Miracle-dz/UniFAR-FTUs huggingface dataset:
Intraspecific Diversity of the 23S rRNA Gene and the Spacer Region Downstream in Escherichia coli

ABSTRACT The molecular microevolution of the 23S rRNA gene (rrl) plus the spacer downstream has been studied by sequencing of different operons from some representative strains of the Escherichia coli ECOR collection. The rrl gene was fully sequenced in six strains showing a total of 67 polymorphic sites, a level of variation per nucleotide similar to that found for the 16S rRNA gene (rrs) in a previous study. The size of the gene was highly conserved (2902 to 2905 nucleotides). Most polymorphic sites were clustered in five secondary-structure helices. Those regions in a large number of operons were sequenced, and several variations were found. Sequences of the same helix from two different strains were often widely divergent, and no intermediate forms existed. Intercistronic variability was detected, although it seemed to be lower than for the rrs gene. The presence of two characteristic sequences was determined by PCR analysis throughout all of the strains of the ECOR collection, and some correlations with the multilocus enzyme electrophoresis clusters were detected. The mode of variation of the rrl gene seems to be quite similar to that of therrs gene. Homogenization of the gene families and transfer of sequences from different clonal lines could explain this pattern of variation detected; perhaps these factors are more relevant to evolution than single mutation. The spacer region between the 23S and 5S rRNA genes exhibited a highly polymorphic region, particularly at the 3′ end.
The ALOHA system

THE ALOHA SYSTEM is composed of a related series of contracts and grants from a variety of funding agencies with principal support from ARPA, which deal with two main themes: computer communications (TASK 1), and computer structures (TASK 2). Under computer-communications there is work in (a) Studies on computer communications using radio and satellites, (b) The development of a prototype radio-linked time-sharing network, (c) System studies and planning for a Pacific area computer communications network linking major universities in the U.S., Japan, Australia and other Pacific countries.Under computer structures, we are engaged in research/development in multiprocessor computing structures, computer networks, and geographically distributed computing systems. This work is being undertaken in two phases: 1) the establishment of a research facility and 2) the research work itself. The research facility is centered around the BCC 500 computing system.
Computation of precise geoid model of Auvergne using current UNB Stokes-Helmert’s approach

Abstract The aim of this paper is to show a present state-of-the-art precise gravimetric geoid determination using the UNB Stokes-Helmert’s technique in a simple schematic way. A detailed description of a practical application of this technique in the Auvergne test area is also provided. In this paper, we discuss the most problematic parts of the solution: correct application of topographic and atmospheric effects including the lateral topographical density variations, downward continuation of gravity anomalies from the Earth surface to the geoid, and the optimal incorporation of the global gravity field into the final geoid model. The final model is tested on 75 GNSS/levelling points supplied with normal Molodenskij heights, which for this investigation are transformed to rigorous orthometric heights. The standard deviation of the computed geoid model is 3.3 cm without applying any artificial improvement which is the same as that of the most accurate quasigeoid.
Using the Phantogram Technique for a Collaborative Stereoscopic Multitouch Tabletop Game

This paper outlines the development of a stereoscopic game included in the design of a pilot transmedia storytelling campaign for health promotion and communication of basic concepts about vision and perception for a target audience of children under six and their families in a research clinic setting. The game utilizes the 3D phantogram technique (anamorphically distorted projection onto a horizontal surface) to implement a two-person multitouch game using the Unity 3D engine and IZ3D drivers on the Microsoft Surface tabletop display. Viewed from an appropriate height and position, virtual objects and characters appear to stand directly on the tabletop, facilitating a direct and intuitive mixed reality interface. The technical challenges included occlusion of stereoscopic images by users' hands, the generation of appropriate perspectives for multiple users, and the integration of a two-dimensional multitouch surface with a three-dimensional stereoscopic display.
View-sequece based indoor/outdoor navigation robust to illumination changes

We propose a view-based indoor/outdoor navigation method as an extension of the view-sequence navigation. The original view-sequence navigation method uses the template matching method with normalized correlation for localization. Because the matching method is sensitive to local illumination changes, it is only used for indoor environment. In this paper, we propose to adopt the accumulated block matching method to improve robustness against locally changing illumination, in which a template is split into small patches and matched by maximizing the average of the normalized correlations of all the patches.We also propose a localization criterion which helps the robot decide its motion. Our experimental results demonstrate that the proposed methods can be applied to both indoor and outdoor environments.
Checking probabilistic noninterference using JOANA

Abstract JOANA is a tool for software security analysis, checking up to 100 kLOC of full multi-threaded Java. JOANA is based on sophisticated program analysis techniques and thus very precise. It includes a new algorithm guaranteeing probabilistic noninterference, named RLSOD. JOANA needs few annotations and has a nice GUI. The tool is open source and was applied in several case studies. The article presents an overview of JOANA and its underlying technology.
Diagonalization in Parallel Space

Matrix diagonalization is an important component of many aspects of computational science. There are a variety of algorithms to accomplish this task. Jacobi’s algorithm is a good choice for parallel environments. Jacobi’s algorithm consists of a series of matrix plane rotations, the ordering of which can dramatically affect performance. We show a new ordering which cuts the number of necessary operations approximately in half. Additionally, Jacobi’s algorithm can be made parallel in space as well as time. This is an advantage when dealing with very large matrices, such as those found in quantum chemistry. 1 Matrix Diagonalization There are two major families of matrix diagonalization methods, those based on Jacobi rotations and those based on householder reflections. It has long been noted that while Householder methods are faster in a serial environment [1], Jacobi rotation-based methods have much more inherent parallelism, as well as better numerical properties and, therefore, greater accuracy [5]. Furthermore, there are refinements to the Jacobi algorithm available in a parallel environment that have been largely unused in serial approaches. The careful and selective use of these refinements has the potential to significantly improve the performance of the algorithm over the serial version, and makes the appearance of super-linear speedups for parallel diagonalization possible. The basic problem in matrix diagonalization is this: given a matrix A, to find matrices Q and S such that A = QSQ (1) where S has all zero off-diagonal elements. The diagonal elements of S are the eigenvalues of A, and the columns of Q are the corresponding eigenvectors. The eigenvalues and corresponding eigenvectors of a matrix are the key targets of many matrix operations. The efficient computation of these quantities is of great use in many applications, such as signal processing [4], computer graphics [8], and computational chemistry [3], among other fields. The motivation of this study is the use of this technique to calculate the quantum mechanical wave functions of noble gas complexes by solving the Schrödinger equation using basis set methods. The matrices for problems of this type can grow to be very large, on the order of 10 elements for non-linear molecules and 10 for simple linear molecules, so parallelization in space as well as in time is highly desirable.
Using Language Technologies to support individual formative feedback

Smithies, A. , Braidman, I. , Berlanga, A. J., Haley, D. , & Wild, F. (2010). Using Language Technologies to support individual formative feedback. In P. Escudeiro (Ed.), Proceedings of the 9th European Conference on e-Learning (ECEL 2010) (pp. 570-577). Oporto, Portugal. November, 4-5, 2010.
Referential uncertainty and word learning in high-dimensional, continuous meaning spaces

This paper discusses lexicon word learning in high-dimensional meaning spaces from the viewpoint of referential uncertainty. We investigate various state-of-the-art Machine Learning algorithms and discuss the impact of scaling, representation and meaning space structure. We demonstrate that current Machine Learning techniques successfully deal with high-dimensional meaning spaces. In particular, we show that exponentially increasing dimensions linearly impact learner performance and that referential uncertainty from word sensitivity has no impact.
Radio monitoring of NGC 7469: late-time radio evolution of SN 2000ft and the circumnuclear starburst in NGC 7469

We present the results of an eight-year long monitoring of the radio emission from the luminous infrared galaxy (LIRG) NGC 7469, using 8.4 GHz Very Large Array (VLA) observations at 0.3 arcsec resolution. Our monitoring shows that the late-time evolution of the radio supernova (RSN) SN 2000ft follows a decline very similar to that displayed at earlier times of its optically thin phase. The late-time radio emission of SN 2000ft is, therefore, still being powered by its interaction with the pre-SN stellar wind, and not with the interstellar medium (ISM). Indeed, the ram pressure of the pre-SN wind is ρ w υ 2 w ≈ 7.6 x 10- 9 dyn cm ―2 , at a SN age of t ≈ 2127 d, which is significantly larger than the expected pressure of the ISM around SN 2000ft. At this age, the SN shock has reached a distance r sh ≈ 0.06 pc, and our observations are probing the interaction of the SN with dense material that was ejected by the pre-SN star about 5820 yr prior to its explosion. From our VLA monitoring, we estimate that the swept-up mass by the SN shock after about six years of expansion is M sw ≈ 0.29 M ⊙ , assuming an average expansion speed of the SN of 10 4 km s ―1 . We also searched for recently exploded core-collapse SNe in our VLA images. Apart from SN 2000ft (S v ≈ 1760 μJy at its peak, corresponding to 1.1 × 10 28 erg s ―1 Hz ―1 ), we found no evidence for any other RSN more luminous than ≈6.0 × 10 26 erg s ―1 Hz ―1 , which suggests that no other Type IIn SN has exploded since 2000 in the circumnuclear starburst of NGC 7469.
A Pipelined Framework for Online Cleaning of Sensor Data Streams

Data captured from the physical world through sensor devices tends to be noisy and unreliable. The data cleaning process for such data is not easily handled by standard data warehouse-oriented techniques, which do not take into account the strong temporal and spatial components of receptor data. We present Extensible receptor Stream Processing (ESP), a declarative query-based framework designed to clean the data streams produced by sensor devices.
Dendrimer, Liposomes, Carbon Nanotubes and PLGA Nanoparticles: One Platform Assessment of Drug Delivery Potential

Liposomes (LIP), nanoparticles (NP), dendrimers (DEN), and carbon nanotubes (CNTs), represent eminent classes of drug delivery devices. A study was carried out herewith by employing docetaxel (DTX) as model drug to assess their comparative drug delivery potentials. Under optimized conditions, highest entrapment of DTX was observed in CNT-based formulation (DTX-CNTs, 74.70 ± 4.9%) followed by nanoparticles (DTX-NP, 62.34 ± 1.5%), liposome (49.2 ± 1.51%), and dendrimers (28.26 ± 1.74%). All the formulations were found to be of nanometric size. In vitro release studies were carried out in PBS (pH 7.0 and 4.0), wherein all the formulations showed biphasic release pattern. Cytotoxicity assay in human cervical cancer SiHa cells inferred lowest IC50 value of 1,235.09 ± 41.93 nM with DTX-CNTs, followed by DTX-DEN, DTX-LIP, DTX-NP with IC50 values of 1,571.22 ± 151.27, 1,653.98 ± 72.89, 1,922.75 ± 75.15 nM, respectively. Plain DTX showed higher hemolytic toxicity of 22.48 ± 0.94%, however loading of DTX inside nanocarriers drastically reduced its hemolytic toxicity (DTX-DEN, 17.22 ± 0.48%; DTX-LIP, 4.13 ± 0.19%; DTX-NP, 6.43 ± 0.44%; DTX-CNTs, 14.87 ± 1.69%).
Benefits of a multidisciplinary pulmonary rehabilitation program.

We evaluated the conditions of 33 patients who completed an outpatient pulmonary rehabilitation program to determine what types of improvements occurred, and whether these changes were related to the baseline degree of ventilatory impairment, to determine whether rehabilitation was beneficial to patients, regardless of the degree of underlying lung dysfunction. Endurance measurements, including sustained submaximal performance on a cycle ergometer and the 12-minute walk distance (1,349 ± 625 feet to 1,700 ± 670 feet) increased significantly (p<0.01), as did multiple educational and subjective parameters. Maximal exercise performance on a graded cycle test improved very little, with a decline in the ventilatory equivalent for oxygen consumption ( V ˙ e/ V ˙ O 2 ) being the only significant change (48.2 ± 28.3 L/ml to 36.6 ± 8.7 L/ml). Of the observed changes, only one endurance measurement, the sustained submaximal exercise performance, correlated with FEV 1 (r = 0.5, p
Critical path selection for delay fault testing based upon a statistical timing model

Critical path selection is an indispensable step for testing of small-size delay defects. Historically, this step relies on the construction of a set of worst-case paths, where the timing lengths of the paths are calculated based upon discrete-valued timing models. The assumption of discrete-valued timing models may become invalid for modeling delay effects in the deep submicron domain, where the effects of timing defects and process variations are often statistical in nature. This paper studies the problem of critical path selection for testing small-size delay defects, assuming that circuit delays are statistical. We provide theoretical analysis to demonstrate that the new path-selection problem consists of two computationally intractable subproblems. Then, we discuss practical heuristics and their performance with respect to each subproblem. Using a statistical defect injection and timing-simulation framework, we present experimental results to support our theoretical analysis.
Method for Detecting Core Malware Sites Related to Biomedical Information Systems

Most advanced persistent threat attacks target web users through malicious code within landing (exploit) or distribution sites. There is an urgent need to block the affected websites. Attacks on biomedical information systems are no exception to this issue. In this paper, we present a method for locating malicious websites that attempt to attack biomedical information systems. Our approach uses malicious code crawling to rearrange websites in the order of their risk index by analyzing the centrality between malware sites and proactively eliminates the root of these sites by finding the core-hub node, thereby reducing unnecessary security policies. In particular, we dynamically estimate the risk index of the affected websites by analyzing various centrality measures and converting them into a single quantified vector. On average, the proactive elimination of core malicious websites results in an average improvement in zero-day attack detection of more than 20%.
The University of Hawaii Wide‐Field Imager (UHWFI)

The University of Hawaii Wide‐Field Imager (UHWFI) is a focal compressor system designed to project the full half‐degree field of the UH 2.2 m telescope onto the refurbished UH 8K × 8K CCD camera. The optics use Ohara glasses and are mounted in an oil‐filled cell to minimize light loss and ghost images from the large number of internal lens surfaces. The UHWFI is equipped with a six‐position filter wheel and a rotating sector blade shutter, both driven by stepper motors. The instrument saw first light in 2004 in an engineering mode. After filling the lens cell with index‐matched oil, integrating all software components into the user interface, tuning the CCD performance, and purchasing the final filter set, the UHWFI is now fully commissioned at the UH 2.2 m telescope.
High Baseline Insulin Levels Associated With 6-Year Incident Observed Sleep Apnea

OBJECTIVE Obstructive sleep apnea is common in patients with type 2 diabetes, and its association with insulin and insulin resistance has been examined in cross-sectional studies. We evaluate risk factors for incident observed sleep apnea in a general population not selected for sleep disturbances. RESEARCH DESIGN AND METHODS A total of 1,780 men and 1,785 women, aged 33 to 68 years, from the cohort Data from an Epidemiologic Study on the Insulin Resistance Syndrome (D.E.S.I.R.) responded to the question, “Has someone said to you that you stop breathing during your sleep? ” at baseline and 6 years. Anthropometric, clinical, and biological factors were recorded at both time points. RESULTS At baseline, 14% of men and 7% of women reported having observed sleep apnea (positive response to question); 6-year incidences were 14 and 6%, respectively. Age, anthropometric parameters, blood pressure, and sleep characteristics were all associated with prevalent, observed apnea episodes, in both sexes. Baseline waist circumference was the strongest predictor of incident apnea: standardized odds ratio (OR), adjusted for age and sex, 1.34 (95% CI 1.19–1.52). After adjustment for age, sex, and waist circumference, the standardized ORs for incident observed apnea were identical for fasting insulin and the homeostasis model assessment of insulin resistance: 1.31 (1.13–1.51) and 1.24 (1.09–1.41) for triglycerides and 1.52 (1.12–2.05) for smoking. Observed apnea at baseline was not associated with changes in anthropometric or biological parameters over the 6-year follow-up. CONCLUSIONS The most important baseline risk factor for incident apnea was adiposity. After accounting for adiposity, other risk factors were high insulin, insulin resistance, high triglycerides, and smoking, factors amenable to lifestyle intervention.
Statistical and computational tradeoffs in biclustering

We consider the problem of identifying a small sub-matrix of activation in a large noisy matrix. We establish the minimax rate for the problem by showing tight (up to constants) upper and lower bounds on the signal strength needed to identify the sub-matrix. We consider several natural computationally tractable procedures and show that under most parameter scalings they are unable to identify the sub-matrix at the minimax signal strength. While we are unable to directly establish the computational hardness of the problem at the minimax signal strength we discuss connections to some known NP-hard problems and their approximation algorithms.
11-magic : Recovery of sparse signals via convex programming

For maximum computational efficiency, the solvers for each of the seven problems are implemented separately. They all have the same basic structure, however, with the computational bottleneck being the calculation of the Newton step (this is discussed in detail below). The code can be used in either “small scale” mode, where the system is constructed explicitly and solved exactly, or in “large scale” mode, where an iterative matrix-free algorithm such as conjugate gradients (CG) is used to approximately solve the system.
Differential Metabolism of Organic Nitrates by Aldehyde Dehydrogenase 1a1 and 2: Substrate Selectivity, Enzyme Inactivation, and Active Cysteine Sites

Organic nitrate vasodilators (ORN) exert their pharmacologic effects through the metabolic release of nitric oxide (NO). Mitochondrial aldehyde dehydrogenase (ALDH2) is the principal enzyme responsible for NO liberation from nitroglycerin (NTG), but lacks activity towards other ORN. Cytosolic aldehyde dehydrogenase (ALDH1a1) can produce NO from NTG, but its activity towards other ORN is unknown. Using purified enzymes, we showed that both isoforms could liberate NO from NTG, isosorbide dinitrate (ISDN), and nicrorandil, while only ALDH1a1 metabolized isosorbide-2-mononitrate and isosorbide-5-mononitrate (IS-5-MN). Following a 10-min incubation with purified enzyme, 0.1 mM NTG and 1 mM ISDN potently inactivated ALDH1a1 (to 21.9% ± 11.1% and 0.44% ± 1.04% of control activity, respectively) and ALDH2 (no activity remaining and 4.57% ± 7.92% of control activity, respectively), while 1 mM IS-5-MN exerted only modest inactivation of ALDH1a1 (reduced to 89% ± 4.3% of control). Cytosolic ALDH in hepatic homogenates incubated at the vascular EC50 concentrations of ORN was inactivated by NTG (to 45.1% ± 8.1% of control activity) while mitochondrial ALDH was inactivated by NTG and nicorandil (to 68.2% ± 10.0% and 78.7% ± 19.8% of control, respectively). Via site-directed mutagenesis, the active sites of ORN metabolism of ALDH2 (Cys-319) and ALDH1a1 (Cys-303) were found to be identical to those responsible for their dehydrogenase activity. Cysteine-302 of ALDH1a1 and glutamate-504 of ALDH2 were found to modulate the rate of ORN metabolism. These studies provide further characterization of the substrate selectivity, inactivation, and active sites of ALDH2 and ALDH1a1 toward ORN.
Follow the heart or the head? The interactive influence model of emotion and cognition

The experience of emotion has a powerful influence on daily-life decision making. Following Plato’s description of emotion and reason as two horses pulling us in opposite directions, modern dual-system models of decision making endorse the antagonism between reason and emotion. Decision making is perceived as the competition between an emotion system that is automatic but prone to error and a reason system that is slow but rational. The reason system (in “the head”) reins in our impulses (from “the heart”) and overrides our snap judgments. However, from Darwin’s evolutionary perspective, emotion is adaptive, guiding us to make sound decisions in uncertainty. Here, drawing findings from behavioral economics and neuroeconomics, we provide a new model, labeled “The interactive influence model of emotion and cognition,” to elaborate the relationship of emotion and reason in decision making. Specifically, in our model, we identify factors that determine when emotions override reason and delineate the type of contexts in which emotions help or hurt decision making. We then illustrate how cognition modulates emotion and how they cooperate to affect decision making.