Miracle-dz/UniFAR-FTUs huggingface dataset:
Flow cytometric enumeration of DNA-stained oceanic planktonic protists

The aim of this study was to test the practicality of enumerating fixed, DNA-stained heterotrophic protists (H) and phototrophic protists (P) in contrasting regions of the Atlantic Ocean. Oceanic protists were enumerated using a standard flow cytometer (FACSort, BD) at an enhanced flow rate of up to 1.0 mL min–1 to increase numbers of counted cells. The enumeration error of protists decreased hyperbolically from 30–40 to 2000) of enumerated cells. H and P were discriminated using the extra red chlorophyll-derived plastidic fluorescence of the latter. The relationship between counts of stained and unstained fixed and unfixed P was statistically close to 1:1, confirming the accuracy of stained protist counting by flow cytometry and adequate discrimination of P from H cells. The estimated average abundance of H in the surface mixed layer of the southern and northern oligotrophic gyres was remarkably similar, with 400 ± 140 and 450 ± 60 cells mL–1, respectively, adding further evidence to the suggestion that these regions are in steady state. In agreement with earlier studies in more productive aquatic environments, a significant correlation (correlation coefficient 0.84, P < 0.0001) was found between the H and the total bacterioplankton numbers, with an average ratio of 1300 prokaryotes to 1 H cell, suggesting a relatively constant trophic interaction between these two groups. This study demonstrates that flow cytometric enumeration of protists is 100 times faster compared with microscopy and, thus, represents a major improvement for quantifying protists in ocean waters, including oligotrophic gyres.
High-Resolution Inverse Synthetic Aperture Radar Imaging and Scaling With Sparse Aperture

In high-resolution radar imaging, the rotational motion of targets generally produces migration through resolution cells (MTRC) in inverse synthetic aperture radar (ISAR) images. Usually, it is a challenge to realize accurate MTRC correction on sparse aperture (SA) data, which tends to degrade the performance of translational motion compensation and SA-imaging. In this paper, we present a novel algorithm for high-resolution ISAR imaging and scaling from SA data, which effectively incorporates the translational motion phase error and MTRC corrections. In this algorithm, the ISAR image formation is converted into a sparsity-driven optimization via maximum a posterior (MAP) estimation, where the statistics of an ISAR image is modeled as complex Laplace distribution to provide a sparse prior. The translational motion phase error compensation and cross-range MTRC correction are modeled as joint range-invariant and range-variant phase error corrections in the range-compressed phase history domain. Our proposed imaging approach is performed by a two-step process: 1) the range-invariant and range-variant phase error estimations using a metric of minimum entropy are employed and solved by using a coordinate descent method to realize a coarse phase error correction. Meanwhile, the rotational motion can be obtained from the estimation of range-variant phase errors, which is used for ISAR scaling in the cross-range dimension; 2) under a two-dimensional (2-D) Fourier-based dictionary by involving the slant-range MTRC, joint MTRC-corrected ISAR imaging and accurate phase adjustment are realized by solving the sparsity-driven optimization with SA data, where the residual phase errors are treated as model error and removed to achieve a fine correction. Finally, some experiments based on simulated and measured data are performed to confirm the effectiveness of the proposed algorithm.
Physical and Genetic Map of the Pasteurella multocida A:1 Chromosome

ABSTRACT A physical and genetic map of the Pasteurella multocidaA:1 genome was generated by using the restriction enzymesApaI, CeuI, and NotI. The positions of 23 restriction sites and 32 genes, including 5 rrnoperons, were localized on the 2.35-Mbp single circular chromosome. This report presents the first genetic and physical map for this genus.
Touchdown of Flying Recording Head Sliders on Continuous and Patterned Media

We conduct three-dimensional transient finite-element analysis to study the contact behavior during touchdown detection by a thermal flying-height control (TFC) recording head on continuous and patterned elastic-plastic layered media. The heat generated during touchdown and the plastic strain of the media are calculated in the model. We investigated key factors such as the radius of curvature of the TFC protrusion, media compositions, bit-patterned media (BPM), and the effect of planarization. Our analysis shows that when subjected to the same TFC over-push, BPM is much more likely to result in plastic deformation than the continuous media. The temperature distribution of planarized BPM with <formula formulatype="inline"><tex Notation="TeX">${\hbox{SiO}}_{2}$</tex> </formula> as filling material exhibits a complex and distinctive pattern different from the one without planarization. More importantly, the maximum plastic strain of the planarized BPM is 50% larger than the one without planarization, which means that filling with <formula formulatype="inline"><tex Notation="TeX">${\hbox{SiO}}_{2}$</tex></formula> deteriorates the media's robustness to the touchdown probably due to the mismatch of thermal properties between <formula formulatype="inline"> <tex Notation="TeX">${\hbox{SiO}}_{2}$</tex></formula> and recording material. This suggests the filling material must be carefully chosen to avoid the excessive plastic strain.
Immunochemical identification of desmin in Torpedo postsynaptic membranes and at the rat neuromuscular junction

Preparations of acetylcholine receptor‐rich (AChR‐rich) postsynaptic membranes from electric tissue of electric rays often contain an Mr 55,000 protein (55kD protein) that has not been previously characterized. Using a monoclonal antibody (MAb 1403) against the 55kD protein from Torpedo californica and a pan‐specific, anti‐intermediate filament antibody (Pruss et al., 1981; Cell 27:419–428), we show that the 55kD protein has the properties expected of Torpedo desmin. By the electron microscope immunogold method applied to perfusion‐fixed electric tissue, MAb 1403 labeled only cytoplasmic filaments in the electroplax. These filaments were neither more concentrated nor arranged detectably differently in postsynaptic regions relative to nonpostsynaptic regions. The 55kD protein could also be fractionated away from isolated postsynaptic membranes by gradient centrifugation. The protein is thus a minor component of the postsynaptic membrane in situ and after isolation. On semithin cryosections of rat skeletal muscle, on the other hand, MAb 1403, which recognizes rat desmin but not rat vimentin, gave strong fluorescent labeling of the postsynaptic region, weaker labeling of the Z‐line, and still weaker labeling of the cell surface immediately surrounding extrajunctional nuclei. The pattern of postsynaptic labeling suggests that desmin, presumably in the form of intermediate filaments, occurs near the AChR‐rich crests of the junctional folds, but is particularly concentrated among and around the ends of the folds. Similar results were obtained with a second monoclonal antibody raised against authentic desmin. These results suggest that desmin intermediate filaments may have an important role in organization of the postsynaptic cytoplasm in rat muscle.
Adaptive Velocity PSO for Global Maximum Power Control of a PV Array Under Nonuniform Irradiation Conditions

Nonuniform irradiation conditions (NUIC) of a photovoltaic (PV) array pose a major challenge to optimal power utilization due to multiple power peaks (consisting of multiple local peaks and one global peak) in power–voltage (P–V) characteristics. This paper proposes an adaptive velocity particle swarm optimization (AVPSO) algorithm for tracking the global maximum of the multiple peak P–V characteristics. The AVPSO algorithm continuously adjusts individual particle's weight factor and cognitive acceleration coefficient, depending upon its distance from the global best position during the tracking process. The advantage of the adaptive weight factor is reduced power oscillations in the region of global best position, while adaptive cognitive factor prevents the particles from getting trapped in local minima. Thus, the adaptive nature of the particle's velocity improves the global maximum power point tracking (GMPPT) time and power yield. Another feature involves limiting the particle's velocity to avoid skipping intermediate peaks. Additionally, AVPSO also includes the ability to sort particle's positions in each iteration, which prevents large changes in the PV voltage, thereby reducing the control effort of a PV voltage controller. The effectiveness of the proposed GMPPT algorithm is investigated for static and dynamic performance under different NUIC patterns and mitigation of local minima trapping issues through analysis, simulations, and extensive hardware experiments.
Digital imaging fiber-optic trans-illumination, F-speed radiographic film and depth of approximal lesions.

BACKGROUND Detection of early carious lesions is a prerequisite to an optimal preventive and minimal surgical intervention strategy. The authors conducted this study to determine whether Digital Imaging Fiber-Optic Trans-Illumination (DIFOTI) (Electro-Optical Sciences, Irvington, N.Y.) could be useful in evaluating early approximal lesions and to compare radiographs produced with F-speed film with both histologic lesion depth and cavitation. METHODS The authors created artificial approximal lesions in vitro in extracted teeth over 14 weeks and imaged them using a "bitewing-like" view every two weeks with DIFOTI and F-speed radiographic film. At the end of the 14 weeks, the authors examined the lesions for surface cavitation using visual and tactile methods. They then thin-sectioned the lesions and subjected them to histologic analysis using polarized light microscopy (PLM). RESULTS DIFOTI was not able to measure the depth of a lesion in any of the samples. It was, however, able to show surface changes associated with early demineralization as early as two weeks. The depth of a lesion measured using F-speed radiographic film was not statistically different from the depth of a lesion measured with PLM histologic analysis (P > .05). None of the lesions showed any signs of surface cavitation after 14 weeks of demineralization. CONCLUSIONS AND CLINICAL IMPLICATIONS DIFOTI technology should not be used to decide between surgical or chemical treatment strategies based on lesion depth. We found that F-speed radiographic film was accurate in the approximating the depth of the lesion histologically. Ideally, the clinical decision whether to cut the tooth should be made based on cavitation rather than histologic lesion depth.
EASYPOP (version 1.7): a computer program for population genetics simulations.

If there are many programs for population genetics data analysis, less effort has been devoted to simulation software in this field. However, there are many situations where simulated population genetics datasets would be very useful. Simulations allow exploring situations too complex to be solved analytically. Indeed, outside very simple population genetics models, it is often extremely difficult to obtain the expectations for quantities such as gene correlation or effective size. Simulations also permit us to validate inferences drawn from empirical studies. They can be run with different estimated parameters and compared to the original dataset. It is also possible to build any null hypotheses against which inferences drawn from real data can be tested. Another nice feature of simulated datasets is the possibility of testing new software devoted to population genetics analysis under nontrivial conditions. In addition to their value in research, simulated data can be very useful for educational purposes. Various datasets can be generated and provided to students to train their skills in population genetics data analysis. All these applications prompted me to develop the software EASYPOP, an individual-based model that simulates neutral loci datasets under a very broad range of conditions.
Current density reconstruction from EEG based on a time varying nonlinear physiological model

A new electroencephalographic current density reconstruction method is introduced using a physiologically based nonlinear modeling that describes better the dynamic behavior of the neural activity. In addition, time-variant parameters are considered into the model to capture the dynamics for normal and pathological states measured from signals. The method is implemented by Unscented Kalman filtering approach. The performance of the new method is evaluated (in terms of mean square error) by application to simulated EEG data over several noise conditions, and a considerable improvement over linear estimation approaches is found.
Using preference-enriched faceted search for species identification

Species identification is essentially a decision-making process comprising steps in which the user makes a selection of characters, figures or photographs, or provides an input, that restricts other choices, until reaching one species. In some identification methods such decisions should have a specific order. Consequently, a wrong decision at the beginning of the process, could exclude a big set of options. To make this process more flexible and less vulnerable to wrong decisions, in this paper we investigate how a Preference-enriched Faceted Search PFS process can be used to aid the identification of species. We show how the proposed process covers and advances the existing methods and we report our experience from applying this process over data taken from FishBase. In the sequent, we elaborate on evaluation and we report the results of a task-based evaluation that shows that the PFS-based method can be used effectively by casual users.
SURVEILLANCE OF AVIAN INFLUENZA VIRUSES IN MIGRATORY BIRDS IN EGYPT, 2003–09

Migratory (particularly aquatic) birds are the major natural reservoirs for type A influenza viruses. However, their role in transmitting highly pathogenic avian influenza (HPAI) viruses is unclear. Egypt is a “funnel” zone of wild bird migration pathways from Central Asia and Europe to Eastern and Central Africa ending in South Africa. We sought to detect and isolate avian influenza viruses in migratory birds in Egypt. During September 2003–February 2009, the US Naval Medical Research Unit Number 3, Cairo, Egypt, in collaboration with the Egyptian Ministry of Environment, obtained cloacal swabs from 7,894 migratory birds captured or shot by hunters in different geographic areas in Egypt. Samples were processed by real-time reverse transcriptase PCR for detection of the influenza A matrix gene. Positive samples were processed for virus isolation in specific-pathogen-free embryonated eggs and isolates were subtyped by PCR and partial sequencing. Ninety-five species of birds were collected. Predominant species were Green-Winged Teal (Anas carolinensis; 32.0%, n=2,528), Northern Shoveler (Anas clypeata; 21.4%, n=1,686), and Northern Pintail (Anas acuta; 11.1%, n=877). Of the 7,894 samples, 745 (9.4%) were positive for the influenza A matrix gene (mainly from the above predominant species). Thirteen of the 745 (1.7%) were H5-positive by PCR (11 were low-pathogenic avian influenza and two were HPAI H5N1). The prevalences of influenza A was among regions were 10–15%, except in Middle Egypt (4%). Thirty-nine influenza isolates were obtained from PCR-positive samples. Seventeen subtypes of avian influenza viruses (including H5N1 and H7N7) were classified from 39 isolates using PCR and partial sequencing. Only one HPAI H5N1 was isolated in February 2006, from a wild resident Great Egret (Ardea alba). No major die-offs or sick migratory birds were detected during the study. We identified avian influenza virus subtypes not previously reported in Egypt. The HPAI H5N1 isolated or detected indicates that migratory birds may play a role in the dispersal of HPAI virus, but a detailed mechanism of this role needs to be elucidated.
Serum cytokine profiles of children with human enterovirus 71‐associated hand, foot, and mouth disease

Cytokine profiles may impact the pathogenicity and severity of hand, foot, and mouth disease caused by human enterovirus (HEV) 71. In 91 severe or mild HEV 71‐associated hand, foot, and mouth disease children, serum was collected between days 2 and 10 or day >10. Serum cytokines including Type 1 T helper (Th1) cytokines: interleukin (IL)‐2, interferon‐gamma (IFN‐γ), IL‐12, and IL‐18, Type 1 T helper (Th2) cytokines: IL‐4, IL‐10, IL‐13, proinflammatory cytokines: IL‐1α, IL‐1β, IL‐6, IL‐8, IL‐17, and tumor necrosis factor alpha (TNF‐α), were assessed during the early stage and recovery. In the patients with mild illness, the peaks of IL‐8 and IL‐10 were observed on day 6 and that of IL‐18 was on day 4. In the patients with severe illness, all cytokines spiked on day 3 and peaked on day 11. All cytokines except IL‐6, IL‐8, IL‐18, and TNF‐α were significantly correlated with immunoglobulin M levels by the end of the disease course. Cytokine profile variations between the patients with mild and severe illness may indicate prognosis and strain virulence, useful in clinical treatment of patients. J. Med. Virol. 86:1377–1385, 2014. © 2014 Wiley Periodicals, Inc.
QT Interval Shortening With Isavuconazole: In Vitro and In Vivo Effects on Cardiac Repolarization

The effects of isavuconazole (active moiety of isavuconazonium sulfate) on cardiac ion channels in vitro and cardiac repolarization clinically were assessed in a phase I, randomized, double‐blind study in healthy individuals who received isavuconazole (after 2‐day loading dose), at therapeutic or supratherapeutic doses daily for 11 days, moxifloxacin (400 mg q.d.), or placebo. A post‐hoc analysis of the phase III SECURE trial assessed effects on cardiac safety. L‐type Ca2+ channels were most sensitive to inhibition by isavuconazole. The 50% inhibitory concentrations for ion channels were higher than maximum serum concentrations of nonprotein‐bound isavuconazole in vivo. In the phase I study (n = 161), isavuconazole shortened the QT interval in a dose‐ and plasma concentration‐related manner. There were no serious treatment‐emergent adverse events; palpitations and tachycardia were observed in placebo and supratherapeutic isavuconazole groups; no cardiac safety signals were detected in the SECURE study (n = 257). Isavuconazole was associated with a shortened cardiac QT interval.
A NOVEL SYSTEM TO CLASSIFY RISK FACTORS TO PREDICT OUTCOMES AFTER SURGERY USING FUZZY METHODS

The aim of this study is to develop a system to recognize most important risk factors which can help to predict outcomes such as mortality or morbidity before performing the specific surgery by the integration a standard assessment checklist based on theoretical considerations and methodological aspects to evaluate the study quality of each publication, fuzzy analytic hierarchy process (FAHP) to order the risk factors, and fuzzy c-means clustering in order to classification. A fundamental idea of this study for applying FAHP was to consider scoring systems as experts to decision making and use of triangular fuzzy number (TFNs) to represent pairwise comparison of odd ratios in order to capture the vagueness. To illustrate the system implementation, the information of scoring systems developed to predict early mortality after CABG (Coronary artery bypass graft) is considered as input and the reasonable results are concluded. This implementation demonstrates the effectiveness and feasibility of the proposed system.
Patient expectations and experiences of nutrition care in general practice: Type II Diabetes as a case study

The role of Australian general practitioners (GPs) in providing nutrition care to patients for chronic disease management is currently receiving increased attention. However, limited literature explores the experiences of patients receiving nutrition care in this setting, as well as the nutrition-related expectations placed upon GPs by patients. This study explored the nutrition-related experiences, expectations and satisfaction of individuals diagnosed with Type II Diabetes under the care of an Australian GP. A cross-sectional retrospective online survey was developed using a review of relevant literature and practice guidelines for management of Type II diabetes in general practice to guide specifi c lines of enquiry. The survey was sent to all members of Diabetes Australia, Queensland with a registered author-address. Sixty-three survey items were clustered into fi ve groups, including general and diabetesrelated demographics; nutrition-related self effi cacy; perspectives on ideal GP nutrition care; and refl ections of previous GP nutrition care. Nine hundred and seventeen participants completed the survey (RR = 11%). Despite 81% of participants claiming that receiving nutrition care will be benefi cial to their diabetes management, only 49% of participants state that their GP has provided some nutrition care in relation to their diabetes. Of these participants, 86% are satisfi ed with the nutrition care received; however only 27% of participants believe that the nutrition care they have received from their GP has positively infl uenced their diabetes management. Patients report high levels of satisfaction with nutrition care received by GPs however varied perceptions regarding the effectiveness of this care.
A Recognition Algorithm for Electrocardiogram Based on Wavelet Transform and Feature Selection

In order to improve survival rate of patients suffering from sudden cardiac arrest, it is very important to develop high accurate and quick recognition algorithm for shockable electrocardiogram (ECG). In this paper, we propose a new ECG recognition algorithm based on some features which are derived by analyzing ECG signals via wavelet transform, and evaluate useful feature parameters by a feature selection approach.
Human Factors Issues on the Design of Telepresence Systems

The overall aim of this work is to provide some guidelines for the design of tele-presence systems from a human factors point of view. Developers of such human-machine systems face at least two major problems: There are hardly any standard input devices, and guiding design principles are almost missing. Further, most often telepresence systems should enable both a high degree of performance and a high sensation of presence, and yet the relationship between these two variables is still a subject of research. To cope with some of the problems, two experimental studies are presented. Each focuses on a different aspect of interface design, which is of widespread interest in the field of telepresence systems. The first is related to the control of multiple degrees of freedom and the second refers to bimanual input control. Beyond this work, a meta-analytical study is presented to describe the relationship between presence and performance more precisely. Certainly there are more issues that have to be studied (e.g., perceptual aspects) to guide the design of telepresence systems. To provide a framework for these and further human factor aspects, a computer based design guide is suggested at the end. This tool addresses system developers and assists in realizing new interfaces more effectively.