bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proton beam therapy for muscle-invasive bladder cancer: A systematic review and analysis with Proton-Net, a multicenter prospective patient registry database
Authors: Araya Masayuki , Ishikawa Hitoshi , Nishioka Kentaro , Maruo Kazushi , Asakura Hirofumi , Iizumi Takashi , Takagi Masaru , Murakami Masao , Azuma Haruhito , Obara Wataru , Aoyama Hidefumi , Sakurai Hideyuki 
Published: April 2023

Abstract
To assess the safety and efficacy of proton beam therapy (PBT) for muscle-invasive bladder cancer (MIBC), we examined the outcomes of 36 patients with MIBC (cT2-4aN0M0) who were enrolled in the Proton-Net prospective registry study and received PBT with concurrent chemotherapy from May 2016 to June 2018. PBT was also compared with X-ray chemoradiotherapy in a systematic review (X-ray (photon) radiotherapy). The radiotherapy consisted of 40–41.4 Gy (relative biological effectiveness (RBE) delivered in 20–23 fractions to the pelvic cavity or the entire bladder using X-rays or proton beams, followed by a boost of 19.8–36.3 Gy (RBE) delivered in 10–14 fractions to all tumor sites in the bladder. Concurrently, radiotherapy was given with intra-arterial or systemic chemotherapy of cisplatin alone or in combination with methotrexate or gemcitabine. Overall survival (OS), progression-free survival (PFS) and local control (LC) rates were 90.8, 71.4 and 84.6%, respectively, after 3 years. Only one case (2.8%) experienced a treatment-related late adverse event of Grade 3 urinary tract obstruction, and no severe gastrointestinal adverse events occurred. According to the findings of the systematic review, the 3-year outcomes of XRT were 57–84.8% in OS, 39–78% in PFS and 51–68% in LC. The weighted mean frequency of adverse events of Grade 3 or higher in the gastrointestinal and genitourinary systems was 6.2 and 2.2%, respectively. More data from long-term follow-up will provide us with the appropriate use of PBT and validate its efficacy for MIBC.
Propyl-cyanide isomer formation on interstellar ices from radical association: a quantum theoretical study
Authors: Kerkeni Boutheïna , Gámez Victoria , Ouerfelli Ghofrane , Senent Maria Luisa , Feautrier Nicole 
Published: April 2023

ABSTRACT
Both linear and branched isomers of propyl cyanide (PrCN; C3H7CN) are ubiquitous in interstellar space. To date, PrCN is one of the most complex molecules found in the interstellar medium. Furthermore, it is the only one observed species to share the branched atomic backbone of amino acids, some of the building blocks of life. Radical–radical chemical reactions are examined in detail using density functional theory, ab initio methods, and the energy resolved master equation formalism to compute rate constants at a low pressure value prevalent in the ISM. Quantum chemical studies are reported for both isomers considering two possibilities: the gas phase association and the surface reactions of radicals on a 34-water amorphous ice model. The reaction mechanism involves the following radicals association: CH3CHCH3 + CN, CH3 + CH3CHCN and CH3CH2 + CH2CN, CH3 + CH2CH2CN, CN + CH3CH2CH2 for iso-PrCN and n-PrCN formation, respectively. Two DFT methods: M062X and ωB97XD with the 6-311++G(d,p) basis set were tested for reactions in gas phase and on the ice mantle. In the gas phase, MP2/aug-cc-pVTZ level of theory is also used, and the energetics of the five reactions are calculated using explicitly correlated coupled cluster (CCSD(T)-F12) method. All reaction paths are exoergic and barrierless in the gas phase and on the ice-model, suggesting that the formation of iso-PrCN and n-PrCN is efficient on the ice model adopted in this paper. The gas phase rate constants of formation of both isomers can be eventually used as a high limit for the solid state reactions.
The XMM cluster survey: exploring scaling relations and completeness of the dark energy survey year 3 redMaPPer cluster catalogue
Authors: Upsdell E W , Giles P A , Romer A K , Wilkinson R , Turner D J , Hilton M , Rykoff E , Farahi A , Bhargava S , Jeltema T , Klein M , Bermeo A , Collins C A , Ebrahimpour L , Hollowood D , Mann R G , Manolopoulou M , Miller C J , Rooney P J , Sahlén Martin , Stott J P , Viana P T P , Allam S , Alves O , Bacon D , Bertin E , Bocquet S , Brooks D , Burke D L , Carrasco Kind M , Carretero J , Costanzi M , da Costa L N , Pereira M E S , De Vicente J , Desai S , Diehl H T , Dietrich J P , Everett S , Ferrero I , Frieman J , García-Bellido J , Gerdes D W , Gutierrez G , Hinton S R , Honscheid K , James D J , Kuehn K , Kuropatkin N , Lima M , Marshall J L , Mena-Fernández J , Menanteau F , Miquel R , Mohr J J , Ogando R L C , Pieres A , Raveri M , Rodriguez-Monroy M , Sanchez E , Scarpine V , Sevilla-Noarbe I , Smith M , Suchyta E , Swanson M E C , Tarle G , To C , Weaverdyck N , Weller J , Wiseman P 
Published: April 2023

ABSTRACT
We cross-match and compare characteristics of galaxy clusters identified in observations from two sky surveys using two completely different techniques. One sample is optically selected from the analysis of 3 years of Dark Energy Survey observations using the redMaPPer cluster detection algorithm. The second is X-ray selected from XMM observations analysed by the XMM Cluster Survey. The samples comprise a total area of 57.4 deg2, bounded by the area of four contiguous XMM survey regions that overlap the DES footprint. We find that the X-ray-selected sample is fully matched with entries in the redMaPPer catalogue, above λ &gt; 20 and within 0.1 &lt;$z$ &lt;0.9. Conversely, only 38 per cent of the redMaPPer catalogue is matched to an X-ray extended source. Next, using 120 optically clusters and 184 X-ray-selected clusters, we investigate the form of the X-ray luminosity–temperature (LX –TX ), luminosity–richness (LX –λ), and temperature–richness (TX –λ) scaling relations. We find that the fitted forms of the LX –TX relations are consistent between the two selection methods and also with other studies in the literature. However, we find tentative evidence for a steepening of the slope of the relation for low richness systems in the X-ray-selected sample. When considering the scaling of richness with X-ray properties, we again find consistency in the relations (i.e. LX –λ and TX –λ) between the optical and X-ray-selected samples. This is contrary to previous similar works that find a significant increase in the scatter of the luminosity scaling relation for X-ray-selected samples compared to optically selected samples.
Large-scale density and velocity field reconstructions with neural networks
Authors: Ganeshaiah Veena Punyakoti , Lilow Robert , Nusser Adi 
Published: April 2023

ABSTRACT
We assess a neural network (NN) method for reconstructing 3D cosmological density and velocity fields (target) from discrete and incomplete galaxy distributions (input). We employ second-order Lagrangian Perturbation Theory to generate a large ensemble of mock data to train an auto-encoder (AE) architecture with a Mean Squared Error (MSE) loss function. The AE successfully captures non-linear features arising from gravitational dynamics and the discreteness of the galaxy distribution. It preserves the positivity of the reconstructed density field and exhibits a weaker suppression of the power on small scales than the traditional linear Wiener filter (WF), which we use as a benchmark. In the density reconstruction, the reduction of the AE MSE relative to the WF is $\sim 15~{{\ \rm per\ cent}}$ , whereas for the velocity reconstruction a relative reduction of up to a factor of two can be achieved. The AE is advantageous to the WF at recovering the distribution of the target fields, especially at the tails. In fact, trained with an MSE loss, any NN estimate approaches the unbiased mean of the underlying target given the input. This implies a slope of unity in the linear regression of the true on the NN-reconstructed field. Only for the special case of Gaussian fields, the NN and WF estimates are equivalent. Nonetheless, we also recover a linear regression slope of unity for the WF with non-Gaussian fields.
A potential histone-chaperone activity for the MIER1 histone deacetylase complex
Authors: Wang Siyu , Fairall Louise , Pham Trong Khoa , Ragan Timothy J , Vashi Dipti , Collins Mark O , Dominguez Cyril , Schwabe John W R 
Published: April 2023

Abstract
Histone deacetylases 1 and 2 (HDAC1/2) serve as the catalytic subunit of six distinct families of nuclear complexes. These complexes repress gene transcription through removing acetyl groups from lysine residues in histone tails. In addition to the deacetylase subunit, these complexes typically contain transcription factor and/or chromatin binding activities. The MIER:HDAC complex has hitherto been poorly characterized. Here, we show that MIER1 unexpectedly co-purifies with an H2A:H2B histone dimer. We show that MIER1 is also able to bind a complete histone octamer. Intriguingly, we found that a larger MIER1:HDAC1:BAHD1:C1QBP complex additionally co-purifies with an intact nucleosome on which H3K27 is either di- or tri-methylated. Together this suggests that the MIER1 complex acts downstream of PRC2 to expand regions of repressed chromatin and could potentially deposit histone octamer onto nucleosome-depleted regions of DNA.
Co-activation for enhanced K-ion storage in battery anodes
Authors: Feng Yanhong , Lv Yawei , Fu Hongwei , Parekh Mihir , Rao Apparao M , Wang He , Tai Xiaolin , Yi Xianhui , Lin Yue , Zhou Jiang , Lu Bingan 
Published: April 2023

ABSTRACT
The relative natural abundance of potassium and potentially high energy density has established potassium-ion batteries as a promising technology for future large-scale global energy storage. However, the anodes’ low capacity and high discharge platform lead to low energy density, which impedes their rapid development. Herein, we present a possible co-activation mechanism between bismuth (Bi) and tin (Sn) that enhances K-ion storage in battery anodes. The co-activated Bi-Sn anode delivered a high capacity of 634 mAh g–1, with a discharge plateau as low as 0.35 V, and operated continuously for 500 cycles at a current density of 50 mA g–1, with a high Coulombic efficiency of 99.2%. This possible co-activation strategy for high potassium storage may be extended to other Na/Zn/Ca/Mg/Al ion battery technologies, thus providing insights into how to improve their energy storage ability.
Culture-Positive and Culture-Negative Empyema After Thoracoscopic Decortication: A Comparison of Short-term and Long-term Outcomes
Authors: Cheng Ya-Fu , Chen Yi-Ling , Cheng Ching-Yuan , Huang Chang-Lun , Hung Wei-Heng , Wang Bing-Yen 
Published: April 2023

AbstractBackgroundEmpyema thoracis is a serious infectious disease and is associated with high morbidity and mortality. The perioperative outcomes between culture-positive and culture-negative empyema after thoracoscopic decortication remained controversial, especially since there were no studies that reported the survival outcomes between culture-positive and culture-negative empyema.MethodsThis single-institute study involved a retrospective analysis. Patients with empyema thoracis who underwent thoracoscopic decortication between January 2012 and December 2021 were included in the study. Patients were grouped into a culture-positive group and a culture-negative group according to culture results obtained no later than 2 weeks after surgery.ResultsA total of 1087 patients with empyema received surgery, and 824 were enrolled after exclusion. Among these, 366 patients showed positive culture results and 458 patients showed negative results. Longer intensive care unit stays (11.69 vs 5.64 days, P &lt; .001), longer ventilator usage (24.70 vs 14.01 days, P = .002), and longer postoperative hospital stays (40.83 vs 28.37 days, P &lt; .001) were observed in the culture-positive group. However, there was no significant difference in 30-day mortality between the 2 groups (5.2% in culture negative vs 5.0% in culture positive, P = .913). The 2-year survival was not significantly different between the 2 groups (P = .236).ConclusionsPatients with culture-positive or culture-negative empyema who underwent thoracoscopic decortication showed similar short-term and long-term survival outcomes. A higher risk of death was associated with advanced age, a higher Charlson Comorbidity Index score, phase III empyema, and a cause other than pneumonia.
Glyceraldehyde-3-phosphate dehydrogenase subunits A and B are essential to maintain photosynthetic efficiency
Authors: Simkin Andrew J , Alqurashi Mohammed , Lopez-Calcagno Patricia E , Headland Lauren R , Raines Christine A 
Published: April 2023

Abstract
In plants, glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12) reversibly converts 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate coupled with the reduction of NADPH to NADP+. The GAPDH enzyme that functions in the Calvin–Benson cycle is assembled either from 4 glyceraldehyde-3-phosphate dehydrogenase A (GAPA) subunit proteins forming a homotetramer (A4) or from 2 GAPA and 2 glyceraldehyde-3-phosphate dehydrogenase B (GAPB) subunit proteins forming a heterotetramer (A2B2). The relative importance of these 2 forms of GAPDH in determining the rate of photosynthesis is unknown. To address this question, we measured the photosynthetic rates of Arabidopsis (Arabidopsis thaliana) plants containing reduced amounts of the GAPDH A and B subunits individually and jointly, using T-DNA insertion lines of GAPA and GAPB and transgenic GAPA and GAPB plants with reduced levels of these proteins. Here, we show that decreasing the levels of either the A or B subunits decreased the maximum efficiency of CO2 fixation, plant growth, and final biomass. Finally, these data showed that the reduction in GAPA protein to 9% wild-type levels resulted in a 73% decrease in carbon assimilation rates. In contrast, eliminating GAPB protein resulted in a 40% reduction in assimilation rates. This work demonstrates that the GAPA homotetramer can compensate for the loss of GAPB, whereas GAPB alone cannot compensate fully for the loss of the GAPA subunit.
Impact of the COVID-19 pandemic on patients with rheumatoid arthritis: data from the Ontario Best Practices Research Initiative (OBRI)
Authors: Wong-Pack Matthew , Hepworth Elliot , Movahedi Mohammad , Kuriya Bindee , Pope Janet , Keystone Edward , Thorne Carter , Ahluwalia Vandana , Cesta Angela , Mously Carol , Bombardier Claire , Lau Arthur , Aydin Sibel Zehra 
Published: April 2023

Abstract

Objective
The coronavirus disease 2019 (COVID-19) pandemic created challenges for patients with RA. We examined the potential impact of the pandemic on patient-reported outcomes (PROs), disease activity and medication profiles, comparing the periods pre-pandemic and during the pandemic.

Methods
Patients enrolled in the Ontario Best Practices Research Initiative were included if they had at least one visit to a physician or study interviewer within 12 months before and after the start of pandemic-related closures in Ontario (15 March 2020). Baseline characteristics, disease activity, PROs [i.e. health assessment questionnaire disability index, RA disease activity index (RADAI), European quality of life five-dimension questionnaire], medication use and changes were included. Student’s paired two-sample t-tests and McNamar’s tests were performed for continuous and categorical variables between time periods.

Results
The sample for analysis consisted of 1508 patients, with a mean (s.d.) age of 62.7 (12.5) years, and 79% were female. Despite decreases in the number of in-person visits during the pandemic, there was no significant negative impact on disease activity or PRO scores. The DASs in both periods remained low, with either no clinically significant differences or slight improvement. Scores for mental, social and physical health were either stable or improved. There were statistically significant decreases in conventional synthetic DMARD use (P &lt; 0.0001) and increased Janus kinase inhibitor usage (P = 0.0002). Biologic DMARD use remained stable throughout the pandemic.

Conclusion
In this cohort, disease activity and PROs of RA patients remained stable during the COVID-19 pandemic. The longer-term outcomes of the pandemic warrant investigation.
Characteristics and Outcomes of Squamous Cell Carcinoma and Other Cutaneous Malignancies in Epidermolysis Bullosa: A Systematic Review
Authors: Kim Patrick Jinhyung , Abduelmula Abrahim , Mistry Jenna , Mufti Asfandyar , Sibbald R. Gary 
Published: April 2023

ABSTRACT

OBJECTIVE
To identify cases and summarize outcomes of cutaneous malignancies in patients with epidermolysis bullosa (EB).

DATA SOURCES
MEDLINE and EMBASE databases were searched on February 8, 2022.

STUDY SELECTION
Original observational or experimental studies with cases of cutaneous malignancy in patients with inherited EB were included.

DATA EXTRACTION
Data were extracted by two reviewers in duplicate.

DATA SYNTHESIS
A total of 87 articles with 367 patients were included in this systematic review. Squamous cell carcinomas were the most common malignancy (94.3%) with a median survival of 60 months. The presence of metastasis was investigated at diagnosis in 77 patients; 18.8% of patients had detectable metastasis. Patients with squamous cell carcinoma with metastasis at diagnosis had significantly shorter median survival (16.8 months) than those without (72 months; P = .027). The remission rate was 47.6%. At the end of follow-up, 15.1% were alive with disease, and 41.6% were deceased. Other malignancies included malignant melanoma and basal cell carcinoma. The most common initial modes of management were excisions (71.9%) and amputations (17.6%). Other modes included chemotherapy (4.6%), radiation (3.9%), and no treatment (2.6%). The overall rate of recurrence or new lesions was 38.8%, with a median time of 16 months to recurrence or new lesions. Immediate recurrence was lowest following amputation (4.3%). There were no statistically significant differences in median survival among initial excision, amputation, and all other modes combined (P = .30).

CONCLUSIONS
Squamous cell carcinomas in patients with EB have a high likelihood of metastasis and mortality. Surgical excision is the most common intervention. There are no significant differences in survival among different initial management options. There is a need for research that documents and monitors outcomes of the treatment options.
Type-2-low severe asthma endotypes for new treatments: the new asthma frontier
Authors: Chung Kian Fan 
Published: April 2023

Purpose of review
Type-2 (T2)-high asthma represents a well defined group of severe eosinophilic asthma for which there are now effective biologic therapies targetting the interleukins (ILs) 4, 5 and 13, and Immunoglobulin E. T2-low asthma detected in the clinic by a low blood eosinophil count remains ill-defined and is the focus of this review.

Recent findings
By analysing transcriptomic and proteomic expression in sputum samples in U-BIOPRED cohort, both T2-high and -low molecular phenotypes have been described. Using clustering approaches, a neutrophilic-predominant cluster associated with activation markers of neutrophilic and inflammasome activation with interferon and tumour necrosis factor expression, together with a cluster of paucigranulocytic inflammation linked to oxidative phosphorylation and senescence pathways have been described. Using gene set variation analysis, specific molecular phenotypes driven by IL-6 trans-signalling pathway, or those by IL-6, IL-17 and IL-22 pathways were identified linked to a mixed granulocytic or neutrophilic inflammation.

Summary
Previous trials of antineutrophilic agents in asthma have failed because enrolled patients were not specifically chosen for these targeted treatments. Although the T2-low molecular pathways should be validated in other cohorts, the availability of targeted therapies indicated for other autoimmune conditions should encourage a trial of these respective biological therapies for these specific molecular phenotypes.
Postoperative delirium: identifying the patient at risk and altering the course
Authors: Hoogma Danny Feike , Milisen Koen , Rex Steffen , Al tmimi Layth 
Published: April 2023

Postoperative delirium (POD) is a common neurocognitive syndrome seen in older patients after major surgery. POD is linked to longer stays in hospital and intensive care, a greater incidence of postoperative complications, worse functional outcome, and higher mortality. Researchers have not yet fully elucidated the exact pathophysiology of POD. Several risk factors that contribute to the development of POD have been identified, such as advanced age, cardiac or hip surgery, preoperative cognitive decline or delirium, disturbances in brain levels of neurotransmitters and information processing, oxidative stress and neuro-inflammation.
Identifying patients at risk for POD enables a more precise and efficient allocation of medical resources and facilitates POD prevention and management.
The present review addresses how to identify patients at risk of POD and summarizes the currently available evidence and best-practice recommendations for peri-operative management and prevention of POD.
Matrisome gene-based subclassification of patients with liver fibrosis identifies clinical and molecular heterogeneities
Authors: Chen Wei , Sun Yameng , Chen Shuyan , Ge Xiaodong , Zhang Wen , Zhang Ning , Wu Xiaoning , Song Zhuolun , Han Hui , Desert Romain , Yan Xuzhen , Yang Aiting , Das Sukanta , Athavale Dipti , Nieto Natalia , You Hong 
Published: April 2023

Background & Aims:
Excessive deposition and crosslinking of extracellular matrix increases liver density and stiffness, promotes fibrogenesis, and increases resistance to fibrinolysis. An emerging therapeutic opportunity in liver fibrosis is to target the composition of the extracellular matrix or block pathogenic communication with surrounding cells. However, the type and extent of extracellular changes triggering liver fibrosis depend on the underlying etiology. Our aim was to unveil matrisome genes not dependent on etiology, which are clinically relevant to liver fibrosis.

Approach & Results:
We used transcriptomic profiles from liver fibrosis cases of different etiologies to identify and validate liver fibrosis-specific matrisome genes (LFMGs) and their clinical and biological relevance. Dysregulation patterns and cellular landscapes of LFMGs were further explored in mouse models of liver fibrosis progression and regression by bulk and single-cell RNA sequencing. We identified 35 LFMGs, independent of etiology, representing an LFMG signature defining liver fibrosis. Expression of the LFMG signature depended on histological severity and was reduced in regressive livers. Patients with liver fibrosis, even with identical pathological scores, could be subclassified into LFMGLow and LFMGHigh, with distinguishable clinical, cellular, and molecular features. Single-cell RNA sequencing revealed that microfibrillar-associated protein 4+ activated HSC increased in LFMGHigh patients and were primarily responsible for the LFMG signature expression and dysregulation.

Conclusions:
The microfibrillar-associated protein 4+ -activated HSC-derived LFMG signature classifies patients with liver fibrosis with distinct clinical and biological characteristics. Our findings unveil hidden information from liver biopsies undetectable using traditional histologic assessments.