Miracle-dz/UniFAR-FTUs huggingface dataset:
High aspect ratio electrodes for high yield electroporation of cells

HIGH ASPECT RATIO ELECTRODES FOR HIGH YIELD ELECTROPORATION OF CELLS by Anil B. Shrirao Electroporation is a widely used process in cell biology studies. It uses an electric field to create pores on the cell membrane in order to either insert exogenous molecules inside the cells or disrupt the cell membrane to kill the cells. Current micro-fluidic electroporation devices use the planar electrodes situated at the bottom of a microchannel. These planar electrodes i) require a high voltage and ii) generate a nonuniform electric field which result in low yield of the electroporation. The standard silicon microfabrication technologies are not suitable to fabricate non-planar electrodes required to increase the yield of electroporation. In this research, an electroporation device is fabricated with an array of five pairs of three dimensional (3D) electrodes situated along the sidewalls of a microchannel. These 3D electrodes are fabricated by filling the molten indium inside the chosen microchannels. The indium filling method allows the fabrication of microstructures with planar dimensions larger than ~30 μm regardless of their height, integrated into the PDMS device. The selective electroporation of fibroblast cells is successfully demonstrated using a fabricated device by applying a low voltage (1.67 V). The uniform electric field generated in cross sections of microchannel by 3D electrodes will avoid the limitations of planar electrodes by i) preventing cell death due to an excessive electric field and ii) preventing lack of electroporation due to a low electric field. As a result, these 3D electrodes should be capable of increasing the yield of electroporation. HIGH ASPECT RATIO ELECTRODES FOR HIGH YIELD ELECTROPORATION OF CELLS
A new robotic context-based object recognition algorithm for humanoid robots

Ihis paper proposes a new object recognition algorithm using robotic context information for humanoid robots. For more robust object recognition for less textured objects, we combine shape-based interest points and local appearance-based descriptors computed in a neighborhood around each detected interest point. The combination is used as a basic feature for matching, and candidate feature correspondences are first computed based on the k-nearest neighbor algorithm. Then, all possible pairs of features are considered in terms of geometric deformation. In order to deal with pairwise geometric relationship between features, the spectral matching algorithm with pairwise constraints is applied. In the spectral matching process, a new robotic context-based correspondence filtering method is combined to obtain improved feature matching with less false correspondences. Finally, the RANSAC-based refinement is carried out to remove outliers. Also, we propose a new assessment method to obtain the final decision to accept or reject the matching results based on an affine distortion measure between model features and the matched image features. Experimental results show that the proposed object recognition algorithm can robustly identity less texture objects.
Sparse Matrix Computations on Parallel Processor Arrays

This paper investigates the balancing of distributed compressed storage of large sparse matrices on a massively parallel computer. For fast computation of matrix–vector and matrix–matrix products on a rectangular processor array with efficient communications along its rows and columns it is required that the nonzero elements of each matrix row or column be distributed among the processors located within the same array row or column, respectively. Randomized packing algorithms are constructed with such properties, and it is proved that with high probability the algorithms produce well-balanced storage for sufficiently large matrices with bounded number of nonzeros in each row and column, but no other restrictions on structure. Then basic matrix–vector multiplication routines are described with fully parallel interprocessor communications and intraprocessor gather and scatter operations. Their efficiency isdemonstrated on the 16,384-processor MasPar computer.
Distributed Representations for Building Profiles of Users and Items from Text Reviews

In this paper, we propose an approach to learn distributed representations of users and items from text comments for recommendation systems. Traditional recommendation algorithms, e.g. collaborative filtering and matrix completion, are not designed to exploit the key information hidden in the text comments, while existing opinion mining methods do not provide direct support to recommendation systems with useful features on users and items. Our approach attempts to construct vectors to represent profiles of users and items under a unified framework to maximize word appearance likelihood. Then, the vector representations are used for a recommendation task in which we predict scores on unobserved user-item pairs without given texts. The recommendation-aware distributed representation approach is fully supported by effective and efficient learning algorithms over massive text archive. Our empirical evaluations on real datasets show that our system outperforms the state-of-the-art baseline systems.
Hybrid TCP-UDP transport for Web traffic

Most of the web traffic today uses the HyperText Transfer Protocol (HTTP), with Transmission Control Protocol (TCP) as the underlying transport protocol. Unfortunately, TCP is poorly suited for the short conversations that comprise a significant component of web traffic. The overhead of setting up and tearing down TCP state amortizes poorly for these small connections. Moreover, emerging modern web server systems employ HTTP redirection for server load-balancing and content distribution; such schemes require setting up (and tearing down) multiple TCP connections for servicing a single client request. We have designed and analyzed a hybrid scheme to address these issues. The scheme uses either TCP, or the User Datagram Protocol (UDP) as the underlying transport protocol for carrying web traffic. UDP is used for short transfers (including HTTP redirection), while TCP is used for all other transfers. In this manner, we avoid the extra TCP overhead for short connections, but still benefit from the reliable delivery and congestion control that TCP provides. We ran trace-based simulations to quantify the effects of various network parameters (i.e., packet loss rates) on the performance of the hybrid scheme. We observed performance gains exceeding 20-25% with HTTP/1.1-style persistent connections, and over 40-50% without persistent connections. These gains can be improved with further performance optimizations that we describe.
A novel flex sensor-based flexible smart garment for monitoring body postures

Posture monitoring and investigation in wearable technology play a significant role in the analysis of body postures. This study aims to develop a new flexible smart garment realized by stitching flex sensors at different joint positions for sensing flexion angles in static and kinematic motions. Calibration tests were conducted by systematically flexing wrist, elbow, and knee joints, respectively. A male subject then wore the developed flexible smart garment to sense different body postures. The measured data from flex sensors inside the smart garment exhibited immediate response after each joint movement of the male subject. The minimum measurement sensitivities of flex sensors mounted at the knee, elbow, and wrist was 0.94°, 0.8°, and 0.56°, respectively. Measured flexion angle changes were within 80°, 95°, and 140° ranges from knee, elbow, and wrist. Both stand and walk tests at a velocity of 4 km/h indicate that the flexion angles of three joint positions include wrist, elbow, and knee joints can be effectively monitored using the flex sensor–based smart garment. Flex sensor can be employed to monitor body joint movement and future to identify different postures of body joints in practice. The flexible smart garments cannot be washed.
Regeneration of Critical-Size Canine Calvarial Defect by Silica-Calcium Phosphate-Composite (SCPC) and Human Adipose Derived Stem Cells

Reconstruction of large maxillofacial bone defects remains challenging even with diverse current treatment modalities. Silica-calcium phosphate nano composite (SCPC) is a resorbable bioactive bone graft material with a strong stimulatory effect on osteogenic gene expression of osteoblasts and mineralized tissue formation. In a prospective experimental study we investigated the ability of SCPC scaffold seeded with human adipose derived stem cells (ADSCs) to regenerate bone in a critical-size canine calvarial defect. Porous SCPC discs were prepared by powder metallurgy method. ADSCs were isolated from human breast adipose tissue, expanded in vitro and differentiated along osteogenic lineage. Bilateral critical-sized defects, 2.5 cm in diameter each, were made in the calvaria of 12 adult dogs. One calvarial defect was filled by either SCPC disc alone (Group I) or SCPC disc seeded with 2.5 x106 osteoblast-like cells (Group II) while other defect was left empty (ungrafted). Bone tissue regeneration and graft material resorption was evaluated 3 and 6 months postoperative using CT and histology. Calvarial defects grafted with SCPC alone or SCPC-Cell construct were grossly repaired while control ungrafted defect did not repair. Microscopically the newly formed bone in the grafted defects was compact and integrated with the surrounding host tissues. Near complete resorption of the graft material was observed. Histomorphometric analysis demonstrated higher bone surface area and more graft material resorption in defects grafted with SCPC-cell hybrid compared to SCPC alone.
Markov Chain Analysis of the PageRank Problem

The PageRank is a notion used by search engines to reflect a popularity and importance of a page based on its citation ranking. Such ranking was first introduced in 1998 by Google search engine [4]. The PageRank of a page i reflects the importance of this page basing on: 1) how many pages link to i, and 2) how important are the pages that link to i. Since the web changes very fast, the PageRank has to be regularly updated. Such update is an intricate task due to the huge size of the World Wide Web. Consequently, the analysis of the PageRank has become a hot topic with vast literature ranging from the original paper by Brin and Page [4], to the latest preprints by specialists in Markov chains, linear algebra, numerical methods, information retrieval, operations research, and other fields [11]. In the proposed PhD project, we shall concentrate on the Markov chain formulation of the PageRank problem. Specifically, we suggest to analyze the effectiveness of aggregationdisaggregation methods [15, 5, 14] in PageRank computation. Such methods exploit the block structure of the web and seem to be very promising [7]. The analysis will be based on the theory of discrete-time Markov chains, Perron-Frobenius theory, perturbation theory [8], and the theory of quasi-stationary distributions [6, 9]. The project will also involve extensive numerical studies. A student may start with the following problem. Consider two completely disconnected communities (blocks of pages) and assume that they tailor several links to each other. Such strategy is called reprocicating and is widely used by web-administrators in hope to increase their ranking [12]. The question is whether the trick really works. In [2], we studied a completely decomposable web and we analyzed the situation when one of communities gives a link to another without receiving a link back. The results insinuate that in case of reprocicating, only one of the communities wins in ranking, whereas the other one looses. This issue however requires a rigorous analysis. The results will be interesting from the practical point of view, as they will either confirm or ruin the common reprocicating myth. Besides, it will be a useful and insightful first step in the analysis of aggregation-disaggregation methods in PageRank computation. After the first problem is been (partly) solved, the direction of research might deviate from the original plan, depending on the used methods, obtained results, and the interests of the student. Possible directions could be, for instance, the analysis of on-line algorithms [1] or Monte Carlo methods [3, 10].
Involvement of PTPN5, the gene encoding the striatal-enriched protein tyrosine phosphatase, in schizophrenia and cognition

Objective Striatal-enriched protein tyrosine phosphatase (STEP) is a brain-specific member of the protein tyrosine phosphatase (PTP) family that has been implicated in learning and memory. In this study, we examined the association of the protein tyrosine phosphatase non-receptor 5 (PTPN5) gene, which encodes for STEP, with both schizophrenia and cognitive functioning in the Israeli Jewish population. Methods A schizophrenia (SZ) case–control study of 868 participants was carried out (286 patients and 582 controls). Eleven PTPN5 tagging single-nucleotide polymorphisms (SNPs) were selected and single markers and haplotype association analyses were carried out. A cognitive variability study included 437 healthy women who completed a computerized cognitive battery. We performed univariate associations between the SNPs and cognitive performance. The possible functional role of these variants was examined by studying their association with gene expression levels in the brain. Results In the SZ study, we found a nominal association in the whole sample between rs4075664 and SZ. Male patients with SZ showed a more significant association for three SNPs (rs4075664, rs2278732, and rs4757710). Haplotypes of the studied SNPs were associated with SZ both in the overall sample and within the male subsample. Expression analysis provided some support for the effects of the associated SNPs on PTPN5 expression level. The cognitive variability study showed positive associations between PTPN5 SNPs and different cognitive subtests. Principal component analysis showed an ‘attention index’ neurocognitive component that was associated with two SNP pairs (rs10832983×rs10766504 and rs7932938×rs4757718). Conclusion The results imply a model in which PTPN5 may play a role in normal cognitive functioning and contribute to aspects of the neuropathology of SZ.
Heterogeneity of Influenza B Virus Strains in One Epidemic Season Differentiated by Monoclonal Antibodies and Nucleotide Sequences

ABSTRACT Seventy-three B/Victoria group strains isolated in the 1996–1997 influenza season were divided into three groups according to the degree of reactivity to monoclonal antibody 8E6. Analysis of nucleotide sequences of the HA1 region clarified that single amino acid substitutions were responsible for the difference in reactivity to 8E6.
Differentiation of Bacillus anthracis, B. cereus, and B. thuringiensis on the Basis of the csaB Gene Reflects Host Source

ABSTRACT csaB gene analysis clustered 198 strains of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis into two groups related to mammalian and insect hosts, respectively. Mammal-related group I strains also have more S-layer homology (SLH) protein genes than group II strains. This indicates that csaB-based differentiation reflects selective pressure from animal hosts.
i-LAND: an interactive landscape for creativity and innovation

We describe the i-LAND environment which constitutes an exampleof our vision of the workspaces of the future, in this casesupporting cooperative work of dynamic teams with changing needs.i-LAND requires and provides new forms of human-computerinteraction and new forms of computer-supported cooperative work.Its design is based on an integration of information andarchitectural spaces, implications of new work practices and anempirical requirements study informing our design. i-LAND consistsof several roomware components, i.e. computer-aug- mented objectsintegrating room elements with information technology. We presentthe current realization of i-LAND in terms of an interactiveelectronic wall, an interactive table, two computer-enhancedchairs, and two bridges for the Passage-mechanism. This iscomplemented by the description of the creativity supportapplication and the technological infrastructure. The paper isaccompanied by a video figure in the CHI99 video program.
Survival probabilities with time‐dependent treatment indicator: quantities and non‐parametric estimators

The ‘landmark’ and ‘Simon and Makuch’ non‐parametric estimators of the survival function are commonly used to contrast the survival experience of time‐dependent treatment groups in applications such as stem cell transplant versus chemotherapy in leukemia. However, the theoretical survival functions corresponding to the second approach were not clearly defined in the literature, and the use of the ‘Simon and Makuch’ estimator was criticized in the biostatistical community.
Gaussian Processes for Global Optimization

We introduce a novel Bayesian approach to global optimization using Gaussian processes. We frame the optimization of both noisy and noiseless functions as sequential decision problems, and introduce myopic and non-myopic solutions to them. Here our solutions can be tailored to exactly the degree of confidence we require of them. The use of Gaussian processes allows us to benefit from the incorporation of prior knowledge about our objective function, and also from any derivative observations. Using this latter fact, we introduce an innovative method to combat conditioning problems. Our algorithm demonstrates a significant improvement over its competitors in overall performance across a wide range of canonical test problems.
Extended Virtual Spring Mesh (EVSM): The Distributed Self-Organizing Mobile Ad Hoc Network for Area Exploration

Mobile Ad hoc NETworks (MANETs) are distributed self-organizing networks that can change locations and configure themselves on the fly. This paper focuses on an algorithmic approach for the deployment of a MANET within an enclosed area, such as a building in a disaster scenario, which can provide a robust communication infrastructure for search and rescue operations. While a virtual spring mesh (VSM) algorithm provides scalable, self-organizing, and fault-tolerant capabilities required by a MANET, the VSM lacks the MANET's capabilities of deployment mechanisms for blanket coverage of an area and does not provide an obstacle avoidance mechanism. This paper presents a new technique, an extended VSM (EVSM) algorithm that provides the following novelties: 1) new control laws for exploration and expansion to provide blanket coverage, 2) virtual adaptive springs enabling the mesh to expand as necessary, 3) adapts to communications disturbances by varying the density and movement of mobile nodes, and 4) new metrics to assess the performance of the EVSM algorithm. Simulation results show that EVSM provides up to 16% more coverage and is 3.5 times faster than VSM in environments with eight obstacles.
Synthesis and characterization of gold doped zinc oxide nanostructure for biosensor application

Zinc oxide (ZnO), a representative of group II-IV metal-oxide semiconductor material with its wide direct band-gap (3.37eV) and high exciton binding energy (60meV) which providing the advantages of their electrical and optical properties. Due to these unique properties, ZnO is widely studied in the current research community. In addition, the fabrication of doped ZnO thin films have been reported could significantly enhance the device sensitivity by Au adsorption. Thus, this work demonstrated the process development of gold doped zinc oxide (Au-ZnO) thin films using sol-gel method. The effect of different Au thickness layer deposited onto ZnO thin films were studied using various characterization method. The structural properties of ZnO thin films before and after modified with Au layer were investigated by using scanning electron microscope (SEM) and energy dispersive x-ray (EDX). The results show that the element existence on the prepared ZnO thin films sample consist the peak of silicon (Si), zinc (Zn) and oxide (O) as well as gold (Au) for Au modified ZnO sample. The optical properties of ZnO thin films and Au-ZnO thin films were also characterized using ultraviolet-visible spectroscopy (UV-VIS). The results indicate the existence of the ZnO characteristic at particular absorbance peak of 380 nm. The formation of Au-ZnO was further confirmed by obtained the characteristic Au absorbance band at wavelength ranged from 500 nm to 600 nm.Zinc oxide (ZnO), a representative of group II-IV metal-oxide semiconductor material with its wide direct band-gap (3.37eV) and high exciton binding energy (60meV) which providing the advantages of their electrical and optical properties. Due to these unique properties, ZnO is widely studied in the current research community. In addition, the fabrication of doped ZnO thin films have been reported could significantly enhance the device sensitivity by Au adsorption. Thus, this work demonstrated the process development of gold doped zinc oxide (Au-ZnO) thin films using sol-gel method. The effect of different Au thickness layer deposited onto ZnO thin films were studied using various characterization method. The structural properties of ZnO thin films before and after modified with Au layer were investigated by using scanning electron microscope (SEM) and energy dispersive x-ray (EDX). The results show that the element existence on the prepared ZnO thin films sample consist the peak of silicon (Si), zinc (Zn).
From numerical concepts to concepts of number

Abstract Many experiments with infants suggest that they possess quantitative abilities, and many experimentalists believe that these abilities set the stage for later mathematics: natural numbers and arithmetic. However, the connection between these early and later skills is far from obvious. We evaluate two possible routes to mathematics and argue that neither is sufficient: (1) We first sketch what we think is the most likely model for infant abilities in this domain, and we examine proposals for extrapolating the natural number concept from these beginnings. Proposals for arriving at natural number by (empirical) induction presuppose the mathematical concepts they seek to explain. Moreover, standard experimental tests for children's understanding of number terms do not necessarily tap these concepts. (2) True concepts of number do appear, however, when children are able to understand generalizations over all numbers; for example, the principle of additive commutativity (a+b=b+a). Theories of how children learn such principles usually rely on a process of mapping from physical object groupings. But both experimental results and theoretical considerations imply that direct mapping is insufficient for acquiring these principles. We suggest instead that children may arrive at natural numbers and arithmetic in a more top-down way, by constructing mathematical schemas.
Disambiguating Noun Compounds

This paper is concerned with the interaction between word sense disambiguation and the interpretation of noun compounds (NCs) in English. We develop techniques for disambiguating word sense specifically in NCs, and then investigate whether word sense information can aid in the semantic relation interpretation of NCs. To disambiguate word sense, we combine the one sense per collocation heuristic with the grammatical role of polysemous nouns and analysis of word sense combinatories. We built supervised and unsupervised classifiers for the task and demonstrate that the supervised methods arc superior to a number of baselines and also a benchmark state-of-the-art WSD system. Finally, we show that WSD can significantly improve the accuracy of NC interpretation.