bluuebunny/crossref_metadata_2025 huggingface dataset:
ΛsCDM cosmology: alleviating major cosmological tensions by predicting standard neutrino properties
Authors: Yadav Anita , Kumar Suresh , Kıbrıs Cihad , Akarsu Özgür
Published: January 2025

In this work, we investigate a two-parameter extension of the ΛsCDM model, as well as the ΛCDM model for comparison, by allowing variations in the effective number of neutrino species (N
eff) and their total mass (∑mν). Our motivation is twofold: (i) to examine whether the ΛsCDM framework retains its success in fitting the data and addressing major cosmological tensions, without suggesting a need for a deviation from the standard model of particle physics, and (ii) to determine whether the data indicate new physics that could potentially address cosmological tensions, either in the post-recombination universe through the late-time (z ∼ 2) mirror AdS-to-dS transition feature of the ΛsCDM model, or in the pre-recombination universe through modifications in the standard values of N
eff and ∑mν
, or both. Within the extended ΛsCDM model, referred to as ΛsCDM+N
eff+∑mν
, we find no significant tension when considering the Planck-alone analysis. We observe that incorporating BAO data limits the further success of the ΛsCDM extension. However, the weakly model-dependent BAOtr data, along with Planck and Planck+PP&SH0ES, favor an H
0 value of approximately 73 km s-1 Mpc-1, which aligns perfectly with local measurements. In cases where BAOtr is part of the combined dataset, the mirror AdS-dS transition is very effective in providing enhanced H
0 values, and thus the model requires no significant deviation from the standard value of N
eff = 3.044, remaining consistent with the standard model of particle physics. Both the H
0 and S
8 tensions are effectively addressed, with some compromise in the case of the Planck+BAO dataset. Finally, the upper bounds obtained
on total neutrino mass, ∑mν
≲ 0.50 eV, are fully compatible with neutrino oscillation experiments. Our findings provide evidence that late-time physics beyond ΛCDM, such as ΛsCDM, without altering the standard description of the pre-recombination universe, can suffice to alleviate the major cosmological tensions, as indicated by our analysis of ΛsCDM+N
eff+∑mν
.
Impact of quadrupole and hexadecapole deformations and associated orientations on a variety of asymmetric nuclear reactions
Authors: . Diksha , SHARMA HARSHIT , Sharma Manoj K
Published: January 2025

The present manuscript investigates the fusion-ER cross-sections for different projectile-targetcombinations, 16O + 148,150Nd, 165Ho, 194Pt, 18O+ 148Nd, 194Pt, 192Os, and 19F + 188Os consisting of quadrupole (β2) and hexadecapole (β4) deformed target nuclei. The study analyzes the influenceof higher-order deformations and corresponding orientation criterias adopted for the exploration ofthe dynamics of the considered nuclei. The influence of these parameters has been studied in termsof capture cross-section (σcap), Compound nucleus (CN) formation probability (PCN ), survivalprobability (Wsur ), and the fusion-ER cross-sections across the center of mass energies (Ec.m.).The study recognizes the importance of the fission barrier in determining the survival probability(Wsur ) of the compound nucleus and subsequently the ER cross-sections. A discrepancy among thecalculated and experimental ER cross-sections is observed, particularly in reactions with lower fissionbarriers. In the reactions with a lower fission barrier of formed CN, the level density parameter ratio(af /an) for the fission and neutron-evaporation channels helps to address the experimental data.
Evaluation of neoclassical transport in nearly quasi-isodynamic stellarator magnetic fields using MONKES
Authors: Escoto F.J. , Velasco J.L. , Calvo I. , Sánchez E.
Published: January 2025

Stellarator magnetic fields that are perfectly optimized for neoclassical transport (with levels of radial neoclassical transport comparable to tokamaks) are called omnigenous. Quasi-isodynamic (QI) magnetic fields are a subset of omnigenous magnetic fields in which the isolines of the magnetic field strength close poloidally, which grants them the additional property of producing zero bootstrap current. A frequent strategy in the quest for QI configurations is to optimize the magnetic field indirectly by minimizing proxies that vanish in an exactly QI field. The recently developed code MONKES enables fast computations of the neoclassical radial transport and bootstrap current monoenergetic coefficients, and therefore facilitates enormously to assess the efficiency of such indirect approach. By evaluating the large database of intermediate configurations that led to the configuration CIEMAT-QI, the inefficiency of the indirect optimization strategy for minimizing the bootstrap current is illustrated. In addition, MONKES is used to take the first steps in the exploration of a region of the configuration space of piecewise omnigenous fields, a novel family of optimized magnetic fields that has broadened the configuration space of stellarators with low levels of radial neoclassical transport.
Development of a novel compact and fast SiPM-based RICH detector for the future ALICE 3 PID system at LHC
Authors: Mazziotta M.N. , Altamura A.R. , Congedo L. , De Robertis G. , Di Mauro A. , Guerra-Pulido J.O. , Licciulli F. , Lorusso L. , Martinengo P. , Nappi E. , Nicassio N. , Paić G. , Panzarini G. , Pillera R. , Volpe G.
Published: January 2025

A dedicated R&D is ongoing for the charged particle identification system of the ALICE 3 experiment proposed for the LHC Run 5 and beyond.
One of the subsystems for the high-energy charged particle identification will be a Ring-Imaging Cherenkov (RICH) detector.
The possibility of integrating Cherenkov-based charged particle timing measurements is currently under study.
The proposed system is based on a proximity-focusing RICH configuration including an aerogel radiator separated from a SiPM array layer by an expansion gap. A thin high-refractive index window of transparent material, acting as a second Cherenkov radiator, is glued on the SiPM array to enable time-of-flight measurements of charged particles by exploiting the yield of Cherenkov photons in the thin window.
We assembled a small-scale prototype instrumented with different Hamamatsu SiPM array sensors with pitches ranging from 1 to 3 mm, readout by custom boards equipped with the front-end Petiroc 2A ASICs to measure charges and times.
The primary Cherenkov radiator consisted of a 2 cm thick aerogel tile, while various window materials, including SiO2 and MgF2, were used as secondary Cherenkov radiators.
The prototype was successfully tested in a campaign at the CERN PS T10 beam line with pions and protons. This paper summarizes the results achieved in the 2023 test beam campaign.
A methodology for timing performance optimization
of the pre-amplifier design in High Energy Physics
Authors: Gan Y. , Casanova R. , Degerli Y. , Guilloux F. , Grinstein S. , Meyer J.-P. , Schwemling P. , Huang G.
Published: January 2025

Particle colliders operating at an increasing luminosity for High Energy Physics (HEP) experiments often present greater challenges in the design of the front-end readout circuits, especially when exploring the possibility of employing Depleted Monolithic Active Pixel Sensors (DMAPS) for timing in HEP. This paper presents a methodology for the timing performance optimization in the context of the future collider experiments. First a simplified model is presented for theoretical performance analysis and the validity is tested. Then an optimization process is done to find the best parameters regarding the trade-offs from the application requirements.
Degradation and residual life assessment of thermocouples with damaged sheaths in corrosive environments
Authors: Kumar Valipi Dinesh , Bhattacharyya Anindya , Behera Rajendra Prasad , M Kasinathan , Prabakar Krishnamurthy
Published: January 2025

Mineral-Insulated Metal-Sheathed thermocouples exhibit
extended lifespan and resilience in harsh environments, owing to
their protective sheath. However, these thermocouples are prone to
failure in a highly acidic medium such as nuclear fuel reprocessing
plants. This paper investigates the degradation phenomena and its
effect on measurement accuracy when a thermocouple with damage to
its protective sheath is immersed in a corrosive medium. The
objective is to assess the thermocouple's reliability by micro
machining a small hole to simulate sheath damage, facilitating
direct contact between the corrosive medium and the sensing
materials of a K-type thermocouple. The thermocouples with sheath
defects were subjected to aging in different concentrations of
acidic medium at a constant temperature, leading to eventual
failure. The time-to-failure data of thermocouples at each
concentration is analyzed using the Weibull distribution. This study
establishes a thermocouple accelerated life-stress relationship
using the Inverse Power Law under a ruptured sheath condition. The
study also explores the correlation between the residual life and
the position of simulated ruptures. ANOVA is employed to test the
hypotheses regarding the influence of rupture position on
thermocouple performance. It is shown that the location of damage is
statistically significant in determining the thermocouple's residual
life under damaged sheath condition.
Numerical modelling of active target time projection chamber for low-energy nuclear physics
Authors: Das Pralay Kumar , Datta Jaydeep , Majumdar Nayana , Mukhopadhyay Supratik
Published: January 2025

A numerical model based on hydrodynamic approach has been
developed to emulate the device dynamics of active target Time
Projection Chamber which is utilized for studying nuclear reaction
through three-dimensional tracking of concerned low-energy
particles. The proposed model has been used to investigate the
performance of a prototype active target Time Projection Chamber,
namely SAT-TPC, to be fabricated at Saha Institute of Nuclear
Physics, for its application in nuclear physics experiments. A case
study of non-relativistic elastic scattering 4He + 12C
with beam energy 25 MeV and current 2.3 pA has been opted for this
purpose. The effect of beam induced space charge on the tracking
performance the SAT-TPC prototype has been studied to optimize the
beam current and scheme of the anode readout segmentation. The model
has been validated by comparing its results to that of a particle
model used to explain observed distortion in scattered particle
tracks in a low-energy nuclear physics experiment.
Potential and costs required for methane removal to compete with BECCS as a mitigation option
Authors: Gaucher Yann , Tanaka Katsumasa , Johansson Daniel J A , Boucher Olivier , Ciais Philippe
Published: January 2025

Methane is the second most important anthropogenic greenhouse gas (GHG) causing warming after carbon dioxide, and the emission reductions potentials are known to be limited due to the difficulty of abating agricultural methane. We explore in this study the emerging option of atmospheric methane removal (MR) that could complement carbon dioxide removal (CDR) in mitigation pathways. MR is technologically very challenging and potentially very expensive, so the main question is at which cost per ton of methane removed is MR more cost effective than CDR. To address this question, we use an intertemporal optimization climate-GHG-energy model to evaluate the MR cost and removal potential thresholds that would allow us to meet a given climate target with the same or a lower abatement cost and allowing for equal or higher gross CO2 emissions than if CDR through bioenergy with carbon capture and storage were an option. We also compare the effects of MR and CDR on the cost-effective mitigation pathways achieving four different climate targets. Using the ACC2-GET integrated carbon cycle, atmospheric chemistry, climate and energy system model, we consider a generic MR technology characterized by a given unit cost and a maximal removal potential. We show that to totally replace bioenergy based CDR with MR, the MR potential should reach at least 180–290 MtCH4 per year, i.e. between 50% and 90% of current anthropogenic methane emissions, with maximum unit cost between 11 000 and 69 000 $/tCH4, depending on the climate target. Finally, we found that replacing CDR by MR reshapes the intergenerational distribution of climate mitigation efforts by delaying further the mitigation burden.
Accessible halitosis diagnosis: validating the accuracy of novel AI-based compact VSC measuring instrument
Authors: Enomoto Suguru , Zaitsu Takashi , Aritomi Risa , Akiyama Hiroshi , Aida Jun
Published: January 2025

Halitosis presents a significant global health concern, necessitating the development of precise and efficient testing methodologies owing to the high prevalence and the associated social and psychological effects. The measurement of volatile sulfur compounds (VSCs), recognized as primary contributors to halitosis, is particularly significant. While gas chromatography (GC-MS) offers accurate measurements, its bulky and expensive nature limits widespread accessibility. Hence, this study endeavors to devise a compact yet highly accurate AI-based halitosis measurement apparatus, termed ‘Kunkun dental’ and validate its efficacy. Specifically, we intend to compare the VSC concentrations obtained from halitosis patients’ breath samples using Kunkun dental against those from conventional GC-MS to assess the criterion validity of the new testing method. The study cohort comprised 68 halitosis patients aged 20 years or older, attending the breath freshening outpatient clinic at Tokyo Medical and Dental University Hospital between October 2022 and March 2023, who consented to participate and underwent routine measurements. Participants completed an age and sex questionnaire, while VSC concentrations were determined using both GC-MS and Kunkun dental (H2S, CH3SH, (CH3)2S), enabling a comparative analysis of the results. Pearson product-moment correlation coefficients between GC-MS and Kunkun dental indicated significant correlations for all three gases: 0.719 for H2S, 0.821 for CH3 SH, and 0.637 for (CH3)2S. Moreover, sensitivity and specificity in accordance with the predefined thresholds were confirmed, and their values ranged from 0.59 to 0.86 and 0.53–0.77, respectively. Furthermore, grouping Kunkun dental measurements into low-, medium-, and high-concentration groups revealed significantly higher GC-MS VSC concentrations in samples with elevated Kunkun dental readings. The amalgamation of AI technology and a semiconductor gas sensor holds great promise in creating a compact and precise halitosis analyzer. This study underscores the feasibility and effectiveness of Kunkun dental as a reliable tool for halitosis assessment, affirming its utility in clinical practice.
Effect of Number Seedlings Per Planting Hole and Seeding Media on The Growth And Yield of TSS Shallots
Authors: Latifah E , Harsonowati W , Sudaryono T , Aisyawati L , Antarlina S S , Arifin Z , Krismawati A , Ashari H. , Sihombing D , Sekarsari T D , Prahardini P E R
Published: January 2025

The research aims to determine the effect of the number of seeds per planting hole and the composition of the shallot seeding media on the growth and yield of TSS shallots. This research was conducted in rice fields in Torongrejo Village, Junrejo District, Batu City,from March to July 2024. Factorial research using a Randomized Block Design (RAK) which was repeated three times. The first factor is the treatment of the composition of the seedling media. with different varieties;there are 6 levels, namely humus seedling media of the Merdeka (HM) variety; seeding media for Merdeka variety (KM) goat manure waste; soil seedling media for the Merdeka (TM) variety; humus seedling medium for the Lokananta variety (HL); seeding media for goat manure waste of the Lokananta variety (KL); soil seedling medium for the Lokananta variety (TL), while the second factor was the treatment of the number of seeds per planting hole, namely 1 seed per hole (T1), 2 seeds per hole (T2) and 3 seeds per hole (T3). Next,the data obtained was analyzed using Analysis of Variance and tested further using a BNJ level of 5%. Based on the results of the observations,there is an interaction between seeding media, variety, and the number of plants per planting hole, which affects the growth and yield of TSS shallots. TSS shallot production per unit area (Ha) in the goat fertilizer seedling media treatment; cocopeat; soil: dolomite with a ratio of 4; 4; 6; ¼ of the Merdeka and Lokananta varieties gave better growth and results compared to the control (using soil only), while in the treatment the number of seeds per planting hole affected growth and the best results were the implementation of planting 2 seeds per hole which was more effective and efficient.
Soil Shear Strength Analysis to Determine Landslide Potential Based on UU Triaxial Test
Authors: Agung P A M , Hasan M F R , Baidhowy M S , Susilo A , Suryo E A , Pramusandi S , Adinegara A W , Pradiptiya A
Published: January 2025

Batu City has many areas that are highly susceptible to landslides. The decreasing soil shear strength generally causes landslides, so the parameter of soil shear strength needs to be significantly considered in stability analysis. This research aims to determine the landslide potential and safety factor at Payung Tourism Area, Batu City. This research used the UU triaxial testing method, which was conducted at 2 location points with a depth variation of 5 to 30 meters. The test results were used for slope stability analysis using the SLOPE/W software to determine the value of the safety factor and failure line. The stability analysis considered alteration climate, where point 1 had a safety factor of 1.176 in dry conditions and the lowest safety factor of 0.86 in the rainy season (unstable conditions). Point 2 had a safety factor of 1.938 in the dry condition and the lowest safety factor of 1.066 in the rainy season (unstable condition).
Negative Geotaxis Assay in Three Drosophila Strains Consuming Bisphenol A: Duration and Number of Climbing Successes
Authors: Ramadhan M J , Kharomah S , Kharomah S , Zahrah N A , Maghfiroh H , Fahmi M I N , Zubaidah S , Fauzi A
Published: January 2025

Bisphenol A (BPA) is a substance that can migrate from polycarbonate plastic packaging to food or beverages. Several countries have banned the use of BPA in various food packaging, while other countries still have looser regulations. This study aims to analyze the effect of BPA consumption and strain type on the climbing performance of Drosophila melanogaster. Negative geotaxis assay was conducted on 3 groups of Drosophila: without BPA, consumed 0.25 mg/mL BPA, and consumed 0.50 mg/mL BPA. In the climbing duration, BPA did not have a significant effect (F = 1.682, p = 0.240), strain had a significant effect (F = 8.807, p = 0.008), and the interaction between the two did not have a significant effect (F = 0.267, p = 0.892). In the climbing success, BPA consumption had a significant effect (F = 9.600, p = 0.006), strain had no significant effect (F = 4.200, p = 0.051), while there was a significant interaction between the two factors (F = 12.900, p = 0.001). Therefore, BPA consumption can interfere with the motor skills of Drosophila imago. This study implies that BPA exposure has the potential to be a risk factor for motor disorders in higher organisms, including humans.
Cultural Adaptation in the Utilization of Public Open Spaces in the Riverside Settlements of Kahayan River, Palangka Raya City
Authors: Garib T W , Soemardiono B , Septanti D
Published: January 2025

The riverside settlement along the Kahayan River in Palangka Raya is inhabited predominantly by the Dayak, Banjar, and Javanese ethnic groups, with diverse backgrounds in terms of religion, education, and income. Despite the Javanese community’s land-based cultural background, which contrasts with the river-based traditions of the Dayak and Banjar, they have adapted to the local culture. This study explores how these ethnic communities utilize public open spaces (POS) in the riverside settlements along the Kahayan River, with the objective of understanding the differences in usage patterns. Using a qualitative approach with field observations and in-depth interviews, the research reveals significant differences in POS usage among these communities. The Dayak and Banjar communities make year-round use of POS, even during floods and the dry season, while the Javanese, influenced by their land-based traditions, predominantly use these spaces during the dry season. These findings underscore the role of cultural differences in shaping the utilization of public spaces within the Kahayan River’s riverside settlements.
Interior-Architecture Features for Supporting Resilience in Historic Buildings Based on Place Attachment (Case Study: Bondowoso Railway Museum)
Authors: Darmawan H R , Wahyudie P , Wijayanti A T
Published: January 2025

The resilience of historic buildings is a concept to maintain their historic values and remain relevant to today’s context. A relevant historic building depends on the relationship and interaction between human as users and the building. These can be assessed based on the concept of place attachment which is influenced by the physical form of interior-architecture features that represent value, information, and meaning of the building. Place attachment is evaluated from the aspect of place identity and place affect to know the visitor’s perception of historic buildings. This research aims to examine how interior-architecture features supporting the resilience of historic building through the place attachment. The case study object is Bondowoso Railway Museum, which is related to the historical event named “Peristiwa Gerbong Maut” in 1947. This research uses quantitative methods with data collection techniques including literature studies, observations, and questionnaires to obtain place attachment variables and interior-architecture features that support the resilience of Bondowoso Railway Museum. This research found that the interior-architecture features, such as walls, columns, floors, and ceilings that are still maintained has been supporting the resilient of the Bondowoso Railway Museum Building because it has characteristics that represent Bondowoso and its historical event.
Comparative Study of Physical Design Principles in Green Hospital Concept (Case Study: Teaching Hospital)
Authors: Perdana A , Sedayu A , Permana K A , Maulana R , Nurfadilah R , Jasim M I
Published: January 2025

A teaching hospital that pays attention to environmental impact is the main vision in developing campus teaching hospitals in Indonesia. The concept of a green hospital is a trend that needs to be followed because hospital operational activities have a fairly high impact on users and the surrounding environment. Therefore, this study aims to examine the design principles of a hospital’s physical building with a green hospital concept, especially in teaching hospitals. Using a comparative study method on several study objects, the main design principles that should be applied in developing teaching hospitals with a green hospital concept can be found. Based on the results of the comparison of the three comparative objects studied, the SPETE principle (safety, patient-centeredness, efficiency, timeliness, and effectiveness) was found to be the key to developing a teaching hospital with a green concept. This principle should be applied in the physical design of the building so that the hospital building has a more positive impact on users and the surrounding environment. These five aspects certainly greatly influence the shape and physical arrangement of the hospital building so that they can be guidelines in future teaching hospitals.
Manufacturing and Electrical Design of the Ecoprint Batik Steamer Machine with Automatic Temperature and Timer Control
Authors: Sari H N , Nurhayati  , Tri I A , Budijono A P , Umaroh S T
Published: January 2025

Ecoprint is a type of batik innovation but the application of technology in the process of making ecoprint steam process which is still conventional. Based on these problems, this study identifies problems regarding the need for ecoprint batik steamer machines, where making machine designs that suit consumer needs and manufacturing machines. The method used in this study is reverse engineering. Ecoprint Batik Steamer Machine is designed using solidwork software. Next, the manufacturing process and control assembly will be carried out. Ecoprint Batik Steamer Machine is designed with 304 stainless steel material and advanced control system that allows accurate temperature and duration settings. The results of the study show that the ecoprint batik steamer machine with temperature and time control offers a significant advantage over conventional steamers. In terms of quantity, this machine is able to handle larger batches with better efficiency that can hold 4 times more batik fabric than conventional steamers, as well as optimizing the use of time and resources and also significant fuel savings with a percentage reduction in fuel consumption of up to 37.5% per hour, making it an innovative and sustainable solution for the batik industry.
Morphology and Structure of Bagasse Fiber after Chemical Treatment
Authors: Nusantara F , Suryanto H , Aminnudin A , Puspitasari P , Aldin A , Renandito M P , Osman H
Published: January 2025

Sugarcane as a raw material for the sugar industry plays a strategic role in the Indonesian economy. Higher production of sugar provides sugarcane waste namely bagasse, as a natural fiber, that has potential for a composite material. This study aims to observe the morphology and crystalline structure of bagasse fiber after chemical treatments using sodium hydroxide (NaOH) and 2, 2, 6, 6-tetramethylpiperidiny-l-oxyl (TEMPO). The methods included the immersion of bagasse fiber using 6% NaOH and TEMPO solution for 2 hours, then dried in an oven at 60 °C for 24 h. The dried fiber was then observed under Scanning Electron Microscopy (SEM) for surface morphology, and its structure was analyzed using X-ray diffraction. The bagasse fiber morphologies look different after being treated using 6% NaOH and TEMPO treatment. Both treatments of 6% NaOH and TEMPO solution cause the surface peel of bagasse fibers causing rougher fiber. Both treatments influence the crystallinity properties of bagasse fibers. The highest crystallinity peak was observed at a 22.4° angle for 6% NaOH + TEMPO-treated sample. The highest crystalline index was obtained in 6% NaOH-treated sample (58.38%). The crystalline size of bagasse fiber at 6% NaOH treatment is 7.60 nm and decreases to 2.88 nm with TEMPO treatment.
Deep learning approaches for online signature authentication: a comparative study of pre-trained CNN models
Authors: Swamy M Ranga , P Vijayalakshmi , Rajendran V
Published: January 2025

Authorization is essential for handling document assurance and security. Nowadays, it constitutes one of the top responsibilities for securing information and effectiveness in every domain. Technological advances have made interactions with machinery more effortless. As a result, the demand for authentication for various legitimate causes is growing rapidly. Therefore, biometric-based identification has dramatically accelerated. This is an improvement over the other approaches. The present work is intended to apply convolutional neural networks for mining features and supervised machine-learning techniques to verify handwritten signatures. Raw images of signatures were used to train the CNN models for feature extraction and data augmentation. In the present work, pre-trained CNN models, such as VGG16, Inception-v3, ResNet50, and Xception, were used to separate authentic from fake signatures. Supervised learning methods, including Logistic Regression and SVM, were used to classify features. The test data were obtained from the ICDAR 2011 Signature Dataset. The results obtained from the present work showed a clear improvement over traditional methods over 69 different signatures. VGG-16 with RMSProp achieved an impressive validation accuracy of 83%, demonstrating robustness with minimal overfitting. Compared with existing techniques, the proposed deep learning approach proved to be more accurate and reliable for signature verification.
Bounded Disciplines and Unbounded Problems
Authors: Fischhoff Baruch
Published: January 2025

In their lives, people often face complex, novel, fateful, and wildly unbounded problems. In their work, disciplinary scientists hone their wisdom on the complexities of necessarily bounded problems. Bounded Disciplines and Unbounded Problems offers a vision for schools of management science to bring these worlds together, by doing more of what they do best, co-creating solutions in ways that serve the world and the disciplines. Disciplinary wisdom is illustrated with studies eliciting beliefs and preferences. Collaboration is demonstrated in a wide variety of applications, including climate, energy, health, security, technology, and natural disasters. The proposed strategy for bonding bounded disciplines offers a realistic path forward, at a time when the value of academia is often questioned by the public, students, and even some of its members.
Bounding Complexity
Authors: Fischhoff Baruch
Published: January 2025

Scientific disciplines progress by deepening their understanding of the complexity of the issues that they tackle. But that success often comes at the necessary price of neglecting the complexity of many problems that individuals and societies face. This chapter discusses the inevitable, but potentially productive tensions between usefulness and specialization, between rival disciplines, and between rival subdiscipiines. It discusses the essential strengths and limitations of the heuristics that guide scientists, as well as the people they study. It sketches the origins of management science in addressing these issues, pursuing some in depth. It frames the analysis and proposals in the chapters that follow, positing an academic leadership role for management science.
Slow Science (Beliefs)
Authors: Fischhoff Baruch
Published: January 2025

“Slow science” is a name for an emerging research philosophy that emphasizes the importance of situating results derived through disciplinary science. This chapter applies that perspective to a core management science topic: eliciting individuals’ decision-relevant beliefs. It shows subtleties of research design that have emerged slowly through the trial and error of faster science, a learning process that might be accelerated through the research management strategy proposed in later chapters. It introduces face validity and construct validity, as tests for whether questions and answers mean the same things to the scientists who pose them and to the individuals who respond to them. It describes the mental model methodologies that psychology has used for disciplined slow science.
Slow Science (Preferences)
Authors: Fischhoff Baruch
Published: January 2025

This chapter applies the slow science perspective to the core management science activity of assessing individuals’ preferences. It illustrates challenges to face validity and construct validity in seemingly simple tasks, such as choices among paired options, and notably challenging ones, such as willingness-to-pay judgments for non-market goods. It considers both expressed (or stated) preferences, asking people about questions posed by researchers, and revealed preferences, looking at responses to questions posed by life. It describes the richness emerging from fast science studies looking at preferences regarding technologies, environmental changes, and medical treatments. It concludes by proposing research options when people have no answers to the questions that scientists want to ask.
Change (in)Action
Authors: Fischhoff Baruch
Published: January 2025

As with any theory of change, the value of the proposed strategy for bonding bounded disciplines depends on its usefulness for explaining past experiences and anticipating future ones. This chapter applies the strategy to accounting for a variety of more and less successful experiences in the two focal domains of Chapter 2: COVID-19 and climate change. For COVID-19, it looks at the stories of equitable vaccine allocation recommendations for using face masks, and decisions about reopening movie studios. For climate change, it looks at the failed early attempt to engage management science expertise, along with more collaborative experiences on topics including in-home displays of energy consumption and preserving salmon runs in the Columbia River system.
The Value of Interpretive Labor
Authors: Carithers Kirsten
Published: January 2025

“The Value of Interpretive Labor” explains the genesis of the author’s theory of creative work, lays out its main components, and introduces some of the musicians who will make appearances in the following chapters. The first part discusses the basis for the project: exploring musical indeterminacy through the work involved in realizing unconventional forms of notation. It also addresses some of the various types of experimental/avant-garde music that inform the theory of Interpretive Labor. The second part addresses the theoretical foundation of the book: theories of interpretation and of some of the concepts from labor history that shape the text overall.
The “Scientist” Model
Authors: Carithers Kirsten
Published: January 2025

“The Scientist Model: The Composition Studio as Laboratory” presents the second of the author’s five models of the theory of Interpretive Labor. This chapter explores the parallels between experimental composers and laboratory scientists. One of the main points of connection is through the use of chance-based procedures, which are established and tested in creating musical compositions; this also shows how these ideas relate to interpretation. Musicians Petr Kotík and Lejaren Hiller demonstrate forms of experimentation that correspond to scientific hypotheses, testing, and refinement. The conclusion points toward current aspects of scientific thinking in music, which are especially evident in electronic-music production and in university research centers.
The “Hacker” Model
Authors: Carithers Kirsten
Published: January 2025

“The Hacker Model: Subversion in Theory and Practice” presents the fourth of the author’s five models of the theory of Interpretive Labor. This chapter theorizes musical interpreters as hackers: people who are experts in a system but who subvert that system for aesthetic or functional reasons. This chapter uses Cornelius Cardew’s compositional practice and his writings to illustrate how hacking is a type of interpretation, and vice versa. It discusses several early performances of Cardew’s Treatise, drawing on archival sources. The chapter also considers some of the political implications of hacking, including communitarianism and class division. It addresses other circumstances in which musical norms have been subverted, including in distribution of media and in performance spaces.
Conclusion
Authors: Carithers Kirsten
Published: January 2025

The brief conclusion, “Interpretive Labor beyond Experimentalism” revisits the motivations driving my work on the theory of Interpretive Labor and reviews its main elements, including what is at stake if scholars fail to account for the labor conditions of musical practitioners. The chapter also addresses how this project itself is a form of interpretation, and reflects on the disciplinary conventions shaping its development. It further posits future applications of the theory to artistic practices beyond the scope of this book, argues that this conception of interpretation represents a radical restaging of performance practice, and emphasizes the value of conceiving of creative interpretation as a form of labor.
Evaluating the Equivalency of Teletesting and the Impact of the COVID-19 Pandemic on Measures of Reading Achievement in a Clinically Referred Sample
Authors: Lieb Rebecca W , Jacobson Lisa A , Kalb Luther G , Pritchard Alison E , McDermott Shelley M , Ludwig Natasha N , Peterson Rachel K , Ng Rowena , Wexler Danielle
Published: January 2025

Objective

The COVID-19 pandemic highlighted the need to build an evidence base to support teletesting as an equivalent modality for standardized neuropsychological assessment. As such, the purpose of this study was twofold. First, this study evaluated teletesting equivalency of standardized reading achievement measures during COVID-19 in children ages 6–16. Further, to examine the impact of COVID-19 on reading, achievement scores were compared in two samples of children assessed before and during COVID-19.

Methods

Participants were referred for testing at an outpatient neuropsychology clinic at an urban, academic medical center. Aim one compared assessments administered in-person (n = 1039) versus teletesting (n = 283). A two one-sided test (TOST) was used to determine equivalency. Aim two compared children seen pre-COVID-19 (n = 2125) and during COVID-19 (n = 1322) including a subsample of elementary school-aged children. One-way analyses of covariance were employed, with insurance type and Wechsler Intelligence Scale for Children, Fifth Edition Matrix Reasoning (as a proxy for nonverbal IQ) included as covariates.

Results

Results showed equivalence in reading achievement scores administered via teletesting compared to in-person during COVID-19. For aim two, Nonsense Word Decoding scores were significantly higher for the COVID-19 group compared to the pre-COVID-19 group (p = 0.03). No other significant differences in reading scores were found between groups, including no differences among a subsample of elementary school-aged children (ages 6–10; all ps > 0.05).

Conclusions

This provides additional support for teletesting equivalency and suggests the negative impact of COVID-19 on foundational reading skills is less than predicted in a clinically referred sample.
Deciphering progressive lesion areas in breast cancer spatial transcriptomics via TGR-NMF
Authors: Li Juntao , Xiang Shan , Wei Dongqing
Published: January 2025

Identifying spatial domains is critical for understanding breast cancer tissue heterogeneity and providing insights into tumor progression. However, dropout events introduces computational challenges and the lack of transparency in methods such as graph neural networks limits their interpretability. This study aimed to decipher disease progression-related spatial domains in breast cancer spatial transcriptomics by developing the three graph regularized non-negative matrix factorization (TGR-NMF). A unitization strategy was proposed to mitigate the impact of dropout events on the computational process, enabling utilization of the complete gene expression count data. By integrating one gene expression neighbor topology and two spatial position neighbor topologies, TGR-NMF was developed for constructing an interpretable low-dimensional representation of spatial transcriptomic data. The progressive lesion area that can reveal the progression of breast cancer was uncovered through heterogeneity analysis. Moreover, several related pathogenic genes and signal pathways on this area were identified by using gene enrichment and cell communication analysis.
A novel framework for phage-host prediction via logical probability theory and network sparsification
Authors: Wei Ankang , Zhan Huanghan , Xiao Zhen , Zhao Weizhong , Jiang Xingpeng
Published: January 2025

Bacterial resistance has emerged as one of the greatest threats to human health, and phages have shown tremendous potential in addressing the issue of drug-resistant bacteria by lysing host. The identification of phage–host interactions (PHI) is crucial for addressing bacterial infections. Some existing computational methods for predicting PHI are suboptimal in terms of prediction efficiency due to the limited types of available information. Despite the emergence of some supporting information, the generalizability of models using this information is limited by the small scale of the databases. Additionally, most existing models overlook the sparsity of association data, which severely impacts their predictive performance as well. In this study, we propose a dual-view sparse network model (DSPHI) to predict PHI, which leverages logical probability theory and network sparsification. Specifically, we first constructed similarity networks using the sequences of phages and hosts respectively, and then sparsified these networks, enabling the model to focus more on key information during the learning process, thereby improving prediction efficiency. Next, we utilize logical probability theory to compute high-order logical information between phages (hosts), which is known as mutual information. Subsequently, we connect this information in node form to the sparse phage (host) similarity network, resulting in a phage (host) heterogeneous network that better integrates the two information views, thereby reducing the complexity of model computation and enhancing information aggregation capabilities. The hidden features of phages and hosts are explored through graph learning algorithms. Experimental results demonstrate that mutual information is effective information in predicting PHI, and the sparsification procedure of similarity networks significantly improves the model’s predictive performance.
Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy
Authors: Sánchez-Villanueva José A , N’Guyen Lia , Poplineau Mathilde , Duprez Estelle , Remy Élisabeth , Thieffry Denis
Published: January 2025

Acute Promyelocytic Leukaemia (APL) arises from an aberrant chromosomal translocation involving the Retinoic Acid Receptor Alpha (RARA) gene, predominantly with the Promyelocytic Leukaemia (PML) or Promyelocytic Leukaemia Zinc Finger (PLZF) genes. The resulting oncoproteins block the haematopoietic differentiation program promoting aberrant proliferative promyelocytes. Retinoic Acid (RA) therapy is successful in most of the PML::RARA patients, while PLZF::RARA patients frequently become resistant and relapse. Recent studies pointed to various underlying molecular components, but their precise contributions remain to be deciphered. We developed a logical network model integrating signalling, transcriptional, and epigenetic regulatory mechanisms, which captures key features of the APL cell responses to RA depending on the genetic background. The explicit inclusion of the histone methyltransferase EZH2 allowed the assessment of its role in the resistance mechanism, distinguishing between its canonical and non-canonical activities. The model dynamics was thoroughly analysed using tools integrated in the public software suite maintained by the CoLoMoTo consortium (https://colomoto.github.io/). The model serves as a solid basis to assess the roles of novel regulatory mechanisms, as well as to explore novel therapeutical approaches in silico.
BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction
Authors: Yang Yang , Zheng Zixuan , Xu Yuyang , Wei Huifang , Yan Wenying
Published: January 2025

The automatic and accurate extraction of diverse biomedical relations from literature constitutes the core elements of medical knowledge graphs, which are indispensable for healthcare artificial intelligence. Currently, fine-tuning through stacking various neural networks on pre-trained language models (PLMs) represents a common framework for end-to-end resolution of the biomedical relation extraction (RE) problem. Nevertheless, sequence-based PLMs, to a certain extent, fail to fully exploit the connections between semantics and the topological features formed by these connections. In this study, we presented a graph-driven framework named BioGSF for RE from the literature by integrating shortest dependency paths (SDP) with entity-pair graph through the employment of the graph neural network model. Initially, we leveraged dependency relationships to obtain the SDP between entities and incorporated this information into the entity-pair graph. Subsequently, the graph attention network was utilized to acquire the topological information of the entity-pair graph. Ultimately, the obtained topological information was combined with the semantic features of the contextual information for relation classification. Our method was evaluated on two distinct datasets, namely S4 and BioRED. The outcomes reveal that BioGSF not only attains the superior performance among previous models with a micro-F1 score of 96.68% (S4) and 96.03% (BioRED), but also demands the shortest running times. BioGSF emerges as an efficient framework for biomedical RE.
Bayesian gene set benchmark dose estimation for “omic” responses
Authors: Zilber Daniel , Messier Kyle P , House John , Parham Fred , Auerbach Scott S , Wheeler Matthew W
Published: January 2025

Motivation

Estimating a toxic reference point using tools like the benchmark dose (BMD) is a critical step in setting policy to regulate pollution and ensure safe environments. Toxicity can be measured for different endpoints, including changes in gene expression and histopathology for various tissues, and is typically explored one gene or tissue at a time in a univariate setting that ignores correlation. In this work, we develop a multivariate estimation procedure to estimate the BMD for specified gene sets. Our approach extends the foundational univariate approach by accounting for correlation in a statistically principled way.

Results

We illustrate the method using data from a 5-day rat study and Hallmark gene sets and compare to existing BMD results computed by the EPA for both gene sets and apical histopathology endpoints. In contrast to previous ad-hoc methods, our principled approach provides the needed extension to bring the foundational univariate method into the multivariate world of transcriptomics. In addition to use in a regulatory setting, our method can provide hypothesis generation when gene sets correspond to mechanistic pathways.

Availability and implementation

BS-BMD is implemented in R and C++ and available at https://github.com/NIEHS/BS-BMD.
FlowPacker: Protein side-chain packing with torsional flow matching
Authors: Lee Jin Sub , Kim Philip M
Published: January 2025

Motivation

Accurate prediction of protein side-chain conformations is necessary to understand protein folding, protein-protein interactions and facilitate de novo protein design.

Results

Here we apply torsional flow matching and equivariant graph attention to develop FlowPacker, a fast and performant model to predict protein side-chain conformations conditioned on the protein sequence and backbone. We show that FlowPacker outperforms previous state-of-the-art baselines across most metrics with improved runtime. We further show that FlowPacker can be used to inpaint missing side-chain coordinates and also for multimeric targets, and exhibits strong performance on a test set of antibody-antigen complexes.

Availability

Code is available at https://gitlab.com/mjslee0921/flowpacker.

Supplementary information

Supplementary data are available at Bioinformatics online.