Miracle-dz/UniFAR-FTUs huggingface dataset:
The dihydropyridine-sensitive calcium channel subtype in cone photoreceptors

High-voltage activated Ca channels in tiger salamander cone photoreceptors were studied with nystatin-permeabilized patch recordings in 3 mM Ca2+ and 10 mM Ba2+. The majority of Ca channel current was dihydropyridine sensitive, suggesting a preponderance of L- type Ca channels. However, voltage-dependent, incomplete block (maximum 60%) by nifedipine (0.1-100 microM) was evident in recordings of cones in tissue slice. In isolated cones, where the block was more potent, nifedipine (0.1-10 microM) or nisoldipine (0.5-5 microM) still failed to eliminate completely the Ca channel current. Nisoldipine was equally effective in blocking Ca channel current elicited in the presence of 10 mM Ba2+ (76% block) or 3 mM Ca2+ (88% block). 15% of the Ba2+ current was reversibly blocked by omega-conotoxin GVIA (1 microM). After enhancement with 1 microM Bay K 8644, omega-conotoxin GVIA blocked a greater proportion (22%) of Ba2+ current than in control. After achieving partial block of the Ba2+ current with nifedipine, concomitant application of omega-conotoxin GVIA produced no further block. The P-type Ca channel blocker, omega-agatoxin IVA (200 nM), had variable and insignificant effects. The current persisting in the presence of these blockers could be eliminated with Cd2+ (100 microM). These results indicate that photoreceptors express an L-type Ca channel having a distinguishing pharmacological profile similar to the alpha 1D Ca channel subtype. The presence of additional Ca channel subtypes, resistant to the widely used L-, N-, and P-type Ca channel blockers, cannot, however, be ruled out.
Rapid Foreground Extraction Algorithm Based on Trimap

Foreground extraction is a very important operation in the image processing of the computers. Its purpose is to extract the area that human beings are interested in from the complicated background, which is beneficial for the subsequent operations such as background exchange, changes of the perspective effect and image mosaicing and so on. However, it is actually an ill-posed problem to determine whether a pixel belongs to the foreground. It is usually hard to acquire an accurate solution from the initial image. Therefore, the foreground extraction algorithm generally needs the user interaction. This paper has put forward a kind of rapid foreground extraction algorithm with the user interaction form of Trimap. On the one hand, our Trimap is quite simple. The users are able to understand the influence of Trimap on the productive resultants visually. On the other hand, with the help of Trimap, we are able to lessen the area that needs to be calculated in a large degree, which can rapidly finish the work of foreground extraction.
Page Segmentation for Historical Handwritten Document Images Using Color and Texture Features

In this paper we present a physical structure detection method for historical handwritten document images. We considered layout analysis as a pixel labeling problem. By classifying each pixel as either periphery, background, text block, or decoration, we achieve high quality segmentation without any assumption of specific topologies and shapes. Various color and texture features such as color variance, smoothness, Laplacian, Local Binary Patterns, and Gabor Dominant Orientation Histogram are used for classification. Some of these features have so far not got many attentions for document image layout analysis. By applying an Improved Fast Correlation-Based Filter feature selection algorithm, the redundant and irrelevant features are removed. Finally, the segmentation results are refined by a smoothing post-processing procedure. The proposed method is demonstrated by experiments conducted on three different historical handwritten document image datasets. Experiments show the benefit of combining various color and texture features for classification. The results also show the advantage of using a feature selection method to choose optimal feature subset. By applying the proposed method we achieve superior accuracy compared with earlier work on several datasets, e.g., We achieved 93% accuracy compared with 91% of the previous method on the Parzival dataset which contains about 100 million pixels.
DNA/RNA preparation for molecular detection.

BACKGROUND Effective upstream preparation of nucleic acid (NA) is important for molecular techniques that detect unique DNA or RNA sequences. The isolated NA should be extracted efficiently and purified away from inhibitors of a downstream molecular assay. CONTENT Many NA sample preparation techniques and commercial kits are available. Techniques for cell lysis and isolation or purification of NA were discovered in early NA characterization studies, evolved in the 20th century with molecular techniques, and still serve as the foundation for current methods. Advances in solid phase extraction methods with nonhazardous chemicals and automated systems have changed the way NA is prepared. Factors to consider when selecting NA preparation methods for molecular detection include lysis (from sources as diverse as human cells, viruses, bacterial spores, or protozoan oocysts), DNA vs RNA, sample background, appropriate preparation chemicals, and required detection limits. Methods are also selected on the basis of requirements for a particular application, such as sample volume or removal of inhibitors. Sometimes tradeoffs are made. SUMMARY Good automated and manual methods are available to effectively prepare NA for molecular detection in under an hour. Numerous systems are available for various applications, including techniques that are flexible for multiple sample types, are capable of processing large batches, can be performed in <10 min, or that can yield high-purity NA. When methods are selected using the most applicable combination of lysis isolation efficiency and concentration, NA preparation can be very effective, even for molecular detection of multiple targets from the same sample.
Evidence for Growth of Enterococci in Municipal Oxidation Ponds, Obtained Using Antibiotic Resistance Analysis

ABSTRACT The Christchurch wastewater treatment plant uses a series of six oxidation ponds to reduce the bacterial load of treated effluent before it is discharged into the local estuary. To ensure that this discharge does not adversely affect water quality in the receiving environment, local regulations specify maximum levels in the discharge for a number of parameters, including enterococci. Between 2001 and 2006, regulations required fewer than 300 enterococci per 100 ml in summer. During this period, the discharge intermittently exceeded this limit, with unexplained levels of enterococci of up to 180,000/100 ml. Characterization of these enterococci by antibiotic resistance analysis showed that enterococci sampled over 4 months had almost identical resistance profiles. In contrast, enterococci from raw sewage and wildfowl from around the oxidation ponds had a diverse range of antibiotic resistance profiles that could be distinguished from each other and also from those of enterococci from the discharge. The hypothesis of a clonal nature of the enterococci in the discharge was supported by molecular genotype analysis, suggesting that these bacteria may have replicated in the pond environment rather than being reflective of breakthrough in the sewage treatment process or the result of recent wildfowl inputs to the ponds. This study highlights the usefulness of antibiotic resistance analysis in identifying this phenomenon and is the first report of apparent replication of a specific type of enterococci in an oxidation pond environment.
Ieee Geoscience and Remote Sensing Letters Example-based Retrieval of Alike Land-cover Scenes from Nlcd2006 Database

—Query by image content (QBIC) tools are in demand in geospatial community because they enable exploration and mining of the rapidly increasing database of remotely sensed images. Accompanying the growth of the imagery database is the increase in the number of image-derived products, such as, for example, high resolution, large spatial extent maps of land cover/land use (LCLU). QBIC-like tools for exploration and mining of such products would significantly enhance their value. In this letter we present a method for retrieval of alike scenes from a category-valued geospatial database of which a LCLU map is a particular example. Alikeness between the two scenes is tantamount to similarity between their spatial patterns of class labels. Our method works on the principle of query-by-example, its input is a reference scene and its output is a similarity map indicating a degree of alikeness between a location on the map and the reference. The two core components of the method are: scene signature-an encapsulation of the scene pattern by means of probability distribution of class labels and the sizes of the patches they form, and scene similarity-a mutual information-based function that assigns a level of similarity between any two scenes based on their signatures. The method is described in detail and applied to the National Land Cover Dataset 2006 (NLCD2006). Two examples of queries on this dataset are presented and discussed. The applicability of the method to other datasets is discussed.
Sensitivity of the random demodulation framework to filter tolerances

The aim of the present paper is to demonstrate the impact of low-pass filter non-idealities on compressed sensing signal reconstruction in the random demodulator (RD) architecture. The random demodulator is a compressed sensing (CS) acquisition scheme capable of acquiring signals in continuous time. One of the main advantages of the system is the possibility to use off-the-shelf components to implement this sub-Nyquist framework. Low-pass filtering plays an important role in the RD analog acquisition process, which needs to be modeled carefully in the digital part of the compressive sensing reconstruction. Having a complete model of the analog front-end, CS algorithms conduct almost perfect reconstruction taking far less samples than for traditional Nyquist-rate sampling. This paper investigates reconstruction sensitivity to distortion in the impulse response of the low-pass filter caused by passive component value fluctuations. The authors simulate common CS recovery algorithms and show that the worst-case performance degradation due to filter component tolerances can be substantial, which requires special attention when designing reconstruction algorithms for RD.
Identifying major contents among web pages with search engine suggests by modeling topics

This paper addresses the problem of identifying irrelevant items from a small set of similar documents using Web search engine suggests. Specifically, we collected volumes of Web pages through Web search engines and inspected the page contents using topic models. Among each cluster of pages sharing the same topic indicated by the topic model, our technique discovers potential content organization in the current page cluster and identifies pages that are out of focus from that topic. The metrics in our approach mainly consist of search engine suggest frequency and inter-document similarity measures. The intuition is that Web pages collected via the same search queries are more likely to share similar contents. We verify this intuition by implementing a subtopic based document selection framework and making quantitative evaluation against human made labeled data sets. Our evaluation result reveals that suggest frequency analysis along with inter-document similarity measure is effective at filtering off-topic documents in small data sets with satisfactory performance.
Seven novel MLH1 and MSH2 germline mutations in hereditary nonpolyposis colorectal cancer

Hereditary nonpolyposis colorectal cancer (HNPCC) is the most frequent hereditary form of colorectal cancer and is caused by germline mutations in mismatch repair (MMR) genes. The majority of mutations occur in MLH1 and MSH2. We report hereby seven novel germline mutations in these two genes (five in MLH1 and two in MSH2). All mutations have been found in families fulfilling criteria of the Bethesda guidelines and four of which also fulfilled the Amsterdam criteria. We identified three insertions or deletions of 1 bp leading to premature stop codons (MLH1: c.341delC, c.1413‐1414insA; MSH2: c.1119delG) and three nonsense mutations (MLH1: c.67G>T [E23X], c.436C>T [Q146X]; MSH2: c.1857T>G [Y619X]). The corresponding tumors showed a high level of microsatellite instability (MSI‐H) and a complete loss of expression of the affected protein. In addition, a missense mutation in MLH1 was identified (c.1984A>C [T662P]). The respective tumor also showed a high level of microsatellite instability but a reduced, rather then lost, expression of the MLH1‐protein. This missense mutation was not found in 107 healthy control individuals and in 54 HNPCC patients. © 2001 Wiley‐Liss, Inc.
Comparative Genomic Analysis of Ten Streptococcus pneumoniae Temperate Bacteriophages

ABSTRACT Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage φSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them.
Decomposition Bounds for Marginal MAP

Marginal MAP inference involves making MAP predictions in systems defined with latent variables or missing information. It is significantly more difficult than pure marginalization and MAP tasks, for which a large class of efficient and convergent variational algorithms, such as dual decomposition, exist. In this work, we generalize dual decomposition to a generic power sum inference task, which includes marginal MAP, along with pure marginalization and MAP, as special cases. Our method is based on a block coordinate descent algorithm on a new convex decomposition bound, that is guaranteed to converge monotonically, and can be parallelized efficiently. We demonstrate our approach on marginal MAP queries defined on real-world problems from the UAI approximate inference challenge, showing that our framework is faster and more reliable than previous methods.
Campylobacter jejuni Survives within Epithelial Cells by Avoiding Delivery to Lysosomes

Campylobacter jejuni is one of the major causes of infectious diarrhea world-wide, although relatively little is know about its mechanisms of pathogenicity. This bacterium can gain entry into intestinal epithelial cells, which is thought to be important for its ability to persistently infect and cause disease. We found that C. jejuni is able to survive within intestinal epithelial cells. However, recovery of intracellular bacteria required pre-culturing under oxygen-limiting conditions, suggesting that C. jejuni undergoes significant physiological changes within the intracellular environment. We also found that in epithelial cells the C. jejuni–containing vacuole deviates from the canonical endocytic pathway immediately after a unique caveolae-dependent entry pathway, thus avoiding delivery into lysosomes. In contrast, in macrophages, C. jejuni is delivered to lysosomes and consequently is rapidly killed. Taken together, these studies indicate that C. jejuni has evolved specific adaptations to survive within host cells.
Technique of Stepwise Intracranial Decompression Combined with External Ventricular Drainage Catheters Improves the Prognosis of Acute Post-Traumatic Cerebral Hemispheric Brain Swelling Patients

Background Acute post-traumatic cerebral hemispheric brain swelling (ACHS) is a serious disorder that occurs after traumatic brain injury, and it often requires immediate treatment. The aim of our clinical study was to assess the effects of stepwise intracranial decompression combined with external ventricular drainage (EVD) catheters on the prognosis of ACHS patients. Methods A retrospective study was performed on 172 cases of severe craniocerebral trauma patients with ACHS. The patients were divided into two groups: unilateral stepwise standard large trauma craniectomy (S-SLTC) combined with EVD catheter implants (n = 86) and unilateral routine frontal temporal parietal SLTC (control group, n = 86). Result No significant differences in age, sex, or pre-operative Glasgow Coma Scale score were observed between groups (P < 0.05). There were no significant differences in the ipsilateral subdural effusion incidence rates between the S-SLTC + EVD treatment group and the routine SLTC group. However, the incidence rates of intraoperative acute encephalocele and contralateral epidural and subdural hematoma in the S-SLTC + EVD group were significantly lower than those in the SLTC group (17.4 and 3.5 vs. 37.2 and 23.3%, respectively). The mean intracranial pressure (ICP) values of patients in the S-SLTC + EVD group were also lower than those in the SLTC group at days 1 through 7 (P < 0.05). A positive neurological outcome [Glasgow Outcome Scale (GOS) score 4–5, 50.0%] and decreased mortality (15.1%) was observed in the S-SLTC + EVD group compared to the neurological outcome (GOS score 4–5, 33.8%; 36.0%) in the SLTC group (P < 0.05). Conclusion Our data suggest that S-SLTC + EVD is more effective for controlling ICP, improving neurological outcome, and decreasing mortality rate compared with routine SLTC.
Path Planning for Autonomous Mobile Robot using Potential Field

The popularity of autonomous mobile robots have been rapidly increasing due to their new emerging application areas, from room cleaning, tourist guidance to space explorations. However, the development of a satisfactory control algorithm that will enable the autonomous mobile robots to navigate safely especially in dynamic environments is still an open research problem. In this paper, a newly proposed potential field based control method is implemented, analyzed, and improvements are suggested based on experimental results obtained from simulations. The experimental results are presented to show the effectiveness of the behavior-based control using the proposed potential field generation technique.
Detection and Removal of Bad Smells instantly using a InsRefactor

Software refactoring is one of the essential techniques which are used to improve the software quality without affecting any of the external functionality of the software. There were numerous of software refactoring tools and code smells detection tools which are to be automatic or semi automatic. Most of these tools were human driven, so Software refactoring depends on developers' spontaneity. Due to little experience in software refactoring this may cause poor software quality and delays in refactoring. For this, we have proposed a framework called Instant Refactoring by Monitor framework using Ins Refactor which helps the inexperienced software engineers to do more refactoring quickly. Source code are instantaneously analyzed by the Monitor, if changes occur and it to be a code smells (symbols of possible problem in the code which requires refactoring) then framework invokes smells detection tools which helps the programmer to resolve the bad smells instantly without delay in time. The proposed framework has been evaluated, implemented and compared with the human-driven refactoring tools.
Drift-Free Position Estimation of Periodic or Quasi-Periodic Motion Using Inertial Sensors

Position sensing with inertial sensors such as accelerometers and gyroscopes usually requires other aided sensors or prior knowledge of motion characteristics to remove position drift resulting from integration of acceleration or velocity so as to obtain accurate position estimation. A method based on analytical integration has previously been developed to obtain accurate position estimate of periodic or quasi-periodic motion from inertial sensors using prior knowledge of the motion but without using aided sensors. In this paper, a new method is proposed which employs linear filtering stage coupled with adaptive filtering stage to remove drift and attenuation. The prior knowledge of the motion the proposed method requires is only approximate band of frequencies of the motion. Existing adaptive filtering methods based on Fourier series such as weighted-frequency Fourier linear combiner (WFLC), and band-limited multiple Fourier linear combiner (BMFLC) are modified to combine with the proposed method. To validate and compare the performance of the proposed method with the method based on analytical integration, simulation study is performed using periodic signals as well as real physiological tremor data, and real-time experiments are conducted using an ADXL-203 accelerometer. Results demonstrate that the performance of the proposed method outperforms the existing analytical integration method.
A Novel Control Procedure for Single Axis Roll Forming

In flexible roll forming, the horizontal movable sheet steel can be formed by controlling the servo motor to drive the multi-pass vertical movable roll. Only when the longitudinal movable distance of the roll in every pass matches exactly the contours of the sheet steel in time and space, the designated cross-section shape can be formed. Controlling the servo motor by applying the configuration programming is a common approach to achieve roll motion, but will not be able or difficult to realize by the configuration programming for complex contour without the rules such as hyperbolic, or the molding product in asymmetric cross-section shape, however, there are two other approaches such as simplifying the curves and using similar shapes to fit the process. As for the complex non-symmetrical curvature shapes, this paper adopts the variable time-domain servo motion control method to form the sheet steel. Experiments show that the variable time-domain servo motor control is a good motion control method for the sheet steel forming in complex cross-section shape.