bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do Patients with Inflammatory Bowel Disease Really Know What Other Immune-mediated Inflammatory Diseases They Are Diagnosed with?
Authors: de Francisco Ruth , Pérez-Martínez Isabel , Castaño-García Andrés , Carballo-Folgoso Lorena , Flórez-Díez Pablo , García-Pérez Cristina , Fernández-González Emilia , Rolle Valeria , Chiminazzo Valentina , Queiro Rubén , Alonso-Castro Sara , Santos-Juanes Jorge , Gueimonde Miguel , Riestra Sabino 
Published: July 2024

Abstract

Background and Aims
The association of inflammatory bowel disease [IBD] with other immune-mediated inflammatory diseases [IMIDs] in the same patient is well known. We aimed to evaluate the degree of knowledge that patients with IBD have regarding the coexistence of other IMIDs, and to analyse the factors associated with concordance between self-reported and confirmed medical information.

Methods
Patients with IBD at a tertiary hospital answered a questionnaire on the presence of 54 IMIDs [self-reported diagnosis], and their IMID diagnosis was confirmed in their medical records [reference diagnosis]. Agreement between the self-reported IMID and IMID according to medical records was evaluated. The association between concordance and different predictors was evaluated using logistic regression models.

Results
A total of 1,620 patients were included; 626 [39%] patients were diagnosed with at least one IMID, and 177 [11%] with two or more. Overall agreement between patients´ self-report and medical records was k:0.61. When we grouped IMIDs according to affected organs or systems, agreement on rheumatic IMIDs was moderate [k:0.58], whereas agreement on cutaneous [k:0.66], endocrine [k: 0.74,] and ocular [k:0.73] IMIDs was substantial. Among patients who had IMIDs, the factor associated with greater concordance was female gender; less concordance was associated with a lower educational level and the fact that the IMID had been diagnosed at the same time or later than IBD.

Conclusion
The knowledge that patients with IBD have regarding the coexistence of other IMIDs is poor, particularly in rheumatic IMIDs.
An assemblage-level comparison of genetic diversity and population genetic structure between island and mainland ant populations
Authors: Naughton Ida , Tsutsui Neil D , Ward Philip S , Holway David A 
Published: July 2024

Abstract
Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, e.g., typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare the genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California. As expected, island populations (from Santa Cruz Island) had lower expected heterozygosity and Watterson’s theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision. Within the focal assemblage, pairwise Fst values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal population differences across an assemblage of interacting species and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine conspecific population pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes.
Low-energy building insulation through external wall modification: a case study on Lanzhou Academy of Painting in China
Authors: Wang Xiaoxiao , Xing Kun , Feng Xinshu , Li Ziyi 
Published: July 2024

Abstract
This study analyzes the external wall insulation of Lanzhou Academy of Painting, China, clarifies the thermal storage performance and characteristics of insulation materials according to local conditions, and proposes an insulation technique that combines external insulation of external walls with a double-skin façade. Based on the characteristics of passive low-energy buildings, the passive façade design with high-performance insulation materials was selected according to local conditions. The insulation performance of such buildings is studied under the conditions of no thermal bridge, high air tightness, waterproof and vapor isolation, and a sunlight shield. Our findings can promote the implementation of passive ultra-low energy-consumption designs in China. Based on the design of double outer skin, the use of thermal insulation and environmental protection materials as well as the control of air flow rate is used to improve the thermal insulation performance of the wall, through the computer simulation to compare the new design of the outer skin to Lanzhou Painting Academy as a pilot. It is proved that the composite double outer surface can be used in a large area of public buildings in cold regions. The low energy consumption double composite exterior skin designed in this article can be adjusted through its own air inlet and outlet size, the reasonable use of natural conditions to achieve the effect of heat preservation and heat dissipation. Through the simulation of the spectral diagram to compare the traditional outer skin and the innovative double skin heat storage performance differences, the simulation shows that the traditional thermal insulation outer skin heat storage capacity is uniform and need to be combined with other devices to achieve indoor thermal insulation, double skin through its own regulation using the control of air convection combined with the new thermal insulation materials to achieve lower energy consumption, heat storage effect is better. In order to compare the effect, the Swire room temperature simulation is carried out using the design of local double-layer exterior and traditional outer skin splicing, and the difference in spectral performance of the two types of walls is obtained intuitively. The use of double skin can regulate the heat storage capacity of the wall to directly affect the room temperature, which can be used in large public buildings in cold regions of China to achieve energy saving and carbon reduction.
Selector of amino-acid scales set
Authors: Vrdoljak Anton , Vukičević Damir 
Published: July 2024

Abstract
Experimental and theoretical properties of amino acids as building blocks of peptides and proteins have been extensively researched. Each such method assigns a number to each amino acid, and one such assignment is called amino-acid scale. Their usage in bioinformatics to explain and predict behaviour of peptides and proteins is of essential value. The number of such scales is very large. There are more than a hundred scales related just to hydrophobicity. A large number of scales can be a computational burden for algorithms that try to define peptide descriptors combining several of these scales. Hence, it is of interest to construct a smaller, but still representative set of scales. Here, we present software that does this. We test it on the set of scales using a database constructed by Kawashima and collaborators and show that it is possible to significantly reduce the number of scales observed without losing much of the information. An algorithm is implemented in C#. As a result, we provide a smaller database that might be a very useful tool for the analyses and construction of new peptides. Another interesting application of this database would be to compare the artificial intelligence construction of peptides having as an input the complete Kawashima database and this reduced one. Obtaining in both cases similar results would give much credibility to the constructs of such AI algorithms.
Effects of sulfur dioxide fumigation on mortality of confused flour beetle (Coleoptera: Tenebrionidae) and rice weevil (Coleoptera: Curculionidae)
Authors: Liu Yong-Biao 
Published: July 2024

Abstract
Sulfur dioxide (SO2) fumigation was studied in laboratory to determine its potential as an alternative treatment for postharvest control of stored product insects, confused flour beetle, Tribolium confusum Jacquelin du Val (Coleoptera: Tenebrionidae), and rice weevil, Sitophilus oryzae (L.) (Coleoptera: Curculionidae). Three-hour fumigations with 0.1%–2.0% SO2 were conducted against eggs, immature stages, and adults of the 2 insects at 20 °C. Effective control of both insects was achieved. However, there were considerable variations between the 2 insects and among different life stages. Confused flour beetle was more susceptible to SO2 fumigation than rice weevil. Complete control of adults and all life stages of confused flour beetle was achieved in 3-h fumigations with 0.5% and 2.0% SO2, respectively. For rice weevil, 3-h fumigation with 1.5% SO2 resulted in 96.5% adult mortality and the fumigation with 2.0% SO2 resulted in 99.27% mortality of adults and 87.5% mortality of immature stages. Three-hour fumigations with 1% SO2 resulted in &lt;5% egg survival to adults. The study demonstrated high efficacy of SO2 fumigation against the insects and suggested that SO2 fumigation has good potential for postharvest pest control on stored products.
Stuck in a whirlpool? The role of hope and despair in dealing with risks during Afghan migration journeys
Authors: Kiriscioglu Eda , Van Heelsum Anja 
Published: July 2024

Abstract
Migration journeys are full of risk, navigated not just by physical obstacles but also by emotional tides. This study explores how the fluctuation of hope and despair plays a role in dealing with risks. Drawing upon in-depth interviews with Afghans in Turkey, this paper demonstrates that hope and despair fluctuate along migration journeys contingent upon three elements: (1) empirical evidence about the future, (2) (un)certainty and potential in the future, and (3) the agency or capability to act. The research finds that hope arises when the future is perceived as uncertain, offering individuals alternative pathways and restoring a sense of agency by transforming uncertainty into potentiality. Conversely, despair sets in when individuals perceive their near future as certain, devoid of alternatives. This sense of certainty about the near future leaves migrants feeling trapped, akin to being stuck in a whirlpool.
The Prosōpon of Jesus’ Soul in Origen’s Homilies on Psalm 15 (16)
Authors: Juge Jean-Paul M 
Published: July 2024

Abstract
Prosopological exegesis was integral to the trinitarian theology of several second- and early third-century Christian theologians who argued that the different divine personae or prosōpa that speak in biblical texts were distinct from one another in reality. Unlike these predecessors, Origen’s use of prosopological exegesis in the Psalms occurs in a less polemical context and gravitates towards Christology and ecclesiology rather than trinitarian theology. In his homilies on Psalm 15 (16), Origen identifies the soul of Jesus as a speaking prosōpon distinct from, and acted upon by, the divine Word. This instance of prosopological exegesis highlights the distinctiveness of Origen’s theological use of this literary practice. In particular, I argue that Origen draws conclusions of soteriological and ecclesiological relevance from his notion of the speaking prosōpon of Jesus’ soul, which mediates a kind of communicatio idiomatum between the human Christ and the Church.
Theoretical study of infrared and ultraviolet spectroscopy in SiP interstellar molecules
Authors: Wang Guosen , Zhang Chuanyu , Cheng Xinlu , Zhang Hong 
Published: July 2024

ABSTRACT
Insufficient theoretical investigation is being conducted on the spectroscopic characteristics within the infrared wavelength range of SiP, an identified interstellar molecule. Using the ic-MRCI method, potential energy functions and dipole moment functions for the ground state (${X^2}\Pi $) and low excited states (${{\rm{A}}^2}{\Sigma ^ + }$) of the SiP molecule were calculated. Based on experimental spectroscopy data, least squares fitting was used for the potential energy functions of the ${X^2}\Pi $ and ${{\rm{A}}^2}{\Sigma ^ + }$ states. By combining these potential energy and dipole moment functions, the one-dimensional Schrödinger equation was solved to obtain the vibronic energy levels and Einstein A coefficients for the electronic states. Partition functions of the SiP molecule from 0.1 to 3000 K and the radiative properties of ${X^2}\Pi \leftrightarrow {X^2}\Pi $ and ${X^{\rm{2}}}\Pi \leftrightarrow {{\rm{A}}^2}{\Sigma ^ + }$ were derived. Infrared spectroscopy of the ${X^2}\Pi $ state and ultraviolet spectroscopy of the ${X^{\rm{2}}}\Pi \leftrightarrow {{\rm{A}}^2}{\Sigma ^ + }$ transition at 100 K, a temperature crucial for astronomical research, were calculated. Results indicate that the spectral-line intensity of the ${X^{\rm{2}}}\Pi \leftrightarrow {{\rm{A}}^2}{\Sigma ^ + }$ transition is greater, making it more suitable for astronomical observation. The obtained computational results in this paper yield spectroscopic parameters for the characterization of the interstellar molecule SiP, furnishing theoretical underpinnings for subsequent experimental observations.
Dark scattering: accelerated constraints from KiDS-1000 with ReACT and CosmoPower
Authors: Carrion Karim , Carrilho Pedro , Spurio Mancini Alessio , Pourtsidou Alkistis , Hidalgo Juan Carlos 
Published: July 2024

ABSTRACT
We present constraints on the dark scattering model through cosmic shear measurements from the Kilo Degree Survey (KiDS-1000), using an accelerated pipeline with novel emulators produced with CosmoPower. Our main emulator, for the dark scattering non-linear matter power spectrum, is trained on predictions from the halo model reaction framework, previously validated against simulations. Additionally, we include the effects of baryonic feedback from HMCode2016, whose contribution is also emulated. We analyse the complete set of statistics of KiDS-1000, namely band powers, COSEBIs, and correlation functions, for dark scattering in two distinct cases. In the first case, taking into account only KiDS cosmic shear data, we constrain the amplitude of the dark energy–dark matter interaction to be $\vert A_{\rm ds} \vert \lesssim 20$$\rm b\,GeV^{-1}$ at 68 per cent C.L. Furthermore, we add information from the cosmic microwave background (CMB) from Planck, along with baryon acoustic oscillations (BAO) from 6dFGS, SDSS, and BOSS, approximating a combined weak lensing+CMB+BAO analysis. From this combination, we constrain $A_{\rm ds} = 10.6^{+4.5}_{-7.3}$$\rm b\,GeV^{-1}$ at 68 per cent C.L. We confirm that with this estimated value of $A_{\rm ds}$ the interacting model considered in this work offers a promising alternative to solve the $S_8$ tension.
A kinome drug screen identifies multi-TKI synergies and ERBB2 signaling as a therapeutic vulnerability in MYC/TYR subgroup atypical teratoid rhabdoid tumors
Authors: Golbourn Brian , Ho Ben , Bondoc Andrew , Luck Amanda , Fan Xiaolian , Richardson Elizabeth , Marcellus Richard , Prakesch Michael , Halbert Mathew , Agrawal Nishant , Smith Christian , Huang Annie , Rutka James T 
Published: July 2024

Abstract

Background
Atypical teratoid rhabdoid tumor (ATRT) is a rare, devastating, and largely incurable pediatric brain tumor. Although recent studies have uncovered 3 molecular subgroups of ATRTs with distinct disease patterns, and signaling features, the therapeutic profiles of ATRT subgroups remain incompletely elucidated.

Methods
We examined the effect of 465 kinase inhibitors on a panel of ATRT subgroup-specific cell lines. We then applied multiomics analyses to investigate the underlying molecular mechanism of kinase inhibitor efficacy in ATRT subgroups.

Results
We observed that ATRT cell lines are broadly sensitive to inhibitors of the PI3K and MAPK signaling pathways, as well as CDKs, AURKA/B kinases, and polo-like kinase 1. We identified 2 classes of multikinase inhibitors predominantly targeting receptor tyrosine kinases including PDGFR and EGFR/ERBB2 in MYC/TYR ATRT cells. The PDGFRB inhibitor, Dasatinib, synergistically affected MYC/TYR ATRT cell growth when combined with broad-acting PI3K and MAPK pathway inhibitors, including Rapamycin and Trametinib. We observed that MYC/TYR ATRT cells were also distinctly sensitive to various inhibitors of ERBB2 signaling. Transcriptional, H3K27Ac ChIPSeq, ATACSeq, and HiChIP analyses of primary MYC/TYR ATRTs revealed ERBB2 expression, which correlated with differential methylation and activation of a distinct enhancer element by DNA looping. Significantly, we show the brain penetrant EGFR/ERBB2 inhibitor, Afatinib, specifically inhibited in vitro and in vivo growth of MYC/TYR ATRT cells.

Conclusions
Taken together, our studies suggest combined treatments with PDGFR and ERBB2-directed TKIs with inhibitors of the PI3K and MAPK pathways as an important new therapeutic strategy for the MYC/TYR subgroup of ATRTs.
Atezolizumab plus bevacizumab as first-line systemic therapy for hepatocellular carcinoma: a multi-institutional cohort study
Authors: Storandt Michael H , Zemla Tyler J , Patell Kanchi , Naleid Nikolas , Gile Jennifer J , Tran Nguyen H , Chakrabarti Sakti , Jin Zhaohui , Borad Mitesh , Mahipal Amit 
Published: July 2024

Abstract

Background
Atezolizumab plus bevacizumab is the standard of care for advanced hepatocellular carcinoma (HCC) in the first-line setting, although was only evaluated in patients with Child-Pugh (CP) A liver function in the IMbrave150 trial. We sought to determine the outcomes of these patients based on CP score and ALBI grade in the US population.

Methods
This multicenter cohort study included patients with HCC who received atezolizumab with bevacizumab as first-line systemic therapy between March 2018 and November 2023. Overall survival (OS) was determined using the Kaplan-Meier method and multivariate analyses were performed using Cox proportional hazard regression method.

Results
Among 322 patients, 226, 86, and 10 patients had CP-A, CP-B, and CP-C liver function, respectively. Median age was 66.5 years, 78.6% were male, and 82.6% were White. Median OS (mOS) was 21.6 months for those with CP-A, 9.1 months for those with CP-B7, and 4.7 months for those with CP-B8-C12 (P &lt; .0001). Among patients with CP-A, those with ALBI grade 1 had an mOS of 34.9 months versus 14.2 months in those with grade 2. In multivariate analyses, CP score, ALBI grade, hepatitis B, performance status, and macrovascular invasion were significantly associated with survival.

Conclusions
CP score is an important prognostic tool for patients with HCC receiving atezolizumab plus bevacizumab, and this regimen remains a viable option for patients with CP-B7 with no additional safety concern, although the benefit is significantly less than those with CP-A. ALBI score has independent predictive value in patients with CP-A liver function.
The lowdown on breakdown: Open questions in plant proteolysis
Authors: Eckardt Nancy A , Avin-Wittenberg Tamar , Bassham Diane C , Chen Poyu , Chen Qian , Fang Jun , Genschik Pascal , Ghifari Abi S , Guercio Angelica M , Gibbs Daniel J , Heese Maren , Jarvis R Paul , Michaeli Simon , Murcha Monika W , Mursalimov Sergey , Noir Sandra , Palayam Malathy , Peixoto Bruno , Rodriguez Pedro L , Schaller Andreas , Schnittger Arp , Serino Giovanna , Shabek Nitzan , Stintzi Annick , Theodoulou Frederica L , Üstün Suayib , van Wijk Klaas J , Wei Ning , Xie Qi , Yu Feifei , Zhang Hongtao 
Published: July 2024

Abstract
Proteolysis, including post-translational proteolytic processing as well as protein degradation and amino acid recycling, is an essential component of the growth and development of living organisms. In this article, experts in plant proteolysis pose and discuss compelling open questions in their areas of research. Topics covered include the role of proteolysis in the cell cycle, DNA damage response, mitochondrial function, the generation of N-terminal signals (degrons) that mark many proteins for degradation (N-terminal acetylation, the Arg/N-degron pathway, and the chloroplast N-degron pathway), developmental and metabolic signaling (photomorphogenesis, abscisic acid and strigolactone signaling, sugar metabolism, and postharvest regulation), plant responses to environmental signals (endoplasmic-reticulum-associated degradation, chloroplast-associated degradation, drought tolerance, and the growth-defense trade-off), and the functional diversification of peptidases. We hope these thought-provoking discussions help to stimulate further research.
Enhancing poststroke hand movement recovery: Efficacy of RehabSwift, a personalized brain–computer interface system
Authors: Darvishi Sam , Datta Gupta Anupam , Hamilton-Bruce Anne , Koblar Simon , Baumert Mathias , Abbott Derek 
Published: July 2024

Abstract
This study explores the efficacy of our novel and personalized brain–computer interface (BCI) therapy, in enhancing hand movement recovery among stroke survivors. Stroke often results in impaired motor function, posing significant challenges in daily activities and leading to considerable societal and economic burdens. Traditional physical and occupational therapies have shown limitations in facilitating satisfactory recovery for many patients. In response, our study investigates the potential of motor imagery–based BCIs (MI-BCIs) as an alternative intervention. In this study, MI-BCIs translate imagined hand movements into actions using a combination of scalp-recorded electrical brain activity and signal processing algorithms. Our prior research on MI-BCIs, which emphasizes the benefits of proprioceptive feedback over traditional visual feedback and the importance of customizing the delay between brain activation and passive hand movement, led to the development of RehabSwift therapy. In this study, we recruited 12 chronic-stage stroke survivors to assess the effectiveness of our solution. The primary outcome measure was the Fugl-Meyer upper extremity (FMA-UE) assessment, complemented by secondary measures including the action research arm test, reaction time, unilateral neglect, spasticity, grip and pinch strength, goal attainment scale, and FMA-UE sensation. Our findings indicate a remarkable improvement in hand movement and a clinically significant reduction in poststroke arm and hand impairment following 18 sessions of neurofeedback training. The effects persisted for at least 4 weeks posttreatment. These results underscore the potential of MI-BCIs, particularly our solution, as a prospective tool in stroke rehabilitation, offering a personalized and adaptable approach to neurofeedback training.