Miracle-dz/UniFAR-FTUs huggingface dataset:
Concepts and protocols for electrostatic free energies

Electrostatic free energies play an essential role in numerous biomolecular processes occurring in solution. Difficulties arise when the long-range Coulomb interaction is computed for idealised infinite simulation models with periodic boundary conditions. To maintain a neutral simulation box and a finite per-box energy, a neutralising charge density or ‘gellium’ is commonly used, leading to a mean box potential that is constrained to be rigorously equal to zero at all times. Thus, in considering quantities such as ion solvation free energy, the potential drop to move from solvent into the usual, gas phase reference state is missing. In fact, for an infinite molecular system, the electrostatic potential itself is not uniquely defined, but takes the form of an infinite series that is only conditionally convergent. This leads to several possible computational conventions that give different values for the potential and field, all mathematically valid. For experimentally measurable quantities, however, unique results are obtained when sufficiently large simulation boxes are utilised. These concepts are detailed, as well as a fundamental, linear response theoretical framework that provides qualitative understanding of the physical processes involved, especially dielectric relaxation of the environment in response to a new solute charge. Illustrative applications to ligand binding and biomolecular electron transfer are described.
Genetic dissection of triplicated chromosome 21 orthologs yields varying skeletal traits in Down syndrome model mice

ABSTRACT Down syndrome (DS) phenotypes result from triplicated genes, but the effects of three copy genes are not well known. A mouse mapping panel genetically dissecting human chromosome 21 (Hsa21) syntenic regions was used to investigate the contributions and interactions of triplicated Hsa21 orthologous genes on mouse chromosome 16 (Mmu16) on skeletal phenotypes. Skeletal structure and mechanical properties were assessed in femurs of male and female Dp9Tyb, Dp2Tyb, Dp3Tyb, Dp4Tyb, Dp5Tyb, Dp6Tyb, Ts1Rhr and Dp1Tyb;Dyrk1a+/+/− mice. Dp1Tyb mice, with the entire Hsa21 homologous region of Mmu16 triplicated, display bone deficits similar to those of humans with DS and served as a baseline for other strains in the panel. Bone phenotypes varied based on triplicated gene content, sex and bone compartment. Three copies of Dyrk1a played a sex-specific, essential role in trabecular deficits and may interact with other genes to influence cortical deficits related to DS. Triplicated genes in Dp9Tyb and Dp2Tyb mice improved some skeletal parameters. As triplicated genes can both improve and worsen bone deficits, it is important to understand the interaction between and molecular mechanisms of skeletal alterations affected by these genes.
Geometric bistellar flips: the setting, the context and a construction

We give a self-contained introduction to the theory of secondary polytopes and geometric bistellar flips in triangulations of polytopes and point sets, as well as a review of some of the known results and connections to algebraic geometry, topological combinatorics, and other areas. As a new result, we announce the construction of a point set in general position with a disconnected space of triangulations. This shows, for the first time, that the poset of strict polyhedral subdivisions of a point set is not always connected.
Iron loss calculation considering temperature influence in non-oriented steel laminations

In this study, the temperature influence on iron loss of non-oriented steel laminations is investigated. The iron loss variation under different flux densities, frequencies and temperatures is systematically measured and analysed by testing two typical non-oriented steel laminations, V300-35 A and V470-50 A. The iron loss variation with temperature is almost linear in the typical operating temperature range of electrical machines. Furthermore, the varying rate of iron loss with temperature varies with flux density and frequency. A coefficient which can fully consider the temperature influence is introduced to the existing iron loss model to improve the iron loss prediction accuracy. The predicted and measured results show that the temperature influence on the iron loss can be effectively considered by utilising the improved model, i.e. the prediction accuracy of the improved iron loss model remains constant, even when the temperature varies significantly. A potential simplification of this improved model is also discussed in this study.
Boundary Control Problems in Convective Heat Transfer with Lifting Function Approach and Multigrid Vanka-Type Solvers

This paper deals with boundary optimal control problems for the heat and Navier-Stokes equations and addresses the issue of defining controls in function spaces which are naturally associated to the volume variables by trace restriction. For this reason we reformulate the boundary optimal control problem into a distributed problem through a lifting function approach. The stronger regularity requirements which are imposed by standard boundary control approaches can then be avoided. Furthermore, we propose a new numerical strategy that allows to solve the coupled optimality system in a robust way for a large number of unknowns. The optimality system resulting from a finite element discretization is solved by a local multigrid algorithm with domain decomposition Vanka-type smoothers. The purpose of these smoothers is to solve the optimality system implicitly over subdomains with a small number of degrees of freedom, in order to achieve robustness with respect to the regularization parameters in the cost functional. We present the results of some test cases where temperature is the observed quantity and the control quantity corresponds to the boundary values of the fluid temperature in a portion of the boundary. The control region for the observed quantity is a part of the domain where it is interesting to match a desired temperature value.
Surgical Instrument Designers and Inventors—Where are the Women?

Historically, surgical instruments were designed by men for male surgeons. Although instrumentation has changed with the changing paradigms of surgery, it has failed to adapt to the changing surgical workforce. Almost 30% of surgeons are female and nearly 90% of surveyed female surgeons report poor instrument design and associated musculoskeletal injuries from use. Understanding the current state of handheld surgical instrument design, published literature was reviewed, surgical instrument collections were contacted, and the U.S. Patent and Trademark databases were queried to identify public patents and pre-granted applications of female inventors of handheld surgical instruments. Twenty-five female inventors were identified from published literature and 1551 unique females hold patents. This number pales when the denominator of male inventors is considered. Hence, to address the female surgeon’s lack of instrumentation and design, there is a critical need for participatory ergonomics whereby both the female surgeon and engineer collaborate on design.
Native Missing Persons Cases Will Not be Solved by Police Alone: The Case for “Missing Persons Advocates”

This study explored the potential role of victim advocacy in Native American missing person cases. Interviews with 25 tribal and non-tribal victim/social service providers were conducted to assess their perspectives on the factors which make Native Americans vulnerable to going missing, the barriers and challenges regarding reporting and investigating missing persons, as well as how victim/social service providers might better support the families of missing persons. Findings suggest that advocates perceive that responding to and offering services for Native families who experience a missing loved one will be extremely difficult because of the intersection of isolation, poverty, and jurisdictional complexities among tribal lands, combined with social service providers and law enforcement officers’ lack of resources and training regarding cultural sensitivity. At the same time, advocates suggest that additional training and resources could help overcome many of these barriers and see a role for victim service providers in responding to missing and murdered Native American persons. Implications and suggestions for practice are discussed.
Design and Development of Fast Dissolving Cinnarizine Tablets by Sublimation Technique

Cinnarizine is a piperazine derivative with antihistamine, sedative and calcium channel blocking activity. It is used for the systematic treatment of nausea and vertigo for the prevention and treatment of motion sickness. In the present invention Fast dissolving tablets of Cinnarizine were prepared by sublimation method. The prepared formulations were evaluated for pre-compressional and post-compressional parameters. The compatibility of drug with other ingredients was checked by FTIR and DSC studies, these results revealed that there was no interaction between dug and other excipients. The values of pre-compressional parameters were within prescribed limits and indicated good free flowing properties. In all the formulations the hardness test indicates good mechanical strength. Friability of all formulations was less than 1. Drug content was found to be high (≥ 101.50%) and uniform in all the formulations. The tablet thickness was found to be 3.59 – 3.62. The weight variation results revealed that average percentage deviation was less then ± 7.5%, which provides good uniformity in all formulations. The disintegration time of the tablets decreased significantly with increase in the concentration of subliming agent. The formulations C4 50% of drug released in 6.25 min, and 90% of drug released in 19.74 min. Stability study carried out as per ICH guidelines for three months and results revealed that upon storage disintegration time of tablets decreased significantly (p<0.05). The results concluded that fast dissolving tablets of Cinnarizine with sublimation technique, an optimum point can be reached in the shortest time with minimum efforts and this technique would be an effective alternative approach compared with the use of more expensive adjuvants in the formulations.
The continuity between representations of small and large numbers: a neural model

It is debated whether there are two kinds of different numerosity representation systems for small number and large number,nrespectively. We built a model with the numerosity detector neurons to simulate cognitive process of numerositiynrepresentation. Our results are consistent with the electrophysiological data and show the continuity between small andnlarge numbers.
14th Annual University of Pennsylvania Conference on statistical issues in clinical trials/subgroup analysis in clinical trials: Opportunities and challenges (afternoon panel discussion)

Pam Shaw: It is my great pleasure to introduce our discussant panelists. I’ll start with Dr. Mark Rothmann, who is the Director of the US Food and Drug Administration (FDA) Division of Biometrics 2 within the Center for Drug Evaluation and Research, which reviews cardiology, nephrology, diabetes, lipids, obesity, and general endocrinology products. He has been with the FDA since 1999, I believe, and before that, he spent several years in academia. He’s done a lot of work in the areas of subgroup analysis. We heard the morning speakers citing some of that work, including the Drug Trials Snapshots Program of the US Food and Drug Administration, heterogeneous treatment effects, and diversity in precise medicine.
Performance of different dental age estimation methods on Saudi children.

AIM To evaluate and compare the performance of six dental age estimation methods (Moorrees, Fanning and Hunt, Demirjian, Gleiser and Hunt, Nolla, Chaillet et al., and Nicodemo et al.) on a sample of Saudi children. METHOD This cross-sectional study was based on the evaluation of a sample of 400 archived digital panoramic radiographs of healthy Saudi children (200 each from boys and girls) aged 6 to 15.99 years. Panoramic radiographs acquired during 2018-2021 were obtained from the information technology department of the dental clinics at King Saud University, Riyadh, Saudi Arabia. Dental age was evaluated using the six dental age estimation methods on the developing permanent dentition in both jaws of the left side. The accuracy of each method was assessed in relation to chronological age, and a comparison between these methods was made. RESULT For all the tested methods, significant differences were found between chronological and dental age (P<0.001). The mean difference between dental and chronological age was (-2.19 years) for Chaillet et al. method, (0.15 years) for the Demirjian method, (-1.01 years) for the Moorrees, Fanning and Hunt method, (-1.72 years) for Nicodemo et al. method, (-1.29 years) for Nolla method, and (-1.00 years) for Gleiser and Hunt method. CONCLUSION Among the tested methods, the accuracy in Saudi subjects was the highest for Demirjian's method, followed by the Moorrees, Fanning and Hunt method. The methods proposed by Nicodemo et al., and Chaillet et al., were the least accurate.
Bootstrap LR Tests for Sign and Amplitude Asymmetries

Using threshold autoregressive specifications, this paper develops new parametric tests for level asymmetries. It proposes bootstrap likelihood ratio statistics to test the symmetric adjustment null against sign and amplitude asymmetries or a combination of both. Monte Carlo simulations show that the proposed tests have good size properties and reasonable power for n>=300. An application to three US dollar nominal exchange rates, 1973:2-2000:2, shows pervasive evidence of amplitude asymmetry. \t
Principal Component Analysis of the UK Term Structure & Its Application to Immunisation Strategies

This study will consist of a fully comprehensive analysis of UK term structure of interest rates using the well known statistical model called the Principal Component Analysis (PCA) and it is considered as the main drive for a successful immunization strategy for the time period concerned. Term structure of interest rates from year 1992 to 2003 has been taken as the sample data set and it s very important for carrying out detailed analysis due to the reason that in the beginning of the time period, the term structure has undergone major variations as a result of macro economic changes. Principal Component Analysis will describe the behaviour of correlated random variables in terms of a small number of uncorrelated “principal components”, that means these complex movements of the term structure will be explained by the first three factors the “level”, “steepness” and “curvature”. The core expectation of this study is to analyze the immunization strategies based on the PC based and Moment based durations and to identify the method with a better approximated return to the portfolio. The results concluded that the PC based duration provides a comparatively better approximated return than the Moment based duration strategy. The study found that 99 percent of the total variation of the term structure can be explained by the first three factors and the first factor is significantly constant throughout the time period except the first few years. In addition to the above, it has been found that the standard deviation and the eigenvalue of the first PC are negatively correlated.
Climate-driven variability of the Southern Ocean CO2 sink

The Southern Ocean is a major sink of atmospheric CO2, but the nature and magnitude of its variability remains uncertain and debated. Estimates based on observations suggest substantial variability that is not reproduced by process-based ocean models, with increasingly divergent estimates over the past decade. We examine potential constraints on the nature and magnitude of climate-driven variability of the Southern Ocean CO2 sink from observation-based air–sea O2 fluxes. On interannual time scales, the variability in the air–sea fluxes of CO2 and O2 estimated from observations is consistent across the two species and positively correlated with the variability simulated by ocean models. Our analysis suggests that variations in ocean ventilation related to the Southern Annular Mode are responsible for this interannual variability. On decadal time scales, the existence of significant variability in the air–sea CO2 flux estimated from observations also tends to be supported by observation-based estimates of O2 flux variability. However, the large decadal variability in air–sea CO2 flux is absent from ocean models. Our analysis suggests that issues in representing the balance between the thermal and non-thermal components of the CO2 sink and/or insufficient variability in mode water formation might contribute to the lack of decadal variability in the current generation of ocean models. This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.
Macadamia nut effects on cardiometabolic risk factors: a randomised trial

Abstract We sought to examine the effects of daily consumption of macadamia nuts on body weight and composition, plasma lipids and glycaemic parameters in a free-living environment in overweight and obese adults at elevated cardiometabolic risk. Utilising a randomised cross-over design, thirty-five adults with abdominal obesity consumed their usual diet plus macadamia nuts (~15 % of daily calories) for 8 weeks (intervention) and their usual diet without nuts for 8 weeks (control), with a 2-week washout. Body composition was determined by bioelectrical impedance; dietary intake was assessed with 24-h dietary recalls. Consumption of macadamia nuts led to increased total fat and MUFA intake while SFA intake was unaltered. With mixed model regression analysis, no significant changes in mean weight, BMI, waist circumference, percent body fat or glycaemic parameters, and non-significant reductions in plasma total cholesterol of 2⋅1 % (−4⋅3 mg/dl; 95 % CI −14⋅8, 6⋅1) and low-density lipoprotein (LDL-C) of 4 % (−4⋅7 mg/dl; 95 % CI −14⋅3, 4⋅8) were observed. Cholesterol-lowering effects were modified by adiposity: greater lipid lowering occurred in those with overweight v. obesity, and in those with less than the median percent body fat. Daily consumption of macadamia nuts does not lead to gains in weight or body fat under free-living conditions in overweight or obese adults; non-significant cholesterol lowering occurred without altering saturated fat intake of similar magnitude to cholesterol lowering seen with other nuts. Clinical Trial Registry Number and Website: NCT03801837 https://clinicaltrials.gov/ct2/show/NCT03801837? term = macadamia + nut&draw = 2&rank = 1
Distance, Origin and Category Constrained Paths

Recommending a Point of Interest (PoI) or a sequence of PoIs to visit based on user’s preferences and geo-locations has been one of the most popular applications of Location-Based Services (LBS). Variants have also been considered which take other factors into consideration, such as broader (implicit or explicit) semantic constraints as well as the limitations on the length of the trip. In this work, we present an efficient algorithmic solution to a novel query – PaDOC (Paths with Distance, Origin, and Category constraints) – which combines the generation of a path that (a) can be traversed within a user-specified budget (e.g., limit on distance), (b) starts at one of the user-specified origin locations (e.g., a hotel), and (c) contains PoIs from a user-specified list of PoI categories. We show that the problem of deciding whether such a path exists is an NP-hard problem. Based on a novel indexing structure, we propose two efficient algorithms for approximate PaDOC query processing based on both conservative and progressive distance estimations. We conducted extensive experiments over real, publicly available datasets, demonstrating the benefits of the proposed methodologies over straightforward solutions.
Hybrid Block Storage for Efficient Cloud Volume Service

The migration of traditional desktop and server applications to the cloud brings challenge of high performance, high reliability, and low cost to the underlying cloud storage. To satisfy the requirement, this article proposes a hybrid cloud-scale block storage system called Ursa. Trace analysis shows that the I/O patterns served by block storage have only limited locality to exploit. Therefore, instead of using solid state drives (SSDs) as a cache layer, Ursa proposes hybrid storage structure that directly stores primary replicas on SSDs and replicates backup replicas on hard disk drives (HDDs). At the core of Ursa’s hybrid storage design is an adaptive journal that can bridge the performance gap between primary SSDs and backup HDDs for random writes by transforming small backup writes into journal appends, which are then asynchronously replayed and merged to backup HDDs. To efficiently index the journal, we design a novel range-optimized merge-tree structure that combines a continuous range of keys into a single composite key {offset,length}. Ursa integrates the hybrid structure with designs for high reliability, scalability, and availability. Experiments show that Ursa in its hybrid mode achieves almost the same performance as in its SSD-only mode (storing all replicas on SSDs), and outperforms other block stores (Ceph and Sheepdog) even in their SSD-only mode while achieving much higher CPU efficiency (IOPS and throughput per core).
Image Denoising via 2-D FIR Filtering Approach

Image denoising has received much concern for decades. One of the simplest methods for image denoising is the 2-D FIR lowpass filtering approach. Firstly, the authors make a comparative study of the conventional lowpass filtering approach, including the classical mean filter and three 2-D FIR LowPass Filters (LPF) designed by McClellan transform. Then an improved method based on learning method is presented, where pixels are filtered by five edge-oriented filters, respectively, facilitated to their edge details. Differential Evolution Particle Swarm Optimization (DEPSO) algorithm is exploited to refine those filters. Computer simulation demonstrates that the proposed method can be superior to the conventional filtering method, as well as the modern Bilateral Filtering (BF) and the Stochastic Denoising (SD) method. DOI: 10.4018/978-1-4666-3958-4.ch007 Image Denoising via 2-D FIR Filtering Approach 185 the original visual information as much as possible has become a major concern for decades. Generally, the deblurring issue can be viewed as a denoising problem and typical noise models include the Gaussian noise, the salt and pepper noise, the speckle noise and the Brownian noise (Lim, 1990). In this chapter, we focus on the lowpass filtering approach on denoising the image corrupted by the Gaussian noise but via a new perspective.