Miracle-dz/UniFAR-FTUs huggingface dataset:
High Fidelity Scan Merging

For each scanned object 3D triangulation laser scanners deliver multiple sweeps corresponding to multiple laser motions and orientations. The problem of aligning these scans has been well solved by using rigid and, more recently, non‐rigid transformations. Nevertheless, there are always residual local offsets between scans which forbid a direct merging of the scans, and force to some preliminary smoothing. Indeed, the tiling and aliasing effects due to the tiniest normal displacements of the scans can be dramatic. This paper proposes a general method to tackle this problem. The algorithm decomposes each scan into its high and low frequency components and fuses the low frequencies while keeping intact the high frequency content. It produces a mesh with the highest attainable resolution, having for vertices all raw data points of all scans. This exhaustive fusion of scans maintains the finest texture details. The method is illustrated on several high resolution scans of archeological objects.
GEO-RBAC: a spatially aware RBAC

Securing access to data in location-based services and mobile applications requires the definition of spatially aware access control systems. Even if some approaches have already been proposed either in the context of geographic database systems or context-aware applications, a comprehensive framework, general and flexible enough to cope with spatial aspects in real mobile applications, is still missing. In this paper, we make one step towards this direction and we present GEO-RBAC, an extension of the RBAC model to deal with spatial and location-based information. In GEO-RBAC, spatial entities are used to model objects, user positions, and geographically bounded roles. Roles are activated based on the position of the user. Besides a physical position, obtained from a given mobile terminal or a cellular phone, users are also assigned a logical and device independent position, representing the feature (the road, the town, the region) in which they are located. To make the model more flexible and re-usable, we also introduce the concept of role schema, specifying the name of the role as well as the type of the role spatial boundary and the granularity of the logical position. We then extend GEO-RBAC to cope with hierarchies, modeling permission, user, and activation inheritance.
A 0.5-V 1.56-mW 5.5-GHz RF transceiver IC module with J-shaped folded monopole antenna

This paper presents a low-power RF-CMOS-transceiver IC-module with small antennas on a printed circuit board (PCB). Active mixer-first architecture is employed on a receiver for achieving both acceptable sensitivity and lower power. We also show strategies for lowering power consumption of the transmitter and the phase locked loop (PLL): a high-gain inverter-based resonant-driver and a current-reuse voltage controlled oscillator (VCO). Power saving of the RF circuits is achieved with low supply-voltage design under 0.5V by exploiting forward body bias technique. The use of 5.5-GHz band and a J-shaped folded monopole antennas (JFMA) on the PCB enable to reduce the module footprint, and the module size of 0.78 cc is realized. The proposed transceiver circuit is fabricated in 65 nm CMOS process technology and is mounted on the PCB. 5.5-GHz RF-transceiver operation is succeeded with small power consumption of 1.56 mW under 0.5-V power supply. Output signal-power of the transmitter is -23.2 dBm, and receiver sensitivity is -61.2 dBm.
Detection of ROS Induced Proteomic Signatures by Mass Spectrometry

Reversible and irreversible post-translational modifications (PTMs) induced by endogenously generated reactive oxygen species (ROS) in regulatory enzymes and proteins plays an essential role in cellular signaling. Almost all cellular processes including metabolism, transcription, translation and degradation have been identified as containing redox regulated proteins. Specific redox modifications of key amino acids generated by ROS offers a dynamic and versatile means to rapidly alter the activity or functional structure of proteins in response to biochemical, environmental, genetic and pathological perturbations. How the proteome responds to these stimuli is of critical importance in oxidant physiology, as it can regulate the cell stress response by reversible and irreversible PTMs, affecting protein activity and protein-protein interactions. Due to the highly labile nature of many ROS species, applying redox proteomics can provide a signature footprint of the ROS species generated. Ideally redox proteomic approaches would allow; (1) the identification of the specific PTM, (2) identification of the amino acid residue that is modified and (3) the percentage of the protein containing the PTM. New developments in MS offer the opportunity of a more sensitive targeted proteomic approach and retrospective data analysis. Subsequent bioinformatics analysis can provide an insight into the biochemical and physiological pathways or cell signaling cascades that are affected by ROS generation. This mini-review will detail current redox proteomic approaches to identify and quantify ROS induced PTMs and the subsequent effects on cellular signaling.
Saving our Future: James Comer and the School Development Program

Since the founding of the School Development Program (SDP) by Dr. James Comer in 1968, the manner in which child development is addressed in many schools has changed drastically. By working together using the SDP model, schools, parents, and child development experts are able to foster healthy social, emotional, and academic development in children, resulting in improvement in all areas. This review briefly describes the creation and implementation of the SDP model by Dr. James Comer.
A Simple and Reliable PDMS and SU-8 Irreversible Bonding Method and Its Application on a Microfluidic-MEA Device for Neuroscience Research

Polydimethylsiloxane (PDMS) and SU-8 are currently two very commonly used polymeric materials in the microfluidics field for biological applications. However; there is a pressing need to find a simple, reliable, irreversible bonding method between these two materials for their combined use in innovative integrated microsystems. In this paper, we attempt to investigate the aminosilane-mediated irreversible bonding method for PDMS and SU-8 with X-Ray Photoelectron Spectroscopy (XPS) surface analysis and bonding strength tests. Additionally, the selected bonding method was applied in fabricating a microelectrode array (MEA) device, including microfluidic features, which allows electrophysiological observations on compartmentalized neuronal cultures. As there is a growing trend towards microfluidic devices for neuroscience research, this type of integrated microdevice, which can observe functional alterations on compartmentalized neuronal culture, can potentially be used for neurodegenerative disease research and pharmaceutical development.
Accessible Wayfinding Testbed: Infrastructure and Components

Despite considerable recent interest in research related to wayfinding and navigation of pedestrians, the needs and preferences of people with disabilities (PWDs) are not yet fully addressed. Some of still unaddressed issues are related to understanding the different mobility challenges of PWDs, while others are related to the accessibility of routes and navigation systems/services. Emergence of advanced systems and services that can assist PWDs in wayfinding and navigation calls for the development of an accessible wayfinding platform facilitating the evaluation of accessibility of indoor and outdoor routes. In this paper, we propose and present an accessible wayfinding testbed which has three components: database, accessibility index, and visualization. The database component includes networks of sidewalks outdoors and building elements indoors with accessibility elements for PWDs. The accessibility index determines the level of accessibility of each element in a network as is perceived by PWDs. The visualization component visualizes the routes, accessible and others, in a simple form allowing PWDs, urban planners, and software developers, among others, to evaluate the accessibility of the travelling environment. The paper discusses the details of the testbed and a prototype accessible wayfinding testbed.
Alternative Splicing and Nonsense-Mediated RNA Decay Contribute to the Regulation of SHOX Expression

The human SHOX gene is composed of seven exons and encodes a paired-related homeodomain transcription factor. SHOX mutations or deletions have been associated with different short stature syndromes implying a role in growth and bone formation. During development, SHOX is expressed in a highly specific spatiotemporal expression pattern, the underlying regulatory mechanisms of which remain largely unknown. We have analysed SHOX expression in diverse embryonic, fetal and adult human tissues and detected expression in many tissues that were not known to express SHOX before, e.g. distinct brain regions. By using RT-PCR and comparing the results with RNA-Seq data, we have identified four novel exons (exon 2a, 7-1, 7-2 and 7-3) contributing to different SHOX isoforms, and also established an expression profile for the emerging new SHOX isoforms. Interestingly, we found the exon 7 variants to be exclusively expressed in fetal neural tissues, which could argue for a specific role of these variants during brain development. A bioinformatical analysis of the three novel 3′UTR exons yielded insights into the putative role of the different 3′UTRs as targets for miRNA binding. Functional analysis revealed that inclusion of exon 2a leads to nonsense-mediated RNA decay altering SHOX expression in a tissue and time specific manner. In conclusion, SHOX expression is regulated by different mechanisms and alternative splicing coupled with nonsense-mediated RNA decay constitutes a further component that can be used to fine tune the SHOX expression level.
Equilibrium curves and growth models to deal with forests in transition to uneven-aged structure : application in two sample stands

Stem number distributions in uneven-aged forests are assumed to be stable, if they follow special functions, e.g. de Liocourt’s reverse J-shaped breast height diameter distribution. These distributions therefore are frequently regarded as a target in all-aged forests. Intending to convert an even-aged forest or any other forest, not yet exhibiting this sort of equilibrium, towards a steady state forest, the question rises, how to choose an appropriate equilibrium curve and how to achieve this stem number distribution by an appropriate thinning and harvesting schedule. Two stands are investigated: One dominated by Norway spruce (Picea abies), having developed from a 120 year old even-aged stand 25 years ago, after several “target diameter thinnings”. The other one is a mixed species stand of Norway spruce, white fir (Abies alba), larch (Larix europea), common beech (Fagus silvatica), and Scots pine (Pinus sylvestris), having lost its typical uneven-aged structure 20 years ago. These stands were used, together with the distance independent individual tree growth model PROGNAUS, to reveal that 1) there are more than only one equilibrium curve per stand, 2) not every hypothesised equilibrium can be reached with any stand, 3) an equilibrium in stem number does not necessarily mean a stable species distribution, and 4) growth models provide an excellent help to decide between several equilibrium curves and harvesting schedules to reach them.
Parallel comba multiplication in GF(2163) using homogenous multicore microcontroller

Comba Multiplication is considered as one of the most important multiplication techniques used in public key cryptography computations be it in modular form in RSA or in finite field form in Elliptic Curve Cryptography for example. The efficiency of these Public Key Cryptography implementations depends heavily on the efficiency of the implementation of the multiplication operation. Multicore architectures are becoming increasingly important platforms for modern computation. However cryptography implementations on these platforms is still at its infancy. In this paper, we propose a parallel software implementation of the comba multiplication in GF(2163) using a homogenous multicore microcontroller. We obtain performance results and compare these to sequential implementation of comba multiplications with and without modular reduction for different word size 8, 16 and 32 bits on single core microcontrollers. Our obtained results outperform most of the published single core modular multiplication implementations and require much fewer cycles. We achieve more than 85% enhancement of the measured time in comparison to a single core implementation.
Differential expression of lysosomal associated membrane protein (LAMP‐1) during mammalian spermiogenesis

The mammalian acrosome is a secretory vesicle of mature sperms that plays an important role in fertilization. Recent evidence had pointed out that some components found at endosomes in somatic cells are associated with the developing acrosome during the early steps of spermiogenesis. Moreover, the mammalian acrosome contains many enzymes found within lysosomes in somatic cells. In this work, we studied the dynamics of some components of the endosome/lysosome system, as a way to understand the complex membrane trafficking circuit established during spermatogenesis. We show that the cation independent‐mannose‐6‐phosphate receptor (CI‐MPR) is transiently expressed in the cytoplasm of mid‐stage spermatids (steps 5–11). On the other hand, γ‐adaptin, an adaptor molecule of a complex involved in trafficking from the Golgi to lysosomes, was expressed in cytoplasmic vesicles only in pachytene and Cap‐phase spermatids (steps 1–5). Our major finding is that the lysosomal protein LAMP‐1 is differentially expressed during spermiogenesis. LAMP‐1 appears late in spermatogenesis (Acrosome‐phase) contrasting with LAMP‐2, which is present throughout the complete process. Both proteins appear to be associated with cytoplasmic vesicles and not with the developing acrosome. None of the studied proteins is present in epididymal spermatozoa. Our results suggest that the CI‐MPR could be involved in membrane trafficking and/or acrosomal shaping during spermiogenesis. Mol. Reprod. Dev. 66: 202–209, 2003. © 2003 Wiley‐Liss, Inc.
Dietary Protein, Protein to Carbohydrate Ratio and Subsequent Changes in Lipid Profile after a 3-Year Follow-Up: Tehran Lipid and Glucose Study

Abstract Background Data regarding the effects of dietary protein on modifying serum lipid and lipoprotein levels are controversial. In this study we have investigated the hypothesis whether dietary protein and protein to carbohydrate ratio could be related to subsequent changes in lipid profile in adults. Methods This 3-yaers follow-up_longitudinal study was conducted on a sample of participants (845 men and 1043 women, aged 19-70 years) of the Tehran Lipid and Glucose Study. Dietary intakes were assessed using a validated semi-quantitative food frequency questionnaire. Anthropometric and serum lipid and lipoprotein levels were measured both at baseline (2006–2008) and after 3 years. Results After adjustment for potential confounding variables and dietary factors, the highest quartile energy intakes from protein was inversely associated with changes in total cholesterol (β= -6.5; 95% CI= -11.5, -1.5) and HDL-C levels (β= -6.7; 95% CI= -12.2, -1.4) in men during the follow-up. Increased proportion of energy intake from protein, compared to that of carbohydrate also had favorable effect on 3-years changes in triglycerides (β= -18.2; 95% CI= -36.7, -0.1) and total cholesterol (β= -8.4; 95% CI= -15.1, -1.8) in men. Higher dietary P/C ratio (median ≥ 0.23) was associated with a significant decrease in serum total cholesterol at 3-years follow-up in men with the higher intake of protein (median ≥ 13.4 % of energy). Conclusion Higher intakes of dietary protein and more importantly, higher proportion of energy intakes from protein, compared to carbohydrate, had favorable effects on modifying lipid levels during a 3-year follow-up.
Functions of Peptidoglycan Recognition Proteins (Pglyrps) at the Ocular Surface: Bacterial Keratitis in Gene-Targeted Mice Deficient in Pglyrp-2, -3 and -4

Purpose Functions of antimicrobial peptidoglycan recognition proteins (Pglyrp1-4) at the ocular surface are poorly understood. Earlier, we reported an antibacterial role for Pglyrp-1 in Pseudomonas aeruginosa keratitis. Here we investigated functions of three other related genes Pglyrp-2, -3 and -4 in a mouse model of P. aeruginosa keratitis. Methods Wild type (WT) and each of the Pglyrp-null genotypes were challenged with P. aeruginosa keratitis. The eyes were scored in a blinded manner 24 and 48h post infection. Viable bacterial counts and inflammatory factors (IL-12, TNF-α, IFN-γ, CCL2, IL-6 and IL-10) were measured in whole eye homogenates using cytometric bead arrays. Expressions of Pglyrp-1-4, mouse beta defensins (mBD)-2,-3, cathelicidin-related antimicrobial peptide (CRAMP) were determined by qRTPCR in total RNA extracts of uninfected and infected eyes of WT and each of the Pglyrp-null mouse types. Results The Pglyrp-2 -/- mice showed reduced disease and lower induction of pro-inflammatory TNF-α (p = 0.02) than WT or the other Pglyrp null mice. Viable bacterial yield was significantly lower in the Pglyrp-2-/- (p = 0.0007) and the Pglyrp-4-/- (p = 0.098) mice. With regards to expression of these antimicrobial genes, Pglyrp-2 expression was induced after infection in WT mice. Pglyrp-3 expression was low before and after infection in WT mice, while Pglyrp-4 expression was slightly elevated after infection in WT, Pglyrp-2 and -3 null mice. Pglyrp-1 expression was slightly elevated after infection in all genotypes without statistical significance. Transcripts for antimicrobial peptides mBD2, mBD3 and CRAMP were elevated in infected Pglyrp-2 -/- males without statistical significance. Conclusions Efficient resolution of keratitis in the Pglyrp-2 -/- mice may be due to a reduced pro-inflammatory microenvironment and synergistic antibacterial activities of defensins, CRAMP and Pglyrp-1. Therefore, in ocular infections the pro-inflammatory functions of Pglyrp-2 must be regulated to benefit the host.
An Improved MapReduce Design of Kmeans with Iteration Reducing for Clustering Stock Exchange Very Large Datasets

This paper targets the problem of clustering very large datasets as one of the most challenging tasks for data mining and processing. We propose an improved MapReduce design of Kmeans algorithm with an iteration reducing method. Experiments show that this method reduces the number of iterations and the execution time of the Kmeans algorithm while keeping 80% of the clustering accuracy. The employment of MapReduce programming paradigm and iterations reducing techniques offers the possibility to process the huge volume of data generated by stock exchanges daily transactions which performs a better decision making by analysts.
GIS analysis for vulnerability assessment of salt damage on coastal agricultural fields: a case of Taro Patch in the Republic of Palau

Due to the global climate change, sea level rise and storm surges are worried to accelerate salt damage to coastal agricultural fields. The Republic of Palau, a small island nation in the Pacific Ocean is suffering from increasing taro patch abandonment. The purpose of this paper is to clarify the characteristics of taro patches which are damaged by seawater based on the GIS analysis and clusterings, such as elevation, distance from the sea, slope, catchment area, and area of a taro patch. The target area was the Babeldaob Island, which is the largest island in Palau. The results showed that the taro patches were mostly distributed in less than 10 m in elevation, within 1 km in distance from seawater and on slopes below 3%. We divided taro patches into two clusters by k-means clustering; cluster 1 which the elevation was low with catchment area and area of taro patch were small; cluster 2 which the elevation was high with catchment area and area of taro patch were large. These results imply that the large catchment area might lead to suppression of salt damage.
"Good" versus "Bad" Opinion on Micro Blogging Networks: Polarity Classification of Twitter

Information-gathering has always been an important part to find what other person is thinking. Millions of users tweet on different aspects of life every day. Therefore micro blogging websites are a very good source for polarity classification. We introduce a novel approach which automatically classifies the polarity of Twitter message. These messages so called tweets are classified as positive or negative or neutral. These results are useful for the customers or any general user who wants to research about the polarity of products before purchases, or it can be useful for the companies that want to analyze the reviews from people of their brands in the market. Most of the previous research on classifying the polarity of messages has tried to achieve some good results but have ignored the neutral tweets which lead to wrong polarity classification, so we have tried to solve this issue in our project. We present an approach for classifying the polarity of tweets using machine learning algorithms using a novel feature vector. Our training data cont ains publically available tweets which are obtained using twitter API‟s available. The following report shows the steps for preprocessing the dataset to achieve high accuracy. The novel feature vector of weighted unigrams that are used to train the machine learni ng classifiers is the main contribution of our project.
Circuit Failure Prediction and Its Application to Transistor Aging

Circuit failure prediction predicts the occurrence of a circuit failure before errors actually appear in system data and states. This is in contrast to classical error detection where a failure is detected after errors appear in system data and states. Circuit failure prediction is performed during system operation by analyzing the data collected by sensors inserted at various locations inside a chip. We demonstrate this concept of circuit failure prediction for a dominant PMOS aging mechanism induced by negative bias temperature instability (NBTI). NBTI-induced PMOS aging slows down PMOS transistors over time. As a result, the speed of a chip can significantly degrade over time and can result in delay faults. The traditional practice is to incorporate worst-case speed margins to prevent delay faults during system operation due to NBTI aging. A new sensor design integrated inside a flip-flop enables efficient circuit failure prediction at a low cost. Simulation results using 90nm and 65nm technologies demonstrate that this technique can significantly improve system performance by enabling close to best-case design instead of traditional worst-case design.
An overview of decoding techniques for large vocabulary continuous speech recognition

Abstract A number of decoding strategies for large vocabulary continuous speech recognition (LVCSR) are examined from the viewpoint of their search space representation. Different design solutions are compared with respect to the integration of linguistic and acoustic constraints, as implied by m -gram language models (LM) and cross-word (CW) phonetic contexts. This study is structured along two main axes: the network expansion and the search algorithm itself. The network can be expanded statically or dynamically while the search can proceed either time-synchronously or asynchronously which leads to distinct architectures. Three broad classes of decoding methods are briefly reviewed: the use of weighted finite state transducers (WFST) for static network expansion, the time-synchronous dynamic-expansion search and the asynchronous stack decoding. Heuristic methods for further reducing the search space are also considered. The main approaches are compared and some prospective views are formulated regarding possible future avenues.