Miracle-dz/UniFAR-FTUs huggingface dataset:
Getting the foot out of the pelvis: modeling problems affecting use of SNOMED CT hierarchies in practical applications

OBJECTIVES (a) To determine the extent and range of errors and issues in the Systematised Nomenclature of Medicine-Clinical Terms (SNOMED CT) hierarchies as they affect two practical projects. (b) To determine the origin of issues raised and propose methods to address them. METHODS The hierarchies for concepts in the Core Problem List Subset published by the Unified Medical Language System were examined for their appropriateness in two applications. Anomalies were traced to their source to determine whether they were simple local errors, systematic inferences propagated by SNOMED's classification process, or the result of problems with SNOMED's schemas. Conclusions were confirmed by showing that altering the root cause and reclassifying had the intended effects, and not others. MAIN RESULTS Major problems were encountered, involving concepts central to medicine including myocardial infarction, diabetes, and hypertension. Most of the issues raised were systematic. Some exposed fundamental errors in SNOMED's schemas, particularly with regards to anatomy. In many cases, the root cause could only be identified and corrected with the aid of a classifier. LIMITATIONS This is a preliminary 'experiment of opportunity. ' The results are not exhaustive; nor is consensus on all points definitive. CONCLUSIONS The SNOMED CT hierarchies cannot be relied upon in their present state in our applications. However, systematic quality assurance and correction are possible and practical but require sound techniques analogous to software engineering and combined lexical and semantic techniques. Until this is done, anyone using SNOMED codes should exercise caution. Errors in the hierarchies, or attempts to compensate for them, are likely to compromise interoperability and meaningful use.
Elevation of the Yields of Very Long Chain Polyunsaturated Fatty Acids via Minimal Codon Optimization of Two Key Biosynthetic Enzymes

Eicosapentaenoic acid (EPA, 20:5Δ5,8,11,14,17) and Docosahexaenoic acid (DHA, 22:6Δ4,7,10,13,16,19) are nutritionally beneficial to human health. Transgenic production of EPA and DHA in oilseed crops by transferring genes originating from lower eukaryotes, such as microalgae and fungi, has been attempted in recent years. However, the low yield of EPA and DHA produced in these transgenic crops is a major hurdle for the commercialization of these transgenics. Many factors can negatively affect transgene expression, leading to a low level of converted fatty acid products. Among these the codon bias between the transgene donor and the host crop is one of the major contributing factors. Therefore, we carried out codon optimization of a fatty acid delta-6 desaturase gene PinD6 from the fungus Phytophthora infestans, and a delta-9 elongase gene, IgASE1 from the microalga Isochrysis galbana for expression in Saccharomyces cerevisiae and Arabidopsis respectively. These are the two key genes encoding enzymes for driving the first catalytic steps in the Δ6 desaturation/Δ6 elongation and the Δ9 elongation/Δ8 desaturation pathways for EPA/DHA biosynthesis. Hence expression levels of these two genes are important in determining the final yield of EPA/DHA. Via PCR-based mutagenesis we optimized the least preferred codons within the first 16 codons at their N-termini, as well as the most biased CGC codons (coding for arginine) within the entire sequences of both genes. An expression study showed that transgenic Arabidopsis plants harbouring the codon-optimized IgASE1 contained 64% more elongated fatty acid products than plants expressing the native IgASE1 sequence, whilst Saccharomyces cerevisiae expressing the codon optimized PinD6 yielded 20 times more desaturated products than yeast expressing wild-type (WT) PinD6. Thus the codon optimization strategy we developed here offers a simple, effective and low-cost alternative to whole gene synthesis for high expression of foreign genes in yeast and Arabidopsis.
Clash of the Lambdas

The introduction of lambdas in Java 8 completes the slate of statically-typed, mainstream languages with both object-oriented and functional features. The main motivation for lambdas in Java has been to facilitate stream-based declarative APIs, and, therefore, easier parallelism. In this paper, we evaluate the performance impact of lambda abstraction employed in stream processing, for a variety of high-level languages that run on a virtual machine (C#, F#, Java and Scala) and runtime platforms (JVM on Linux and Windows, .NET CLR for Windows, Mono for Linux). Furthermore, we evaluate the performance gain that two optimizing libraries (ScalaBlitz and LinqOptimizer) can offer for C#, F# and Scala. Our study is based on small-scale throughput-benchmarking, with significant care to isolate different factors, consult experts on the systems involved, and identify causes and opportunities. We find that Java exhibits high implementation maturity, which is a dominant factor in benchmarks. At the same time, optimizing frameworks can be highly effective for common query patterns.
Min- and Max-Relative Entropies and a New Entanglement Monotone

Two new relative entropy quantities, called the min- and max-relative entropies, are introduced and their properties are investigated. The well-known min- and max-entropies, introduced by Renner, are obtained from these. We define a new entanglement monotone, which we refer to as the max-relative entropy of entanglement, and which is an upper bound to the relative entropy of entanglement. We also generalize the min- and max-relative entropies to obtain smooth min-and max-relative entropies. These act as parent quantities for the smooth Renyi entropies (ETH Zurich, Ph.D. dissertation, 2005), and allow us to define the analogues of the mutual information, in the smooth Renyi entropy framework. Further, the spectral divergence rates of the information spectrum approach are shown to be obtained from the smooth min- and max-relative entropies in the asymptotic limit.
Remarks on piecewise-linear algebra

This note studies some of the basic properties of the category whose objects are finite unions of (open and closed) polyhedra and whose morphisms are (not necessarily continu- ous) piecewise-linear maps. Introduction* A function f: V —>W between real vector spaces is piecewise-linear (PL) if there exists a partition of V into "open polyhedra" X€ (i.e., relative interiors of polyhedra) such that / is affine on each Xt. (As distinct to the case of PL-topology, no continuity is required of /.) Images and preimages under PL-maps give rise to finite unions of open polyhedra, or PL-seίs; conversely PL functions can be characterized by the fact that their graphs are PL-sets. This paper studies some basic algebraic properties of the category PL, proving in particular that it is an exact category, and in fact a pretopos. A classification is given for the isomorphism classes of objects of PL, in terms of a two-generator semiring. The first section recalls without proof some facts from polyhedral geometry needed in the paper. Except for the setting of a unified notation and for minor generalizations, the material there is well known. The second section defines PL maps and sets, and studies the category. The main results (leading to the classification theorem) are given in the last section. 1* Review of polyhedral geometry* The following conventions and definitions hold throughout. All vector spaces are finite- dimensional spaces over the reals R; a flat means an affine sub- manifold of some such space V, and the closed half-spaces associated to a linear /: V —> R and an r in R (or associated to the hyperplane {x\f(x) = r},) are the sets {x\f(x) ^ r} and {x\f(x) ^ r}. The cor- responding open half-spaces are obtained by using strict inequalities in the above. A half-line (closed or open) is the intersection of a line L in V with a (closed or open) half-space not containing L.
Supplemental Information Unreliable Evoked Responses in Autism

Fig u re S 1 (re late d to all m ain fig u re s): This figure shows the design of our experiments. Fig u re S 2 (re late d to ma in Fig u re 1): This figure shows how we selected our regions of interest (ROIs) based on responses presented in main Figure1. Fig u re S 3 (re late d to ma in Fig u re s 2, 3, & 4): This figure shows how we calculated response amplitude and trial-by-trial variability – the basis for most of the presented results. Fig u re S 4 (re late d to ma in Fig u re 2): This figure shows that the results presented in Figure 2 were also apparent when assessing other trial types (adapted, un-adapted, no-test, and when combining all three) using the same analysis. Fig u re S 5 (re late d to ma in Fig u re 2): This figure shows that the results presented in Figure 2 were also apparent when assessed using a different methodology – GLM analysis. Fig u re S6 (re late d to ma in Figure 7): This figure shows an additional behavioral analysis (trial-by-trial reaction time variability), which is related to the task responses presented in Figure 7. Fig u re S 7 (re late d to all m ain fig u re s): This figure contains control analyses showing that head motion was not significantly different across groups. This is an important control for interpreting all of our results. Ta b le S 1 (re la te d to a ll m a in fig u re s): This table contains behavioral scores of the individuals with autism who participated in the experiments. This is important information for interpreting the entire study. Ta b le S 2 (re la te d to m a in Fig u re 1): This table lists the locations of our regions of interest, which were selected based on the response maps presented in main Figure 1.
Neonatal Testicular Torsion; a Review Article

Neonatal testicular torsion, also known as perinatal testicular torsion is a subject of debate among surgeons. Neonatal testicular torsion either intrauterine or postnatal results into extravaginal torsion which is a different entity than intravaginal type but has the same devastating consequences if not diagnosed and managed well in time. Testicular torsion results into acute ischemia with its resultant sequelae such as abnormality of testicular function and fertility. Urgent surgical exploration and fixation of the other testis are the key points in the management. General anesthesia is not a contraindication for exploration as thought before. Diagnosis and controversies on management of testicular torsion are discussed in this review.
Towards emergency vehicle routing using Geolinked Open Data: the case study of the Municipality of Catania

Linked Open Data (LOD) has gained significant momentum over the past years as a best practice of promoting the sharing and publi- cation of structured data on the semantic Web. Currently LOD is reach- ing significant adoption also in Public Administrations (PAs), where it is often required to be connected to existing platforms, such as GIS-based data management systems. Bearing on previous experience with the pi- oneering data.cnr. it, through Semantic Scout, as well as the Agency for Digital Italy recommendations for LOD in Italian PA, we are working on the extraction, publication, and exploitation of data from the Geographic Information System of the Municipality of Catania, referred to as SIT ("Sistema Informativo Territoriale"). The goal is to boost the metropolis towards the route of a modern Smart City by providing prototype inte- grated solutions supporting transport, public health, urban decor, and social services, to improve urban life. In particular a mobile application focused on real-time road traffic and public transport management is currently under development to support sustainable mobility and, espe- cially, to aid the response to urban emergencies, from small accidents to more serious disasters. This paper describes the results and lessons learnt from the first work campaign, aiming at analyzing, reengineering, linking, and formalizing the Shape-based geo-data from the SIT.
Rising Midlife Obesity Will Worsen Future Prevalence of Dementia

Background Midlife body weight status has been found to affect late life dementia outcomes. A cohort projections model was developed to assess the impact of midlife body mass index (BMI) profile on dementia in older Australians. Methods A baseline projection using age-sex specific dementia prevalence rates was constructed and the results of scenarios that took account of midlife BMI were compared with those from population ageing only. Results This modelling predicts that if the rising trend in midlife obesity and declining trend in midlife normal weight in Australia are to be taken into account in projecting future numbers of Australians with dementia then the number of people aged 65 or more years with dementia, by 2050, would be 14% higher than that expected from demographic ageing only. If midlife obesity prevalence was decreased to 20% and normal weight increased to 40% over the period of 2015–2025, then dementia cases among persons aged 65–69 years would be lower by about 10% in 2050 compared with the “doing nothing to stop current trends in obesity” projection. Conclusion The rising tide of obesity in Australian adults will increase the dementia epidemic expected in future years.
Visualization of missing values using the R-package VIM

This paper introduces new tools for the visualization of missing values. The tools can be used for exploring the data and the structure of the missing values. Depending on this structure, the tools can be helpful for identifying the mechanism generating the missings. This knowledge is important for selecting an appropriate imputation method to reliably estimate the missing values. The visualization tools are implemented in the R-package VIM (visualization and imputation of missing values). A graphical user interface allows an easy handling of the plot methods. The developed tool can be used for data from official statistics, but also for data from various other fields. Special attention is given to data with spatial coordinates, and in that case the missing data information can be displayed with maps.
Differential heme release from various hemoglobin redox states and the upregulation of cellular heme oxygenase‐1

Despite advances in our understanding of the oxidative pathways mediated by free hemoglobin (Hb), the precise contribution of its highly reactive redox forms to tissue and organ toxicities remains ambiguous. Heme, a key degradation byproduct of Hb oxidation, has recently been recognized as a damage‐associated molecular pattern (DAMP) molecule, able to trigger inflammatory responses. Equally damaging is the interaction of the highly redox active forms of Hb with other biological molecules. We determined the kinetics of heme loss from individual Hb redox states—ferrous (Fe2+), ferric (Fe3+), and ferryl (Fe4+)—using two different heme receptor proteins: hemopexin (Hxp), a naturally occurring heme scavenger in plasma, and a double mutant (H64Y/V86F), apomyoglobin (ApoMb), which avidly binds heme released from Hb. We show for the first time that ferric Hb (Fe3+) loses heme at rates substantially higher than that of ferryl Hb (Fe4+). This was also supported by a higher expression of heme oxygenase‐1 (HO‐1) when ferric Hb was added to cultured lung alveolar epithelial cells (E10). The reported cytotoxicity of Hb may therefore be attributed to a combination of accelerated heme loss from the ferric form and protein radical formation associated with ferryl Hb. Targeted therapeutic interventions can therefore be designed to curb specific oxidative pathways of Hb in hemolytic anemias and when Hb is used as an oxygen‐carrying therapeutic.
The Quality of Value at Risk Via Univariate GARCH

The estimation of value at risk using univariate GARCH models is examined. A long history of the S&P 500 is used to compare these estimators with several other common approaches to value at risk estimation. The test results indicate that GARCH estimates are superior to the other methods in terms of the accuracy and consistency of the probability level. Although all of the GARCH models tested performed relatively well, the quality of the value at risk estimate does depend on which particular GARCH model is used. Weighting recent observations more heavily when fitting the GARCH model seems to be beneficial.
Multiplexing pH and temperature in a molecular biosensor

Robust and reliable measurements in electrochemical biosensing of molecules are crucial for personalized medicine. Electrochemical sensors based on cytochrome P450 can detect the large majority of drugs commonly used in pharmacological treatments. The same cytochrome can detect different substrates; each of them changes the electrochemical response of the enzyme in a specific manner. Our system exploits the measure of electrical potential to identify the drug type, while current measurements decode the drug concentration. Since potential and current are affected by pH and temperature, and since variations occur in the patient samples, we propose a novel design for multiplexing biosensing with pH and temperature control, which ensures more precise measurements for drugs identification and their quantification.
Knowledge Sharing in is Personnel: Organizational Behavior's Perspective

This research investigates the roles of sense of self-worth, in-role behavior, and organizational citizenship behavior in supporting individuals' knowledge sharing behavior, by incorporating a motivational aspect into the theory of reasoned action. Structural equation modeling analysis of survey data from a group of 116 Information Systems personnel revealed that two variables (i.e., sense of self-worth and in-role behavior) are positively related to the attitude toward knowledge sharing. Both subjective norm and organizational citizenship behavior are independent and positively related to an intention to share knowledge, while the attitude toward knowledge sharing is negatively related to intention to share knowledge. Individuals' knowledge sharing behavior is predicted with more favorable intention to share knowledge. This research and its findings have implications for organizational administrators in Information Technology (IT) firms to enhance intrinsic motivation among employees, and develop better reciprocal relationships and interpersonal interactions of employees to facilitate successful knowledge sharing.
Smooth nonexpected utility without state independence

We propose a notion of smoothness of nonexpected utility functions, which extends the variational analysis of nonexpected utility functions to more general settings. In particular, our theory applies to state dependent utilities, as well as the multiple prior expected utility model, both of which are not possible in previous literatures. Other nonexpected utility models are shown to satisfy smoothness under more general conditions than the Frechet and Gateaux differentiability used in the literature. We give more general characterizations of monotonicity and risk aversion without assuming state independence of utility function.
Traces of Terror: Counter-Terrorism Law, Policing, and Race

1. Traces in Counter-Terrorism: An Introduction 2. The Hegemony of Race 3. A Motive for Terror: Law and Islam 4. 'No Crime Scenes': The Police and Extremism 5. Policing Social Cohesion: Community Policing for Counter-Terrorism 6. 'We just want to get to know you': The Function of Informal Questioning 7. Disrupting Diaspora: Policing Terrorist Organisations 8. Without an Inventory
Finite dimensional adaptive H∞ control for flexible arms preceded by input nonlinearites

The problem of constructing model reference adaptive H∞ control for flexible arms preceded by unknown input nonlinearities such as dead-zone or backlash, is considered in this paper. Control schemes of flexible arms are mixed parameter systems composed of distributed parameter systems of hyperbolic type (flexible arms) and lumped parameter systems (motor control systems). An adaptive inverse model is introduced to estimate and compensate input nonlinearities. The stabilizing control signal is added to regulate the effect of spill-over terms, and it is derived as a solution of certain H∞ control problem where the residual part of the inverse model and the spill-over term are considered as external disturbances.
Modeling Concept-Attribute Structure

We apply hierarchical Latent Dirichlet Allocation (hLDA) to the problem of ontology annotation; automatically extending WORDNET with new concepts and annotating existing concepts with generic property fields, or attributes. The resulting annotations are evaluated along two dimensions: (1) the precision of the ranked lists of attributes at each concept, and (2) the specificity of the attribute assignments to WORDNET concepts. We find that hLDA and several variants outperform previously proposed heuristic methods, significantly improving the resulting annotation quality, and confirming the ability of topic models to reduce extraction noise.
A new infrared view of evolved stars in IZw 18

We report results from near-infrared imaging of IZw 18, the most metal-poor galaxy in the local universe, with NICMOS on board the Hubble Space Telescope (HST). Observations were obtained in the broad F205W filter (∼K) and in the medium-wide bands F171M and F180M, the latter which cover strong molecular absorption features in cool stars. The new data, together with previously obtained HST/NICMOS images in the F110W (∼J )a ndF160W (∼H) filters, provide a census of the cool stellar population in this chemically unevolved galaxy. We find that stars as old as ∼1 Gyr are required to explain the observed colour-magnitude diagrams. Combining broad and medium-wide band photometry, we have classified the observed stars. The observed stellar populations, to the depth of our data, are dominated by luminous red supergiant stars. However, an intermediate-age component is also present. We have identified carbon star candidates, and show that they dominate the stellar content for intermediate mass and age. We show that low metallicity intermediate-age stars have, for a given colour, a F110W (∼J-band) excess compared to local carbon stars. The carbon stars identified in IZw 18 are the most distant (more than 10 Mpc) resolved examples yet discovered.
Speaker independent speech recognition using features based on glottal sound source

We discussed utilization of features based on the glottal sound source for speaker independent speech recognition. It has been thought that such features as pitch cannot contribute to speaker independent speech recognition because of the dominant speaker dependent factor. In this paper, we tried to utilize pitch, power, LPC residual power, voicing rate, and their regression coefﬁcients as feature parameters for speaker independent speech recognition, and found that regression parameters of F0, power and LPC residual power could improve the performance, especially using covariances be-tween each parameter and conventional MFCC. This showed that the procedure to derive the regression parameters could reduce the speaker dependent factor which appeared as biases of those features, and that the correlation between glottal source information and spectral envelope information (MFCC) worked well. We also tested the parameters on a large-vocabulary continuous speech recognition task and obtained the performance improvement.