Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous Detection of Five Pathogens from Cerebrospinal Fluid Specimens Using Luminex Technology

Early diagnosis and treatment are crucial for the outcome of central nervous system (CNS) infections. In this study, we developed a multiplex PCR-Luminex assay for the simultaneous detection of five major pathogens, including Mycobacterium tuberculosis, Cryptococcus neoformans, Streptococcus pneumoniae, and herpes simplex virus types 1 and 2, which frequently cause CNS infections. Through the hybridization reaction between multiplex PCR-amplified targets and oligonucleotide “anti-TAG” sequences, we found that the PCR-Luminex assay could detect as low as 101–102 copies of synthetic pathogen DNAs. Furthermore, 163 cerebrospinal fluid (CSF) specimens from patients with suspected CNS infections were used to evaluate the efficiency of this multiplex PCR-Luminex method. Compared with Ziehl-Neelsen stain, this assay showed a high diagnostic accuracy for tuberculosis meningitis (sensitivity, 90.7% and specificity, 99.1%). For cryptococcal meningitis, the sensitivity and specificity were 92% and 97.1%, respectively, compared with the May Grunwald Giemsa (MGG) stain. For herpes simplex virus types 1 and 2 encephalitis, the sensitivities were 80.8% and 100%, and the specificities were 94.2% and 99%, respectively, compared with Enzyme Linked Immunosorbent Assay (ELISA) assays. Taken together, this multiplex PCR-Luminex assay showed potential efficiency for the simultaneous detection of five pathogens and may be a promising supplement to conventional methods for diagnosing CNS infections.
Galaxy Zoo : Dust lane early-type galaxies are tracers of recent, gas-rich minor mergers

We present the second of two papers concerning the origin and evolution of local early-type galaxies exhibiting dust features. We use optical and radio data to examine the nature of AGN activity in these objects, and compare these with carefully constructed control samples. We find that dust lane early-type galaxies are much more likely to host emission-line AGN than the control samples. Moreover, there is a strong correlation between radio and emission-line AGN activity in dust lane early-types, but not the control samples. Dust lane early-type galaxies show the same distribution of AGN properties in rich and poor environments, suggesting a similar triggering mechanism. By contrast, this is not the case for early-types with no dust features. These findings strongly suggest that dust lane early-type galaxies are starburst systems formed in gas-rich mergers. Further evidence in support of this scenario is provided by enhanced star formation and black hole accretion rates in these objects. We derive radio AGN ages and show that these are younger in dust lane galaxies than in the control sample. Dust lane early-types therefore represent an evolutionary stage between starbursting and quiescent galaxies. In these objects, the AGN has already been triggered but has not as yet completely destroyed the gas reservoir required for star formation.
Peranan Tpack terhadap Kemampuan Menyusun Perangkat Pembelajaran Calon Guru Fisika dalam Pembelajaran Post-pack

The aim of this research is to study the role of TPACK toward the lesson plan designing ability. Subjects of this research are 19 prospective physics teachers that rolled in P3F class that taught with the POST-PACK learning model. Research design that researcher applied is mixed method embedded experimental model. Results of analysis data show that TPACK has important role and has strong influence toward the lesson plan designing ability. Besides that, results of this research show that the TPACK and the lesson plan designing ability of prospective physics teachers increased because the intervention. Tujuan penelitian ini adalah untuk mengetahui peranan TPACK terhadap kemampuan menyusun perangkat pembelajaran. Subjek penelitian adalah sembilan belas calon guru fisika yang mengikuti perkuliahann P3F yang diajar dengan menggunakan model pembelajaran POST-PACK. Desain penelitian yang digunakan adalah mixed method embedded experimental model. Hasil analisis menunjukkan bahwa TPACK memiliki peranan yang penting dan memiliki pengaruh yang kuat terhadap kemampuan menyusun perangkat pembelajaran. Selain itu, hasil penelitian menunjukkan bahwa TPACK dan kemampuan menyusun perangkat pembelajaran calon guru fisika mengalami peningkatan dikarenakan perlakuan yang diberikan.
Conjecture of Nonlinear Filtering with Dependent Data ∗

We establish the innovations conjecture for a nonlinear filtering problem in which the signal to be estimated is conditioned by the observations. The approach uses only elementary stochastic analysis, together with a variant due to J.M. C. Clark of a theorem of Yamada and Watanabe on pathwise-uniqueness and strong solutions of stochastic differential equations.
The neural correlates of sex differences in emotional reactivity and emotion regulation

Sex differences in emotional responding have been repeatedly postulated but less consistently shown in empirical studies. Because emotional reactions are modulated by cognitive appraisal, sex differences in emotional responding might depend on differences in emotion regulation. In this study, we investigated sex differences in emotional reactivity and emotion regulation using a delayed cognitive reappraisal paradigm and measured whole‐brain BOLD signal in 17 men and 16 women. During fMRI, participants were instructed to increase, decrease, or maintain their emotional reactions evoked by negative pictures in terms of cognitive reappraisal. We analyzed BOLD responses to aversive compared to neutral pictures in the initial viewing phase and the effect of cognitive reappraisal in the subsequent regulation phase. Women showed enhanced amygdala responding to aversive stimuli in the initial viewing phase, together with increased activity in small clusters within the prefrontal cortex and the temporal cortex. During cognitively decreasing emotional reactions, women recruited parts of the orbitofrontal cortex, the anterior cingulate, and the dorsolateral prefrontal cortex to a lesser extent than men, while there was no sex effect on amygdala activity. In contrast, compared to women, men showed an increased recruitment of regulatory cortical areas during cognitively increasing initial emotional reactions, which was associated with an increase in amygdala activity. Clinical implications of these findings are discussed. Hum Brain Mapp, 2010. © 2009 Wiley‐Liss, Inc.
Current opportunities and challenges in microbial metagenome analysis—a bioinformatic perspective

Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large metagenomes and studying multiple metagenomes over time or space. Recently, a new type of holistic ecosystem study has emerged that seeks to combine metagenomics with biodiversity, meta-expression and contextual data. Such ‘ecosystems biology’ approaches bear the potential to not only advance our understanding of environmental microbes to a new level but also impose challenges due to increasing data complexities, in particular with respect to bioinformatic post-processing. This mini review aims to address selected opportunities and challenges of modern metagenomics from a bioinformatics perspective and hopefully will serve as a useful resource for microbial ecologists and bioinformaticians alike.
3D-LD: a Graphical Wavelet-based Tool for Analyzing Non-stationary and Scaling Processes

This paper proposes a novel graphical tool based on wavelets for studying the nonstationary and scaling properties of general signals, which we call the 3D-LD. We show that it allows to better study the timescale-dependent qualitative properties of non-stationary and scaling signals, compared to the classical techniques. Based on the 3D-LD, this paper analyzes several long network traffic traces spanning the years from 1993 to 2001, to understand the actual nature of scaling in TCP flows arrivals. The study of these traces shows that the TCP flows arrivals is a complex scaling process, which is highly non-stationarity from several point of views. Based on this analysis, we propose an analytical model for the dynamics of the TCP flows arrivals process, which takes into account all timescales ranging from seconds to hours. Finally, we show that simulating realistic TCP flows arrivals conforming to this model is feasible.
Capacity of optical reading, Part 1: Reading boundless error-free bits using a single photon

We show that nature imposes no fundamental upper limit to the number of information bits per expended photon that can, in principle, be read reliably when classical data is encoded in a medium that can only passively modulate the amplitude and phase of the probe light. We show that with a coherent-state (laser) source, an on-off (amplitude-modulation) pixel encoding, and shot-noise-limited direct detection (an overly-optimistic model for commercial CD/DVD drives), the highest photon information efficiency achievable in principle is about 0.5 bit per transmitted photon. We then show that a coherent-state probe can read unlimited bits per photon when the receiver is allowed to make joint (inseparable) measurements on the reflected light from a large block of phase-modulated memory pixels. Finally, we show an example of a spatially-entangled non-classical light probe and a receiver design---constructable using a single-photon source, beam splitters, and single-photon detectors---that can in principle read any number of error-free bits of information. The probe is a single photon prepared in a uniform coherent superposition of multiple orthogonal spatial modes, i.e., a W-state. The code, target, and joint-detection receiver complexity required by a coherent-state transmitter to achieve comparable photon efficiency performance is shown to be much higher in comparison to that required by the W-state transceiver.
Why Not Have Fun While Learning : Using Programming Games in Software Programming Education

In this research, we examine how computer-based programming games and contests could be used in the information technology education to increase the learning effectiveness for learners. We conduct a field study in a unique community of software developers who participated in IBM Robocode game. In our field study, we address the following research questions: (1) how do computer-based games influence the learner’s learning outcomes? Did the learner’s programming skills and knowledge improve after participating in the programming game? (2) Is the programming game appealing to learner groups with different ages, education backgrounds and skill levels? (3) What do the learners like most about the programming game? (4) What are the factors that influence the learner’s motivation to engage in the programming game? (5) What programming stages are of more intrinsic fun value and how to design the programming game accordingly? Through our case study, we found that (1) computer-based programming games and contests could significantly increase the intrinsic motivation of the learners across all learning levels, ages and education backgrounds. (2) These programming games could improve the learning effectiveness very efficiently. (3) Different stages of programming have various intrinsic fun values. Researchers and practitioners could design programming games and contests accordingly to improve the intrinsic fun factors.
Attribute-based vehicle search in crowded surveillance videos

We present a novel application for searching for vehicles in surveillance videos based on semantic attributes. At the interface, the user specifies a set of vehicle characteristics (such as color, direction of travel, speed, length, height, etc.) and the system automatically retrieves video events that match the provided description. A key differentiating aspect of our system is the ability to handle challenging urban conditions such as high volumes of activity and environmental factors. This is achieved through a novel multi-view vehicle detection approach which relies on what we call motionlet classifiers, i.e. classifiers that are learned with vehicle samples clustered in the motion configuration space. We employ massively parallel feature selection to learn compact and accurate motionlet detectors. Moreover, in order to deal with different vehicle types (buses, trucks, SUVs, cars), we learn the motionlet detectors in a shape-free appearance space, where all training samples are resized to the same aspect ratio, and then during test time the aspect ratio of the sliding window is changed to allow the detection of different vehicle types. Once a vehicle is detected and tracked over the video, fine-grained attributes are extracted and ingested into a database to allow future search queries such as "Show me all blue trucks larger than 7ft length traveling at high speed northbound last Saturday, from 2pm to 5pm".
The ice nucleation ability of one of the most abundant types of fungal spores found in the atmosphere

Abstract. Recent atmospheric measurements show that biological particles are a potentially important class of ice nuclei. Types of biological particles that may be good ice nuclei include bacteria, pollen and fungal spores. We studied the ice nucleation properties of water droplets containing fungal spores from the genus Cladosporium , one of the most abundant types of spores found in the atmosphere. For water droplets containing a Cladosporium spore surface area of ~217 μm 2 (equivalent to ~5 spores with average diameters of 3.2 μm ), 1% of the droplets froze by −28.5 °C and 10% froze by –30.1 °C. However, there was a strong dependence on freezing temperature with the spore surface area of Cladosporium within a given droplet. Mean freezing temperatures for droplets containing 1–5 spores are expected to be approximately −35.1 ± 2.3 °C (1σ S. D.). Atmospheric ice nucleation on spores of Cladosporium sp. , or other spores with similar surface properties, thus do not appear to explain recent atmospheric measurements showing that biological particles participate as atmospheric ice nuclei. The poor ice nucleation ability of Cladosporium sp. may be attributed to the surface which is coated with hydrophobins (a class of hydrophobic proteins that appear to be widespread in filamentous fungi). Given the ubiquity of hydrophobins on spore surfaces, the current study may be applicable to many fungal species of atmospheric importance.
Serum Circulating microRNA Profiling for Identification of Potential Breast Cancer Biomarkers

MicroRNAs (miRNAs) are a class of small, non-coding RNA molecules that can regulate gene expression, thereby affecting crucial processes in cancer development. miRNAs offer great potential as biomarkers for cancer detection because of their remarkable stability in blood and their characteristic expression in different diseases. We investigated whether quantitative RT-PCR miRNA profiling on serum could discriminate between breast cancer patients and healthy controls. We performed miRNA profiling on serum from breast cancer patients, followed by construction of ROC (Receiver Operating Characteristic) curves to determine the sensitivity and specificity of the assay. We found that seven miRNAs (miR-10b, miR-21, miR-125b, miR-145, miR-155 miR-191 and miR-382) had different expression patterns in serum of breast cancer patients compared to healthy controls. ROC curve analyses revealed that three serum miRNAs could be valuable biomarkers for distinguishing BC from normal controls. Additionally, a combination of ROC curve analyses of miR-145, miR-155 and miR-382 showed better sensitivity and specificity of our assay. miRNA profiling in serum has potential as a novel method for breast cancer detection in the Mexican population.
Two competing influences that may explain concomitant tumor resistance.

A second tumor inoculum is often inhibited in its growth by the presence in the recipient animal of an earlier implanted, growing tumor. The tumor resulting from the first inoculum may, paradoxically, continue to grow despite the simultaneous inhibition of the growth of the second inoculum, a phenomenon usually called "concomitant immunity. " Evidence now suggests that the phenomenon can be observed in the absence of any recognizable type of immune reaction and might often be named more appropriately "concomitant tumor resistance. " Consideration of a variety of probably related observations suggests that concomitant tumor resistance can best be explained by the competitive interaction of two opposing influences: a local diffusible, tumor-facilitating environment, produced by both tumor and normal tissues, that is counteracted by circulating inhibitors that are also produced by both tumor and by normal tissues. In an implanted small tumor, because of geometric considerations and diffusion, the action of the local facilitating environment is weak; in a larger tumor the local facilitating environment has a relatively greater influence and thus the larger tumor can continue to grow despite levels of circulating tumor inhibitors capable of inhibiting the smaller growth.
The Use of Documentary Research Methods in Social Research

Social research is an activity that is undertaken to find an answer or explanation regarding a particular social phenomenon. It involves systematic collection of data about such a social phenomenon for the purpose of finding and or understanding patterns and regularities in it. Social science departments in most universities require some of their final year students to undertake a small piece of social research, commonly referred to as a ‘research project’ in partial fulfilment of the requirements for the award of a degree. A social research project is normally small in scale and is intended to gauge the student’s ability to convert social research knowledge (acquired in class) into social research skills. Depending on how the student performs in the research project, the department will know whether the student is competent to undertake independent research in the future or to work with little supervision as a research assistant. To the majority of social scientists the idea of a research project is that it is something that is ‘original’ and for which ‘new data’ must be collected. To this end the social survey method, sometimes supplemented by in-depth interviews and participant observation, is selected as the method of choice, and very few social scientists ever think of re-analysing existing data sets (Hakim 1982).
The radio luminosity distribution of pulsars in 47 Tucanae

We have used the Australia Telescope Compact Array to seek the integrated radio flux from all the pulsars in the core of the globular cluster 47 Tucanae. We have detected an extended region of radio emission and have calibrated its flux against the flux distribution of the known pulsars in the cluster. We find the total 20-cm radio flux from the pulsars in the cluster to be S = 2.0 ± 0.3 mJy. This implies the lower limit to the radio luminosity distribution to be m/n L 1400 = 0.4 mJy kpc 2 and the size of the observable pulsar population to be N? 30.
A shunt active filter based on voltage detection for harmonic termination of a radial power distribution line

This paper is focused on a shunt active filter based on detection of harmonic voltages at the point of installation. The objective of the active filter is to attenuate harmonic propagation resulting from series/parallel resonance between capacitors for power factor correction and line inductors in a power distribution line. The active filter acts as a low resistor to the external circuit for harmonic frequencies, and it is installed on the end bus of the power distribution line, just like a 50 /spl Omega/ terminator installed on the end terminal of a signal transmission line. Therefore, the function of the active filter is referred to as "harmonic termination" in this paper. Experimental results obtained from a laboratory system rated at 200 V and 20 kW verify that the active filter for the purpose of harmonic termination has the capability of harmonic damping throughout the power distribution line.
Single Incision Laparoscopic Colectomy: Technical Aspects, Feasibility, and Expected Benefits

Background. This paper studied technical aspects and feasibility of single incision laparoscopic colectomy (SILC). Methods. Bibliographic search was carried out up to October 2009 including original articles, case reports, and technical notes. Assessed criteria were techniques, operative time, scar length, conversion, complications, and hospitalization duration. Results. The review analyzed seventeen SILCs by seven surgical teams. A single port system was used by four teams. No team used the same laparoscope. Two teams used two laparoscopes. All teams used curved instruments. SILC time was 116 ± 34 minutes. Final scar was longer than port incision (31 ± 7 versus 24 ± 8 mm; P = .036). No conversion was reported. The only complication was a bacteremia. Hospitalization was 5 ± 2 days. Conclusion. SILC is feasible. A single incision around the umbilical scar represents cosmetic progress. Comparative studies are needed to assess potential abdominal wall and recovery benefits to justify the increased cost of SILC.
The XMM-Newton Wide-Field Survey in the COSMOS Field. IV. X-Ray Spectral Properties of Active Galactic Nuclei

We present a detailed spectral analysis of pointlike X-ray sources in the XMM-Newton COSMOS field. Our sample of 135 sources only includes those that have more than 100 net counts in the 0.3-10 keV energy band and have been identified through optical spectroscopy. The majority of the sources are well described by a simple power-law model with either no absorption (76%) or a significant intrinsic, absorbing column (20%). The remaining ~4% of the sources require a more complex modeling by incorporating additional components to the power law. For sources with more than 180 net counts (bright sample), we allowed both the photon spectral index Γ and the equivalent hydrogen column NH to be free parameters. For fainter sources, we fix Γ to the average value and allow NH to vary. The mean spectral index of the 82 sources in the bright sample is = 2.06 ± 0.08, with an intrinsic dispersion of ~0.24. Each of these sources has fractional errors on the value of Γ below 20%. As expected, the distribution of intrinsic absorbing column densities is markedly different between AGNs with or without broad optical emission lines. We find within our sample four type 2 QSO candidates (LX > 1044 ergs s-1, NH > 1022 cm-2), with a spectral energy distribution well reproduced by a composite Seyfert 2 spectrum, that demonstrates the strength of the wide-field COSMOS XMM-Newton survey to detect these rare and underrepresented sources. In addition, we have identified a Compton-thick (NH > 1.5 × 1024 cm-2) AGN at z = 0.1248. Its X-ray spectrum is well fitted by a pure reflection model and a significant Fe Kα line at rest-frame energy of 6.4 keV.