Miracle-dz/UniFAR-FTUs huggingface dataset:
The Motion Blur Filter : An Algorithm for Extracting Confinement Forces & Diffusivity from a Single “ Blurred ” Trajectory

Single Particle Tracking (SPT) data can aid in understanding a variety of complex spatio-temporal processes (e.g., chromatin remodeling in the nucleus). However, quantifying diffusivity and confinement forces from individual live cell trajectories is complicated by inter& intra-trajectory kinetic heterogeneity, thermal fluctuations, and (experimentally resolvable) statistical temporal dependence inherent to the underlying molecule’s time correlated confined dynamics experienced in the cell. The problem is further complicated by experimental artifacts such as localization uncertainty and motion blur; the latter is caused by the tagged molecule emitting photons at different spatial positions during the exposure time of a single frame. The aforementioned experimental artifacts induce spurious time correlations in measured SPT time series that obscure the information of interest (e.g., confinement forces and diffusivity). We develop a new maximum likelihood estimation (MLE) technique that decouples the above noise sources and systematically treats temporal correlation (permitting the extraction of effective force or velocity) via a likelihood function. We illustrate how our approach avoids complications inherent to mean square displacement (MSD) or autocorrelation techniques typically used to calibrate SPT motion models. The approach can also systematically utilize localization uncertainty estimates afforded by image analysis if available. To our knowledge, this is the first SPT technique treating confinement and motion blur within an MLE framework (our approach does not make ad hoc statistical approximations of the likelihood). Our new estimator is demonstrated to be consistent over a wide range of exposure times (5− 100 ms), diffusion coefficients 1× 10−3 1× 10 μm/s, and confinement “radii” (100nm− 3μm). We demonstrate that neglecting motion blur and confinement can substantially bias estimation of kinetic parameters of interest to researchers in biophysics and cell biology. The technique also readily permits one to check statistical model assumptions against measured individual trajectories without “ground truth” (this feature is important in trusting the assumed model). The ability to reliably and consistently extract motion parameters independent of exposure time in trajectories exhibiting confined and/or non-stationary dynamics is expected to aid in directly comparing trajectories obtained from different experiments or imaging modalities. A Python implementation is provided (code will be maintained on GitHub). ar X iv :1 51 0. 06 06 2v 1 [ qbi o. Q M ] 2 0 O ct 2 01 5
IS '97 model curriculum: where do enterprise resource planning systems fit?

As businesses world-wide begin to adopt Enterprise Resource Planning (ERP) systems in increasing numbers, academics are deciding how to utilise these types of systems in Information Systems (IS) curricula. Alliances with some of the ERP vendors have enabled some universities to develop innovative courses and subjects. Nevertheless, the limited research in this area has only outlined case studies or examples of ERP use in IS. In this paper we outline how ERP systems can be incorporated into a broad IS curriculum model such as IS’97 thus providing a guide to institutions that may be contemplating the use of ERP in their curriculum.
Analysis of Twitter Data for Postmarketing Surveillance in Pharmacovigilance

Postmarketing surveillance (PMS) has the vital aim to monitor effects of drugs after release for use by the general population, but suffers from under-reporting and limited coverage. Automatic methods for detecting drug effect reports, especially for social media, could vastly increase the scope of PMS. Very few automatic PMS methods are currently available, in particular for the messy text types encountered on Twitter. In this paper we describe first results for developing PMS methods specifically for tweets. We describe the corpus of 125,669 tweets we have created and annotated to train and test the tools. We find that generic tools perform well for tweet-level language identification and tweet-level sentiment analysis (both 0.94 F1-Score). For detection of effect mentions we are able to achieve 0.87 F1-Score, while effect-level adverse-vs.-beneficial analysis proves harder with an F1-Score of 0.64. Among other things, our results indicate that MetaMap semantic types provide a very promising basis for identifying drug effect mentions in tweets.
Data Delivery by Mobile Agents with Energy Constraints over a fixed path

We consider $k$ mobile agents of limited energy that are initially located at vertices of an edge-weighted graph $G$ and have to collectively deliver data from a source vertex $s$ to a target vertex $t$. The data are to be collected by an agent reaching $s$, who can carry and then hand them over another agent etc., until some agent with the data reaches $t$. The data can be carried only over a fixed $s-t$ path of $G$; each agent has an initial energy budget and each time it passes an edge, it consumes the edge's weights in energy units and stalls if its energy is not anymore sufficient to move. The main result of this paper is a 3-approximation polynomial time algorithm for the data delivery problem over a fixed $s-t$ path in the graph, for identical initial energy budgets and at most one allowed data hand-over per agent.
Threat Assessment Based on Adaptive Intuitionistic Fuzzy Neural Network

This paper proposes a method for threat assessment(TA) based on Adaptive Intuitionistic Fuzzy Neural Network(AIFNN). Firstly, intuitionistic fuzzy proposition is defined and the concept of intuitionistic fuzzy reasoning is discussed and Takagi-Sugeno Kang intuitionistc fuzzy model is developed. Secondly, a model for TA on AIFNN based on Takagi-Sugeno Takagi-Sugeno Kang intuitionistc fuzzy model is established, the attribute functions, ie. membership and non-membership functions, and the inference rules of the system variables are devised with computational relations between layers of input and output and a synthesized computational expression of system outputs ascertained. Thirdly, a learning algorithm of neural based on the extended kalman algorithm is designed. Finally, the validity of the technique is checked and rationality of constructed model is verified by providing TA instances with 400 typical targets. The simulated results show that this method can enhance creditability of TA and improve quality of assessment with precision of synthetic values in reasoning output. Keywords-Threat Assessment; Intuitionistic Fuzzy Set; Adaptive Intuitionistic Fuzzy Neural Networks; Extended Kalman Algorithm
Gender difference in smoking effects on lung function and risk of hospitalization for COPD: results from a Danish longitudinal population study

Gender difference in smoking effects on lung function and risk of hospitalization for COPD: results from a Danish longitudinal population study. E. Prescott, A.M. Bjerg, P.K. Andersen, P. Lange, J. Vestbo. ©ERS Journals Ltd 1997. ABSTRACT: Recent findings suggest that females may be more susceptible than males to the deleterious influence of tobacco smoking in developing chronic obstructive pulmonary disease (COPD). This paper studies the interaction of gender and smoking on development of COPD as assessed by lung function and hospital admission. A total of 13,897 subjects, born after 1920, from two population studies, 9,083 from the Copenhagen City Heart Study (CCHS) and 4,814 from the Glostrup Population Studies (GPS), were followed for 7–16 yrs. Data were linked with information on hospital admissions caused by COPD. Based on cross-sectional data, in the CCHS the estimated excess loss of forced expiratory volume in one second (FEV1) per pack-year of smoking was 7.4 mL in female smokers who inhaled and 6.3 mL in male smokers who inhaled. In the GPS, the corresponding excess loss of FEV1 was 10.5 and 8.4 mL in females and males, respectively. Two hundred and eighteen subjects in the CCHS and 23 in the GPS were hospitalized during follow-up. Risk associated with pack-years was higher in females than in males (relative risks (RRs) for 1–20, 20–40 and >40 pack-years were 7.0 (3.5–14.1), 9.8 (4.9–19.6) and 23.3 (10.7–50.9) in females, and 3.2 (1.1–9.1), 5.7 (2.2–14.3) and 8.4 (3.3–21.6) in males) but the interaction term gender×packyears did not reach significance (p=0.08). Results were similar in the GPS. After adjusting for smoking in more detail, females in both cohorts had an increased risk of hospitalization for COPD compared to males with a RR of 1.5 (1.2–2.1) in the CCHS and 3.6 (1.4–9.0) in the GPS. This was not likely to be caused by a generally increased rate of hospital admission for females. Results were similar when including deaths from COPD as endpoint. In two independent population samples, smoking had greater impact on the lung function of females than males, and after adjusting for smoking females subsequently suffered a higher risk of being admitted to hospital for COPD. Results suggest that adverse effects of smoking on lung function may be greater in females than in males. Eur Respir J 1997; 10: 822–827. *The Copenhagen Center for Prospective Population Studies at the Institute of Preventive Medicine, Copenhagen Hospital Corporation, Copenhagen, Denmark. **Institute of Biostatistics, University of Copenhagen, Denmark. +Danish Epidemiology Science Center, State Serum Institute, Copenhagen, Denmark. ++Dept of Pulmonary Medicine P, Bispebjerg Hospital, Copenhagen, Denmark.
Cached Long Short-Term Memory Neural Networks for Document-Level Sentiment Classification

Recently, neural networks have achieved great success on sentiment classification due to their ability to alleviate feature engineering. However, one of the remaining challenges is to model long texts in document-level sentiment classification under a recurrent architecture because of the deficiency of the memory unit. To address this problem, we present a Cached Long Short-Term Memory neural networks (CLSTM) to capture the overall semantic information in long texts. CLSTM introduces a cache mechanism, which divides memory into several groups with different forgetting rates and thus enables the network to keep sentiment information better within a recurrent unit. The proposed CLSTM outperforms the state-of-the-art models on three publicly available document-level sentiment analysis datasets.
An In-Depth Analysis of Compressive Sensing for High Speed Video Acquisition

Compressive sensing [1, 2] is a novel technique that has been gaining increasing importance in the last years. It states that a signal can be perfectly recovered when sampled at rates below those dictated by the Shannon-Nyquist theorem provided this signal is sparse in some basis (or dictionary) and the sampling pattern meets some conditions. One of the applications showing the great potential of compressive sensing is the capture of high speed high resolution video in a single frame. In their work, Hitomi et al. [3, 4] present a framework capable of recovering a video sequences from a single image where the temporal information is coded with a per-pixel shutter that samples different time instants for every pixel. In this work, we have performed an in-depth analysis of the system they propose, running extensive tests over a range of parameters of influence, possible algorithms of choice, and characteristics of the input videos. We show that there is room for improvement in a number of aspects of their framework, which are detailed below.
Centripetal flow of pseudopodial surface components could propel the amoeboid movement of Caenorhabditis elegans spermatozoa

Latex beads and wheat germ agglutinin (WGA) were used to examine the movement of membrane components on amoeboid spermatozoa of Caenorhabditis elegans. The behavior of beads attached to the cell revealed continuous, directed movement from the tip of the pseudopod to its base, but no movement on the cell body. Lectin receptors are also cleared from the pseudopod (4). Blocking preexisting lectin receptors with unlabeled WGA followed by pulse-labeling wih fluorescent WGA showed that new lectin receptors are continuously inserted at the tip of the pseudopod. Like latex beads, these new lectin receptors move continuously over the pseudopod surface to the cell body-pseudopod junction where they are probably internalized. Mutants altering the rate of membrane flow, and eliminating its topographical asymmetry, have been identified. Together with the observation that fluorescent phospholipids are cleared from the pseudopod of developing spermatozoa at the same rate as lectin receptors (25), these results show that there is bulk membrane flow over the pseudopod with assembly at the tip and apparent disassembly at the base. There are no vesicles visible at either the pseudopodial tip or base, so these spermatozoa must have a novel mechanism for insertion and uptake of membrane components. This membrane flow could provide the forward propulsion of spermatozoa attached to a substrate by their pseudopods.
Lifestyle and Host Defense Mechanisms of the Dung Beetle, Euoniticellus intermedius: The Toll Signaling Pathway

Abstract The dung beetle, Euoniticellus intermedius (Reiche) (Coleoptera: Scarabaeidae) is an important ecological and agricultural agent. Their main activity, the burying of dung, improves quality of the soil and reduces pests that could cause illness in animals. E. intermedius are therefore important for agriculture and for good maintenance of the environment, and are regarded as effective biological control agents for parasites of the gastrointestinal tract in livestock. The ability of E. intermedius to co-exist comfortably with many microorganisms, some of which are important human pathogens, stimulated our interest in its host defense strategies. The aim of this study was to investigate the Toll signaling pathway, which is strongly activated by fungi. Gene expression associated with fungal infection was analyzed by using 2-D gel electrophoresis and mass spectroscopy. Furthermore, the partial adult transcriptome was investigated for the presence of known immune response genes by using high-throughput sequencing and bioinformatics. The results presented here suggest that E. intermedius responds to fungal challenge via the Toll signaling pathway.
Latent pH-responsive ratiometric fluorescent cluster based on self-assembled photoactivated SNARF derivatives

Abstract We have developed a self-assembled fluorescent cluster comprising a seminaphthorhodafluor (SNARF) derivative protected by a photoremovable o-nitrobenzyl group. Prior to UV irradiation, a colorless and nonfluorescent cluster was spontaneously assembled in aqueous solution. After UV irradiation, the self-assembled cluster remained intact and showed a large enhancement in pH-responsive fluorescence. The unique pH responsive fluorescent cluster could be used as a dual-emissive ratiometric fluorescent pH probe not only in the test tube but also in HeLa cell cultures.
Journal of Geography in Higher Education

A BSTRACT The development and testing of a Web-based GIS e-learning resource is described. This focuses on the application of GIS for siting a nuclear waste disposal facility and the associated principles of spatial decision-making using Boolean and weighted overlay methods. Initial student experiences in using the system are analysed as part of a research project on teaching GIS concepts to large numbers of students with little or no prior GIS experience. Some general thoughts on the utility of Web-based GIS for learning and teaching are presented. Results from the ﬁrst cohort of 167 undergraduate/postgraduate geography students using the system indicate that students ﬁnd it easy to use, a useful aid to learning about the issues involved, and a thought-provoking exercise in Internet-based democracy.
Exact symmetry of large N_c QCD

QCD and QED exhibit an infinite set of three–point Green’s functions that contain only OZI rule violating contributions, and (for QCD) vanish exactly in the large Nc limit. This is due to symmetrization, do not follow from any Lagrangian symmetry, and constitutes the discovery of a new symmetry principle in QCD and QED. We prove that the amplitude for a neutral hybrid {1, 3, 5 . }−+ exotic current to create ηπ0 vanishes exactly for QCD in the large Nc limit. Crystal Barrel’s experimental claim of a resonant 1−+ decaying to ηπ0 suggests that the 1−+ is not a hybrid meson.
Intrinsic Sensor Noise Features for Forensic Analysis on Scanners and Scanned Images

A large portion of digital images available today are acquired using digital cameras or scanners. While cameras provide digital reproduction of natural scenes, scanners are often used to capture hard-copy art in a more controlled environment. In this paper, new techniques for nonintrusive scanner forensics that utilize intrinsic sensor noise features are proposed to verify the source and integrity of digital scanned images. Scanning noise is analyzed from several aspects using only scanned image samples, including through image denoising, wavelet analysis, and neighborhood prediction, and then obtain statistical features from each characterization. Based on the proposed statistical features of scanning noise, a robust scanner identifier is constructed to determine the model/brand of the scanner used to capture a scanned image. Utilizing these noise features, we extend the scope of acquisition forensics to differentiating scanned images from camera-taken photographs and computer-generated graphics. The proposed noise features also enable tampering forensics to detect postprocessing operations on scanned images. Experimental results are presented to demonstrate the effectiveness of employing the proposed noise features for performing various forensic analysis on scanners and scanned images.
Molecular Biomarkers of Pancreatic Intraepithelial Neoplasia and Their Implications in Early Diagnosis and Therapeutic Intervention of Pancreatic Cancer

Lack of early detection and effective interventions is a major reason for the poor prognosis and dismal survival rates for pancreatic cancer. Pancreatic intraepithelial neoplasia (PanIN) is the most common precursor of invasive pancreatic ductal adenocarcinoma (PDAC). Each stage in the progression from PanIN to PDAC is well characterized by multiple significant genetic alterations affecting signaling pathways. Understanding the biological behavior and molecular alterations in the progression from PanIN to PDAC is crucial to the identification of noninvasive biomarkers for early detection and diagnosis and the development of preventive and therapeutic strategies for control of pancreatic cancer progression. This review focuses on molecular biomarkers of PanIN and their important roles in early detection and treatment of pancreatic cancer.
Channel Equalization Using Dynamic Fuzzy Neural Networks

Channel equalization is a major method for reducing distortion and interference effects on a communication channel. In this paper, channel equalization using soft computing methods is attempted. To be more specific, Dynamic Fuzzy Neural Networks (DFNN) which combines fuzzy rules and neural networks is adopted. The DFNN is functionally equivalent to a Takagi-Sugeno-Kang (TSK) fuzzy system possessing the learning ability of a Radial Basis Function (RBF) neural network. The hidden neurons (rules) of the DFNN can be added and pruned dynamically during the training process based on the significance of each neuron to achieve a compact topology structure. Simulation studies demonstrate that the performance of the DFNN-based equalizer is superior to some other existing equalizers in terms of Bit Error Rate (BER).
Ribosomal Biogenesis and Translational Flux Inhibition by the Selective Inhibitor of Nuclear Export (SINE) XPO1 Antagonist KPT-185

Mantle cell lymphoma (MCL) is an aggressive B-cell lymphoma characterized by the aberrant expression of several growth-regulating, oncogenic effectors. Exportin 1 (XPO1) mediates the nucleocytoplasmic transport of numerous molecules including oncogenic growth-regulating factors, RNAs, and ribosomal subunits. In MCL cells, the small molecule KPT-185 blocks XPO1 function and exerts anti-proliferative effects. In this study, we investigated the molecular mechanisms of this putative anti-tumor effect on MCL cells using cell growth/viability assays, immunoblotting, gene expression analysis, and absolute quantification proteomics. KPT-185 exhibited a p53-independent anti-lymphoma effect on MCL cells, by suppression of oncogenic mediators (e.g., XPO1, cyclin D1, c-Myc, PIM1, and Bcl-2 family members), repression of ribosomal biogenesis, and downregulation of translation/chaperone proteins (e.g., PIM2, EEF1A1, EEF2, and HSP70) that are part of the translational/transcriptional network regulated by heat shock factor 1. These results elucidate a novel mechanism in which ribosomal biogenesis appears to be a key component through which XPO1 contributes to tumor cell survival. Thus, we propose that the blockade of XPO1 could be a promising, novel strategy for the treatment of MCL and other malignancies overexpressing XPO1.
Optimization of Cell Surface Binding Enhances Efficiency and Specificity of Molecular Conjugate Gene Delivery*

Molecular conjugates, or polyplexes, are promising synthetic vectors for targeted, in vivo gene delivery, if their efficiency can be improved. Gaining mechanistic information on conjugate gene delivery can potentially yield significant improvements in transfer efficiency by revealing barriers to conjugate transfer from the cell surface to the nucleus. We have developed an experimental system that employs epidermal growth factor as the ligand to direct delivery of DNA encoding the green fluorescent protein to mouse fibroblasts. We report here that the initial step of delivery, binding of the conjugate to the cell surface, is a barrier to gene transfer. We examined the effects of conjugate charge, ligand cross-linker spacer length, and ligand valency on polyplex cell surface binding, internalization, and gene transfer. We find that delivery is both efficient and specific only within a relatively narrow window of conjugate charge, results that correlate with binding and internalization of radiolabeled conjugate. In addition, increasing the cross-linker length can improve binding affinity and delivery. Finally, there is a significant optimum in gene delivery as a function of ligand valency, due to saturation of receptor binding and internalization. Optimizing parameters that affect surface binding therefore improves the efficiency and specificity of molecular conjugate gene delivery.
Contact with Cultural Others – The Friendship Family Programme

The Friendship Family Programme is a cultural exchange initiative piloted this year at Edinburgh Napier University. It is designed to give international students a chance to have first-hand experience of the local culture and way of life, in addition to life on campus. Students are paired with volunteer staff families, who also get the chance to better understand international transitions and learn about the students' home countries and cultures. The programme was grounded in research findings which indicate that social support and friendship with host nationals reduce the acculturative stress and ease the transition of international students. Indeed, international students do not have a full-scale support system in the United Kingdom (UK) and tend to experience loneliness and homesickness during their stay. Meanwhile, the literature also indicates the need for all university staff to understand the background of their students and to be aware of the unique challenges that confront them in the UK. Internationalisation includes mutual cultural awareness and respect. This ‘On the horizon’ piece introduces the Friendship Family Programme and the rationale behind the initiative, along with testimonials from participants.