bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hit it hard: qualitative patient perspectives on the optimisation of immune checkpoint inhibition
Authors: Merrick Sophie , Rush Hannah L. , Daniels Susanna , Fielding Alison , Deveson Kell Sharon , Pickering Lisa , Langley Ruth E. , South Annabelle , Gilbert Duncan C. 
Published: June 2024

Abstract
Background
Immune checkpoint inhibitors have transformed the treatment landscape of many cancers, including melanoma and renal cell carcinoma (RCC). Randomised trials are evaluating outcomes from reduced ICI treatment schedules with the aim of improving quality of life, tolerability, and cost-effectiveness. This study aims to provide insight into patient and carer’s perspectives of these trials.

Methods
Seven focus groups were conducted with 31 people with stage IV melanoma, RCC, or caregivers for people receiving ICI. Transcripts were analysed using reflexive thematic analysis.

Results
Three themes were generated: 1) “Treatment and clinic visits provide reassurance”: reducing hospital visits may not improve quality of life. 2) “Assessment of personal risk versus benefit”: the decision to participate in an ICI optimisation trial is influenced by treatment response, experience of toxicity and perceived logistical benefits based on the individual’s circumstances. 3) “Pre-existing experience and beliefs about how treatment and trials work”, including the belief that more treatment is better, influence views around ICI optimisation trials.

Conclusion
This study provides insight into recruitment challenges and recommends strategies to enhance recruitment for ongoing ICI optimisation trials. These findings will influence the design of future ICI optimisation trials ensuring they are acceptable to patients.
Structural basis of S-adenosylmethionine-dependent allosteric transition from active to inactive states in methylenetetrahydrofolate reductase
Authors: Yamada Kazuhiro , Mendoza Johnny , Koutmos Markos 
Published: June 2024

AbstractMethylenetetrahydrofolate reductase (MTHFR) is a pivotal flavoprotein connecting the folate and methionine methyl cycles, catalyzing the conversion of methylenetetrahydrofolate to methyltetrahydrofolate. Human MTHFR (hMTHFR) undergoes elaborate allosteric regulation involving protein phosphorylation and S-adenosylmethionine (AdoMet)-dependent inhibition, though other factors such as subunit orientation and FAD status remain understudied due to the lack of a functional structural model. Here, we report crystal structures of Chaetomium thermophilum MTHFR (cMTHFR) in both active (R) and inhibited (T) states. We reveal FAD occlusion by Tyr361 in the T-state, which prevents substrate interaction. Remarkably, the inhibited form of cMTHFR accommodates two AdoMet molecules per subunit. In addition, we conducted a detailed investigation of the phosphorylation sites in hMTHFR, three of which were previously unidentified. Based on the structural framework provided by our cMTHFR model, we propose a possible mechanism to explain the allosteric structural transition of MTHFR, including the impact of phosphorylation on AdoMet-dependent inhibition.
Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation
Authors: Nacev Benjamin A. , Dabas Yakshi , Paul Matthew R. , Pacheco Christian , Mitchener Michelle , Perez Yekaterina , Fang Yan , Soshnev Alexey A. , Barrows Douglas , Carroll Thomas , Socci Nicholas D. , St. Jean Samantha C. , Tiwari Sagarika , Gruss Michael J. , Monette Sebastien , Tap William D. , Garcia Benjamin A. , Muir Tom , Allis C. David 
Published: June 2024

AbstractDysregulated epigenetic states are a hallmark of cancer and often arise from genetic alterations in epigenetic regulators. This includes missense mutations in histones, which, together with associated DNA, form nucleosome core particles. However, the oncogenic mechanisms of most histone mutations are unknown. Here, we demonstrate that cancer-associated histone mutations at arginines in the histone H3 N-terminal tail disrupt repressive chromatin domains, alter gene regulation, and dysregulate differentiation. We find that histone H3R2C and R26C mutants reduce transcriptionally repressive H3K27me3. While H3K27me3 depletion in cells expressing these mutants is exclusively observed on the minor fraction of histone tails harboring the mutations, the same mutants recurrently disrupt broad H3K27me3 domains in the chromatin context, including near developmentally regulated promoters. H3K27me3 loss leads to de-repression of differentiation pathways, with concordant effects between H3R2 and H3R26 mutants despite different proximity to the PRC2 substrate, H3K27. Functionally, H3R26C-expressing mesenchymal progenitor cells and murine embryonic stem cell-derived teratomas demonstrate impaired differentiation. Collectively, these data show that cancer-associated H3 N-terminal arginine mutations reduce PRC2 activity and disrupt chromatin-dependent developmental functions, a cancer-relevant phenotype.
Landform and lithospheric development contribute to the assembly of mountain floras in China
Authors: Zhao Wan-Yi , Liu Zhong-Cheng , Shi Shi , Li Jie-Lan , Xu Ke-Wang , Huang Kang-You , Chen Zhi-Hui , Wang Ya-Rong , Huang Cui-Ying , Wang Yan , Chen Jing-Rui , Sun Xian-Ling , Liang Wen-Xing , Guo Wei , Wang Long-Yuan , Meng Kai-Kai , Li Xu-Jie , Yin Qian-Yi , Zhou Ren-Chao , Wang Zhao-Dong , Wu Hao , Cui Da-Fang , Su Zhi-Yao , Xin Guo-Rong , Liu Wei-Qiu , Shu Wen-Sheng , Jin Jian-Hua , Boufford David E. , Fan Qiang , Wang Lei , Chen Su-Fang , Liao Wen-Bo 
Published: June 2024

AbstractAlthough it is well documented that mountains tend to exhibit high biodiversity, how geological processes affect the assemblage of montane floras is a matter of ongoing research. Here, we explore landform-specific differences among montane floras based on a dataset comprising 17,576 angiosperm species representing 140 Chinese mountain floras, which we define as the collection of all angiosperm species growing on a specific mountain. Our results show that igneous bedrock (granitic and karst-granitic landforms) is correlated with higher species richness and phylogenetic overdispersion, while the opposite is true for sedimentary bedrock (karst, Danxia, and desert landforms), which is correlated with phylogenetic clustering. Furthermore, we show that landform type was the primary determinant of the assembly of evolutionarily older species within floras, while climate was a greater determinant for younger species. Our study indicates that landform type not only affects montane species richness, but also contributes to the composition of montane floras. To explain the assembly and differentiation of mountain floras, we propose the ‘floristic geo-lithology hypothesis’, which highlights the role of bedrock and landform processes in montane floristic assembly and provides insights for future research on speciation, migration, and biodiversity in montane regions.
NCF4 attenuates colorectal cancer progression by modulating inflammasome activation and immune surveillance
Authors: Li Longjun , Mao Rudi , Yuan Shenli , Xie Qingqing , Meng Jinyu , Gu Yu , Tan Siyu , Xu Xiaoqing , Gao Chengjiang , Liu Hongbin , Ma Chunhong , Man Si Ming , Meng Xiangbo , Xu Tao , Qi Xiaopeng 
Published: June 2024

AbstractThe spatiotemporal regulation of inflammasome activation remains unclear. To examine the mechanism underlying the assembly and regulation of the inflammasome response, here we perform an immunoprecipitation-mass spectrometry analysis of apoptosis-associated speck-like protein containing a CARD (ASC) and identify NCF4/1/2 as ASC-binding proteins. Reduced NCF4 expression is associated with colorectal cancer development and decreased five-year survival rate in patients with colorectal cancer. NCF4 cooperates with NCF1 and NCF2 to promote NLRP3 and AIM2 inflammasome activation. Mechanistically, NCF4 phosphorylation and puncta distribution switches from the NADPH complex to the perinuclear region, mediating ASC oligomerization, speck formation and inflammasome activation. NCF4 functions as a sensor of ROS levels, to establish a balance between ROS production and inflammasome activation. NCF4 deficiency causes severe colorectal cancer in mice, increases transit-amplifying and precancerous cells, reduces the frequency and activation of CD8+ T and NK cells, and impairs the inflammasome-IL-18-IFN-γ axis during the early phase of colorectal tumorigenesis. Our study implicates NCF4 in determining the spatial positioning of inflammasome assembly and contributing to inflammasome-mediated anti-tumor responses.
BCN20000: Dermoscopic Lesions in the Wild
Authors: Hernández-Pérez Carlos , Combalia Marc , Podlipnik Sebastian , Codella Noel C. F. , Rotemberg Veronica , Halpern Allan C. , Reiter Ofer , Carrera Cristina , Barreiro Alicia , Helba Brian , Puig Susana , Vilaplana Veronica , Malvehy Josep 
Published: June 2024

AbstractAdvancements in dermatological artificial intelligence research require high-quality and comprehensive datasets that mirror real-world clinical scenarios. We introduce a collection of 18,946 dermoscopic images spanning from 2010 to 2016, collated at the Hospital Clínic in Barcelona, Spain. The BCN20000 dataset aims to address the problem of unconstrained classification of dermoscopic images of skin cancer, including lesions in hard-to-diagnose locations such as those found in nails and mucosa, large lesions which do not fit in the aperture of the dermoscopy device, and hypo-pigmented lesions. Our dataset covers eight key diagnostic categories in dermoscopy, providing a diverse range of lesions for artificial intelligence model training. Furthermore, a ninth out-of-distribution (OOD) class is also present on the test set, comprised of lesions which could not be distinctively classified as any of the others. By providing a comprehensive collection of varied images, BCN20000 helps bridge the gap between the training data for machine learning models and the day-to-day practice of medical practitioners. Additionally, we present a set of baseline classifiers based on state-of-the-art neural networks, which can be extended by other researchers for further experimentation.
ForametCeTera, a novel CT scan dataset to expedite classification research of (non-)foraminifera
Authors: Luijmes Joost , van Leeuwen Tristan , Renema Willem 
Published: June 2024

AbstractThis paper introduces ForametCeTera, a pioneering dataset designed to address the challenges associated with automating the analysis of benthic foraminifera in sediment cores. Foraminifera are sensitive sentinels of environmental change and are a crucial component of carbonate-denominated ecosystems, such as coral reefs. Studying their prevalence and characteristics is imperative in understanding climate change. However, analysis of foraminifera contained in core samples currently requires washing, sieving and manual quantification. These methods are thus time-consuming and require trained experts. To overcome these limitations, we propose an alternative workflow utilizing 3D X-ray computational tomography (CT) for fully automated analysis, saving time and resources. Despite recent advancements in automation, a crucial lack of methods persists for segmenting and classifying individual foraminifera from 3D scans. In response, we present ForametCeTera, a diverse dataset featuring 436 3D CT scans of individual foraminifera and non-foraminiferan material following a high-throughput scanning workflow. ForametCeTera serves as a foundational resource for generating synthetic digital core samples, facilitating the development of segmentation and classification methods of entire core sample CT scans.
The impact of ZTE-based MR attenuation correction compared to CT-AC in 18F-FBPA PET before boron neutron capture therapy
Authors: Lo Yi-Wen , Lin Ko-Han , Lee Chien-Ying , Li Chia-Wei , Lin Chien-Yuan , Chen Yi-Wei , Wang Ling-Wei , Wu Yuan-Hung , Huang Wen-sheng 
Published: June 2024

AbstractTumor-to-normal ratio (T/N) measurement of 18F-FBPA is crucial for patient eligibility to receive boron neutron capture therapy. This study aims to compare the difference in standard uptake value ratios on brain tumors and normal brains using PET/MR ZTE and atlas-based attenuation correction with the current standard PET/CT attenuation correction. Regarding the normal brain uptake, the difference was not significant between PET/CT and PET/MR attenuation correction methods. The T/N ratio of PET/CT-AC, PET/MR ZTE-AC and PET/MR AB-AC were 2.34 ± 0.95, 2.29 ± 0.88, and 2.19 ± 0.80, respectively. The T/N ratio comparison showed no significance using PET/CT-AC and PET/MR ZTE-AC. As for the PET/MRI AB-AC, significantly lower T/N ratio was observed (− 5.18 ± 9.52%; p < 0.05). The T/N difference between ZTE-AC and AB-AC was also significant (4.71 ± 5.80%; p < 0.01). Our findings suggested PET/MRI imaging using ZTE-AC provided superior quantification on 18F-FBPA-PET compared to atlas-based AC. Using ZTE-AC on 18F-FBPA-PET /MRI might be crucial for BNCT pre-treatment planning.
A novel Hellinger distance-based regret theory method for spherical fuzzy decision making model and its application in logistics
Authors: Ren Haiping , Zhou Hui 
Published: June 2024

AbstractActual decision making problems are often based on the company decision maker’s behavior factors, such as risk attitude, subjective preference, etc. Regret theory can well express the behavior of the decision maker. In this pursuit, a novel decision making method was developed, based on the regret theory for the multi-attribute decision making problem, in which attribute values were expressed by spherical fuzzy numbers. Distance measurement not only has extensive applications in fields such as pattern recognition and image processing, but also plays an important role in the research of fuzzy decision theory. The existing distance measures of spherical fuzzy set either have special cases of anti-intuition or are more complex in calculation, so finding suitable distance measures is also an important research topic in the decision-making theory of spherical fuzzy set. For this reason, we first establish a new distance of spherical fuzzy sets based on Hellinger distance of probability distribution. A decision maker’s perception utility value function is proposed using the new distance formula, which is used to measure the regretful and rejoice value. Then we establish an optimization model for solving the attribute weights, when the information of attribute weight was partially known. Subsequently, the comprehensive perceived utility values were utilized to rank the order of the alternatives. Finally, a numerical example of assessment of logistics providers is used to show that the new decision making method is effective and feasible.
A method to accelerate computational efficiency by more than two orders of magnitude for Monte Carlo simulations of electron-solid interactions
Authors: Shao Lin 
Published: June 2024

AbstractA method has been developed to increase computational efficiency in Monte Carlo simulations of electron transport and interactions in matter. The method serves as the computational engine for the open-source code AMCSET (Aggie Monte Carlo Simulations of Electron and Ion Transport). The key is to combine n consecutive neighboring free flying distances into groups. Within each group, both flying distance and Mott scattering angles are obtained using Monte Carlo sampling under an equal energy approximation. This reduces the number of integrations of the tabulated differential Mott scattering cross-section in scattering angle selection, i.e., from 1000 to 1 if n = 1000. The method increases efficiency by more than 100 times. At the same time, the calculation still guarantees accuracy in calculating electron trajectory, excitation/ionization energy deposition, elastic scattering energy deposition, and displacement creation. For demonstration, 10 MeV electron bombardments of pure Fe with n up to 1000 are used as examples. The method, due to the availability of tabulated scattering cross-sections, is applicable for targets of the entire elemental table up to Z = 118, and for electron energies up to 900 MeV.
Association of blood group O with a recurrent risk for acute lower gastrointestinal bleeding from a multicenter cohort study
Authors: Suzuki Sho , Tominaga Naoyuki , Aoki Tomonori , Sadashima Eiji , Miike Tadashi , Kawakami Hiroshi , Kobayashi Katsumasa , Yamauchi Atsushi , Yamada Atsuo , Omori Jun , Ikeya Takashi , Aoyama Taiki , Sato Yoshinori , Kishino Takaaki , Ishii Naoki , Sawada Tsunaki , Murata Masaki , Takao Akinari , Mizukami Kazuhiro , Kinjo Ken , Fujimori Shunji , Uotani Takahiro , Fujita Minoru , Sato Hiroki , Narasaka Toshiaki , Hayasaka Junnosuke , Funabiki Tomohiro , Kinjo Yuzuru , Mizuki Akira , Kiyotoki Shu , Mikami Tatsuya , Gushima Ryosuke , Fujii Hiroyuki , Fuyuno Yuta , Hikichi Takuto , Toya Yosuke , Narimatsu Kazuyuki , Manabe Noriaki , Nagaike Koji , Kinjo Tetsu , Sumida Yorinobu , Funakoshi Sadahiro , Kobayashi Kiyonori , Matsuhashi Tamotsu , Komaki Yuga , Kaise Mitsuru , Nagata Naoyoshi 
Published: June 2024

AbstractThe relationship between blood group and rebleeding in acute lower gastrointestinal bleeding (ALGIB) remains unclear. This study aimed to investigate the association between blood group O and clinical outcomes in patients with ALGIB. The study included 2336 patients with ALGIB whose bleeding source was identified during initial endoscopy (from the CODE BLUE-J Study). The assessed outcomes encompassed rebleeding and other clinical parameters. The rebleeding rates within 30 days in patients with blood group O and those without blood group O were 17.9% and 14.9%, respectively. Similarly, the rates within 1 year were 21.9% for patients with blood group O and 18.2% for those without blood group O. In a multivariate analysis using age, sex, vital signs at presentation, blood test findings, comorbidities, antithrombotic medication, active bleeding, and type of endoscopic treatment as covariates, patients with blood group O exhibited significantly higher risks for rebleeding within 30 days (odds ratio [OR] 1.31; 95% confidence interval [CI] 1.04–1.65; P = 0.024) and 1 year (OR 1.29; 95% CI 1.04–1.61; P = 0.020) compared to those without blood group O. However, the thrombosis and mortality rates did not differ significantly between blood group O and non-O patients. In patients with ALGIB, blood group O has been identified as an independent risk factor for both short- and long-term rebleeding.
Transformation behavior of hazardous jarosite into recyclable hematite in a solution with high concentrations of K+ and Na+
Authors: Xing Yubo , Deng Zhigan , Wei Chang , Li Xingbin , Li Minting 
Published: June 2024

AbstractIron in the leaching solution with high K+ and Na+ concentrations was usually precipitated as the typical hazardous and toxic jarosite residues. However, this method of treatment has been greatly restricted by increasingly strict environmental regulations. Here we propose that iron can be precipitated from the solution with high K+ and Na+ concentrations as recyclable hematite products by adjusting the concentration ratio of sodium and potassium ions in the solution. The transformation behavior of jarosite into hematite in high concentration potassium ion and sodium ion solution was explained based on collision theory. The results indicated that in instances where the concentration ratio of Na+/K+ is ≥ 4:1, the iron present in the solution can be effectively precipitated as a recyclable hematite product, as opposed to forming the conventional hazardous jarosite residue, even under conditions where the potassium ion concentration reaches levels as high as 4 g/L. On the other hand, thermodynamic and molecular dynamics simulations indicate that at a temperature of 185 °C, the decomposition transformation of Na-jarosite (32.64 kJ and 7.25 eV) is more energetically advantageous compared to that of K-jarosite (61.07 kJ and 15.31 eV). The results were verified by the leaching solution from smelting industry. The iron content in the residues is above 58%, the sulfur content is below 4%, the zinc content is below 1%, and the total iron concentration in the supernatant is about 4 g/L, reaching the production index of the smelting industry. The green, environmentally friendly, and recyclable separation of iron in a solution with high concentrations of potassium and sodium ions is achieved, which is of great significance for the treatment of iron-containing solution and wastewater in the chemical industry and metallurgy fields.
CS-count-optimal quantum circuits for arbitrary multi-qubit unitaries
Authors: Mukhopadhyay Priyanka 
Published: June 2024

AbstractIn quantum computing there are quite a few universal gate sets, each having their own characteristics. In this paper we study the Clifford+CS universal fault-tolerant gate set. The CS gate is used is many applications and this gate set is an important alternative to Clifford+T. We introduce a generating set in order to represent any unitary implementable by this gate set and with this we derive a bound on the CS-count of arbitrary multi-qubit unitaries. Analysing the channel representation of the generating set elements, we infer $${\mathcal {J}}_n^{CS}\subset {\mathcal {J}}_n^T$$

J
n

CS

⊂

J
n
T

, where $${\mathcal {J}}_n^{CS}$$

J
n

CS

and $${\mathcal {J}}_n^T$$

J
n
T

are the set of unitaries exactly implementable by the Clifford+CS and Clifford+T gate sets, respectively. We develop CS-count optimal synthesis algorithms for both approximately and exactly implementable multi-qubit unitaries. With the help of these we derive a CS-count-optimal circuit for Toffoli, implying $${\mathcal {J}}_n^{Tof}={\mathcal {J}}_n^{CS}$$

J
n

Tof

=

J
n

CS

, where $${\mathcal {J}}_n^{Tof}$$

J
n

Tof

is the set of unitaries exactly implementable by the Clifford+Toffoli gate set. Such conclusions can have an important impact on resource estimates of quantum algorithms.
Multi role ChatGPT framework for transforming medical data analysis
Authors: Chen Haoran , Zhang Shengxiao , Zhang Lizhong , Geng Jie , Lu Jinqi , Hou Chuandong , He Peifeng , Lu Xuechun 
Published: June 2024

AbstractThe application of ChatGPTin the medical field has sparked debate regarding its accuracy. To address this issue, we present a Multi-Role ChatGPT Framework (MRCF), designed to improve ChatGPT's performance in medical data analysis by optimizing prompt words, integrating real-world data, and implementing quality control protocols. Compared to the singular ChatGPT model, MRCF significantly outperforms traditional manual analysis in interpreting medical data, exhibiting fewer random errors, higher accuracy, and better identification of incorrect information. Notably, MRCF is over 600 times more time-efficient than conventional manual annotation methods and costs only one-tenth as much. Leveraging MRCF, we have established two user-friendly databases for efficient and straightforward drug repositioning analysis. This research not only enhances the accuracy and efficiency of ChatGPT in medical data science applications but also offers valuable insights for data analysis models across various professional domains.