Miracle-dz/UniFAR-FTUs huggingface dataset:
Hafnium-Indium-Zinc oxide thin film transistors using HfO2 as gate dielectric, with both layers deposited by RF sputtering

The electrical performance of RF magnetron sputtered Hafnium-Indium-Zinc-Oxide-based thin film transistors (HIZO TFTs) is compared using two different gate dielectrics: a) RF sputtered HfO<sub>2</sub> and b) thermally grown SiO<sub>2</sub>. For HfO<sub>2</sub> devices, output characteristics showed higher drain-currents capabilities with a reduction of the TFT operation voltage range from 0-15 V, when using SiO<sub>2</sub>, to 0-8 V. The HfO<sub>2</sub> dielectric constant was around 15, measured at 1 kHz. Vt was less than 2 V for HfO<sub>2</sub> devices and around 5 V for SiO<sub>2</sub> devices.
Drug-adherence questionnaires not valid for patients taking blood-pressure-lowering drugs in a primary health care setting.

PURPOSE To validate two established questionnaires [Morisky and Medication Adherence Report Scale (MARS-5)] for the measurement of medical adherence of patients treated with antihypertensive drugs in primary care in Germany. SETTING General practitioners (GPs) and their patients in North Rhine-Westphalia, Germany. METHODS GPs were asked to recruit 12 consecutive patients using blood-pressure-lowering medication for at least 12 months. Patients were asked to fill out both the Morisky and MARS-5 questionnaires. The medication possession ratio (MPR) was calculated as reference standard for patients' medication adherence by using GPs' electronic patient records. The results of the questionnaires were then compared with the reference standard. RESULTS A total of 14 GPs recruited 163 patients of which 128 were included in the analysis. Of the 128 patients, 52% were females; the age ranged from 44 to 96 years (mean 71). The overall adherence rate measured by the MPR was 62.1%. Compared to the reference standard, the Morisky Scale had a sensitivity of 31.9%, a specificity of 72.8% and a positive likelihood ratio (+LR) of 1.18. The MARS-5 had a sensitivity of 8.5%, a specificity of 97.4% and a +LR of 3.28. CONCLUSION The Morisky Scale and the MARS-5 cannot be recommended for measuring the adherence to antihypertensive drugs in a general practice setting in Germany at this point. These results emphasize the necessity to validate questionnaires in a specific setting before using them as instruments within a trial different from the original setting(s) of validation.
Striim: A streaming analytics platform for real-time business decisions

Real-time decisions and insights over real-time data have become the essential mantra of success for many enterprises. The real-time data is generated from a multitude of sources and they come in a streaming fashion with high volume and velocity. The data could be machine generated e.g. clickstream data, logs, sensor data from IoT devices or human generated e.g. social data, mission critical transactional data. This is causing a technological shift from storage driven architectures to event driven architectures for enterprises to be able to capture, integrate and analyze these large sets of data for real-time decision making. Striim is a novel end-to-end analytics platform that enables business users to easily develop and deploy analytical applications that can generate real-time insights over real-time streaming data; business users and developers use a SQL-like declarative language (that has been extended to include streaming semantics) to write application logic in Striim. Striim provides high-throughput, low-latency event processing on commodity hardware with a scale-out architecture. In this paper, we describe the architecture of Striim and discuss some of the key aspects of the platform (a) built-in real-time data capture including streaming change data capture from transactional databases (ii) a natively built storage and query engine that uses modern data structures like skip lists to store streaming window data and performs query optimization, planning and run-time code generation (iii) enabling application de-coupling using persisted streams.
Context-based Branch Prediction for High-Performance and Low-Power Computing

Advanced processors can simultaneously execute multiple instructions in parallel to achieve better performance. Branches introduce control dependence between instructions. Branch prediction therefore is important for modern processors. Most present predictors use branch history to predict branch outcomes. Using branch history alone results in delay for identifying mispredictions. In this paper, a context-based branch predictor is proposed to resolve branch condition for conditional branches. Simulation results of SimWattch from SPECint95 and MediaBench programs reveal that using our method, on average, the CPI can be improved by 2.12%, the IPC can be improved by 2.19%, and power consumption can be improved by 2.12%.
Lighting Simulation of Augmented Outdoor Scene Based on a Legacy Photograph

We propose a novel approach to simulate the illumination of augmented outdoor scene based on a legacy photograph. Unlike previous works which only take surface radiosity or lighting related prior information as the basis of illumination estimation, our method integrates both of these two items. By adopting spherical harmonics, we deduce a linear model with only six illumination parameters. The illumination of an outdoor scene is finally calculated by solving a linear least square problem with the color constraint of the sunlight and the skylight. A high quality environment map is then set up, leading to realistic rendering results. We also explore the problem of shadow casting between real and virtual objects without knowing the geometry of objects which cast shadows. An efficient method is proposed to project complex shadows (such as tree's shadows) on the ground of the real scene to the surface of the virtual object with texture mapping. Finally, we present an unified scheme for image composition of a real outdoor scene with virtual objects ensuring their illumination consistency and shadow consistency. Experiments demonstrate the effectiveness and flexibility of our method.
An empathy learning problem for HSI: To be empathic, self-improving and ambient

Empathy is a learnable skill that requires experiential learning and practice of empathic ability for it to improve and mature. In the context of human-system interaction (HSI) this can mean that a system should be permitted to have an initial knowledge of empathy provision that is inaccurate or incomplete, but with this knowledge evolving and progressing over time through learning from experience. This problem has yet to be defined and dealt in HSI. This paper is an attempt to state an empathy learning problem for an ambient intelligent system to self-improve its empathic responses based on user affective states.
Normalization of cDNA libraries 99

In a cellular transcriptome, the number of mRNA copies per gene may differ by several orders. In cDNA libraries, performed from mRNA, these proportions are the same. Normalization methods allow us to equalize numbers of gene’s copies in the library. Normalized cDNA libraries are used to discover new genes transcribed at relatively low levels or for functional screenings. Here, we observed different cDNA libraries normalization methods, which were based on hybridization (renaturation) of cDNA or DNA, or RNA. Also we described duplex-specific nuclease (DSN) normalization protocol – simple and effective cDNA libraries normalization method.
Ocular Adnexal Lymphoma: Clinical Presentation, Diagnosis, Treatment and Prognosis

Ocular adnexal lymphoma (OAL) is a rare tumor with an incidence of 0.2 per 1,00,000 individuals. However, it constitutes the most common orbital tumor especially in older population with an incidence ranging from 11% to 24%. OAL can involve conjunctiva, orbital soft tissues, eyelid, or adnexal structures such as lacrimal gland and lacrimal drainage system. The most common primary OAL is low-grade malignant extranodal marginal zone B-cell lymphoma (EMZL) of mucosa-associated lymphoid tissue (MALT) type. Though various classification and staging systems have been proposed for OAL, currently, American joint committee on cancer (AJCC) TNM (tumor node metastasis) staging is most commonly used. Most commonly, conjunctival lymphoma typically presents as ‘salmon-colored patch’ and orbital lymphoma presents as proptosis, which on imaging shows characteristic appearance of molding around the globe without any globe indentation or bone erosion. Orbital radiotherapy and systemic chemotherapy forms the mainstay of treatment. Newer treatment modalities include immunotherapy with interferon and anti-CD20 antibody rituximab that have been shown to be useful either when used alone or in combination with chemotherapy or as radio-immunotherapy.
SerialRank : Spectral Ranking using Seriation

We describe a seriation algorithm for ranking a set of n items given pairwise comparisons between these items. Intuitively, the algorithm assigns similar rankings to items that compare similarly with all others. It does so by constructing a similarity matrix from pairwise comparisons, using seriation methods to reorder this matrix and construct a ranking. We first show that this spectral seriation algorithm recovers the true ranking when all pairwise comparisons are observed and consistent with a total order. We then show that ranking reconstruction is still exact even when some pairwise comparisons are corrupted or missing, and that seriation based spectral ranking is more robust to noise than other scoring methods. An additional benefit of the seriation formulation is that it allows us to solve semi-supervised ranking problems. Experiments on both synthetic and real datasets demonstrate that seriation based spectral ranking achieves competitive and in some cases superior performance compared to classical ranking methods.
Deficiency of Kallikrein Activity in Plsma of Patients with Cystic Fibrosis

Total kallikrein activity and kallikrein activity inhibited by soybean trypsin inhibitor are significantly reduced in the plasma of patients with cystic fibrosis compared to age-matched controls. The level of the STI inhibited kallikrein activity in the plasma of heterozygotes was significantly different from that in either controls or affected children. However, the individual heterozygote could not be reliably identified in each case.
A computer-controlled contracture correction device with low-load and continuous torque: An animal experiment and prototype design for clinical use

The purpose of this study was to clarify the relationship between mechanical stress and tissue response of the contracted knee joint in rats and to propose a new design of contracture correction device for clinical use. Wistar rats were operated on to immobilize their knee joints with a procedure causing periarticular bleeding and were kept in flexed position for 40 days. At day 40, the immobilizing wire was removed, and after day 43, the contracted knee joint had been treated with tunable corrective devices secured by an external fixation method to the rear limb. These devices consisted of four types of motor-driving system which provided several different low-load and continuous stretch torques. Measuring the angle of maximum knee extension, its effectiveness was assessed comparing with a lower load and control group of natural recovery course. The device also had a cyclic joint movement within the acquired range of motion and an oval cam mechanism producing a small distraction force to the joint along its long axis. The results showed that an appropriate range of low-load continuous torque was more effective to correct joint contracture. On the basis of the animal experiment, a new computer-controlled, gas-driven contracture correction device was developed for clinical trial. It was concluded that mechanical application in a condition with low and continuous torque is a useful treatment for fixed joint contracture.
Post-translational proteolysis in polypeptide hormone biosynthesis.

be further conveniently subdivided into the preproteins and proproteins. These two large groups differ significantly in their processing kinetics, in the subcellular localizations of cleavage enzymes, and in their functions. This review focuses primarily on these forms, with special emphasis on recent progress in elucidating their primary enzymic cleavage mechanisms. At this stage it seems most likely that for each subgroup a single proteolytic mecha­ nism accounts for the major processing events, with some specialized fea­ tures requiring additional enzymes for several of the prohormonal systems.
A GPU-Based Method to Approximate Acoustical Reflectivity

Abstract Here we present a GPU-based heuristic method for approximating the size and reflectivity of a room relative to a given sound source origin that can potentially provide interactive response for the appropriate selections of geometry and hardware. The method calculates the average distance to the nearest surfaces in the environment and an approximate measure of the fraction of sound energy that would be reflected from those surfaces. Both of these values are then used to drive the reverberation effects of an audio API. The method can potentially provide interactive response for the appropriate selections of geometry and hardware. Source code is available online at address provided at the end of this paper.
Moving Object Localization with Single Camera Based on Height Model in Video Surveillance

A method of object localization based on man height model is proposed. With the relationship between the project position of the head of object and the distance between object and camera, a man height model can be built. By this model, the two- dimensional position of object on the ground can be located. This method can not only be used outside but can also be used inside with complex background. Experiments with simulated data show that the technique is simple and accurate.
Integral Sliding Mode Control: Performance, Modification, and Improvement

Sliding mode control (SMC) is attractive for nonlinear systems due to its invariance for both parametric and nonparametric uncertainties. However, the invariance of SMC is not guaranteed in a reaching phase. Integral SMC (ISMC) eliminates the reaching phase such that the invariance is achieved in an entire system response. To reduce chattering in ISMC, it was suggested that the switching element is smoothed by using a low-pass filter and an integral sliding variable is modified. This study discusses several crucial problems regarding the performance, modification, and improvement of ISMC. First, the modification of the integral sliding variable is revealed to be unnecessary as it degrades the performance of a sliding phase; second, ISMC is shown to be a kind of global SMC; third, it is manifested that a high-order ISMC design with super twisting involves a stability condition that may be infeasible in theory; finally, an efficient solution is suggested to attenuate chattering in ISMC without the degradation of tracking accuracy and the solution is extended to the case with uncertain control gain functions. Comprehensive simulation results have verified the arguments of this study.
Increased Resistance of DNA Lipoplexes to Protein Binding In Vitro by Surface-modification with a Multivalent Hydrophilic Polymer

The potential of cationic liposomes as DNA delivery vehicles for gene therapy is significantly limited by their instability upon systemic administration. Their strong positive charge induces non-specific binding of serum proteins and subsequent clearance from the circulation. This work investigates the ability of the multivalent reactive copolymer of poly[N-(2-hydroxypropopyl) methacrylamide], pHPMA (MA–GG–ONp) to shield lipoplexes from non-specific protein binding. The polymer was found to react with cationic liposome–DNA complexes (lipoplexes) in both an electrostatic and covalent manner to form an external polymer coat. Polymer coating resulted in an increase in lipoplex diameter (by up to 100 nm) that was proportional to the amount of polymer used, with a concomitant reduction in surface charge from strongly positive to neutral (from 30 to 0 mV). Polymer-coated lipoplexes exhibited increased stability to protein binding compared to untreated liposomes and reduced non-specific uptake into cells in vitro.
Systemic Sclerosis Perturbs the Architecture of the Immunome

Systemic sclerosis (SSc) is an autoimmune disease characterized by excessive fibrosis of skin and internal organs, and vascular dysfunction. Association of T and B cell subsets has been reported in SSc; however, there is lack of systematic studies of functional relations between immune cell subsets in this disease. This lack of mechanistic knowledge hampers targeted intervention. In the current study we sought to determine differential immune cell composition and their interactions in peripheral blood of SSc patients. Mononuclear cells from blood of SSc patients (n = 20) and healthy controls (n = 10) were analyzed by mass cytometry using a 36-marker (cell surface and intracellular) panel. Transcriptome analysis (m-RNA sequencing) was performed on sorted T and B cell subsets. Unsupervised clustering analysis revealed significant differences in the frequencies of T and B cell subsets in patients. Correlation network analysis highlighted an overall dysregulated immune architecture coupled with domination of inflammatory senescent T cell modules in SSc patients. Transcriptome analysis of sorted immune cells revealed an activated phenotype of CD4 and mucosal associated invariant T (MAIT) cells in patients, accompanied by increased expression of inhibitory molecules, reminiscent of phenotype exhibited by functionally adapted, exhausted T cells in response to chronic stimulation. Overall, this study provides an in-depth analysis of the systemic immunome in SSc, highlighting the potential pathogenic role of inflammation and chronic stimulation-mediated “functional adaptation” of immune cells.
An algal toxicity database of organic toxicants derived by a closed‐system technique

The current study presents the toxicity data of 90 organic compounds with various modes of actions to Pseudokirchneriella subcapitata. The assessment was conducted using a closed‐system technique, and a biomass‐type end point based on the cell density was employed. The above toxicity data were compared with test results from ciliate (Tetrahymena pyriformis), water flea (Daphnia magna), fish (Pimephales promelas), and luminescent bacteria (Photobacterium phosphoreum). Satisfactory correlation relationships between toxicity data from algae and other aquatic organisms were found (r2 = 0.66‐0.82). Pseudokirchneriella subcapitata revealed considerably higher sensitivity to organic toxicants compared with other organisms. Benzenes, aldehydes, and alkanes also were highly selective to the test alga. In addition, the results show that conventional algal batch tests tend to underestimate the toxicity of organic compounds, except in the case of 4‐chlorophenol. Toxicity observed from the closed‐system test is approximately 2‐ to 380‐fold higher than that estimated by conventional batch tests. Such a phenomenon can be found in nearly all organic compounds, regardless of the chemical's Henry's law constant. In the risk assessment of chemicals, following the European Union's practice, approximately 30% (7 of 23) of the cases may result in a more strict classification when the batch test is replaced by the closed‐system test. More effort therefore is needed to revise the algal toxicity database using the closed‐system test method.
Modeling and Simulation of Low Speed Wind over the Great Sphinx

In this paper, the low speed wind over the Great Sphinx is simulated in order to investigate the effects of the wind flow structure on the surface of the statue. The three-dimensional incompressible Navier-Stokes equations are solved based on Chorin-type projection method and using finite difference approximations. The computational mesh of such large scale simulation problems contains several millions of points, therefore the MPI-based parallel solution of Navier-Stokes equations is addressed on distributed-memory parallel architecture. The distributed solution methodology of Navier-Stokes equations is optimized to get the best accuracy and performance. Then, this optimized methodology is used to simulate the low speed northwest wind over the Great Sphinx at Reynolds number of 1000. The wind flow structure over the statue is visualized and intensively studied.
The RAxML-VI-HPC Version 2 . 2 . 3 Manual

– Minor bug fixed in estimation of alpha parameter (does not affect the vast majority of datasets) – New option (-k) to optimize model parameters, likelihood and printout branch lengths of bootstrapped trees – New option to define outgroup(s) (-o outgroupName(s)) – Improved tree format for trees with support values computed with -f b – The program will now also generate an appropriately adapted reduced model file, in case completely undetermined columns have been removed from the alignment.
Likelihood-based testing and model selection for hazard functions with unknown change-points

The focus of this work is the development of testing procedures for the existence of change-points in parametric hazard models of various types. Hazard functions and the related survival functions are common units of analysis for survival and reliability modeling. We develop a methodology to test for the alternative of a two-piece hazard against a simpler one-piece hazard. The location of the change is unknown and the tests are irregular due to the presence of the change-point only under the alternative hypothesis. Our approach is to consider the profile log-likelihood ratio test statistic as a process with respect to the unknown change-point. We then derive its limiting process and find the supremum distribution of the limiting process to obtain critical values for the test statistic. We first reexamine existing work based on Taylor Series expansions for abrupt changes in exponential data. We generalize these results to include Weibull data with known shape parameter. We then develop new tests for two-piece continuous hazard functions using local asymptotic normality (LAN). Finally we generalize our earlier results for abrupt changes to include covariate information using the LAN techniques. While we focus on the cases of no censoring, simple right censoring, and censoring generated by staggered-entry; our derivations reveal that our framework should apply to much broader censoring scenarios.
EpiGraphDB: a database and data mining platform for health data science

Motivation The wealth of data resources on human phenotypes, risk factors, molecular traits and therapeutic interventions presents new opportunities for population health sciences. These opportunities are paralleled by a growing need for data integration, curation and mining to increase research efficiency, reduce mis-inference and ensure reproducible research. Results We developed EpiGraphDB (https://epigraphdb.org/), a graph database containing an array of different biomedical and epidemiological relationships and an analytical platform to support their use in human population health data science. In addition, we present three case studies that illustrate the value of this platform. The first uses EpiGraphDB to evaluate potential pleiotropic relationships, addressing mis-inference in systematic causal analysis. In the second case study we illustrate how protein-protein interaction data offer opportunities to identify new drug targets. The final case study integrates causal inference using Mendelian randomization with relationships mined from the biomedical literature to “triangulate” evidence from different sources. Availability The EpiGraphDB platform is openly available at https://epigraphdb.org. Code for replicating case study results is available at https://github.com/MRCIEU/epigraphdb as Jupyter notebooks using the API, and https://mrcieu.github. io/epigraphdb-r using the R package. Contact yi6240.liu@bristol.ac. uk, ben.elsworth@bristol.ac. uk, Tom.Gaunt@bristol.ac. uk