Miracle-dz/UniFAR-FTUs huggingface dataset:
Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

Physiological function and pathology of the Alzheimer’s disease causing amyloid precursor protein (APP) are correlated with its cytosolic adaptor Fe65 encompassing a WW and two phosphotyrosine-binding domains (PTBs). The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD) including the GYENPTY internalization sequence fingerprint. AICD binding to Fe65-PTB2 opens an intra-molecular interaction causing a structural change and altering Fe65 activity. Here we show that in the absence of the AICD, Fe65-PTB2 forms a homodimer in solution and determine its crystal structure at 2.6 Å resolution. Dimerization involves the unwinding of a C-terminal α-helix that mimics binding of the AICD internalization sequence, thus shielding the hydrophobic binding pocket. Specific dimer formation is validated by nuclear magnetic resonance (NMR) techniques and cell-based analyses reveal that Fe65-PTB2 together with the WW domain are necessary and sufficient for dimerization. Together, our data demonstrate that Fe65 dimerizes via its APP interaction site, suggesting that besides intra- also intermolecular interactions between Fe65 molecules contribute to homeostatic regulation of APP mediated signaling.
Efficient Interpolation of SAR Images for Coregistration in SAR Interferometry

An efficient polynomial interpolation method is proposed to reduce the computational burden of the coregistration of synthetic aperture radar images in interferometric processing. The method can be viewed as an application of the Farrow interpolator technique and requires a series of 2-D fast Fourier transforms (FFTs). Mainly, it has two advantages relative to the usual coregistration procedure. First, it does not require to compute or store in memory any kernel sample. Second, it involves less floating-point operations than the conventional coregistration, with a clear advantage if the image needs to be oversampled. The efficiency of the method is based on the fact that the complexity of one 2-D FFT is much smaller than the complexity of one spatial convolution. These advantages are demonstrated by both analyzing the interpolation procedure itself and by defining an efficient code implementation.
Franksum: new feature selection method for protein function prediction

In the study of in silico functional genomics, improving the performance of protein function prediction is the ultimate goal for identifying proteins associated with defined cellular functions. The classical prediction approach is to employ pairwise sequence alignments. However this method often faces difficulties when no statistically significant homologous sequences are identified. An alternative way is to predict protein function from sequence-derived features using machine learning. In this case the choice of possible features which can be derived from the sequence is of vital importance to ensure adequate discrimination to predict function. In this paper we have successfully selected biologically significant features for protein function prediction. This was performed using a new feature selection method (FrankSum) that avoids data distribution assumptions, uses a data independent measurement (p-value) within the feature, identifies redundancy between features and uses an appropriate ranking criterion for feature selection. We have shown that classifiers generated from features selected by FrankSum outperforms classifiers generated from full feature sets, randomly selected features and features selected from the Wrapper method. We have also shown the features are concordant across all species and top ranking features are biologically informative. We conclude that feature selection is vital for successful protein function prediction and FrankSum is one of the feature selection methods that can be applied successfully to such a domain.
The Standardized BHH10 Extract, a Combination of Astragalus membranaceus, Cinnamomum cassia, and Phellodendron amurense, Reverses Bone Mass and Metabolism in a Rat Model of Postmenopausal Osteoporosis

Jasin‐hwan‐gagambang (BHH10), a modified prescription of Jasin‐hwan, contains Astragalus membranaceus, Cinnamomum cassia, and Phellodendron amurense, and it has been traditionally used to treat osteoporosis and other inflammatory diseases. In this study, we systematically investigated the protective effects of BHH10 in ovariectomy (OVX)‐induced rats. Sprague–Dawley rats were randomly divided into sham and OVX subgroups. The rats in the OVX group were treated with vehicle, BHH10, alendronate (ALN), and 17β‐estradiol (E2). BHH10 treatment significantly inhibited OVX‐induced increases in body weight and uterus atrophy. In addition, it significantly increased the bone mineral density (BMD) and prevented a decrease in trabecular bone volume, connectivity density, trabecular number, thickness, and separation at the total femur and femur neck. The OVX rats showed significant decreases in the serum levels of calcium and phosphorous and significant increases in the serum levels of cholesterol, low‐density lipoprotein cholesterol, alkaline phosphatase, osteocalcin, C‐telopeptide type 1 collagen, and bone morphogenetic protein‐2. These changes were significantly reduced to near sham levels by administration of BHH10 to OVX rats. BHH10‐treated rats had a greater bone mass, a better structural architecture of the bone, and higher levels of biochemical markers of the bone than did the ALN‐treated or E2‐treated rats. These results suggest that BHH10 reverses osteoporosis in OVX rats by stimulating bone formation or regulating bone resorption and is not associated with toxicity. © 2014 The Authors. Phytotherapy Research published by John Wiley & Sons Ltd.
Resilient complex event processing in IoT using side-channel information

Internet of Things (IoT) is a paradigm shift towards digital world. To make this scenario better, we delve into the capabilities of IoT to perform Complex Event Processing (CEP) in a secured manner. In this paper, we discuss the functioning of IoT framework to perform CEP on multiple sensor values and make sure that adversaries are not able to tamper our code. Existing implementations of CEP engines do not accommodate changes in rules or addition of new rules. This research aims to implement a framework for such a CEP engine, which allows dynamic updation of rules. This is achieved by designing a new, flexible approach for representing rules and annotating data within the system, and also a standard messaging protocol that IoT nodes have to use. We also add a novel feature to provide security using side-channel information collected through FLUSH and RELOAD method.
CMC-FZU at TRECVID 2010: Semantic Indexing

This paper summarizes our approaches to the semantic indexing task in TRECVID 2010. Several fusion strategies are employed in our detection system, including a low-level feature concatenation, text retrieval fusion, and ontology relation fusion. It can be drawn that the fusion of text retrieval results with a baseline in a proper way can contribute greatly to the system performance. Our approach to ontology relation fusion increases the number of the inferred true shots returned. Two of our runs using fusion schemes have the best infAP for a feature among the 30 features evaluated. We describe our text and ontology relation fusion schemes in detail in this paper. The description of our submission runs for the semantic indexing is as follows:
Electrical Stimulation of Spared Corticospinal Axons Augments Connections with Ipsilateral Spinal Motor Circuits after Injury

Activity-dependent competition shapes corticospinal (CS) axon outgrowth in the spinal cord during development. An important question in neural repair is whether activity can be used to promote outgrowth of CS axons in maturity. After injury, spared CS axons sprout and make new connections, but often not enough to restore function. We propose that electrically stimulating spared axons after injury will enhance sprouting and strengthen connections with spinal motor circuits. To study the effects of activity, we electrically stimulated CS tract axons in the medullary pyramid. To study the effects of injury, one pyramid was lesioned. We studied sparse ipsilateral CS projections of the intact pyramid as a model of the sparse connections preserved after CNS injury. We determined the capacity of CS axons to activate ipsilateral spinal motor circuits and traced their spinal projections. To understand the separate and combined contributions of injury and activity, we examined animals receiving stimulation only, injury only, and injury plus stimulation. Both stimulation and injury alone strengthened CS connectivity and increased outgrowth into the ipsilateral gray matter. Stimulation of spared axons after injury promoted outgrowth that reflected the sum of effects attributable to activity and injury alone. CS terminations were densest within the ventral motor territories of the cord, and connections in these animals were significantly stronger than after injury alone, indicating that activity augments injury-induced plasticity. We demonstrate that activity promotes plasticity in the mature CS system and that the interplay between activity and injury preferentially promotes connections with ventral spinal motor circuits.
Helping Medical Students Understand Postpartum Psychosis Through the Prism of “The Yellow Wallpaper” by Charlotte Perkins Gilman

Objective: We assessed the use of literature to illustrate a postpartum depression lecture. Methods: Medical students and faculty facilitators were surveyed after small group discussions. Results: Students’ ratings and comments were positive, and faculty comments were neutral to positive. Conclusion: Students valued this teaching method, while faculty observations reflected challenges of assessing literature’s contributions to medical education in improving empathy and treatment outcome.
NS fivebranes in type 0 string theory

The massless degrees of freedom of type 0 NS5-branes are derived. A non-chiral, purely bosonic spectrum is found in both type 0A and 0B. This non-chirality is confirmed by a one-loop computation in the bulk. Some puzzles concerning type 0B S-duality are pointed out in this context. An interpretation of the spectra in terms of ``type 0 little strings'' is proposed.
CS 229 Final Project Using WordNet and Clustering for Semantic Role Labeling

In this paper, we compare the performance of several clustering algorithms on the task of semantic role labeling. We use a baseline system based on logistic regression classifiers, and also a distributional clustering algorithm based on word association lists. We use a Latent Semantic Analysis system to compare to two previously implemented clustering algorithms, k-means and a more comprehensive discriminative clustering algorithm. We also focus on features we can extract through specialized corpuses such as WordNet. Overall, we demonstrate that semantically clustering text leads to significant improvements on semantic role labeling tasks.
Robust and Blind Watermarking of Polygonal Meshes Based on Volume Moments

This paper describes a robust and blind watermarking algorithm for polygonal meshes, dedicated to copyright protection. The watermark primitives are intrinsic 3D shape descriptors: the analytic and continuous geometric volume moments. The mesh is first normalized by using its global moments, and decomposed into patches by discretizing its cylindric domain. Then, one bit is inserted in each candidate patch by quantizing its local zero-order moment, through a modified scalar Costa scheme. The patch is then deformed by an iterative process, so as to reach the target quantized moment value; a smooth deformation mask is used to avoid introducing visible distortion. A global moment compensation post-processing is carried out after bit insertion so as to recover the normalized mesh pose; thus, the causality problem is resolved. The watermarking security is ensured by the key-dependent scalar Costa quantization. The blind watermark extraction simply consists of mesh normalization, patch decomposition and bit extraction. Experimental results and comparisons with the state-of-the-art have demonstrated the superiority of the proposed approach in terms of robustness, security and imperceptibility. Moreover, to the authors’ knowledge, it is the first attempt in the literature to tackle the robustness against 3D representation conversions (e.g. discretization of the mesh into voxels).
Inferring functional connectivity using spatial modulation measures of fMRI signals within brain regions of interest

We propose inferring functional connectivity between brain regions by examining the spatial modulation of the blood oxygen level dependent (BOLD) signals within brain regions of interest (ROIs). This is motivated by our previous work, where the spatial distribution of BOLD signals within an ROI was found to be modulated by task. Applying replicator dynamics to our proposed spatial feature time courses on real functional magnetic resonance imaging (fMRI) data detected task-related changes in the composition of the brain's functional networks, whereas using classical mean intensity features resulted in little changes being detected. Thus, our results suggest that intensity is not the only co- activating feature in fMRI data. Instead, spatial modulations may also be used for inferring functional connectivity.
Reducing Phthalate, Paraben, and Phenol Exposure from Personal Care Products in Adolescent Girls: Findings from the HERMOSA Intervention Study

Background: Personal care products are a source of exposure to potentially endocrine-disrupting chemicals such as phthalates, parabens, triclosan, and benzophenone-3 (BP-3) for adolescent girls. Methods: We enrolled 100 Latina girls in a youth-led, community-based participatory research intervention study to determine whether using personal care products whose labels stated they did not contain these chemicals for 3 days could lower urinary concentrations. Pre- and postintervention urine samples were analyzed for phthalate metabolites, parabens, triclosan, and BP-3 using high-performance liquid chromatography/tandem mass spectrometry. Results: Urinary concentrations of mono-ethyl phthalate (MEP) decreased by 27.4% (95% CI: –39.3, –13.2) on average over the 3-day intervention; no significant changes were seen in urinary concentrations of mono-n-butyl phthalate (MnBP) and mono-isobutyl phthalate (MiBP). Methyl and propyl paraben concentrations decreased by 43.9% (95% CI: –61.3, –18.8) and 45.4% (95% CI: –63.7, –17.9), respectively. Unexpectedly, concentrations of ethyl and butyl paraben concentrations increased, although concentrations were low overall and not detected in almost half the samples. Triclosan concentrations decreased by 35.7% (95% CI: –53.3, –11.6), and BP-3 concentrations decreased by 36.0% (95% CI: –51.0, –16.4). Discussion: This study demonstrates that techniques available to consumers, such as choosing personal care products that are labeled to be free of phthalates, parabens, triclosan, and BP-3, can reduce personal exposure to possible endocrine-disrupting chemicals. Involving youth in the design and implementation of the study was key to recruitment, retention, compliance, and acceptability of the intervention. Citation: Harley KG, Kogut K, Madrigal DS, Cardenas M, Vera IA, Meza-Alfaro G, She J, Gavin Q, Zahedi R, Bradman A, Eskenazi B, Parra KL. 2016. Reducing phthalate, paraben, and phenol exposure from personal care products in adolescent girls: findings from the HERMOSA Intervention Study. Environ Health Perspect 124:1600–1607; http://dx.doi. org/10.1289/ehp.1510514
Crime and Community: Continuities, Contradictions and Complexities

This article explores the research on community crime prevention, fear of crime, and alternative crime control strategies that go beyond those of traditional criminal justice agencies. The discussion focuses on the competing paradigms for prevention and control that have been tried over the past 20 years and relates that debate to the larger questions of crime causation and public attitudes toward crime that fuel this competition. Alternative policy options are discussed and recommendations related to the most promising approaches are made.
HD-Eye - visual clustering of high dimensional data: a demonstration

Clustering of large databases is an important research area with a large variety of applications in the data base context. Missing in most of the research efforts are means for guiding the clustering process and understand the results, which is especially important if the data under consideration is high dimensional and has not been collected for the purpose of being analyzed. Visualization technology may help to solve this problem since it allows an effective support of different clustering paradigms and provides means for a visual inspection of the results. Our HD-Eye (high-dimensional eye) system (A. Hinneburg et al., 1999) shows that a tight integration of advanced clustering algorithms and state-of-the-art visualization techniques is powerful for a better understanding and effective guidance of the clustering process, and therefore can help to significantly improve the clustering results. The demonstration shows how the user can visually explore the data by focusing on interesting projections and guide the important steps of the clustering process. Due to its interactive nature, the HD-Eye system allows a combination of multiple clustering paradigms, leading to clustering models, which fit, well to the intended tasks and the users interests. In addition, the integrated data visualization capabilities of the HD-Eye system lead to a better understanding of the clustering results. The applications to be demonstrated include clustering of large image as well as molecular biology databases.
Role of NEK2A in Human Cancer and Its Therapeutic Potentials

Chromosome instability (CIN) has been identified as a common feature of most human cancers. A number of centrosomal kinases are thought to cause CIN in cancer cells. Part of those centrosomal kinases exhibit elevated expression in a wide variety of tumours and cancer cell lines. Additionally, critical roles in many aspects of cancer cell growth, proliferation, metastasis, and drug resistance have been assigned to some of these centrosomal kinases, such as polo-like kinase 1 (PLk1) and Aurora-A kinase. Recent studies from our group and others revealed that a centrosomal kinase, Never in Mitosis (NIMA) Related Kinase 2A (NEK2A), is frequently upregulated in multiple types of human cancers. Uncontrolled activity of NEK2A activates several oncogenic pathways and ABC transporters, thereby leading to CIN, cancer cell proliferation, metastasis, and enhanced drug resistance. In this paper, we highlight recent findings on the aberrant expression and functional significance of NEK2A in human cancers and emphasize their significance for therapeutic potentials.
A new rotation invariant similarity measure for trajectories

We present a new rotation invariant measure for trajectories of dynamically changing locations of mobile objects (vehicles), which appear naturally in applications such as video-tracking, motion capture etc. Similar motion patterns can also be expressed at different orientations. We have modeled each trajectory by its sequence of angles. The similarity measure is defined based on longest common subsequence (LCS) method. To evaluate a system, we have simulated the database consisting of common trajectories of moving vehicles in the cities. First, clustering based on agglomerative algorithm with new similarity measure is applied on the training dataset. To classify new samples, similarity to the median of the clusters is considered and based on the rates of the similarity to the median, some natural language sentences is produced, these sentences express the behavioural descriptions of the vehicles. Experimental results show the accuracy and efficiency of the technique.
Sulfotyrosine Recognition as Marker for Druggable Sites in the Extracellular Space

Chemokine signaling is a well-known agent of autoimmune disease, HIV infection, and cancer. Drug discovery efforts for these signaling molecules have focused on developing inhibitors targeting their associated G protein-coupled receptors. Recently, we used a structure-based approach directed at the sulfotyrosine-binding pocket of the chemokine CXCL12, and thereby demonstrated that small molecule inhibitors acting upon the chemokine ligand form an alternative therapeutic avenue. Although the 50 members of the chemokine family share varying degrees of sequence homology (some as little as 20%), all members retain the canonical chemokine fold. Here we show that an equivalent sulfotyrosine-binding pocket appears to be conserved across the chemokine superfamily. We monitored sulfotyrosine binding to four representative chemokines by NMR. The results suggest that most chemokines harbor a sulfotyrosine recognition site analogous to the cleft on CXCL12 that binds sulfotyrosine 21 of the receptor CXCR4. Rational drug discovery efforts targeting these sites may be useful in the development of specific as well as broad-spectrum chemokine inhibitors.
Backward Motion for Estimation Enhancement in Sparse Visual Odometry

Visual Odometry (VO) aims to estimate camera position and orientation based on the images acquired by the camera. This area is rapidly gaining traction due to the dissemination of utonomous robots (cars, drones etc). It is well understood that different camera translations have different impacts on camera pose estimation. Movement along the optical axis (forward or backward) produces lower parallax than movement perpendicular to the optical axis (sideway translations). In this work, projection characteristics of sparse features for a camera moving away from the scene (backward movement) are discussed and a monocular backward looking camera VO system is suggested to take advantage of those characteristics. Implementation results tested with the KITTI dataset, a forward motion application processed in reversed order to emulate backward movement, show that the proposed system presents superior precision then forward looking published solutions and is suitable for real time operation.
Industry-driven innovative system development for the construction industry: The DIVERCITY project

Collaborative working has become possible using the innovative integrated systems in construction as many activities are performed globally with stakeholders situated in various locations. The Integrated VR based information systems can bind the fragmentation and provide communication and collaboration between the distributed stakeholders n various locations. The development of these technologies is vital for the uptake of these systems by the construction industry. This paper starts by emphasising the importance of construction IT research and reviews some future research directions in this area. In particular, the paper explores how virtual prototyping can improve the productivity and effectiveness of construction projects, and presents DIVERCITY, which is th as a case study of the research in virtual prototyping. Besides, the paper explores the requirements engineering of the DIVERCITY project. DIVERCITY has large and evolving requirements, which considered the perspectives of multiple stakeholders, such as clients, architects and contractors. However, practitioners are often unsure of the detail of how virtual environments would support the construction process, and how to overcome some barriers to the introduction of new technologies. This complicates the requirements engineering process.