bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-cancer analysis of the prognostic and immunological roles of SHP-1/ptpn6
Authors: Cui Ping , Lian Jie , Liu Yang , Zhang Dongsheng , Lin Yao , Lu Lili , Ye Li , Chen Hui , An Sanqi , Huang Jiegang , Liang Hao 
Published: October 2024

AbstractSHP-1, a nonreceptor protein tyrosine phosphatase encoded by ptpn6, has been regarded as a regulatory protein of hematopoietic cell biology for years. However, there is now increasing evidence to support its role in tumors. Thus, the role of ptpn6 for prognosis and immune regulation across 33 tumors was investigated, aiming to explore its functional heterogeneity and clinical significance in pan-cancer. Differential expression of ptpn6 was found between cancer and adjacent normal tissues, and its expression was significantly correlated with the prognosis of tumor patients. In most cancers, ptpn6 expression was significantly associated with immune infiltration. This was further confirmed by ptpn6-related genes/proteins enrichment analysis. Additionally, genetic alterations in ptpn6 was observed in most cancers. As for epigenetic changes, it’s phosphorylation levels significantly altered in 6 tumors, while methylation levels significantly altered in 12 tumors. Notably, the methylation levels of ptpn6 were significantly decreased in 11 tumors, accompanied by its increased expression in 8 of them, suggesting that the hypomethylation may be related to its increased expression. Our results show that ptpn6 plays a specific role in tumor immunity and exerts a pleiotropic effect in a variety of tumors. It can serve as a prognostic factor for some cancers. Especially in LGG, KIRC, UCS and TGCT, the increased expression of ptpn6 is associated with poor prognosis and high immune infiltration. This aids in understanding the role of ptpn6 in tumor biology, and can provide insight into presenting a potential biomarker for poor prognosis and immune infiltration in cancers.
A human progeria-associated BAF-1 mutation modulates gene expression and accelerates aging in C. elegans
Authors: Romero-Bueno Raquel , Fragoso-Luna Adrián , Ayuso Cristina , Mellmann Nina , Kavsek Alan , Riedel Christian G , Ward Jordan D , Askjaer Peter 
Published: October 2024

AbstractAlterations in the nuclear envelope are linked to a variety of rare diseases termed laminopathies. A single amino acid substitution at position 12 (A12T) of the human nuclear envelope protein BAF (Barrier to Autointegration Factor) causes Néstor-Guillermo Progeria Syndrome (NGPS). This premature ageing condition leads to growth retardation and severe skeletal defects, but the underlying mechanisms are unknown. Here, we have generated a novel in vivo model for NGPS by modifying the baf-1 locus in C. elegans to mimic the human NGPS mutation. These baf-1(G12T) mutant worms displayed multiple phenotypes related to fertility, lifespan, and stress resistance. Importantly, nuclear morphology deteriorated faster during aging in baf-1(G12T) compared to wild-type animals, recapitulating an important hallmark of cells from progeria patients. Although localization of BAF-1(G12T) was similar to wild-type BAF-1, lamin accumulation at the nuclear envelope was reduced in mutant worms. Tissue-specific chromatin binding and transcriptome analyses showed reduced BAF-1 association in most genes deregulated by the baf-1(G12T) mutation, suggesting that altered BAF chromatin association induces NGPS phenotypes via altered gene expression.
The role of structure in regulatory RNA elements
Authors: Tants Jan-Niklas , Schlundt Andreas 
Published: October 2024

Abstract
Regulatory RNA elements fulfill functions such as translational regulation, control of transcript levels, and regulation of viral genome replication. Trans-acting factors (i.e., RNA-binding proteins) bind the so-called cis elements and confer functionality to the complex. The specificity during protein-RNA complex (RNP) formation often exploits the structural plasticity of RNA. Functional integrity of cis-trans pairs depends on the availability of properly folded RNA elements, and RNA conformational transitions can cause diseases. Knowledge of RNA structure and the conformational space is needed for understanding complex formation and deducing functional effects. However, structure determination of RNAs under in vivo conditions remains challenging. This review provides an overview of structured eukaryotic and viral RNA cis elements and discusses the effect of RNA structural equilibria on RNP formation. We showcase implications of RNA structural changes for diseases, outline strategies for RNA structure-based drug targeting, and summarize the methodological toolbox for deciphering RNA structures.
Power control system structure of doubly‐fed induction generator connected to current source converter
Authors: Morawiec Marcin , Blecharz Krzysztof , Ryndzionek Roland , Jaderko Andrzej , Vyas Deepak 
Published: October 2024

AbstractThe power control system structures for a doubly‐fed generator (DFIG) are proposed. The classical field oriented control and the feedback control with the multi‐scalar variables were considered. The generator is working in the AC grid connection mode. The rotor side of the generator is connected to the current source converter (CSC); the stator is directly related to the AC grid. The static feedback linearization using the multi‐scalar variables of DFIG is proposed to increase active and reactive power control accuracy. The proposed control structure allows to linearize the generator system, and decoupled between the control paths. The proposed approach can be called voltage control because one of the control variables is the voltage in the DC‐link of the CSC. The simulation and experimental investigations in the 2 kW DFIG system consider the AC grid voltage dips, confirming that the proposed control system remains stable.
Traffic microsimulation for smart cities: Investigating the impact of objective function formulation on calibration efficiency
Authors: Abuamer Ismail M. A. , Tampère Chris M. J. 
Published: October 2024

AbstractTraffic microsimulation models are crucial for intelligent transportation systems evaluation, but careful parameter calibration is required for credible pre‐ and post‐ITS comparisons. However, the back‐box and stochastic nature of the system make calibration challenging. Sensitivity analysis (SA) helps to identify influential parameters, but scenario dependency limits its generalisability. Metrics such as root mean squared relative error (RMSRE) can oversimplify the stochasticity in traffic data, compromising calibration quality. Furthermore, calibration for specific key performance indicators (KPIs) does not ensure the reliability of other KPIs. The authors propose the simultaneous calibration of driving behaviour parameters without prior sensitivity information. They demonstrate the effect of the error metric and objective function facets on the calibration efficiency and parameter convergence consistency. Results indicate that employing SA to identify influential parameters is unnecessary. Each parameter converges to a stable point by responding directly to the information within the objective function or due to the interactions with other parameters. Therefore, simultaneous calibration of multiple KPIs and maintaining the stochasticity structure in the data—enhanced calibration efficiency and parameter convergence consistency. Additionally, using probabilistic dissimilarity metrics that consider the entire distribution, such as the Wasserstein distance, outperform the K–S distance and RMSRE.
Statistical view of orbital circularisation with 14 000 characterised TESS eclipsing binaries
Authors: IJspeert L. W. , Tkachenko A. , Johnston C. , Aerts C. 
Published: October 2024

Context. Eclipsing binaries are crucial for understanding stellar physics, allowing detailed studies of stellar masses, radii, and orbital dynamics. Recent space missions like the Transiting Exoplanet Survey Satellite (TESS) have significantly expanded the catalogue of observed eclipsing binaries with uninterrupted time series photometry, providing an opportunity for large-scale ensemble studies.
Aims. This study aims to analyse the statistical properties of circularisation in a large sample of intermediate-to-high mass eclipsing binaries observed by TESS. We explore the dependence of orbital circularisation on stellar properties and orbital parameters to improve our understanding of the physical processes affecting these systems. We further aim to assess the role of stellar pulsations in circularisation.
Methods. We compiled a catalogue of O- to F-type stars to search for eclipsing binary signals in the data available from the first four years of the TESS mission. Using automated classification and data analysis methodologies, we arrive at a well-characterised sample of 14 573 eclipsing binaries. We supplement our catalogue with Gaia effective temperatures, and investigate the statistical characteristics of the sample as a function of temperature, orbital period, and scaled orbital separation.
Results. The orbital circularisation was measured with statistical methods to obtain three distinct measurements of the critical period and separation in four temperature ranges. These measurements cover a range of orbital periods and separations where both circularised and eccentric systems exist. Pulsations were identified in the g- and p-mode regimes and a reduced fraction of eccentric systems was found among them.
Conclusions. Our analysis revealed the dependence of orbital circularisation on stellar temperatures, also seen in other studies, and confirmed previous findings that additional dissipation is needed as compared to the predictions of turbulent viscosity and non-resonant radiative damping. We speculate that pulsations may play a role in the circularisation of close binaries. Our study highlights the need for dissipative mechanisms that can produce a wide range of critical periods from a range of initial conditions.
Sequential bias-corrected weighted least squares solution of mixed additive and multiplicative error models
Authors: Leyang Wang , Zhenjie Peng , Fei Wu , Weifeng Zhao , Zhanglin Sun 
Published: October 2024

Abstract
In the era of big data, the number of observations in adjustment calculations may reach tens or even hundreds of thousands. When dealing with these large dataset problems, many matrix operations are often required. At this time, the dimensions of the matrix will be large, which will generate a great computational burden. At present, no research results have been published on the computational efficiency of bias-corrected weighted least squares (bcWLS) for mixed additive and multiplicative error models (MAMEM). Sequential adjustment (SEA) groups the observations for calculation and can provide the same computational precision while greatly improving computational efficiency. This paper applies the idea of SEA to the calculation of bcWLS and proposes an iterative solution for sequential bcWLS (SEbcWLS). Using three simulation experiments to verify the effectiveness of our method, it was found that when the number of observations is 10000, the effect is better when the number of groups does not exceed 100, achieving the same precision as the original method while having high computational efficiency. The calculation results of line fitting and plane fitting are not affected by the number of grouping groups. For DEM (Digital elevation model) experiments with strong nonlinearity, when the number of grouping groups is too large, the effect is not very good, but the calculation efficiency is also higher than the original method, and the difference in calculation results is not significant.
Gravitational waves from first-order phase transitions in LISA: reconstruction pipeline and physics interpretation
Authors: Caprini Chiara , Jinno Ryusuke , Lewicki Marek , Madge Eric , Merchand Marco , Nardini Germano , Pieroni Mauro , Pol Alberto Roper , Vaskonen Ville ,   the LISA Cosmology Working Group
Published: October 2024

AbstractWe develop a tool for the analysis of stochastic gravitational wave backgrounds from cosmological first-order phase transitions with LISA: we initiate a template databank for these signals, prototype their searches, and forecast their reconstruction. The templates encompass the gravitational wave signals sourced by bubble collisions, sound waves and turbulence. Accounting for Galactic and extra-Galactic foregrounds, we forecast the region of the parameter space that LISA will reconstruct with better than ∼ 10% accuracy, if certain experimental and theoretical uncertainties are solved by the time LISA flies. We illustrate the accuracy with which LISA can reconstruct the parameters on a few benchmark signals, both in terms of the template parameters and the phase transition ones. To show the impact of the forecasts on physics beyond the Standard Model, we map the reconstructed benchmark measurements into the parameter spaces of the singlet extension of the Standard Model and of the classically conformal invariant U(1)B-Lmodel.
The surface electron transfer strategy promotes the hole of PDI release and enhances emerging organic pollutant degradation
Authors: Yang Yunchuan , Wang Dongyu , Geng Jisheng , Liu Jun , Wang Jun 
Published: October 2024

Abstract
In semiconductor photocatalysts, the easy recombination of photogenerated carriers seriously affects the application of photocatalytic materials in water treatment. To solve the serious problem of electron−hole pair recombination in perylene diimide (PDI) organic semiconductors, we loaded ferric hydroxyl oxide (FeOOH) on PDI materials, successfully prepared novel FeOOH@PDI photocatalytic materials, and constructed a photo-Fenton system. The system was able to achieve highly efficient degradation of BPA under visible light, with a degradation rate of 0.112 min−1 that was 20 times higher than the PDI system, and it also showed universal degradation performances for a variety of emerging organic pollutants and anti-interference ability. The mechanism research revealed that the FeOOH has the electron trapping property, which can capture the photogenerated electrons on the surface of PDI, effectively reducing the compounding rate of photogenerated carriers of PDI and accelerating the iron cycling and H2O2 activation on the surface of FeOOH at the same time. This work provides new insights and methods for solving the problem of easy recombination of carriers in semiconductor photocatalysts and degrading emerging organic pollutants.
Enhancing postural stability in musculoskeletal quadrupedal locomotion through tension feedback for CPG-based controller
Authors: Tanaka Hiroaki , Matsumoto Ojiro , Kawasetsu Takumi , Hosoda Koh 
Published: October 2024

Abstract
A central pattern generator (CPG)-based controller enhances the adaptability of quadrupedal locomotion, for example, by controlling the trunk posture. The conventional CPG-based controllers with attitude control often utilized the posture angle as feedback information. However, if the robot’s body is as soft as a musculoskeletal structure, it can detect the over-tilting of the trunk based on proprioceptive information of the muscles. In general, proprioceptive information such as muscle tension changes more rapidly than posture angle information. Therefore, a feedback loop based on proprioceptive information has great potential to respond to sudden disturbances that occur during locomotion over uneven terrain. In this research, we proposed a CPG-based controller utilizing the tension of soft pneumatic artificial muscles (PAMs). Musculoskeletal quadruped robots driven by PAMs are so soft, which prevents over-tilting of the trunk because the soft leg acts like a suspension. In addition, tension, one of the proprioceptive information of PAMs, exhibits high sensitivity to changes in trunk posture because the soft body’s motion easily is affected by over-tilting of the trunk. To validate the efficacy of the proposed controller, we conducted numerical simulations with a simple quadruped model and experiments with a musculoskeletal quadruped robot. As a result, the tension feedback is not effective for posture stabilization on flat terrain whereas it is effective on uneven terrain. Moreover, the tension feedback improved the running velocity over uneven terrain. These results will enhance the locomotion capability of musculoskeletal quadruped robots, advancing their practical application.
Fock space and field theoretic description of nonequilibrium work relations
Authors: Baish Andrew J , Vollmayr-Lee Benjamin P 
Published: October 2024

Abstract
We consider classical, interacting particles coupled to a thermal reservoir and subject to a local, time-varying potential while undergoing hops on a lattice. We impose detailed balance on the hopping rates and map the dynamics to the Fock space Doi representation, from which we derive the Jarzynski and Crooks relations. Here the local potential serves to drive the system far from equilibrium and to provide the work. Next, we utilize the coherent state representation to map the system to a Doi–Peliti field theory and take the continuum limit. We demonstrate that time reversal in this field theory takes the form of a gauge-like transformation which leaves the action invariant up to a generated work term. The time-reversal symmetry leads to a fundamental identity, from which we are able to derive the Jarzynski and Crooks relations, as well as a far-from-equilibrium generalization of the fluctuation-dissipation relation.
A novel system for removing examinee’s exhaled air using an open, lightweight non-sealing facemask-a proof-of-concept study
Authors: Abu Shkara Danial , Keynan Yoav , Brikman Shay , Dori Guy 
Published: October 2024

Abstract
Patients with respiratory infections (e.g. COVID-19, antimicrobial resistant bacteria) discharge pathogens to the environment, exposing healthcare workers and inpatients to deleterious complications. This study tested the performance of SPEAR-P1 (synchronized personal exhaled air removal system-prototype 1), which actively detects expiration and removes exhaled air using an open, non-sealing lightweight facemask connected to a deep vacuum generating unit. Fourteen healthy examinees practiced breathing through facemasks at 30, 25 and 20 breaths per minute; oxygen and nebulized saline were added at later steps. To test the efficacy of removing exhaled air, CO2 was used as a proxy and its level was measured from the outer surface of the open facemask. Compared to the baseline recording, SPEAR-P1 reduced CO2 escaping from the facemask by 66% on average for all study steps and respiratory rates (p < 0.001), reaching 85.55% on average at 20 breaths per minute (p < 0.001). This study shows that removing exhaled air from examinees using an open, non-sealing lightweight facemask is feasible. Future development of this system will enhance its efficacy and provide a method to remove a patient’s contaminating aerosol without the need to ‘seal’ the patient, especially in settings where isolation rooms are not readily available.
Investigating the impact of curcumin extract incorporation on PVA/Collagen/Chitosan/HAp nanofiber scaffold: morphological, mechanical, wettability, degradation rate, and antibacterial activity
Authors: Hartatiek H , Wuriantika M I , Rahmawati S A , Yudyanto Y , Taufiq A 
Published: October 2024

Abstract
This study investigates the impact of curcumin extract incorporation on the properties of PVA/Collagen/Chitosan/HAp nanofiber scaffolds for bone tissue engineering applications. Nanofibers were fabricated via electrospinning using PVA, collagen, chitosan, hydroxyapatite (HAp), and curcumin. Their morphology, mechanical properties, wettability, degradation rate, and antibacterial activity were comprehensively evaluated. Fourier transform infrared (FTIR) spectroscopy confirmed the successful incorporation of all components into the nanofibers and the potential for interactions between their functional groups. Scanning Electron Microscopy (SEM) revealed bead-free, fine nano-fibers with a decrease in diameter ranging from 139 nm to 108 nm. Simultaneously, enhanced mechanical properties were observed, with ultimate strength increasing from 2.8 MPa to 8.8 MPa as the diameter decreased. Notably, 15% curcumin extract maintained favorable hydrophilicity and degradation rates, crucial factors for tissue regeneration. Antibacterial activity was also enhanced, with an inhibition zone of 6.71 mm against E.coli observed at 15% curcumin treatment. Staphylococcus aureus exhibited the largest zone of inhibition (8.74 mm) at 15% curcumin concentration. This research demonstrates the feasibility of incorporating curcumin into nanofiber scaffolds for bone tissue engineering applications.
Preferences for drinking water temperature in mice vary with ambient temperature
Authors: Akiyama Miyu , Ishikawa Shori , Hosooka Tetsuya , Iwase Mari , Uchida Kunitoshi 
Published: October 2024

Abstract
Temperature detection and temperature preference are critical for the maintenance of thermal homeostasis and protection from noxious temperature. Methods to measure the time spent on plates of different temperatures such as the 2-plate test and thermal-gradient test are generally used to evaluate temperature preference. In this study, we established a temperature preference test that assesses water drinking behavior by modifying the 2-bottle taste preference test. We found that mice in a common-temperature environment of 23 °C avoid drinking water of temperature more than 40 °C. While mice in a common-temperature environment preferred 10 °C and 30 °C water equally, mice in a hot environment at 35 °C preferred 10 °C water to 30 °C water. Moreover, mice in a cold environment of 10 °C preferred to drink 40 °C water compared to 10 °C water. From these results, the temperature preference test that we developed could be used to evaluate temperature preferences owing to the ambient temperature changes.
‘KNOCK NOC’—Non-offending carers experiences with social work in the aftermath of Internet-based child sexual abuse
Authors: McGookin Naomi Katie 
Published: October 2024

Abstract
Children of individuals under investigation for the possession of child sexual abuse material (CSAM) in the UK are referred to social work to assess the risk of potential sexual harm. As a result of their co-parent’s offences, the non-offending carer finds themselves thrown into the centre of child protection investigations and parenting assessments, which is underpinned by the new reality they must face: Their partner is no longer considered safe to be left alone with children. This study was undertaken over the course of two years as part of my participatory action research doctoral thesis in which I worked in collaboration with four women with lived experience of social work intervention. This article focuses specifically on four themes identified that spoke to the women’s experiences with social workers. The themes are presented as messages that participants wished to communicate to child protection practitioners and were titled by the participants as follows: ‘we are terrified’, ‘we are not the perpetrator’, ‘we are on our knees’ and ‘we want to work together to protect out children’. Following a summary of themes, this article goes on to discuss how social workers might better respond to families impacted by CSAM.
Nudging for Tax Compliance: a Meta-Analysis
Authors: Antinyan Armenak , Asatryan Zareh 
Published: October 2024

Abstract
Governments increasingly use nudges to improve tax collection. We synthesise the growing literature on nudging experiments using meta-analytical methods. We find that, relative to the baseline where about a quarter of taxpayers are compliant, simple reminders increase the probability of compliance by 2.7 percentage points, while tax morale and deterrence nudges increase compliance by additional 1.4 and 3.2 percentage points. Our further results highlight the conditions where nudges are more or less effective. Overall, our findings imply that taxpayers are biased by various informational and behavioural constraints, and that nudges can be of some help in overcoming these frictions.