, the likelihood of 90-day mortality was lower in the coinfection group (adjusted odds ratio, 0.43; 95% CI, 0.20–0.91). Severe disease did not differ significantly between the 2 groups.

Conclusions
In this extensive study of &gt;3000 patients with babesiosis in the United States, 4 in 10 patients had coinfecting tick-borne zoonoses. The prevalence rates of coinfection were highest with Borrelia burgdorferi, followed by ehrlichiosis, and lowest with anaplasmosis. Coinfection with other tick-borne infections was not associated with severe disease. It is plausible that this finding is due to the likelihood of treatment of coinfections with doxycycline. Future studies are needed to investigate the possible therapeutic benefits of doxycycline in babesiosis patients as, to date, no trials with doxycycline have been conducted in human patients with Babesia infections.
Indirect Detection for Higgs Portal Majorana Fermionic Dark Matter
Authors: Haba Naoyuki , Ikemoto Junpei , Shimizu Yasuhiro , Yamada Toshifumi 
Published: October 2024

Abstract
We study the $\gamma$-ray signal emitted from dark matter (DM) pair annihilation in the Higgs portal Majorana fermion DM model. In the model, a Majorana fermion DM $\chi$ couples with the Standard Model (SM) Higgs field $H$ through a higher-dimensional term $-{\cal L}\supset H^\dagger H \bar{\chi }\chi /\Lambda$, where $\Lambda$ is a cutoff scale [1]. The pair annihilation of $\chi$ through the above term produces the Higgs boson and the longitudinal modes of $W,Z$ gauge bosons. The Milky Way dwarf spheroidal satellite galaxies (dSphs) are used as the most promising targets to search for the $\gamma$-ray signal of the model, due to high DM density and lack of astrophysical backgrounds. The Fermi Large Area Telescope (Fermi-LAT) is used for the search, for its high sensitivity [2]. In this work, we use 14-year Fermi-LAT data from 16 dSphs, to constrain the DM pair annihilation cross section for the DM mass range from 125 GeV to 100 TeV.
Essential Competencies for Oncology in Physical Therapist Professional Education Programs: Results of a Mixed Methods Modified Delphi Study
Authors: Harrington Shana E , Wilson Christopher M , Rinehart-Ayres Margaret E , Westlake Frances , VanHoose Lisa 
Published: October 2024

Abstract

Objective
The objective was to establish consensus-based competencies for oncology within physical therapist professional education programs in the United States.

Methods
A mixed-methods approach implementing a sequential exploratory design that included 3 phases was used to establish oncology competencies for physical therapist professional education programs. Participants in each phase were physical therapists representing diverse practice settings, experience levels, and geographical regions. Student physical therapists were included in phases 2 and 3. Three online focus groups were followed by an in-person group discussion to establish cancer-related themes, domains of practice, and competencies. Participants evaluated the competencies in a 3-round modified Delphi study for relevance and clarity. Each competency required 80% consensus using a Likert scale (1 = not at all relevant/clear, 5 = extremely relevant/clear). It was not accepted if a competency did not meet the 80% threshold by the end of round 3.

Results
Six domains of practice and 28 competencies were developed and evaluated. Within the 6 domains, 21 competencies were accepted: general cancer concepts (n = 4), musculoskeletal system (n = 3), neurologic system (n = 5), integumentary system (n = 2), cardiovascular and pulmonary system (n = 5), and involvement of multiple systems across the lifespan (n = 2). Along with the 21 competencies, participants also recommended 11 overarching oncology themes to incorporate into physical therapist professional education programs. Delivering cancer content using a body systems approach was recommended.

Conclusion
As the number of survivors of cancer continues to grow, integration of these essential competencies within physical therapist professional education programs will improve the profession’s capacity to provide quality care to meet the societal need of persons living with and beyond cancer.

Impact
Academic and clinical educators should integrate these competencies to ensure that physical therapist professional education programs appropriately prepare physical therapists for providing care for persons living with and beyond cancer across the lifespan.
The relationship between Zoster serology, vaccination uptake and infection rates: a single-centre cross-sectional study
Authors: Ahmed Saad , Lauran Martin , Ugwoke Adaeze , Walton Tom , Holroyd Chris , Galloway James 
Published: October 2024

Abstract

Objective
This study aimed to assess the prevalence of Varicella-Zoster Virus (VZV) immunity, vaccination uptake and incidence of VZV-related events in inflammatory arthritis (IA) patients initiating biologic or targeted synthetic disease-modifying antirheumatic drugs.

Methods
An observational study was conducted in a single hospital between March 2019 and December 2020. Ninety-three IA patients were included. Data were collected from electronic health records and analysed using the chi-squared test.

Results
The majority of patients (91.4%) were seropositive for VZV, reaffirming the necessity for vaccination. In total, 8.6% of the cohort received the Zostavax vaccine, despite a small yet significant number of patients (4.3%) experiencing Herpes Zoster after initiating treatment. Multiple factors contributed to low vaccine uptake, including limited vaccine availability, discrepancies between the British Society for Rheumatology and Joint Committee on Vaccination and Immunisation guidelines, vaccine hesitancy and concerns regarding vaccine efficacy and risks.

Discussion
Significant VZV immunity exists among patients prior to targeted therapy commencement. Risk factors for VZV-related events include Janus kinase inhibition, increasing age and long-term steroid use. VZV-related events occurred exclusively in patients with prior viral immunity. Despite most patients having serological evidence of prior VZV exposure, our study exposes critical gaps between current clinical guidelines and practice, particularly in VZV vaccine uptake. Barriers to vaccination include inconsistent guidelines, limited vaccine availability and patient-level hesitancy. This is concerning as our cohort demonstrated small but significant rates of zoster, mostly among patients on long-term steroids.
Assessment of local diagnostic reference levels (LDRLS) for full-field digital mammography (FFDM) and digital breast tomosynthesis (DBT) mammography in Tamil Nadu, India
Authors: Adhimoolam Saravana Kumar , Kumar Sudhir , Manojkumar Thangavel , Devanand Bala Lakshmoji , Elango Nagappan , Govindarajan Nagarajarao , Sapra Balvinder Kaur 
Published: October 2024

Abstract
The purpose of this study was to assess local diagnostic reference levels (LDRLs) for full-field digital mammography (FFDM) and digital breast tomosynthesis (DBT) mammography in India. Data from 1500 women were collected from five different mammography facilities in major cities in Tamil Nadu, India. The mean of mean glandular dose were used to arrive at an LDRL. The noted mean compressed breast thickness was 55.26 ± 3.4. The recorded mean MGDs for the five centres were 3.1 ± 0.1 and 3.8 ± 0.2 mGy for FFDM and DBT, respectively. The 75th percentile value for all five centers is 3.3 and 4.0 mGy for FFDM and DBT, respectively. The LDRLs found in the current study were also compared with those from earlier studies conducted in other nations, such as the United Kingdom, Malaysia, Morocco, and Ghana. The present study is the first of its kind to determine the LDRL for the FFDM and DBT scanners operating in the Tamil Nadu region, India, and is proposed as a starting point that will allow professionals to evaluate and optimize their practice. Furthermore, similar studies in other regions of India are necessary in order to establish National DRLs.
Development and safety of investigational and approved drugs targeting the RAS function regulation in RAS mutant cancers
Authors: Li Jinjin , Wu Wentong , Chen Jiajia , Xu Zhifei , Yang Bo , He Qiaojun , Yang Xiaochun , Yan Hao , Luo Peihua 
Published: October 2024

Abstract
The RAS gene family holds a central position in controlling key cellular activities such as migration, survival, metabolism, and other vital biological processes. The activation of RAS signaling cascades is instrumental in the development of various cancers. Although several RAS inhibitors have gained approval from the US Food and Drug Administration for their substantial antitumor effects, their widespread and severe adverse reactions significantly curtail their practical usage in the clinic. Thus, there exists a pressing need for a comprehensive understanding of these adverse events, ensuring the clinical safety of RAS inhibitors through the establishment of precise management guidelines, suitable intermittent dosing schedules, and innovative combination regimens. This review centers on the evolution of RAS inhibitors in cancer therapy, delving into the common adverse effects associated with these inhibitors, their underlying mechanisms, and the potential strategies for mitigation.