Miracle-dz/UniFAR-FTUs huggingface dataset:
A Additional Results

Sections A.1–A.3 present more comprehensive empirical results organized to correspond with Sections 4.1–4.3. The objective of ODM is to minimize the system regret, so that should be the primary measure of performance; however, we also provide a variety of other metrics to give a broader picture of how UMPIRE and benchmarks behave. In order of appearance in the sequel: The system loss is defined by Equation 3: Rt(⇡̂, ) :=EXt⇠⇢EỸt⇠⇡̃(·|Xt)EYt⇠⇡⇤(·|Xt)[ (Zt=0|Xt, Ỹt)`(Yt, (Y Ỹt)) + (Zt=1|Xt, Ỹt)(`(Yt, ⇡̂(·|Xt))+kint)+ (Zt=2|Xt, Ỹt)kreq], where we approximate the expectations over multiple samples by averaging over the ten runs of each experiment; loss values are taken as the moving average of a rolling window of width n/5. The system regret is defined by Equation 4: Regret[t] := Pt ⌧=0(R⌧ (⇡̂, ) R⌧ (⇡⇤, ⇤)); that is, regret values are the cumulative sums of system loss less oracle loss (with the oracle mediator policy being the greedy policy ⇤ and the oracle model policy ⇡⇤ approximated by training on the full dataset in advance), where we similarly approximate the expectations over multiple trajectories by averaging over the ten runs of each experiment. The system mistake at each time t is defined as whether or not the decision system S as a whole outputs a final decision Ȳt⇠⇡S(·|X, Ỹ ) that is a mistake; that is, if Ȳt is different from the (observed or unobserved) decision of the expert Yt: EXt⇠⇢EỸt⇠⇡̃(·|Xt)EYt⇠⇡⇤(·|Xt)`(Yt, ⇡̄S(·|Xt, Ỹt)), where we again likewise approximate the expectations over multiple samples by averaging over the ten runs of each experiment; as with system loss, numbers are computed as the moving average of a rolling window of width n/5. Across all evaluation measures, UMPIRE consistently performs better than applying existing methods.
Phage Display.

In crossing a heath, suppose.I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place. [T]he inference, we think, is inevitable, that the watch must have had a maker: that there must have existed.an artificer or artificers, who formed it for the purpose which we find it actually to answer; who comprehended its construction and designed its use. [And] every indication of contrivance, every manifestation of design, which existed in the watch, exists in the works of nature; with the difference, on the side of nature, of being greater or more, and that in a degree which exceeds all computation. ”1
On the Relationship between Code Verifiability and Understandability

Proponents of software verification have argued that simpler code is easier to verify: that is, that verification tools issue fewer false positives and require less human intervention when analyzing simpler code. We empirically validate this assumption by comparing the number of warnings produced by four state-of-the-art verification tools on 211 snippets of Java code with 20 metrics of code comprehensibility from human subjects in six prior studies. Our experiments, based on a statistical (meta-)analysis, show that, in aggregate, there is a small correlation (r = 0.23) between understandability and verifiability. The results support the claim that easy-to-verify code is often easier to understand than code that requires more effort to verify. Our work has implications for the users and designers of verification tools and for future attempts to automatically measure code comprehensibility: verification tools may have ancillary benefits to understandability, and measuring understandability may require reasoning about semantic, not just syntactic, code properties.
The Shallow-Water Stony Corals of the Netherlands Antilles

Although the corals and reefs of Curacao are fairly well known (VAN DER HORST 1927, Roos 1964, 1967), information about coral growth around the other islands of the Netherlands Antilles is still lacking. This paper offers the first comprehensive study of the reef corals of this area: Aruba, Curacao (with Klein Curacao), Bonaire (with Klein Bonaire), St. Martin, Saba and St. Eustatius. Due to practical reasons, however, the survey had to be restricted in several respects.
Newcastle University E-prints Citation for Published Item: Publishers Copyright Statement

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STEPS : modeling and simulating complex reaction-diffusion systems with Python

INTRODUCTION Computational modeling and simulation of signaling pathways has become a valuable and established tool for studying the molecular aspects of biological systems (Bhalla, 2004; Doi et al., 2005; Holmes, 2000; Kuroda et al., 2001; Lindskog et al., 2006; Miller et al., 2005; Smolen et al., 2006; Stefan et al., 2008). Modeling such systems consists of identifying the molecular players and describing the stoichiometry and rate constants of their chemical interactions. The resulting system is then often simulated by converting it to a set of coupled ordinary differential equations that can be numerically integrated (Press et al., 2007). It has long been acknowledged that the discrete nature of reaction events, caused by the very low numbers of key molecules being present, can make biological reaction systems noisy and affect their behavior on a macroscopic level. This aspect can be brought into the simulation by adding noise terms to the differential equations (Kloeden and Platen, 1999; van Kampen, 2007), or more commonly, by simulating the system with Gillespie’s Stochastic Simulation Algorithm or SSA (Gillespie, 1977) or one of its derivations (Gillespie, 2007). For some pathways, however, even more realism is needed. One such case is when the spatial organization and morphology of the cell is known to play an active role in controlling the pathway, e.g. through chemical compartmentalization, spatial gradients and by various transport processes and diffusion (Lemerle et al., 2005). Such cases are common in neurons because of their complex dendritic arborization (Santamaria et al., 2006), but of course are not limited to them. In order to study systems at the level where stochasticity, spatial gradients within complex boundary conditions and diffusion all come into play at the same time, we have developed a simulation platform called STEPS (STochastic Engine for Pathway Simulation) that uses an extension of Gillespie’s SSA to deal with diffusion STEPS: modeling and simulating complex reaction-diffusion systems with Python
A new LDA-based method for face recognition

Linear discriminant analysis (LDA) is a feature extraction technique for classification. In this paper, we propose a new LDA-based method that can overcome the drawback existed in the traditional LDA methods. It redefines the between-class scatter by adding a weight function according to the between-class distance, which helps to separate the classes as much as possible. At the same time, it projects the between-class scatter into the null space of the within-class scatter that contains the most discriminant information. Hence, the transformation matrix composed with the eigenvectors corresponding to the largest eigenvalues of the transferred between-class scatter can maximize the Fisher criteria. Experimental results show our method achieves better performance in comparison with the traditional LDA methods.
Development and clinical applications of the time intensity curve shape analysis in dynamic contrast enhanced MRI: a pixel-by-pixel approach

Purpose: To analyze the distribution of different shapes of time intensity curves (TICs) in synovial tissue of patients with rheumatoid arthritis (RA) and to compare relative numbers of TIC shapes between patients with RA and healthy control subjects. Materials and Methods: This prospective study was approved by the institutional review board; patients and control subjects gave written informed consent. Dynamic contrast magnetic resonance (MR) imaging of the knee joint in five patients with early RA and in five control subjects was performed. Parametric maps showing seven TIC shape types were created. Spatial information of the synovial TIC shape distribution pattern and relative number of TIC shapes were calculated on a three-dimensional region of interest. Relative TIC shape numbers were compared by using a nonparametric Mann-Whitney U test. Results: Synovial enhancement in patients with RA consisted of type 2 TIC shapes (slow enhancement) with heterogeneous zones of types 3 (fast enhancement followed by plateau phase), 4 (fast enhancement followed by early washout phase), and 5 (fast enhancement followed by slow enhancement increase) TIC shapes, compared with almost only type 2 TIC shapes in control subjects. The heterogeneous zones were seen in the lateral and medial knee compartments and around the cruciate ligaments. A significantly higher relative number of type 4 TIC shapes was observed in the patient group compared with the control group (16.5% vs. 6.9%, P = .008). Conclusion: The pixel-by-pixel dynamic contrast enhanced MR imaging TIC shape analysis may help distinguish patients with RA from control subjects on the basis of the relative number of type 4 TIC shapes. This study provides the rationale for future research to evaluate the utility of this approach in clinical practice.
Evaluation of the potentialities of different soil types to yield response of soybean under deficit irrigation

An experiment was conducted in a vinyl house at Gifu University, Japan, from June to November 2007 to evaluate the potentialities of the three soil types under various water deficit conditions to yield of soybean. The soil type was the first factor with three different soil types, comprising of clay loam, sandy clay loam, and sandy loam soils, classified as Inceptisol, Ultisol, and Andisol, respec- tively. Water deficit (D) was the second factor with four levels including D1 (0 - 25 %), D2 (25 - 50 %), D3 (50 - 75 %) and D4 (75 - 100 %) water deficits of total available water (TAW). The crop water requirement (CWR) of soybean in the three soil types significantly decreased with the increas- ing water deficit levels, and the highest was in Incepti- sol, followed by Ultisol and then Andisol under all wa- ter deficit levels. Grain yield of soybean per unit area in Inceptisol was the highest, followed by Ultisol and then Andisol under all water deficit levels. The values of yield efficiency (YE), indicating the grain yield per unit CWR, was strongly influenced by water deficit level, and the max- imum YE occurred at the water deficit level D3 (50 - 75 %) in all the three soil types. However, there were no signif- icant differences at 5 % level among the maximum values of YE in the three soil types. The lowest yield response factor (Ky), indicating the relative yield loss to relative wa- ter deficit, was seen in Inceptisol (Ky = 0.42), followed by Ultisol (Ky = 0.64) and then Andisol (Ky = 0.87) under the water stress lower than 50 - 75 % of TAW. These results indicate that deficit irrigation in Inceptisol contained the finest soil texture is the most effective for economic water usage among the three soil types under the water deficit lower than 50 - 75 % of TAW (D3).
Software Measurement and Functional Programming

Software metrics have been investigated for the assessment of programs writ-ten in a functional programming language. The external attribute of programs considered in this thesis is their comprehensibility to novice programmers. This attribute has been operationalized in a number of experiments. The in-ternal attribute of software which is examined is the structure. Two models for the structure of software have been employed: callgraphs and flowgraphs. The proposed control-flow model captures the operational semantics of function definitions. The objective measurement of the attributes has been supported by tools. The validation of structure metrics has been addressed in certain ex-periments for programming-in-the-small. The structure of type expressions in functional programs has been analysed in a case study. A simple framework for software metrication proved to be useful. The validation of metrics has been linked with axioms from the representational measurement theory. The control-flow model for functional programs showed its value in the set-up of an experiment regarding the influence of the structure on the comprehensibility. A programming style rule on the use of guards in function definitions has been validated by the findings in this experiment.
ECDP: Energy Consumption Disaggregation Pipeline for Energy Optimization in Lightweight Robots

Limited resources and resulting energy crises occurring all over the world highlight the importance of energy efficiency in technological developments such as robotic manipulators. Efficient energy consumption of manipulators is necessary to make them affordable and spread their application in the future industry. Previously, the power consumption of the robot motion was the main factor considered in the evaluation of energy efficiency. Lately, the paradigm in industrial robotics shifted towards lightweight robot manipulators which require a new investigation on the disaggregation of robot energy consumption. In this paper, we propose a novel pipeline to identify and disaggregate the energy use of mechatronic devices and apply it to lightweight industrial robots. The proposed method allows the identification of the electronic components consumption, mechanical losses, electrical losses, and required mechanical energy for robot motion. We evaluate the pipeline and understand the distribution of energy consumption using four different manipulators, namely, Universal Robot's UR5e, UR10e, Franka Emika's FR3, and Kinova Gen3. The experimental results show that most of the energy (60–90%) is consumed by the electronic components of the robot control box. Using this knowledge, the approaches to further optimize their energy consumption need to shift towards efficient robot electronic design instead of efficient robot mass distribution or motion control. Finally, our disaggregation pipeline allows an understanding of the power consumption of any mechatronic device and thus enables deliberate optimization of energy consumption.
Matrix invariants for program equivalence in LCTRSs

When transforming a program into a more efficient version (for example by translating recursive functions into iterative ones), it is important that the input-output-behavior remains the same. One approach to assure this uses Logically Constrained Term Rewriting Systems (LCTRSs). Two versions of a program are translated into LCTRSs and compared in a proof system (Rewriting Induction). Proving their equivalence in this system often requires the introduction of a lemma. In this paper we present a new technique for generating invariants, using matrix calculations, and show how it can be combined with an existing method by Fuhs, Kop and Nishida to produce a lemma.
Prototype Kran Air Wudhu Otomatis Berbasis Sensor Infrared

Penggunaan air setiap berwudhu bervariasi dari 1 sampai 3 liter per orang tergantung pada cara membuka kran dan kecepatan aliran. Untuk kecepatan aliran rendah dengan kran terbuka penuh air yang terpakai antara 1 – 1,5 liter sedang dengan kran terbuka setengah hanya menghabiskan antara 0,75 – 1 liter. Padahal menurut hadits, Rasullulaah berwudhu dengan satu mud air ( satu mud kurang lebih setengah liter air). Penghematan air wudhu bisa dilakukan dengan mengurangi jumlah pemakaian air yang dikeluarkan oleh kran. Pada penelitian ini dirancang sebuah sistem air wudhu yang merupakan integrasi dari kran otomatis yang dilengkapi sensor infra merah dan solenoid dengan menggunakan mikrokontroller Arduino Uno. Pada sistem ini juga digunakan sistem pompa otomatis untuk daur ulang air wudhu menggunakan sensor pH dan sensor kekeruhan. Pada sistem ini, keran hanya akan terbuka jika ada kaki/tangan yang berada di bawah keran, dan tertutup saat tidak ada halangan. Sistem bisa mengurangi kekeruhan yang dihasilkan dari air wudhu. Hasil pengujian menunjukkan sistem ini bisa menghemat pemakaian air wudhu sebesar 10,87 %.
Theory of the linear sampling method for time-dependent fields

The linear sampling method seeks to localize the unknown source of an observed, time-dependent field. The unknown source could be, for example, a scatterer embedded within a medium, or an impulsive excitation such as an earthquake or explosion. The source of the observed field is localized by means of solving the so-called near-field equation and mapping the obtained solutions through an indicator functional over a test region assumed to contain the source. In its current formulation, however, the linear sampling method suffers from an ambiguous time parameter that strongly influences its ability to localize the unknown source. Our paper consists of two fundamental results central to the theoretical understanding of the linear sampling method and its numerical implementation. First, we prove the so-called blowup behavior of solutions to the near-field equation for a general source function that is separable in space and time. Second, we show that the linear sampling method can be formulated such that the ambiguous time parameter is irrelevant. We demonstrate that a dependence of the linear sampling method on the time parameter arises from an incorrect implementation of a convolution-type operator found in the near-field equation. When the operator is implemented correctly, the dependence on the time parameter vanishes. We provide detailed algorithms for efficient and proper implementations of the convolutional operator in both the time and frequency domains. The crucial result of the improved implementations is that they allow the linear sampling method to be completely automated, as one does not need to know the space-time dependence of the unknown source. We demonstrate the effectiveness of the improved time- and frequency-domain implementations using several numerical examples applied to imaging scatterers.
The Giant Protein Titin A Major Player in Myocardial Mechanics , Signaling , and Disease

The sarcomere contains, in addition to thin and thick filaments, a filament composed of the giant protein titin (also known as connectin). Titin molecules anchor in the Z-disc and extend to the M-line region of the sarcomere. The majority of titin’s I-band region functions as a molecular spring. This spring maintains the precise structural arrangement of thick and thin filaments, and gives rise to passive muscle stiffness; an important determinant of diastolic filling. Earlier work on titin has been reviewed before. In this study, our main focus is on recent findings vis-à-vis titin’s molecular spring segments in cardiac titins, including the discovery of fetal cardiac isoforms with novel spring elements. We also discuss new insights regarding the role of titin as a biomechanical sensor and signaling molecule. We will end with focusing on the rapidly growing knowledge regarding titinopathies. (Circ Res. 2004;94:284-295.)
Regulation of G Protein–Coupled Receptor Signaling By Scaffold Proteins G Protein–Coupled Receptor Oligomerization: Implications for G Protein Activation and Cell Signaling Multi-Tasking RGS Proteins in the Heart: The Next Therapeutic Target?

Regulator of G-protein–signaling (RGS) proteins play a key role in the regulation of G-protein–coupled receptor (GPCR) signaling. The characteristic hallmark of RGS proteins is a conserved 120-aa RGS region that confers on these proteins the ability to serve as GTPase-activating proteins (GAPs) for G proteins. Most RGS proteins can serve as GAPs for multiple isoforms of G and therefore have the potential to influence many cellular signaling pathways. However, RGS proteins can be highly regulated and can demonstrate extreme specificity for a particular signaling pathway. RGS proteins can be regulated by altering their GAP activity or subcellular localization; such regulation is achieved by phosphorylation, palmitoylation, and interaction with protein and lipid-binding partners. Many RGS proteins have GAP-independent functions that influence GPCR and non-GPCR–mediated signaling, such as effector regulation or action as an effector. Hence, RGS proteins should be considered multifunctional signaling regulators. GPCR-mediated signaling is critical for normal function in the cardiovascular system and is currently the primary target for the pharmacological treatment of disease. Alterations in RGS protein levels, in particular RGS2 and RGS4, produce cardiovascular phenotypes. Thus, because of the importance of GPCR-signaling pathways and the profound influence of RGS proteins on these pathways, RGS proteins are regulators of cardiovascular physiology and potentially novel drug targets as well. (Circ Res. 2005;96:401-411.)
New Data Network Architecture: From Reactive Post-collecting to Intelligent Proactive Pre-sensing

With the emergence of scenarios that consume large amounts of data such as AI/ML (artificial intelligence and machine learning) and ISAC (Integrated sensing and communication) technologies, how to efficiently utilize data while protecting data privacy and security, reducing communication overhead, and improving data utilization efficiency have become one of the major research interests for 6G network technologies. Current mobile communication networks only use external data service nodes, and the sensing of data is based on consumer subscription, which cannot meet the data service requirements of 6G networks. We propose a data service network architecture for mobile communication networks that supports intelligent collaboration of distributed data service nodes; transforms reactive subscription mode into proactive sensing mode with the assistance of AI/ML analysis; enhances data sensing, processing and storage mechanisms through the flexible use of data rules and knowledge, thus effectively improving the overall data service capability; further, with this architecture, possible solutions are discussed in detail with emphasis on data sensing difficulties.
A Self-decoupled Two Closely Antenna Array with Reconfigurable Polarization Using Characteristic Mode Theory

In this paper, a self-decoupled two closely antenna array with reconfigurable polarization was proposed. This antenna array is composed of two patches with short-pins loaded. Characteristic mode analysis was introduced, which offers a unique physical insight on the decoupling mechanism through manipulating the odd mode and the even mode. Through the loading of pins, the even mode and the odd mode of two orthogonal linear polarization are converged together with overlapped resonant frequency. By feeding one patch to excite the both modes together, the currents would be canceled out on the other patch, thus leading to high isolation. Meanwhile, the two orthogonal polarization have a phase difference of 90 degree and circular polarization can be generated by exciting them together. Through controlling the feeding network with P-I-N diodes, the modes with different polarization are excited. The simulation results showed that significant reduction of mutual coupling have been achieved for dual-linear and circular polarization.