Miracle-dz/UniFAR-FTUs huggingface dataset:
Solving multiobjective clustering using an immune-inspired algorithm

In this study, we introduced a novel multiobjective optimization algorithm, Nondominated Neighbor Immune Algorithm (NNIA), to solve the multiobjective clustering problems. NNIA solves multiobjective optimization problems by using a nondominated neighbor-based selection technique, an immune inspired operator, two heuristic search operators and elitism. The main novelty of NNIA is that the selection technique only selects minority isolated nondominated individuals in current population to clone proportionally to the crowding-distance values, recombine and mutate. As a result, NNIA pays more attention to the less-crowded regions in the current trade-off front. The experimental results on seven artificial data sets with different manifold structure and six real-world data sets show that the NNIA is an effective algorithm for solving multiobjective clustering problems, and the NNIA based multiobjective clustering technique is a cogent unsupervised learning method.
The crystal structure of anhydrous alpha,alpha-trehalose at -150 degrees.

The crystal structure of alpha,alpha-trehalose (alpha-D-glucopyranosyl alpha-D-glucopyranoside), C12H22O11, is monoclinic, P2(1), Z = 2, with unit cell dimensions at -150 degrees [20 degrees] of a = 12.971(5) [13.003(5)], b = 8.229(4) [8.252(4)], c = 6.789(3) [6.799(3)] A, beta = 98.12(4) [98.33(4)]. The crystal structure was solved by using MULTAN, and refined to R = 0.059, Rw = 0.048 for 1564 intensities, measured with MoK alpha radiation. The molecular structure is very similar to that observed in the dihydrate crystals. It has approximate C2 symmetry. Both glucopyranosyl groups are in the 4C1 conformation. The linkage torsion angles, O-5-C-1-O-1-C-1, are +60.8 degrees and +60.1 degrees. The primary alcohol groups are oriented gauche/gauche and gauche/trans, as in the dihydrate structure. A comparison of the cross-polarization, magic-angle-spinning (c.p.-m.a.s.), 13C-n.m. r. spectra for powders of the crystalline anhydrous and dihydrate forms shows differences in resonances assigned to C-1 and C-4 that would not be anticipated from the results of the crystal-structure analyses.
Differential Privacy of Mathematical Functions

Differential privacy is a privacy notion in statistical databases. However, we find that the notion can be extended to mathematical functions. By studying the differential privacy problem of a simple mathematical function we find two differentially private mechanisms which are applicable for almost all query functions. By using these mechanisms each query function can have custom-designed mechanisms, which implies that our mechanisms are not based on (global or local) sensitivitybased methods—some methods extensively used to construct differentially private mechanisms. Our mechanisms are so flexible that they can be used to balance the accuracy of the outputs of different datasets. We also present some interesting impossibility results of differential privacy. The above results motivate us to explore the mathematical treatment of differential privacy. We present an abstract model of differential privacy in which a differential privacy problem is modeled as finding a randomized mapping between two metric spaces. Some basic structures of differential privacy are presented, such as the {I i }i, {Ri }i sequences. Some of the properties of these structures, such as the convergence, are also discussed (for some special cases). Finally, we apply our theoretical results to the subgraph counting problem and the linear query problem. The experiments show that our mechanisms (in most cases) have more accurate results than the state of the art mechanisms. ar X iv :1 70 2. 02 72 1v 1 [ cs . C R ] 9 F eb 2 01 7
Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing

Small RNAs triggering RNA silencing are loaded onto Argonautes and then sequence-specifically guide them to target transcripts. Epitope-tagged human Argonautes (hAgo1, hAgo2, hAgo3, and hAgo4) are associated with siRNAs and miRNAs, but only epitope-tagged hAgo2 has been shown to have Slicer activity. Contrarily, how endogenous hAgos behave with respect to small RNA association and target RNA destruction has remained unclear. Here, we produced monoclonal antibodies for individual hAgos. High-throughput pyrosequencing revealed that immunopurified endogenous hAgo2 and hAgo3 associated mostly with miRNAs. Endogenous hAgo3 did not show Slicer function but localized in P-bodies, suggesting that hAgo3 endogenously expressed is, like hAgo2, involved in the miRNA pathway but antagonizes the RNAi activity of hAgo2. Sequence variations of miRNAs were found at both 5′ and 3′ ends, suggesting that multiple mature miRNAs containing different “seed” sequences can arise from one miRNA precursor. The hAgo antibodies we raised are valuable tools for ascertaining the functional behavior of endogenous Argonautes and miRNAs in RNA silencing.
A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, 13C Metabolic Flux Analysis (13C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during 13C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based 13C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species.
Statistical Analysis of the Primary Outcome in Acute Stroke Trials

Common outcome scales in acute stroke trials are ordered categorical or pseudocontinuous in structure but most have been analyzed as binary measures. The use of fixed dichotomous analysis of ordered categorical outcomes after stroke (such as the modified Rankin Scale) is rarely the most statistically efficient approach and usually requires a larger sample size to demonstrate efficacy than other approaches. Preferred statistical approaches include sliding dichotomous, ordinal, or continuous analyses. Because there is no best approach that will work for all acute stroke trials, it is vital that studies are designed with a full understanding of the type of patients to be enrolled (in particular their case mix, which will be critically dependent on their age and severity), the potential mechanism by which the intervention works (ie, will it tend to move all patients somewhat, or some patients a lot, and is a common hazard present), a realistic assessment of the likely effect size, and therefore the necessary sample size, and an understanding of what the intervention will cost if implemented in clinical practice. If these approaches are followed, then the risk of missing useful treatment effects for acute stroke will diminish.
An Effective General Purpose Approach for Automated Biomedical Document Classification

Automated document classification can be a valuable tool for biomedical tasks that involve large amounts of text. However, in biomedicine, documents that have the desired properties are often rare, and special methods are usually required to address this issue. We propose and evaluate a method of classifying biomedical text documents, optimizing for utility when misclassification costs are highly asymmetric between the positive and negative classes. The method uses chi-square feature selection and several iterations of cost proportionate rejection sampling followed by application of a support vector machine (SVM), combining the resulting classifier results with voting. It is straightforward, fast, and achieves competitive performance on a set of standardized biomedical text classification evaluation tasks. The method is a good general purpose approach for classifying biomedical text.
A Genetic Method for Sex Identification of Raccoons (Procyon lotor) with Using the ZFX and ZFY Genes

ABSTRACT A genetic method for sex determination in raccoons was developed based on nucleotide differences of the zinc finger protein genes ZFX and ZFY. Four novel internal primers specific for ZFX or ZFY were designed. PCR amplification using two primer sets followed by agarose gel electrophoresis enabled sex determination. 141-bp and 447-bp bands were in both sex, and 346-bp band was specific only in male with primer set I. 345-bp and 447-bp bands were in both sex, and 141-bp band was specific only in male with primer set II, which could distinguish raccoon’s electrophoresis pattern from three native carnivores in Hokkaido. This method will be useful for conservation genetics studies or biological analyses of raccoons.
Proteome studies of Saccharomyces cerevisiae: Identification and characterization of abundant proteins

Two‐dimensional (2‐D) gel electrophoresis can now be coupled with protein identification techniques and genome sequence information for direct detection, identification, and characterization of large numbers of proteins from microbial organisms. 2‐D electrophoresis, and new protein identification techniques such as amino acid composition, are proteome research techniques in that they allow direct characterization of many proteins at the same time. Another new tool important for yeast proteome research is the Yeast Protein Database (YPD), which provides the sequence‐derived protein properties needed for spot identification and tabulations of the currently known properties of the yeast proteins. Studies presented here extend the yeast 2‐D protein map to 169 identified spots based upon the recent completion of the yeast genome sequence, and they show that methods of spot identification based on predicted isoelectric point, predicted molecular mass, and determination of partial amino acid composition from radiolabeled gels are powerful enough for the identification of at least 80% of the spots representing abundant proteins. Comparison of proteins predicted by YPD to be detectable on 2‐D gels based on calculated molecular mass, isoelectric point and codon bias (a predictor of abundance) with proteins identified in this study suggests that many glycoproteins and integral membrane proteins are missing from the 2‐D gel patterns. Using the 2‐D gel map and the information available in YDP, 2‐D gel experiments were analyzed to characterize the yeast proteins associated with: (i) an environmental change (heat shock), (ii) a temperature‐sensitive mutation (the prp2 mRNA splicing mutant), (iii) a mutation affecting post‐translational modification (N‐terminal acetylation), and (iv) a purified subcellular fraction (the ribosomal proteins). The methods used here should allow future extension of these studies to many more proteins of the yeast proteome.
Serious adverse events after measles-mumps-rubella vaccination during a fourteen-year prospective follow-up.

BACKGROUND Several disorders have been attributed to measles-mumps-rubella (MMR) vaccination during the past decade. The aim of this prospective follow-up study was to identify serious adverse events causally related to MMR vaccination. METHODS When the MMR vaccination program was launched in Finland in 1982, a countrywide surveillance system was set up to detect serious adverse events associated with MMR. To obtain detailed case histories vaccinees' clinical charts were reviewed. Serum samples were analyzed to trace concurrent infections. SETTING All hospitals and health centers in Finland from 1982 through 1996. RESULTS Immunization of 1.8 million individuals and consumption of almost 3 million vaccine doses by the end of 1996 gave rise to 173 potentially serious reactions claimed to have been caused by MMR vaccination. In all, 77 neurologic, 73 allergic and 22 miscellaneous reactions and 1 death were reported, febrile seizure being the most common event. However, 45% of these events proved to be probably caused or contributed by some other factor, giving an incidence of serious adverse events with possible or indeterminate causal relation with MMR vaccination of 5.3 per 100,000 vaccinees or 3.2 per 100,000 vaccine doses. CONCLUSIONS Causality between immunization and a subsequent untoward event cannot be estimated solely on the basis of a temporal relation. Comprehensive analysis of the reported adverse reactions established that serious events causally related to MMR vaccine are rare and greatly outweighed by the risks of natural MMR diseases.
Fountain-Code Aided File Transfer in 802.11 WLANs

Abstract —Fountain codes constitute novel erasure codes, whichhave been standardized for Forward Error Correction (FEC)in broadcast network protocols and by the Third-GenerationPartnersonhip Project (3GPP). The basic operational units ofFountain codes are source packets, which have a particular ﬁxedlength. These codes are invoked here in an 802.11 Wireless LocalArea Network (WLAN) scenario for protecting ﬁle transfers.More speciﬁcally, the optimal packet length is selected by con-sidering the 802.11 Media Access Control (MAC) retransmissionrate and the properties of the physical layer’s modulation scheme.Naturally, owing to the limited memory of the encoders/decoders,large source ﬁles must be decomposed into shorter transportblocks. Therefore, methods for partitioning the ﬁle and acknowl-edging the successful transmission of each block are also proposedhere. Compared to the ﬁle transfer regime operating without FECover the classic TCP protocol, the proposed regime requires alower threshold SNR for accomplishing a successful ﬁle transferand hence enhances the transmission efﬁciency by about 50%.
External Lexical Information for Multilingual Part-of-Speech Tagging

Morphosyntactic lexicons and word vector representations have both proven useful for improving the accuracy of statistical part-of-speech taggers. Here we compare the performances of four systems on datasets covering 16 languages, two of these systems being feature-based (MEMMs and CRFs) and two of them being neural-based (bi-LSTMs). We show that, on average, all four approaches perform similarly and reach state-of-the-art results. Yet better performances are obtained with our feature-based models on lexically richer datasets (e.g. for morphologically rich languages), whereas neural-based results are higher on datasets with less lexical variability (e.g. for English). These conclusions hold in particular for the MEMM models relying on our system MElt, which benefited from newly designed features. This shows that, under certain conditions, feature-based approaches enriched with morphosyntactic lexicons are competitive with respect to neural methods.
Gain-scheduled Smith PID controllers for LPV first order plus time varying delay systems

Practical control problems often deal with parameter varying uncertain systems that can be described by a first order plus delay (FOPD) model. In this paper, a new approach to design gain scheduled robust linear parameter varying (LPV) PID controllers with pole placement constraints (through LMI regions) is proposed. The controller structure includes a Smith predictor, real time measured parameters that schedule the controller (including the known part of the delay) and unstructured dynamic uncertainty which covers the unknown portion of the delay. Finally, this proposed control technique is validated in an academic example.
The Robert Gordon University

Blogs are highly rich in opinion making their automatic processing appealing to marketing companies, the media, costumer centres, etc. TREC ran a Blog track in 2006 with two tasks: opinion retrieval and an open task. This document reports the experiments conducted at The Robert Gordon University (RGU) where we used Statistical Language Models combined with shallow parsing techniques for the opinion retrieval problem.
Comparison of two atmospheric correction methods for the classification of spaceborne urban hyperspectral data depending on the spatial resolution

ABSTRACT For remote-sensing applications such as spectra classification or identification, atmospheric correction constitutes a very important pre-processing step, especially in complex urban environments where a lot of phenomenons alter the shape of the signal. The objective of this article is to compare the efficiency of two atmospheric correction algorithms, COCHISE (atmospheric COrrection Code for Hyperspectral Images of remote-sensing SEnsors) and an empirical method, on hyperspectral data and for classification applications. Classification is carried out on several simulated spaceborne data sets with different spatial resolutions (from 1.6 to 9.6 m). Four classifiers are considered in the study: a k-means, a Support Vector Machine (SVM), and a sun/shadow version of each of them, which processes sunlit and shadowed pixels separately. Results show that the most relevant atmospheric method for classification depends on the spatial resolution of the processed data set. Indeed, if the empirical method performs better on high-resolution data sets (up to 4%), its superiority fades out as the spatial resolution decreases, especially with the lower spatial resolution where COCHISE can be 10% more accurate than the empirical method.
Twice‐ vs. thrice‐weekly MPD PUVA in psoriasis: a randomized‐controlled efficacy study

Background: Oral psoralen‐ultraviolet A (PUVA) has been the treatment of choice of moderate to severe forms of psoriasis, however there is no standardized worldwide protocol. Twice‐ and thrice‐weekly regimens had been used. In this study we compare the efficacy of these regimens.
An analytic design of 2-space-time trellis code by function range set expansion

We offer an analytic design of optimal 2-space-time trellis codes. The design uses function range set expansion, which achieves better performance compared to known codes. The function range set is the encoder output value range of this trellis finite state machine. The output then is used to modulate the phase (m-PSK) to transmit. The resultant code is non-uniform and can be viewed as an extension of Tarokh's (see IEEE Transactions on Information Theory, vol.44, p.744-65, March 1998) work. When the range set size equals to the number of states it reduces to Tarokh's uniform code. Simulations also show that function range set expansion design outperforms state space expansion design in both frame error rate (FER) and decoding complexity. Our 4 states16-PSK STTC can achieve the similar performance of Tarokh's 32 states 4-PSK STTC.
Nonpharmacological treatment of agitation: a controlled trial of systematic individualized intervention.

OBJECTIVE The objective of this study was to examine the efficacy of a systematic algorithm for providing individualized, nonpharmacological interventions for reducing agitated behaviors in nursing home residents with dementia. METHODS This placebo-controlled study combined nomothetic and ideographic methodologies. The study was conducted in 12 nursing home buildings in Maryland; 6 were used as treatment facilities, and 6 as control facilities. Participants were 167 elderly nursing home residents with dementia. Interventions were tailored to the individual profiles of agitated participants using a systematic algorithm that considered type of agitation and unmet needs. Interventions were then designed to fulfill the need in a manner that matched the person's cognitive, physical, and sensory abilities, and their lifelong habits and roles. Interventions were provided for 10 days during the 4 hours of greatest agitation. Direct observations of agitation were recorded by trained research assistants via the Agitated Behavior Mapping Instrument (ABMI). Evaluation of positive and negative affect was also based on direct observation and assessed via Lawton's Modified Behavior Stream. Data analysis was performed via SPSS software. RESULTS The implementation of personalized, nonpharmacological interventions resulted in statistically significant decreases in overall agitation in the intervention group relative to the control group from baseline to treatment (F(1,164) = 10.22, p =. 002). In addition, implementation of individualized interventions for agitation resulted in statistically significant increases in pleasure and interest (F(1,164) = 24.22, p <. 001; F(1,164) = 20.66, p <. 001). CONCLUSIONS The findings support the use of individualized nonpharmacological interventions to treat agitation in persons with dementia and underscore the importance for clinicians of searching for underlying reasons for agitated behaviors.
Improved accuracy in periodontal pocket depth measurement using optical coherence tomography

Purpose The purpose of this study was to examine whether periodontal pocket could be satisfactorily visualized by optical coherence tomography (OCT) and to suggest quantitative methods for measuring periodontal pocket depth. Methods We acquired OCT images of periodontal pockets in a porcine model and determined the actual axial resolution for measuring the exact periodontal pocket depth using a calibration method. Quantitative measurements of periodontal pockets were performed by real axial resolution and compared with the results from manual periodontal probing. Results The average periodontal pocket depth measured by OCT was 3.10±0.15 mm, 4.11±0.17 mm, 5.09±0.17 mm, and 6.05±0.21 mm for each periodontal pocket model, respectively. These values were similar to those obtained by manual periodontal probing. Conclusions OCT was able to visualize periodontal pockets and show attachment loss. By calculating the calibration factor to determine the accurate axial resolution, quantitative standards for measuring periodontal pocket depth can be established regardless of the position of periodontal pocket in the OCT image.