Miracle-dz/UniFAR-FTUs huggingface dataset:
LAMPhimerus: A novel LAMP assay for detecting Amphimerus sp. DNA in human stool samples

Background Amphimeriasis is a fish-borne disease caused by the liver fluke Amphimerus spp. that has recently been reported as endemic in the tropical Pacific side of Ecuador with a high prevalence in humans and domestic animals. The diagnosis is based on the stool examination to identify parasite eggs, but it lacks sensitivity. Additionally, the morphology of the eggs may be confounded with other liver and intestinal flukes. No immunological or molecular methods have been developed to date. New diagnostic techniques for specific and sensitive detection of Amphimerus spp. DNA in clinical samples are needed. Methodology/Principal findings A LAMP targeting a sequence of the Amphimerus sp. internal transcribed spacer 2 region was designed. Amphimerus sp. DNA was obtained from adult worms recovered from animals and used to optimize the molecular assays. Conventional PCR was performed using outer primers F3-B3 to verify the proper amplification of the Amphimerus sp. DNA target sequence. LAMP was optimized using different reaction mixtures and temperatures, and it was finally set up as LAMPhimerus. The specificity and sensitivity of both PCR and LAMP were evaluated. The detection limit was 1 pg of genomic DNA. Field testing was done using 44 human stool samples collected from localities where fluke is endemic. Twenty-five samples were microscopy positive for Amphimerus sp. eggs detection. In molecular testing, PCR F3-B3 was ineffective when DNA from fecal samples was used. When testing all human stool samples included in our study, the diagnostic parameters for the sensitivity and specificity were calculated for our LAMPhimerus assay, which were 76.67% and 80.77%, respectively. Conclusions/Significance We have developed and evaluated, for the first time, a specific and sensitive LAMP assay for detecting Amphimerus sp. in human stool samples. The procedure has been named LAMPhimerus method and has the potential to be adapted for field diagnosis and disease surveillance in amphimeriasis-endemic areas. Future large-scale studies will assess the applicability of this novel LAMP assay.
Robust multicast beamforming using covariance channel state information

The problem of transmit beamforming design for multicast wireless system is considered in this paper. We focus on the robust long-term transmit beamforming design with only imperfect knowledge of the channel covariance from two view points: minimizing total transmission power with prescribed signal-to-noise ratio (SNR) constraints at the receivers and maximizing the minimum SNR to achieve the relative max-min fairness. Only infrequent feedback is required from the users in such an algorithm. Furthermore, the algorithm shows great tolerance of imperfect channel state information (CSI) on both transceiver sides. It is shown that we can formulate both of the optimizations as convex semidefinite programming (SDP) problems by applying semidefinite relaxation (SDR) techniques. Extensive simulation results are presented to corroborate the performance of our proposed design.
Photocuring by Infrared Irradiation Using Upconversion Emission

Infrared-to-visible upconversion emission was used for photocuring of a pentaerythritol tetraacrylate (PETA) by infrared laser irradiation to achieve local polymerization on an upconversion phosphor. Submillimeter-sized, cone-shaped and solid poly (PETA) was successfully formed on a Y2O3 compact doped with 5 mol% Er under 985 nm diode laser irradiation with about 900 mW power. By changing the irradiation time, it was found that the formation of the cone starts in seconds and takes minutes to form a millimeter-sized cone. The correlation between the irradiation time and the cone volume was linear in the seconds-to-minutes time region with 800-900 mW irradiation powers.
Computational intelligence in software cost estimation: an emerging paradigm

One of the key features for the failure of project estimation techniques is the selection of inappropriate estimation models. Further, noisy data poses a challenge to build accurate estimation models. Therefore, the software cost estimation (SCE) is a challenging problem that has attracted many researchers over the past few decades. In the recent times,the use of computational intelligence methodologies for software cost estimation have gained prominence. This paper reviews some of the commonly used computational intelligence (CI) techniques and analyzes their application in software cost estimation and outlines the emerging trends in this area
Caspartin and Calprismin, Two Proteins of the Shell Calcitic Prisms of the Mediterranean Fan Mussel Pinna nobilis*

We used the combination of preparative electrophoresis and immunological detection to isolate two new proteins from the shell calcitic prisms of Pinna nobilis, the Mediterranean fan mussel. The amino acid composition of these proteins was determined. Both proteins are soluble, intracrystalline, and acidic. The 38-kDa protein is glycosylated; the 17-kDa one is not. Ala, Asx, Thr, and Pro represent the dominant residues of the 38-kDa protein, named calprismin. An N-terminal sequence was obtained from calprismin. This sequence, which comprises a pattern of 4 cysteine residues, is not related to any known protein. The second protein, named caspartin, exhibits an unusual amino acid composition, since Asx constitutes by far the main amino acid residue. Preliminary sequencing surprisingly suggests that the first 75 N-terminal residues are all Asp. Caspartin self-aggregates spontaneously into multimers. In vitro tests show that it inhibits the precipitation of calcium carbonate. Furthermore, it strongly interferes with the growth of calcite crystals. A polyclonal antiserum raised against caspartin was used to localize this protein in the shell by immunogold. The immunolocalization demonstrates that caspartin is distributed within the prisms and makes a continuous film at the interface between the prisms and the surrounding insoluble sheets. Our finding emphasizes the prominent role of aspartic acid-rich proteins for the building of calcitic prisms among molluscs.
An Efficient Approach to Enhance Classifier and Cluster Ensembles Using Genetic algorithms for Mining Drifting Data Streams

Mining data streams is concerned with extracting knowledge structures represented in models and patterns in high-speed streams of information. It raises new problems for the data mining community in terms of how to mine continuous highspeed data items that you can only have one look. The increasing focus of applications that generate and receive data streams stimulates the need for online data stream analysis tools. Recently, mining data streams with concept drifts has become an important and challenging task for a wide range of applications such as target marketing, network intrusion detection, credit card fraud protection, etc. Clustering and classification ensemble learning is a frequently used tool for building prediction models from data streams, due to its fundamental nature of managing large volumes of stream data. These both are the tools which help in improving the performance of mining systems. In order to improve the accuracy and error rate of traditional ensemble models, we propose a new ensemble model which combines both classifiers and clusters together and utilizes genetic algorithms for mining data streams. The main reason for using genetic algorithms along with clustering and classification is its high ability to solve optimization.
Probing the Structure of the Nicotinic Acetylcholine Receptor Ion Channel with the Uncharged Photoactivable Compound [3H]Diazofluorene*

The uncharged photoactivable probe 2-[3H]diazofluorene ([3H]DAF) was used to examine structural changes in the Torpedo californica nicotinic acetylcholine receptor (AChR) ion channel induced by agonists. Photoincorporation of [3H]DAF into the AChR consisted of the following two components: a nonspecific component consistent with incorporation into residues situated at the lipid-protein interface, and a specific component, inhibitable by noncompetitive antagonists and localized to the M2 hydrophobic segments of AChR subunits. The nonspecific [3H]DAF incorporation was characterized in the M4 segment of each AChR subunit. The observed distribution and periodicity of labeled residues reinforce the conclusion that the M4 segments are organized as transmembrane α-helices with a common “face” of each helix in contact with lipid. Within the M2 segments, in the absence of agonist [3H]DAF specifically labeled homologous residues βVal-261 and δVal-269, with incorporation into δVal-269 at a 5-fold greater efficiency than into βVal-261. This observation, coupled with the lack of detectable incorporation into α-M2 including the homologous αVal-255, indicates that within the resting channel [3H]DAF is bound with its photoreactive diazo group oriented toward δVal-269. In the presence of agonist, there is an ∼90% reduction in the labeling of βVal-261 and δVal-269 accompanied by specific incorporation into residues (βLeu-257, βAla-258, δSer-262, and δLeu-265) situated 1 or 2 turns of an α-helix closer to the cytoplasmic end of the M2 segments. The results provide a further characterization of agonist-induced rearrangements of the M2 (ion channel) domain of the AChR.
Who's choosing whom? A sociological study of the specialty choices in a Danish context

Objectives: The purpose of this study was to investigate if habitus, the unconscious and embodied mental structures founded early in life, can contribute to our understanding of how individuals choose a medical specialty. Methods A qualitative approach was employed using standardized open-ended interviews. In the present research, sampling was purposive, with an aim to illuminating the study objective. A sample of six juniors and three senior doctors were recruited from gynecology and obstetrics, vascular surgery and general practice via a snowball method. The interview guide and the subsequent analysis were based on Bourdieu’s sociological theory. Results Three central themes emerged, labeled as “the use of distinctions and dichotomies”, “the shaping of habitus” and “consequences of the shaping of habitus”. These represent values and preferences developed through childhood education and experiences which may contribute to explaining specialty choices. Participants distinguished between specialties by referring to dichotomous characteristics of the specialty (such as sick/healthy patients; young/elderly patients; fine/coarse surgery). Conclusions Bourdieu’s theory is useful for broadening our understanding of specialty choice, as his central concept, habitus, was found to direct the choice of specialty and constrain the number of possible specialties for the individual doctor. Research is needed to better understand how various factors affect the specialty choices of medical school graduates.
Friction and Wear Performance of Titanium Alloys against Tungsten Carbide under Dry Sliding and Water Lubrication

The friction and wear properties of titanium alloys TC4, TC18, and TA19 against tungsten carbide under both dry sliding and water-lubricated conditions were investigated using a ball-on-flat sliding friction apparatus under a load of 3 N and at a sliding speed of 112 mm/s. These investigated titanium alloys were observed by scanning electron microscopy (SEM) and energy-dispersive spectrometry (EDS). The results indicated that the kinetic friction coefficients as a function of sliding time increased at the initial friction stage under dry conditions and vary within a small range under water-lubricated conditions. Furthermore, the coefficient of friction of the TA19/WC-Co tribopair was lower than that of both TC4/WC-Co and TC18/WC-Co tribopairs. However, under water-lubricated conditions, the friction coefficients and wear volume of both TC4/WC-Co and TA19/WC-Co tribopairs decreased obviously compared to that under dry conditions, and the abrasion resistance increased. On the other hand, the effect of water lubrication on the TC18/WC-Co tribopair was limited. The results showed that TC4, TC18, and TA19 alloys have different tribological behaviors and wear mechanisms when sliding against tungsten carbide under different friction conditions.
F eb 2 00 8 C-Functions in Lovelock Gravity

We present C-functions for static and spherically symmetric spacetimes in Lovelock gravity theories. These functions are monotonically increasing functions of the outward radial coordinate and aquire their minima when evaluated on the horizon. Unlike the case of Einstein gravity, where there is a single C-function, we find that this function is non-unique in the case of Lovelock gravity. We define two C-functions, which agree at the horizon giving the black hole entropy, and state the different energy conditions that must hold in order for these functions to satisfy the monotonicity condition. manber@physics.umass. edu kastor@physics.umass. edu
Hydrogen-bonded chains of rings in 1-(4-chloroanilinomethyl)-5-(4-chlorophenyl)-1,3,5-triazinane-2-thione and hydrogen-bonded sheets in 1-anilinomethyl-5-phenyl-1,3,5-triazinane-2-thione.

In 1-(4-chloroanilinomethyl)-5-(4-chlorophenyl)-1,3,5-triazinane-2-thione, C(16)H(16)Cl(2)N(4)S, there are two independent molecules in the asymmetric unit which form inversion dimers via two weak N-H.S hydrogen bonds. The dimers are then linked into C(9)C(14) chains by a C-H.S hydrogen bond and a C-H.Cl contact. In 1-(anilinomethyl)-5-phenyl-1,3,5-triazinane-2-thione, C(16)H(18)N(4)S, molecules are linked into complex sheets via a combination of N-H.S and C-H.pi hydrogen bonds.
Easy Navigation through Instructional Videos using Automatically Generated Table of Content

The amount of instructional videos available online, already in tens of thousands of hours, is growing steadily. A major bottleneck in their wide spread usage is the lack of tools for easy consumption of these videos. In this demonstration, we present MMToC: Multimodal Method for Table of Content, a technique that automatically generates a table of content for a given instructional video and enables text-book-like efficient navigation through the video. MMToC quantifies word saliency for visual words extracted from the slides and spoken words obtained from the lecture transcript. These saliency scores are combined using a dynamic programming based segmentation algorithm to identify likely points in the video where the topic has changed. MMToC is a web-based modular solution that can be used as a stand alone video navigation solution or can be integrated with any e-platform for multimedia content management. MMToC can be seen in action on a sample video at http://104.130. 241.45:8080/TopicTransitionV2/index.html.
Optimising networks for ultra-high definition video

The increase in real-time ultra-high definition video services is a challenging issue for current network infrastructures. The high bitrate traffic generated by ultra-high definition content reduces the effectiveness of current live video distribution systems. Transcoders and application layer multicasting (ALM) can reduce traffic in a video delivery system, but they are limited due to the static nature of their implementations. To overcome the restrictions of current static video delivery systems, an OpenFlow based migration system is proposed. This system enables an almost seamless migration of a transcoder or ALM node, while delivering real-time ultra-high definition content. Further to this, a novel heuristic algorithm is presented to optimise control of the migration events and destination. The combination of the migration system and heuristic algorithm provides an improved video delivery system, capable of migrating resources during operation with minimal disruption to clients. With the rise in popularity of consumer based live streaming, it is necessary to develop and improve architectures that can support these new types of applications. Current architectures introduce a large delay to video streams, which presents issues for certain applications. In order to overcome this, an improved infrastructure for delivering real-time streams is also presented. The proposed system uses OpenFlow within a content delivery network (CDN) architecture, in order to improve several aspects of current CDNs. Aside from the reduction in stream delay, other improvements include switch level multicasting to reduce duplicate traffic and smart load balancing for server resources. Furthermore, a novel max-flow algorithm is also presented. This algorithm aims to optimise traffic within a system such as the proposed OpenFlow CDN, with the focus on distributing traffic across the network, in order to reduce the probability of blocking.
Homogeneous Temporal Activity Patterns in a Large Online Communication Space

The many-to-many social communication activity on the popular technology-news website Slashdot has been studied. We have concentrated on the dynamics of message production without considering semantic relations and have found regular temporal patterns in the reaction time of the community to a news-post as well as in single user behavior. The statistics of these activities follow log-normal distributions. Daily and weekly oscillatory cycles, which cause slight variations of this simple behavior, are identified. The findings are remarkable since the distribution of the number of comments per users, which is also analyzed, indicates a great amount of heterogeneity in the community. The reader may find surprising that only two parameters, those of the log-normal law, allow a detailed description, or even prediction, of social many-to-many information exchange in this kind of popular public spaces.
Do Conservation Easements Reduce Land Prices? The Case of South Central Wisconsin

While theory strongly suggests that restricting development rights should reduce land prices, empirical evidence of this effect has been notoriously hard to obtain. Indeed, largely based on this difficulty a Congressional committee has recently recommended that tax benefits for such restrictions be severely curtailed. We collect data on 131 land transactions in South Central Wisconsin, including 19 cases of developmentrestricted parcels. When we use the whole sample to estimate the impact of conservation easements we replicate the results of Nickerson and Lynch (2001), finding a negative but statistically insignificant effect. However we then show that when the sample is appropriately restricted to a more homogenous group of land parcels, our ability to detect an effect increases dramatically. In particular, for vacant agricultural land we find a statistically significant negative impact of conservation easements that ranges up to 50% of land values.
On packetization of JPEG2000 code-streams in wireless channels

The JPEG2000 standard adopts an error-resilient structure to organize its code-stream. Meanwhile, this robust structure also provides potential optimization space for packetization algorithms. In this paper, we study the optimal packetization issue for JPEG2000 code-streams over wireless channels. We first discuss the best strategy for packetization hits from an individual code-block into channel packets. Then, we extend it to bits from a group of code-blocks. Experimental results indicate that our scheme is outperforming the normal method by significant margins.
Land cover monitoring using coarse resolution data series

* Corresponding author. Abstract – This study focuses on the use of coarse spatial resolution (CR, pixel size about 1 km) remote sensing data for land cover change detection and estimation. Since, in the presence of some changes, both the multitemporal class features and the pixel composition in terms of classes are unknown, the proposed algorithm is based on the iterative alternate estimation of each unknown variable: class features, and pixel composition. Final estimation of the pixel composition is constrained using a Markovian chain model, introducing the previous land cover map as a 'memory' term. This approach has been validated both using simulated data and actual data (SPOT/VGT and NOAA/AVHRR). The thematic application was the study of the evolution of an agricultural watershed during the last two decades.
Learning and using context on a humanoid robot using latent dirichlet allocation

In this work, we model context in terms of a set of concepts grounded in a robot's sensorimotor interactions with the environment. For this end, we treat context as a latent variable in Latent Dirichlet Allocation, which is widely used in computational linguistics for modeling topics in texts. The flexibility of our approach allows many-to-many relationships between objects and contexts, as well as between scenes and contexts. We use a concept web representation of the perceptions of the robot as a basis for context analysis. The detected contexts of the scene can be used for several cognitive problems. Our results demonstrate that the robot can use learned contexts to improve object recognition and planning.
Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners

Agrobacterium tumefaciens infects its plant hosts by a mechanism of horizontal gene transfer. This capability has led to its widespread use in artificial genetic transformation. In addition to DNA, the bacterium delivers an abundant ssDNA binding protein, VirE2, whose roles in the host include protection from cytoplasmic nucleases and adaptation for nuclear import. In Agrobacterium, VirE2 is bound to its acidic chaperone VirE1. When expressed in vitro in the absence of VirE1, VirE2 is prone to oligomerization and forms disordered filamentous aggregates. These filaments adopt an ordered solenoidal form in the presence of ssDNA, which was characterized previously by electron microscopy and three-dimensional image processing. VirE2 coexpressed in vitro with VirE1 forms a soluble heterodimer. VirE1 thus prevents VirE2 oligomerization and competes with its binding to ssDNA. We present here a crystal structure of VirE2 in complex with VirE1, showing that VirE2 is composed of two independent domains presenting a novel fold, joined by a flexible linker. Electrostatic interactions with VirE1 cement the two domains of VirE2 into a locked form. Comparison with the electron microscopy structure indicates that the VirE2 domains adopt different relative orientations. We suggest that the flexible linker between the domains enables VirE2 to accommodate its different binding partners.
Detecting Incomplete Learners in a Blended Learning Environment Among Japanese University Students

To examine the feasibility of identifying incomplete participants who had not eventually completed a course in a blended learning environment using current learning behavioral data, access log data of complete and incomplete participants were analyzed. There is a significant difference between the two sets, and the number of accesses correlates with the final test score. Discrimination analysis was conducted using several variables across the learning process, and the ratio of those taking part in online tests was significant. Discrimination performance improved in relation to the number of accesses. The estimation performance was determined for two disparate courses in order to detect incomplete participants.