Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of computation time for estimation of dominant frequency of atrial electrograms: Fast fourier transform, blackman tukey, autoregressive and multiple signal classification

Dominant frequency (DF) of electrophysiological data is an effective approach to estimate the activation rate during Atrial Fibrillation (AF) and it is important to understand the pathophysiology of AF and to help select candidate sites for ablation. Frequency analysis is used to find and track DF. It is important to minimize the catheter insertion time in the atria as it contributes to the risk for the patients during this procedure, so DF estimation needs to be obtained as quickly as possible. A comparison of computation tim- es taken for spectrum estimation analysis is presented in this paper. Fast Fourier Transform (FFT), Blackman-Tukey (BT), Autoregressive (AR) and Multiple Signal Classification (MUSIC) methods are used to obtain the frequency spectrum of the signals. The time to produce DF was measured for each method. The method which takes the shortest time for analysis is selected for real time application purpose.
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA

An improved potential mean force (PMF) scoring function, named KScore, has been developed by using 23 redefined ligand atom types and 17 protein atom types, as well as 28 newly introduced atom types for nucleic acids (DNA and RNA). Metal ions and water molecules embedded in the binding sites of receptors are considered explicitly by two newly defined atom types. The individual potential terms were devised on the basis of the high-resolution crystal and NMR structures of 2,422 protein-ligand complexes, 300 DNA-ligand complexes, and 97 RNA-ligand complexes. The optimized atom pairwise distances and minima of the potentials overcome some of the disadvantages and ambiguities of current PMF potentials; thus, they more reasonably explain the atomic interaction between receptors and ligands. KScore was validated against five test sets of protein-ligand complexes and two sets of nucleic-acid-ligand complexes. The results showed acceptable correlations between KScore scores and experimentally determined binding affinities (log K i's or binding free energies). In particular, KScore can be used to rank the binding of ligands with metalloproteins; the linear correlation coefficient ( R) for the test set is 0.65. In addition to reasonably ranking protein-ligand interactions, KScore also yielded good results for scoring DNA/RNA--ligand interactions; the linear correlation coefficients for DNA-ligand and RNA-ligand complexes are 0.68 and 0.81, respectively. Moreover, KScore can appropriately reproduce the experimental structures of ligand-receptor complexes. Thus, KScore is an appropriate scoring function for universally ranking the interactions of ligands with protein, DNA, and RNA.
rrecsys: An R-package for Prototyping Recommendation Algorithms

We introduce rrecsys, an open source extension package in R for rapid prototyping and intuitive assessment of recommender system algorithms. As the only currently available R package for recommender algorithms (recommenderlab) did not include popular algorithm implementations such as matrix factorization or One-class Collaborative Filtering algorithms we developed rrecsys as an easily accessible tool that can, for instance, be employed for interactive demonstrations when teaching. This package replicates state-of-the-art Collaborative Filtering algorithms for rating and binary data and we compare results with the Java-based LensKit implementation and recommederlab for the purpose of benchmarking the implementation. Therefore this work can also be seen as a contribution in the context of replication of algorithm implementations and reproduction of evaluation results.
Grand Cayman blue iguana

The critically endangered Blue Iguana is globally unique to Grand Cayman. Urgent wide ranging conservation measures are vital if this Caymanian flagship animal is to be saved from extinction. This document is a detailed plan for such measures, developed by the IUCN Iguana Specialist Group in consultation with the Cayman Islands Government and the National Trust for the Cayman Islands. It covers the period 2001 to 2006, and will be implemented by the National Trust in collaboration with local and international partners.
The online median problem

We introduce a natural variant of the (metric uncapacitated) k-median problem that we call the online median problem. Whereas the k-median problem involves optimizing the simultaneous placement of k facilities, the on-line median problem imposes the following additional constraints: the facilities are placed one at a time; a facility cannot be moved once it is placed, and the total number of facilities to be placed, k, is not known in advance. The objective of an online median algorithm is to minimize the competitive ratio, that is, the worst-case ratio of the cost of an online placement to that of an optimal offline placement. Our main result is a linear-time constant-competitive algorithm for the online median problem. In addition, we present a related, though substantially simpler linear-time constant-factor approximation algorithm for the (metric uncapacitated) facility location problem. The latter algorithm is similar in spirit to the recent primal-dual-based facility location algorithm of Jain and Vazirani, but our approach is more elementary and yields an improved running time.
Adaptable Categorization of Hands and Tools in Prosthesis Users

Some theories propose that tools become incorporated into the neural representation of the hands (a process known as tool embodiment; Maravita & Iriki, 2004). Others suggest that conceptual body representation is rigid and that experience with one’s own body is insufficient for adapting bodily cognition, as shown in individuals born without hands (Vannuscorps & Caramazza, 2016) and in amputees with persistent phantom hand representation (Kikkert et al., 2016). How sharp is the conceptual boundary between hands and tools? This question is particularly relevant for individuals who have lost one hand and use prosthetic hands as tools to supplement their missing hand function. Although both congenital one-handers (i.e., amelia patients) and one-handed amputees are encouraged to use prostheses, the former show a greater tendency than the latter to use prosthetic hands in daily tasks (Jang et al., 2011). One-handers have a fully functional remaining hand (allowing them to use handheld tools, etc.), which makes them less likely to show semantic distortions in hand and tool representation. However, their bodies and their interactions with their environment are fundamentally altered by their disability (Makin et al., 2013; Makin, Wilf, Schwartz, & Zohary, 2010). To determine how real-world experience shapes conceptual categorization of hands, tools, and prostheses, we recruited one-handers with congenital or acquired unilateral hand loss to take part in a study involving a priming task. We predicted that one-handers, particularly congenital one-handers, would show more conceptual blurring between hands and tools than control participants would, as a result of less experience with a hand and more reliance on prostheses (which are essentially tools) for typical hand functions. We further predicted that individual differences in prosthesis usage would be reflected in implicit categorization of hands, manual tools, and prostheses.
Spatiotemporal variation vegetation cover and their relationship to climate in Yangtze River watershed area

Based on the SPOT/ NDVI data and meteorological data of Jianghuai watershed area, the temporal and spatial variation characteristics of NDVI and their correlation with climate factors (temperature and precipitation) are analyzed from 1998 to 2013 by utilizing the maximum value composite and linear regression method. The results showed that the vegetation growth has changed year by year with an overall trend in Jianghuai watershed region, and the number of pixels in the growing area accounts for 85.8% of the total. From the space point of view, expect for some regions in Hefei, Chuzhou and Luan are obviously decreasing, most of the other regions showing a growth trend. Vegetation was not positively correlated with temperature and precipitation, and the correlation between NDVI and temperature was higher than that of precipitation. Due to the differences of topography, geography and human activities, the correlation in different regions is different. In addition, human activities are also the influencing factors of vegetation change.
Acquisition of “Start” and “Stop” response thresholds in peak-interval timing is differentially sensitive to protein synthesis inhibition in the dorsal and ventral striatum

Time-based decision-making in peak-interval timing procedures involves the setting of response thresholds for the initiation (“Start”) and termination (“Stop”) of a response sequence that is centered on a target duration. Using intracerebral infusions of the protein synthesis inhibitor anisomycin, we report that the acquisition of the “Start” response depends on normal functioning (including protein synthesis) in the dorsal striatum (DS), but not the ventral striatum (VS). Conversely, disruption of the VS, but not the DS, impairs the acquisition of the “Stop” response. We hypothesize that the dorsal and ventral regions of the striatum function as a competitive neural network that encodes the temporal boundaries marking the beginning and end of a timed response sequence.
Small RNA Analysis in Sindbis Virus Infected Human HEK293 Cells

Introduction In contrast to the defence mechanism of RNA interference (RNAi) in plants and invertebrates, its role in the innate response to virus infection of mammals is a matter of debate. Since RNAi has a well-established role in controlling infection of the alphavirus Sindbis virus (SINV) in insects, we have used this virus to investigate the role of RNAi in SINV infection of human cells. Results SINV AR339 and TR339-GFP were adapted to grow in HEK293 cells. Deep sequencing of small RNAs (sRNAs) early in SINV infection (4 and 6 hpi) showed low abundance (0.8%) of viral sRNAs (vsRNAs), with no size, sequence or location specific patterns characteristic of Dicer products nor did they possess any discernible pattern to ascribe to a specific RNAi biogenesis pathway. This was supported by multiple variants for each sequence, and lack of hot spots along the viral genome sequence. The abundance of the best defined vsRNAs was below the limit of Northern blot detection. The adaptation of the virus to HEK293 cells showed little sequence changes compared to the reference; however, a SNP in E1 gene with a preference from G to C was found. Deep sequencing results showed little variation of expression of cellular microRNAs (miRNAs) at 4 and 6 hpi compared to uninfected cells. Twelve miRNAs exhibiting some minor differential expression by sequencing, showed no difference in expression by Northern blot analysis. Conclusions We show that, unlike SINV infection of invertebrates, generation of Dicer-dependent svRNAs and change in expression of cellular miRNAs were not detected as part of the Human response to SINV.
Dialysis-Requiring Acute Kidney Injury in Denmark 2000-2012: Time Trends of Incidence and Prevalence of Risk Factors—A Nationwide Study

Introduction Dialysis-requiring acute kidney injury is a severe illness associated with poor prognosis. However, information pertaining to incidence rates and prevalence of risk factors remains limited in spite of increasing focus. We evaluate time trends of incidence rates and changing patterns in prevalence of comorbidities, concurrent medication, and other risk factors in nationwide retrospective cohort study. Materials and Methods All patients with dialysis-requiring acute kidney injury were identified between January 1st 2000 and December 31st 2012. By cross-referencing data from national administrative registries, the association of changing patterns in dialysis treatment, comorbidity, concurrent medication and demographics with incidence of dialysis-requiring acute kidney injury was evaluated. Results A total of 18,561 adult patients with dialysis-requiring AKI were identified between 2000 and 2012. Crude incidence rate of dialysis-requiring AKI increased from 143 per million (95% confidence interval, 137–144) in 2000 to 366 per million (357–375) in 2006, and remained stable hereafter. Notably, incidence of continuous veno-venous hemodialysis (CRRT) and use of acute renal replacement therapy in elderly >75 years increased substantially from 23 per million (20–26) and 328 per million (300–355) in 2000, to 213 per million (206–220) and 1124 per million (1076–1172) in 2012, respectively. Simultaneously, patient characteristics and demographics shifted towards increased age and comorbidity. Conclusions Although growth in crude incidence rate of dialysis-requiring AKI stabilized in 2006, continuous growth in use of CRRT, and acute renal replacement therapy of elderly patients >75 years, was observed. Our results indicate an underlying shift in clinical paradigm, as opposed to unadulterated growth in incidence of dialysis-requiring AKI.
NichingEDA: Utilizing the diversity inside a population of EDAs for continuous optimization

Since the estimation of distribution algorithms (EDAs) have been introduced, several single model based EDAs and mixture model based EDAs have been developed. Take Gaussian models as an example, EDAs based on single Gaussian distribution have good performance on solving simple unimodal functions and multimodal functions whose landscape has an obvious trend towards the global optimum. But they have difficulties in solving multimodal functions with irregular landscapes, such as wide basins, flat plateaus and deep valleys. Gaussian mixture model based EDAs have been developed to remedy this disadvantage of single Gaussian based EDAs. A general framework NichingEDA is presented in this paper from a new perspective to boost single model based EDAspsila performance. Through adopting a niching method and recombination operators in a population of EDAs, NichingEDA significantly boosts the traditional single model based EDAspsila performance by making use of the diversity inside the EDA population on hard problems without estimating a precise distribution. Our experimental studies have shown that NichingEDA is very effective for some hard global optimization problems, although its scalability to high dimensional functions needs improving. Analyses and discussions are presented to explain why NichingEDA performed well/poorly on certain benchmark functions.
Validation of the Short Obsessive–Compulsive Disorder Screener (SOCS) in children and adolescents

Background The Short Obsessive–Compulsive Disorder Screener (SOCS) is recommended by the National Institute for Health and Care Excellence as a suitable and validated screening tool for 11- to 15-year olds. Despite its excellent sensitivity and specificity in detecting obsessive–compulsive disorder (OCD), it has limitations. Aims To empirically examine whether the SOCS is suitable for assessing OCD symptoms across a wide age range of children and adolescents and to provide new data about its psychometric properties. Method Participants were 94 patients (9–19 years) with OCD, and 880 healthy controls. Results The results supported the SOCS’ unidimensional factor structure and metric invariance across samples. It showed good reliability in terms of internal consistency and temporal stability. Furthermore, it had significantly high correlations with other OCD measures and an acceptable sensitivity and specificity for detecting OCD. Conclusions The SOCS is a brief screening tool suitable for detecting OCD in children and adolescents. Declaration of interest None. Copyright and usage © The Royal College of Psychiatrists 2015. This is an open access article distributed under the terms of the Creative Commons Non-Commercial, No Derivatives (CC BY-NC-ND) licence.
Cryptanalysis of a class of cryptographic hash functions

We apply new cryptanalytical techniques to perform the generic multi-block multicollision, second preimage and herding attacks on the Damgard-Merkle hash functions with linear-XOR/additive checksums. The computational work required to perform these attacks on the Damgard-Merkle hash functions with linear-XOR/additive checksum of message blocks (GOST), intermediate states (3C, MAELSTROM-0, F-Hash) or both is only a little more than what is required on the Damgard-Merkle hash functions. Our generic attacks on GOST answers the open question of Hoch and Shamir at FSE 2006 on the security of the iterated hash functions with the linear mixing of message blocks.
Clinical and Biological Significance of CDK4 Amplification in Well-Differentiated and Dedifferentiated Liposarcomas

Purpose: The MDM2 and HMGA2 genes are consistently amplified in well-differentiated/dedifferentiated liposarcomas (WDLPS/DDLPS) whereas CDK4 is frequently but not always amplified in these tumors. Our goal was to determine whether the absence of CDK4 amplification was (a) correlated to a specific clinico-histopathologic profile; and (b) compensated by another genomic anomaly involving the CCND1/CDK4/P16INK4a/RB1/E2F pathway. Experimental Design: We compared the clinical characteristics of a series of 143 WDLPS/DDLPS with amplification of both MDM2 and CDK4 (MDM2+/CDK4+) to a series of 45 WDLPS/DDLPS with MDM2 amplification and no CDK4 amplification (MDM2+/CDK4-). We used fluorescence in situ hybridization, real time quantitative reverse transcription PCR, and immunohistochemistry to explore the status of CCND1, P16INK4a, P14ARF, and RB1. Results: We found that MDM2+/CDK4- WDLPS/DDLPS represent a distinct clinical subgroup with favorable prognostic features, including low-grade lipoma-like histology, peripheral location, and lower rate of recurrence. By using fluorescence in situ hybridization, we found that genomic aberrations expected to be alternative mechanisms for compensating the lack of CDK4 amplification, such as RB1 and CDKN2A deletions or CCND1 amplification, were very uncommon. In contrast, by using real time quantitative reverse transcription PCR and immunohistochemistry, we observed that overexpression of P16INK4a (and P14ARF) and CCND1 and reduced expression of RB1 were very frequent, independently of the CDK4 status. Conclusions: Our results underscore the complex coordinated regulation of the RB and p53 growth-control pathways in WDLPS/DDLPS. Because the absence of CDK4 amplification is not specifically counterbalanced by a genomic alteration of the CCND1/CDK4/P16INK4a/RB1/E2F pathway, CDK4 amplification may only represent a “MDM2-HMGA2-helper” in WDLPS/DDLPS tumorigenesis. (Clin Cancer Res 2009;15(18):5696–703)
Four Hundred Seventeen Squamous Cell Cancers in a Heart Transplant Patient

Squamous cell carcinoma (SCC) is the most common malignancy in organ transplant recipients. In this patient population it pursues a much more aggressive course than in the general population: it occurs with higher frequency and displays a greater tendency to recur locally and metastasize, even after surgical excision. Hence, prophylactic measures assume a very important role in these patients. Patients should minimize their sun exposure and have their skin examined routinely. For those with large numbers of SCCs, systemic retinoids and reduction in immunosuppressive regimen may be of benefit. We present the case of a 70-year-old male heart transplant recipient who developed 334 SCCs, 83 SCCs in situ, and innumerable actinic keratoses during the course of 19 years posttransplant. His cancerous lesions were all excised surgically, but over the years, his cancer assumed a progressively more aggressive course. His immunosuppressive regimen was eventually reduced.
Serum eosinophil cationic protein as a marker of eosinophilic inflammation in asthma

The serum level of eosinophil cationic protein (ECP) has been used as a clinical marker in asthma, on the assumption that it reflects ongoing eosinophilic inflammation of the airways. However, only a few studies have investigated this issue, using bronchial secretions but not tissue specimens.
Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome

Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy.
Risk Analysis Model Based on Prototype Theory

In risk analysis in health insurance, one fundamental duty is to classify the insured into the risk categories which are essentially the vague concepts. A defining feature of vague concepts that their boundaries are uncertain. Inthis paper, we take a prototype theory approach to represent risk categories. In this representation, each label is associated with a prototype and has a probability density function. One main contribution of this paper is that a learning procedure is proposed to obtain a label representation from the given data set. The idea of learning algorithm is that the training dataset can be considered as the samples generated from the label, and hence the data set has a generating probability distribution from the underlying label. By taking the Mahalanobis distance to measure the distance between elements and label, an iterative learning algorithm is proposed to obtain the label representation.The basic procedure includes two iterations. The first is to generate a label representation from the training data set with a probability distribution. The second is to generate the probability distribution associated with the training data from the label representation. These two iterations continue till the termination condition is satisfied.
Relationship Between Osteoporosis and Cardiovascular Disease in Postmenopausal Women

In the placebo group of the MORE study, including 2576 postmenopausal women (mean age, 66.5 years), the authors describe a strong linear association between the severity grade of osteoporosis (from low BMD to presence of severe vertebral fractures) and the future risk of cardiovascular events. Accordingly, treatment of postmenopausal osteoporosis should include consideration of measures to prevent adverse cardiovascular outcomes.