Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation-Tolerant Capture and Multiplex Detection of Nucleic Acids: Application to Detection of Microbes

ABSTRACT In contrast to ordinary PCRs, which have a limited multiplex capacity and often return false-negative results due to target variation or inhibition, our new detection strategy, VOCMA (variation-tolerant capture multiplex assay), allows variation-tolerant, target-specific capture and detection of many nucleic acids in one test. Here we demonstrate the use of a single-tube, dual-step amplification strategy that overcomes the usual limitations of PCR multiplexing, allowing at least a 22-plex format with retained sensitivity. Variation tolerance was achieved using long primers and probes designed to withstand variation at known sites and a judicious mix of degeneration and universal bases. We tested VOCMA in situations where enrichment from a large sample volume with high sensitivity and multiplexity is important (sepsis; streptococci, enterococci, and staphylococci, several enterobacteria, candida, and the most important antibiotic resistance genes) and where variation tolerance and high multiplexity is important (gastroenteritis; astrovirus, adenovirus, rotavirus, norovirus genogroups I and II, and sapovirus, as well as enteroviruses, which are not associated with gastroenteritis). Detection sensitivities of 10 to 1,000 copies per reaction were achieved for many targets. VOCMA is a highly multiplex, variation-tolerant, general purpose nucleic acid detection concept. It is a specific and sensitive method for simultaneous detection of nucleic acids from viruses, bacteria, fungi, and protozoa, as well as host nucleic acid, in the same test. It can be run on an ordinary PCR and a Luminex machine and is suitable for both clinical diagnoses and microbial surveillance.
Publication bias in qualitative research: what becomes of qualitative research presented at conferences?

Background: Less than half of studies presented at conferences remain unpublished two years later, and these studies differ systematically from those that are published. In particular, the unpublished studies are less likely to report statistically significant findings, and this introduces publication bias. This has been well documented for quantitative studies, but has never been explored in relation to qualitative research. Methods: We reviewed the abstracts of qualitative research presented at the 1998 (n = 110) and 1999 (n = 114) British Sociological Association (BSA) Medical Sociology meetings, and attempted to locate those studies in databases or by contacting authors. We also appraised the quality of reporting in each abstract. Results: We found an overall publication rate for these qualitative studies of 44.2%. This is nearly identical to the publication rate for quantitative research. The quality of reporting of study methods and findings in the abstract was positively related to the likelihood of publication. Conclusion: Qualitative research is as likely to remain unpublished as quantitative research. Moreover, non-publication appears to be related to the quality of reporting of methodological information in the original abstract, perhaps because this is a proxy for a study with clear objectives and clear findings. This suggests a mechanism by which “qualitative publication bias” might work: qualitative studies that do not show clear, or striking, or easily described findings may simply disappear from view. One implication of this is that, as with quantitative research, systematic reviews of qualitative studies may be biased if they rely only on published papers.
ICA Filtering Based Channel Estimation for Massive MIMO TDD Systems

A novel ICA-based channel estimation method for massive MIMO systems has been proposed in this letter. The proposed method first employs the systems' very large transmit antennas to obtain channel time-delay vectors through classical ICA schemes, and then employs the independent and slowly time-varying time-delay vectors to filter the pilot contamination in the least-squares channel estimate during the time-delay vectors' coherence interval, which is much longer than the channel's coherence interval. The proposed method can efficiently suppress the pilot contamination without increasing the system pilot overhead. The simulation results demonstrate the effectiveness of the proposed method.
MulTIS : A Gesture Based Interaction Model for iDTV

The existence of digital artefacts commonly used to interact with today’s television systems does not guarantee that those devices are adequate to mediate the use of Interactive Digital Television (iDTV) and its new types of applications. This is especially true in the context of developing countries where iDTV is a promise to cope with the digital divide. This technical report reviews the state of the art of physical artefacts of interaction with iDTV. In addition it presents a gesture based interaction model for iDTV that could inform the design of a new interaction language based on gesture and physical artefacts of interaction with iDTV.
The forgotten ureteric stent: what next?

The forgotten ureteric stent is a ‘never event’, because it is entirely preventable and conveys the potential for serious harm. Forgotten stents tend to encrust and encrusted stents are difficult to remove, frequently entailing significant complications [1]. Singh et al. [2], from a retrospective series of 19 forgotten ureteric stents, even reported one death as a direct consequence. Clearly, strategies for the prevention of this harm are essential.
Analysis and characterization of the integrated dielectric slab waveguide-wedge antenna using iterative mode-matching technique

ANALYSIS AND CHARACTERIZATION OF THE INTEGRATED DIELECTRIC SLAB WAVEGUIDE-WEDGE ANTENNA USING ITERATIVE MODE-MATCHING TECHNIQUE by Chairat Pinthong A rigorous solution for the TE and TM polarization to the dielectric wedge antenna fed by a slab waveguide of the same material is presented. The method of solution involves modeling the wedge as a sequence of step discontinuities and using an iterative procedure to track forward and backward partial wave fields, expressed as modal expansions, to obtain the rigorous field solution. Radiation patterns of directive gain are presented. All patterns smoothly decrease from a maximum in the endfire direction and exhibit very low side lobes. Longer length wedges are shown to produce higher directivity and smaller half-power beamwidths (HPBW). For TE polarization, wedges with larger values of dielectric constant yield smaller directivity and broader HPBW. In contrast, for TM polarization, wedges with larger values of dielectric constant have essentially same directivity and HPBW as wedges of smaller dielectric constant material. For TE or TM polarization, slender, gradually tapered wedges, yield a reflection coefficient of the guided surface wave on the feed guide at the base of the antenna that is very small. This indicates that tapered dielectric antennas produce low VSWR values. In addition, there appears to be no gain limitation with antenna length for these antennas. Frequency characteristics are examined to show that the dielectric wedge antenna is a broadband antenna. The method of solution is general and can be applied to a broad class of dielectric antennas having different geometries. ANALYSIS AND CHARACTERIZATION OF THE INTEGRATED DIELECTRIC SLAB WAVEGUIDE-WEDGE ANTENNA USING ITERATIVE MODE-MATCHING TECHNIQUE
Occipital network for W gure / ground organization

To study the cortical mechanism of Wgure/ ground categorization in the human brain, we employed fMRI and the temporal-asynchrony paradigm. This paradigm is able to eliminate any diVerential activation for local stimulus features, and thus to identify only global perceptual interactions. Strong segmentation of the image into diVerent spatial conWgurations was generated solely from temporal asynchronies between zones of homogeneous dynamic noise. The Wgure/ground conWguration was a single geometric Wgure enclosed in a larger surround region. In a control condition, the Wgure/ground organization was eliminated by segmenting the noise Weld into many identical temporal-asynchrony stripes. The manipulation of the type of perceptual organization triggered dramatic reorganization in the cortical activation pattern. The Wgure/ground conWguration generated suppression of the ground representation (limited to early retinotopic visual cortex, V1 and V2) and strong activation in the motion complex hMT+/ V5+; conversely, both responses were abolished when the Wgure/ground organization was eliminated. These results suggest that Wgure/ground processing is mediated by topdown suppression of the ground representation in the earliest visual areas V1/V2 through a signal arising in the motion complex. We propose a model of a recurrent cortical architecture incorporating suppressive feedback that operates in a topographic manner, forming a Wgure/ground categorization network distinct from that for “pure” scene segmentation and thus underlying the perceptual organization of dynamic scenes into cognitively relevant components.
High-crystallinity and large-grain CH3NH3PbI3 thin films for efficient TiO2 nanorod array perovskite solar cells

The high-crystallinity, large-grain and full-coverage CH3NH3PbI3 thin films are successfully prepared by converting the PbI2·dimethyl sulphoxide (DMSO) complex thin films at the optimum annealing temperature and time of 140°C and 10 min in the glove box with the relative humidity of 10–15%. The influence of the annealing temperature and time on the crystallinity, surface morphology, optical absorption of CH3NH3PbI3 thin films is systematically investigated and the photovoltaic performance of the corresponding TiO2 nanorod array perovskite solar cells is evaluated. The results reveal that the crystallinity of CH3NH3PbI3 thin films can be improved and their grain sizes gradually increase from 200–300 to 300–500 and 500–800 nm with the increase of the annealing temperature from 100 to 120 and 140°C. The TiO2 nanorod array perovskite solar cells with the optimum annealing temperature and time of 140°C and 10 min exhibit the best photoelectric conversion efficiency (PCE) of 16.11% and the average PCE of 15.62 ± 0.49%.
Firewall Rules Sorting Based on Markov Model

Firewall technique is a major measure to solve network security problems for enterprises. However, firewall efficiency is compromised by lots of tuple-comparisons. In this research, we established a Markov model for package matching statistics and prediction based on status investigation of rules matching in rule table. Then an optimization method which sorts the rules ranking is proposed, and the theoretical demonstration is provided as well. The experiment proved that this method (1) reduces the total operation of package matching; (2) improves the speed and effective of firewall filtering; and (3) adept to large rules set. The result also could be used to some package classification system.
Project Scheduling under Resource and Mode Identity Constraints. Part II: An Application to Audit-Staff Scheduling

When scheduling its audit-staff, the management of an auditing firm encompasses a number of different decisions which differ markedly in terms of organizational echelon involved, length of the planning horizon and the planning periods, degree of aggregation of the audit tasks, degree of detail of the required information, and decision objective. We outline an hierarchical planning approach for the audit-staff scheduling problem and demonstrate how the first level can be expressed in terms of the MIRCPSP, which has been presented in Part I of this paper. For solving this problem, we also demonstrate how the solution approach RAMSES, also presented in Part I of this paper, can be adapted to it. We provide a number of different priority rules which can be employed alternatively. The results of an extensive computational study indicate that RAMSES is capable of producing "good" solutions in neglectable amounts of time.
A STUDY OF THE STRUCTURE AND DISTRIBUTION OF THE NEXUS

Nexuses, that is, fusions of plasma membranes of adjacent cells, are described in mammalian smooth and cardiac muscle, median giant axon of earthworm, frog skin, and rat submandibular gland. In smooth muscle they usually occur where a process from one cell either meets a process of, or projects into a neighboring cell. On the other hand, in mammalian heart muscle and in earthworm giant axon the nexuses occur along the intercalated disc and intercellular segmental septa, respectively. Their occurrence between these excitable cells is correlated with propagation of action potentials by an electrical rather than chemical mechanism. Since the nexuses may offer pathways for electric current between cell interiors, it seems possible that they constitute a link in the structural basis for electrical transmission in these systems. In epithelia, nexuses usually appear as part of a terminal bar complex. This is true in the rat salivary gland studied here. In the epidermis of frog skin, nexuses are less numerous between the basilar columnar cells than between the subjacent squamous cells. The nexuses which occur in epithelia in frog skin and rat salivary gland are distributed as though to provide seals against electrochemical backleaks and sites of chemical exchange between cell interiors.
DR-11. DEVELOPMENT OF BIOCOMPATIBLE GLASS SUBSTRATE WITH SURFACE NANOTOPOGRAPHY

The wide application of nanomaterials allows us to reconsider common methods in various fields of science. Thus, in biology science, both submolecular and molecular interactions play a major role in cell processes and nanomaterials have great potential of application due to their selectivity in cellular mechanisms [1]. For example, it is possible to control both the cell-cell interaction and the cell-substrate interaction by iron oxide magnetic nanoparticles (MNPs), defining the cell fate [2]. Besides MNPs exhibit unique magnetic properties that increase controllability in the development and the usage of biocompatible glass substrate [3]. In this study, we introduce the method of coating of the glass surface by magnetic nanoparticles. The nanoparticles were synthesized by the method of chemical co-precipitation of iron salts in aqueous solution. Cytotoxicity of MNPs at concentrations of 24–360 g/well was measured by colorimetric assays (MTT-assay and resazurin redaction assay) on Human skin fibroblasts (HSF) in 96-well plate after 24 hours of exposure. Magnetic nanoparticles were characterized by atomic-force microscopy (AFM), DLS technique and hyperspectral imaging. Modification of the glass surface was based on the principle of self-assembly of nanoparticles. The surface nanotopography of substrate was examined by AFM and dark-field microscopy. Morphology changes of cells were observed with confocal and bright-field microscopy. DLS results showed that size and zeta-potential of MNPs was 141,7 ±2,8 nm and –48 ±1,9 mV respectively. Spectral libraries of nanoparticles were collected by the method of hyperspectral imaging. Morphology of synthesized nanoparticles is spherical according to AFM images. The viability of cells increased up to 20 % at the highest concentration of nanoparticles (360 g/well) by results of colorimetric assays. Morphology of cells cultivated on the modified surface wasn’t significantly changed regarding the control group. The received results characterize MNPs as a biocompatible nanomaterial which allows us to plan further research in the field of the interaction of mammalian cells with modified surfaces.
Protocol analysis in intrusion detection using decision tree

Network based intrusion detection are the most deployed IDS. They frequently rely on signature matching detection method and focus on the security of low level network protocols. Because of the large number of false positives from one side, and the incapacity to detect some attack types from another side, IDS must allow more interest to the monitoring of application level protocols. We propose in this paper a combination of pattern matching and protocol analysis approaches. While the first method of detection relies on a multipattern matching strategy, the second one benefits from an efficient decision tree adaptive to the network traffic characteristics.
Churn prediction of mobile and online casual games using play log data

Internet-connected devices, especially mobile devices such as smartphones, have become widely accessible in the past decade. Interaction with such devices has evolved into frequent and short-duration usage, and this phenomenon has resulted in a pervasive popularity of casual games in the game sector. On the other hand, development of casual games has become easier than ever as a result of the advancement of development tools. With the resulting fierce competition, now both acquisition and retention of users are the prime concerns in the field. In this study, we focus on churn prediction of mobile and online casual games. While churn prediction and analysis can provide important insights and action cues on retention, its application using play log data has been primitive or very limited in the casual game area. Most of the existing methods cannot be applied to casual games because casual game players tend to churn very quickly and they do not pay periodic subscription fees. Therefore, we focus on the new players and formally define churn using observation period (OP) and churn prediction period (CP). Using the definition, we develop a standard churn analysis process for casual games. We cover essential topics such as pre-processing of raw data, feature engineering including feature analysis, churn prediction modeling using traditional machine learning algorithms (logistic regression, gradient boosting, and random forests) and two deep learning algorithms (CNN and LSTM), and sensitivity analysis for OP and CP. Play log data of three different casual games are considered by analyzing a total of 193,443 unique player records and 10,874,958 play log records. While the analysis results provide useful insights, the overall results indicate that a small number of well-chosen features used as performance metrics might be sufficient for making important action decisions and that OP and CP should be properly chosen depending on the analysis goal.
Bayes risk approximations using time overlap with an application to system combination

The computation of the Minimum Bayes Risk (MBR) decoding rule for word lattices needs approximations. We investigate a class of approximations where the Levenshtein alignment is approximated under the condition that competing lattice arcs overlap in time. The approximations have their origins in MBR decoding and in discriminative training. We develop modified versions and propose a new, conceptually extremely simple confusion network algorithm. The MBR decoding rule is extended to scope with several lattices, which enables us to apply all the investigated approximations to system combination. All approximations are tested on a Mandarin and on an English LVCSR task for a single system and for system combination. The new methods are competitive in error rate and show some advantages over the standard approaches to MBR decoding. Index Terms: speech recognition, minimum bayes risk, confusion network, system combination, discriminative training
Immunologic Response to Tumor Ablation with Irreversible Electroporation

Background Irreversible electroporation (IRE) is a promising technique for the focal treatment of pathologic tissues, which involves placing minimally invasive electrodes within the targeted region. However, the knowledge about the therapeutic efficacy and immune reactions in response to IRE remains in its infancy. Methods In this work, to detect whether tumor ablation with IRE could trigger the immunologic response, we developed an osteosarcoma rat model and applied IRE directly to ablate the tumor. In the experiment, 118 SD rats were randomized into 4 groups: the control, sham operation, surgical resection, and IRE groups. Another 28 rats without tumor cell implantation served as the normal non-tumor-bearing group. We analyzed the changes in T lymphocyte subsets, sIL-2R and IL-10 levels in the peripheral blood one day before operation, as well as at 1, 3, 7,14 and 21 days after the operation. Moreover, splenocytes were assayed for IFN-γ and IL-4 production using intracellular cytokine staining one day before the operation, as well as at 7 and 21 days after operation. Results We found that direct IRE completely ablated the tumor cells. A significant increase in peripheral lymphocytes, especially CD3+ and CD4+ cells, as well as an increased ratio of CD4+/CD8+ were detectable 7 days after operation in both the IRE and surgical resection groups. Compared with the surgical resection group, the IRE group exhibited a stronger cellular immune response. The sIL-2R level of the peripheral blood in the IRE group decreased with time and was significantly different from that in the surgical resection group. Moreover, ablation with IRE significantly increased the percentage of IFN-γ-positive splenocytes. Conclusion These findings indicated that IRE could not only locally destroy the tumor but also change the status of cellular immunity in osteosarcoma-bearing rats. This provides experimental evidence for the clinical application of IRE in osteosarcoma treatment.
No association between seniority of surgeon and postoperative recurrence of chronic subdural haematoma.

INTRODUCTION Neurosurgical trainees should achieve competency in chronic subdural haematoma (CSDH) drainage at an early stage in training. The effect of surgeon seniority on recurrence following surgical drainage of CSDH was examined. METHODS All CSDH cases performed at St George's Hospital in London between March 2009 and March 2012 were analysed. Recurrence was defined as clinical deterioration with computed tomography evidence of CSDH requiring reoperation within six months. The following risk factors were considered: seniority of primary and supervising surgeons, timing of surgery (working hours, outside working hours), patient related factors (age, antiplatelets, warfarin) and operative factors (general vs local anaesthesia, burr holes vs craniotomy, drain use). For recurrent cases, we examined the distance of the cranial opening from the thickest part of the CSDH. RESULTS A total of 239 patients (median age: 79 years, range: 33-98 years) had 275 CSDH drainage operations. The overall recurrence rate was 13.1%. The median time between the initial procedure and reoperation was 16 days (range: 1-161 days). The only statistically significant risk factor for recurrence was antiplatelets (odds ratio: 2.62, 95% confidence interval: 1.13-6.10, p<0.05). Warfarin, grade of surgeon, timing of surgery, type of anaesthesia, type of operation and use of drains were not significant risk factors. In 26% of recurrent CSDH cases, the burr holes or craniotomy flaps were placed with borderline accuracy. CONCLUSIONS CSDH drainage is a suitable case for neurosurgical trainees to perform without increasing the chance of recurrence.
TRAMP

Though partially automated, developing schema mappings remains a complex and potentially error-prone task. In this paper, we present TRAMP (TRAnsformation Mapping Provenance), an extensive suite of tools supporting the debugging and tracing of schema mappings and transformation queries. TRAMP combines and extends data provenance with two novel notions, transformation provenance and mapping provenance, to explain the relationship between transformed data and those transformations and mappings that produced that data. In addition we provide query support for transformations, data, and all forms of provenance. We formally define transformation and mapping provenance, present an efficient implementation of both forms of provenance, and evaluate the resulting system through extensive experiments.