Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptation of Pseudomonas aeruginosa to Phage PaP1 Predation via O-Antigen Polymerase Mutation

Adaptation of bacteria to phage predation poses a major obstacle for phage therapy. Bacteria adopt multiple mechanisms, such as inhibition of phage adsorption and CRISPR/Cas systems, to resist phage infection. Here, a phage-resistant mutant of Pseudomonas aeruginosa strain PA1 under the infection of lytic phage PaP1 was selected for further study. The PaP1-resistant variant, termed PA1RG, showed decreased adsorption to PaP1 and was devoid of long chain O-antigen on its cell envelope. Whole genome sequencing and comparative analysis revealed a single nucleotide mutation in the gene PA1S_08510, which encodes the O-antigen polymerase Wzy that is involved in lipopolysaccharide (LPS) biosynthesis. PA1_Wzy was classified into the O6 serotype based on sequence homology analysis and adopts a transmembrane topology similar to that seem with P. aeruginosa strain PAO1. Complementation of gene wzy in trans enabled the mutant PA1RG to produce the normal LPS pattern with long chain O-antigen and restored the susceptibility of PA1RG to phage PaP1 infection. While wzy mutation did not affect bacterial growth, mutant PA1RG exhibited decreased biofilm production, suggesting a fitness cost of PA1 associated with resistance of phage PaP1 predation. This study uncovered the mechanism responsible for PA1RG resistance to phage PaP1 via wzy mutation and revealed the role of phages in regulating bacterial behavior.
Standardized Radiation Shield Design Method: 2005 HZETRN

Research committed by the Langley Research Center through 1995 resulting in the HZETRN code provides the current basis for shield design methods according to NASA STD-3000 (2005). With this new prominence, the database, basic numerical procedures, and algorithms are being re-examined with new methods of verification and validation being implemented to capture a well defined algorithm for engineering design processes to be used in this early development phase of the Bush initiative. This process provides the methodology to transform the 1995 HZETRN research code into the 2005 HZETRN engineering code to be available for these early design processes. In this paper, we will review the basic derivations including new corrections to the codes to insure improved numerical stability and provide benchmarks for code verification.
Quantification of uncertainties in conifer sap flow measured with the thermal dissipation method.

Trees play a key role in the global hydrological cycle and measurements performed with the thermal dissipation method (TDM) have been crucial in providing whole-tree water-use estimates. Yet, different data processing to calculate whole-tree water use encapsulates uncertainties that have not been systematically assessed. We quantified uncertainties in conifer sap flux density (Fd ) and stand water use caused by commonly applied methods for deriving zero-flow conditions, dampening and sensor calibration. Their contribution has been assessed using a stem segment calibration experiment and 4 yr of TDM measurements in Picea abies and Larix decidua growing in contrasting environments. Uncertainties were then projected on TDM data from different conifers across the northern hemisphere. Commonly applied methods mostly underestimated absolute Fd . Lacking a site- and species-specific calibrations reduced our stand water-use measurements by 37% and induced uncertainty in northern hemisphere Fd . Additionally, although the interdaily variability was maintained, disregarding dampening and/or applying zero-flow conditions that ignored night-time water use reduced the correlation between environment and Fd . The presented ensemble of calibration curves and proposed dampening correction, together with the systematic quantification of data-processing uncertainties, provide crucial steps in improving whole-tree water-use estimates across spatial and temporal scales.
Waveform Optimization for Target Estimation by Cognitive Radar with Multiple Antennas

A new scheme based on Kalman filtering to optimize the waveforms of an adaptive multi-antenna radar system for target impulse response (TIR) estimation is presented. This work aims to improve the performance of TIR estimation by making use of the temporal correlation between successive received signals, and minimize the mean square error (MSE) of TIR estimation. The waveform design approach is based upon constant learning from the target feature at the receiver. Under the multiple antennas scenario, a dynamic feedback loop control system is established to real-time monitor the change in the target features extracted form received signals. The transmitter adapts its transmitted waveform to suit the time-invariant environment. Finally, the simulation results show that, as compared with the waveform design method based on the MAP criterion, the proposed waveform design algorithm is able to improve the performance of TIR estimation for extended targets with multiple iterations, and has a relatively lower level of complexity.
Musical Rendering of Mathematical Objects

This project explored methods of applying mathematics to the generation of music, and the methods for analysing music with mathematics. Music was generated randomly using Markov Chains, with specific start nodes, end nodes, and lengths. We applied specific transition probabilities and were able to generate random melodies with consistent and similar structures. Music was also generated deterministically using a binary operation across pitch patterns called composition. We proved that the composition operation is associative. Green’s relations, a set of equivalence relations that describe how a binary operation acts in a semigroup, were scrutinized. Finally, the project has added to a software suite which produces and plays melodies utilizing these methods.
. cerevisiae mRNA in ASH 1 localization of A nucleoporin , Nup 60 p , affects the nuclear and cytoplasmic Material Supplemental

The biogenesis of a localization-competent mRNP begins in the nucleus. It is thought that the coordinated action of nuclear and cytoplasmic components of the localization machinery is required for the efficient export and subsequent subcellular localization of these mRNAs in the cytoplasm. Using quantitative poly(A) and transcript-specific fluorescent in situ hybridization, we analyzed different nonessential nucleoporins and nuclear pore-associated proteins for their potential role in mRNA export and localization. We found that Nup60p, a nuclear pore protein located on the nucleoplasmic side of the nuclear pore complex, was required for the mRNA localization pathway. In a Dnup60 background, localized mRNAs were preferentially retained within the nucleus compared to nonlocalized transcripts. However, the export block was only partial and some transcripts could still reach the cytoplasm. Importantly, downstream processes were also affected. Localization of ASH1 and IST2 mRNAs to the bud was impaired in the Dnup60 background, suggesting that the assembly of a localization competent mRNP (‘‘locasome’’) was inhibited when NUP60 was deleted. These results demonstrate transcript specificity of a nuclear mRNA retention defect and identify a specific nucleoporin as a functional component of the localization pathway in budding yeast.
The role of habitat heterogeneity in the relationships between soil properties and earthworm assemblages: A case study in Pomerania (Northern Poland)

The vastness of the research on earthworm assemblages in agricultural lands focus on the comparison of agricultural treatments of different intensity. Consequently, spatial complexity of the landscape is less emphasised. Our study addresses this knowledge gap. The field study taken in West Pomeranian Lake District in Poland during four campaigns (spring and autumn) revealed that the mosaic of fields (MF) supported higher earthworm abundance than the similarly managed but homogeneous field (HF). Number and biomass of earthworm individuals both reflect the relationships with electrical conductivity, pH and in some situations also soil organic carbon and soil moisture effectively. We argue that autumn sampling is more preferable for biomonitoring.
Signal identification in ERP data by decorrelated Higher Criticism Thresholding

Event-related potentials (ERPs) are intensive recordings of electrical activity along the scalp time-locked to motor, sensory, or cognitive events. A main objective in ERP studies is to select (rare) time points at which (weak) ERP amplitudes (features) are significantly associated with experimental variable of interest. The Higher Criticism Thresholding (HCT), as an optimal signal detection procedure in the " rare-and-weak " paradigm, appears to be ideally suited for identifying ERP features. However, ERPs exhibit complex temporal dependence patterns violating the assumption under which signal identification can be achieved efficiently for HCT. This article first highlights this impact of dependence in terms of instability of signal estimation by HCT. A factor modeling for the covariance in HCT is then introduced to decorrelate test statistics and to restore stability in estimation. The detection boundary under factor-analytic dependence is derived and the phase diagram is correspondingly extended. Using simulations and a real data analysis example, the proposed method is shown to estimate more efficiently the support of signals compared with standard HCT and other HCT approaches based on a shrinkage estimation of the covariance matrix.
Evaluation of Antimicrobial Susceptibility by Staphylococcus aureus Isolated from the Nutrition Service of a Teaching Hospital

The bacteria Staphylococcus aureus is found in the nasal passages, mouth and skin of the human population and stands out among foodborne diseases. Some causes of foodborne illness are related with food, handlers, and utensils contamination in a hospital’s nutrition service. The aim of this study was to investigate the presence of S. aureus in food handlers, equipment, counter-tops and utensils of the nutrition service of a teaching hospital. Samples of the environment, hands and nasal mucosa of employees of a nutrition service were collected with two sterile swabs, in 2016, March and June. A total of 134 samples were obtained, which were submitted to characterization tests Biochemistry and morphotinorial (gram staining, catalase and coagulase tests in tube), phenotypic evaluation by drug diffusion technique and D-test approach, and the biofilm phenotype characterization by culture on Congo Red Agar. Results showed high rates of S. aureus colonization, mainly in the kitchen, high frequency of antimicrobial resistance, especially erythromycin and the presence of multi-resistant microorganisms. Large number of positive samples was also found for biofilm production, with totality for the samples of handlers. We highlight the relevance of the data in virtue of the serious consequences and risks that can be triggered in the hospital environment.
Analysis as an Approximation to Gaussian Ordination

Canonical Correspondence Analysis is an approximation to maximum likelihood estimation for Gaussian ordination under certain restrictions of the ordination model (Ter Braak, 1987b). Species tolerances must :t>e equal, and species maxima must be equal or at least indepe11dent of the location of the optima. These assumptions are often violated in practice. This paper develops graphical displays to explore how well species abundances approximate Gaussian curves along the derived environmental axes. As well, a simulation study was performed to determine how well Canonical Correspondence Analysis recovered the true axes when the Gaussian model for species abundance is correct, but the assumptions about the tolerances, maxima and location of optima are violated. The methods were applied to an analysis of an observational study conducted on a fen in the Black Hills of South Dakota.
Traditional test administration and proactive interference undermine visual-spatial working memory performance in schizophrenia-spectrum disorders

ABSTRACT Introduction Working-memory (WM) is a core cognitive deficit among individuals with Schizophrenia Spectrum Disorders (SSD). However, the underlying cognitive mechanisms of this deficit are less known. This study applies a modified version of the Corsi Block Test to investigate the role of proactive interference in visuospatial WM (VSWM) impairment in SSD. Methods Healthy and SSD participants completed a modified version of the Corsi Block Test involving both high (typical ascending set size from 4 to 7 items) and low (descending set size from 7 to 4 items) proactive interference conditions. Results The results confirmed that the SSD group performed worse overall relative to a healthy comparison group. More importantly, the SSD group demonstrated greater VSWM scores under low (Descending) versus high (Ascending) proactive interference; this pattern is opposite to that of healthy participants. Conclusions This differential pattern of performance supports that proactive interference associated with the traditional administration format contributes to VSWM impairment in SSD. Further research investigating associated neurocognitive mechanisms and the contribution of proactive interference across other domains of cognition in SSD is warranted.
Cyber-physical manufacturing system Development: A test-driven design method and exploratory case study

Today, manufacturing engineering companies still struggle developing cyber-physical solutions. Studies suggest that inappropriate engineering methods dominated by mechanical design decisions and incompatible engineering tool landscapes are key problems that lead to isolated and potentially inconsistent specifications. To overcome the current situation, in this paper we propose a test-driven approach to cyber-physical manufacturing system design based on an integrated modeling technique and engineering tool called MACON. Then, we explore the applicability and potential benefits of the approach for an industry-close example. Therefore, we analyze empirical data about the development process collected during tool usage. The data indicates that test-driven development is applicable in principle to the cyber-physical manufacturing systems domain resulting both in early test specification at various levels of the component architecture as well as in early identification of design flaws.
First record and new species of Tortopsis Molineri, 2010 (Ephemeroptera, Polymitarcyidae) from Brazil

A new species of the recently erected genus Tortopsis is described from males and females imagos collected in Macae river, Rio de Janeiro State. Tortopsis canum sp. nov. can be recognized by the color pattern of the head and pronotum, strongly shaded with black in both sexes, male genitalia with parastyli long and straight and female parastyli receptor “C” shaped, with receptors large, occupying nearly all extension of sternum VIII. This new species represents the first record of the genus Tortopsis in Brazil.
Comparison of Larval and Adult Stages of Chthamalus Dalli and Chthamalus Fissus (Cirripedia: Thoracica)

ABSTRACT Adult and larval forms of Chthamalus dalli and Chthamalus fissus are compared and distinguishing characteristics described. Adult forms of these species differ in malate dehydrogenase enzyme allozymes, in the setae of the second cirrus, and in shell characteristics. Larval forms are morphologically identical, although larvae cultured from adults collected at Monterey Bay differ in size at naupliar stages I-III and at the cyprid stage.
Isolation of Cinnamic Acid Derivatives from the Bulbs of Allium tripedale

Background: Allium genus with 750 species is the most diverse genus in the Amaryllidaceae family. Historically, Allium species have been used as medicinal plants, especially for prevention and treatment of cardiovascular diseases and considered as valuable sources of phytonutrients. Phytochemical investigation of Allium tripedale, locally called “Anashq,” which is an edible plant of the “Zagros” region (west of Iran) was conducted in the present study. Materials and Methods: Air-dried bulbs of the plant were extracted in a four-step extraction method with increasing polarity using hexane, chloroform, chloroform–methanol (9:1), and methanol. Chloroform-methanol (9:1) extract was fractionated by medium-pressure liquid chromatography on a RP-18 column using a linear gradient solvent system of H2O to MeOH. Phenolic-rich fractions were subjected to the final isolation and purification of the constituents by reversed-phase high-performance liquid chromatography method. Structure elucidation of the compounds was performed through comprehensive methods including 1D-and 2D-NMR and mass spectroscopy. Results: Two cinnamic acid derivatives were isolated from the bulbs of A. tripedale; using spectroscopic methods, their chemical structures were determined as 6,7-dimethoxy N-trans-caffeoyltyramine (1) and N-trans-feruloyltyramine (2). Conclusion: Cinnamic acid derivatives are pharmacologically active phenolic compounds, which have been isolated from different Allium species. Isolation of these compounds from A. tripedale is reported for the first time in this study and could be used as a chemical basis for explanation of the plant biological and pharmacological activities.
Comparison of a smartphone-based ECG recording system with a standard cardiac event monitor in the investigation of palpitations in children

Background The AliveCor (Kardia) monitor attaches to a smartphone and allows a single-lead ECG to be recorded during symptoms. In 2016, we introduced the use of this smartphone device for investigating palpitations, without syncope, in children. The aim of our study was to review our experience with the smartphone device, comparing it with our previous standard conventional approach to cardiac event monitoring using the Cardiocall monitor, which uses skin electrodes and is given for a finite period. Methods Over a period of 24 months, 80 smartphone monitors were issued and compared with the most recent 100 conventional event monitors. The number of ECG recordings received, arrhythmias documented, quality of ECG recordings and patient satisfaction were evaluated. Results Median patient age was 11 years in the smartphone monitor group compared with 10 years in the conventional group. Seventy-nine of 80 (98%) patients with a smartphone monitor sent an ECG recorded during symptoms, compared with 62/100 (62%) from the conventional group. A total of 836 ECG recordings were sent from the smartphone monitors compared with 752 from the conventional group. Eight per cent of ECG recordings in each group were of inadequate quality for analysis. Twenty of 80 (25%) patients with a smartphone monitor had documented tachyarrhythmia compared with 6/100 (6%) patients with the conventional monitor (p<0.001). On comparison with the conventional approach, the smartphone monitor outperformed with respect to diagnostic yield and patient satisfaction. Conclusions A smartphone-based event monitor allows simple, effective, long-term ECG event monitoring in children that is highly acceptable to the patient and parent.
A novel filter approach for efficient selection and small round blue-cell tumor cancer detection using microarray gene expression data

Feature selection is a vital task in machine learning and data mining to reduce the dimensionality of the data and also improves the classification performance of an algorithm in terms of high precision, low computational cost, and low vulnerability. Various many technologies have been successfully applied in the previous experimental studies for tumor detection. The foremost challenging task of gene selection method is extracting informative genes contribution in the classification from the DNA microarray datasets with lesser computational load. In this paper, we propose the conglomeration of the Kendall Correlation (KC) and Filter based Feature Selection (FS) method for better classification and prediction. We demonstrate the extensive comparison of the effect of Kendall Correlation with FS methods, using Relief-F, Joint Mutual Information (JMI), and Mutual Information based feature selection (MIFS), Conditional mutual information maximization (CMIM), and Max-relevance & Min-Redundancy (mRMR). To measure the classification performance of four diverse supervised classifiers K-Nearest Neighbor (KNN), Support Vector Machines (SVM), Naïve Bayes (NB), and Decision Tree (DT) have been used on small round blue cell tumors (SRBCT) dataset. The result demonstrates that Kendall Correlation in accumulation with mRMR performances better than other combinations.
Proposal submitted to the 2016 ARIA Annual Meeting An Extended Lee-Carter Model for Mortality Differential by Long-Term Care Status

This paper aims to propose a new methodology to forecast mortality rates of the longterm care (LTC) population with longevity risk. A major obstacle to devising such a method is lack of data on the number of deaths in LTC populations, which prevents us from using the conventional mortality model such as the Lee-Carter model. To overcome this difficulty, we propose an extended Lee-Carter model with a term representing mortality differential due to LTC status which does not require the data on the number of deaths in LTC populations. We apply the proposed model to the data from the Japanese long-term care insurance system. Our preliminary results shows that the proposed method captures the heterogeneity in the mortality rate between the LTC statuses properly. We plan to deliver a more detailed investigation at the conference.
Interest-Aware Content Discovery in Peer-to-Peer Social Networks

With the increasing popularity and rapid development of Online Social Networks (OSNs), OSNs not only bring fundamental changes to information and communication technologies, but also make an extensive and profound impact on all aspects of our social life. Efficient content discovery is a fundamental challenge for large-scale distributed OSNs. However, the similarity between social networks and online social networks leads us to believe that the existing social theories are useful for improving the performance of social content discovery in online social networks. In this article, we propose an interest-aware social-like peer-to-peer (IASLP) model for social content discovery in OSNs by mimicking ten different social theories and strategies. In the IASLP network, network nodes with similar interests can meet, help each other, and co-operate autonomously to identify useful contents. The presented model has been evaluated and simulated in a dynamic environment with an evolving network. The experimental results show that the recall of IASLP is 20% higher than the existing method SESD while the overhead is 10% lower. The IASLP can generate higher flexibility and adaptability and achieve better performance than the existing methods.