Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting community patterns capturing exceptional link trails

We present a new method for detecting descriptive community patterns capturing exceptional (sequential) link trails. For that, we provide a novel problem formalization: We model sequential data as first-order Markov chain models, mapped to an attributed weighted network represented as a graph. Then, we detect subgraphs (communities) using exceptional model mining techniques: We target subsets of sequential transitions between nodes that are exceptional in that sense that they either conform strongly to a specific reference or show significant deviations, estimated by a quality measure. In particular, such a community is described by a community pattern composed of descriptive features (of the attributed graph) covering the respective community. We present a comprehensive modeling approach and discuss results of a case study analyzing data from two real-world social networks.
Solitaire Flow-Restoration Device for Treatment of Acute Ischemic Stroke: Safety and Recanalization Efficacy Study in a Swine Vessel Occlusion Model

BACKGROUND AND PURPOSE: The extended time window and theoretic reduction in hemorrhage make mechanical strategies an attractive approach in the treatment of patients with ischemic stroke. My purpose was to evaluate the recanalization efficacy and safety of the Solitaire FR Revascularization Device in a swine vessel occlusion model. MATERIALS AND METHODS: For recanalization efficacy, radio-opaque clots were used in 6 ascending pharyngeal arteries of the swine. Safety was assessed in 8 renal arteries with 3 passes of the device. Four vessels were harvested at 30 days, and 4, at 90 days, with microscopic examination to assess vessel damage. RESULTS: On deployment, immediate flow was seen in 3/6 vessels; and on retrieval, TIMI-3 recanalization was seen in 6/6. Vasospasm, which resolved on follow-up angiography with no distal emboli or vessel damage, was noted. In the renal vessels, safety evaluation findings were unremarkable, with the exception of 2 vessels harvested from a kidney at 90 days. These 2 vessels appeared without damage on microscopy; however, angiography showed shrinkage of the entire kidney, which was attributed to damage and stenosis of the main renal artery at the site of the guide-catheter insertion, likely leading to a chronic low-flow state and resultant atrophy of the entire kidney. CONCLUSIONS: The Solitaire Device showed good recanalization efficacy with acceptable safety. The unique stent-like design allows immediate flow restoration, a distinct advantage of the device. On the basis of this study, the device has good potential as a tool in the treatment of patients with ischemic stroke.
Investigation of the Gas Barrier Properties of PP/Clay Nanocomposite Films with EVA as a Compatibiliser Prepared by the Melt Intercalation Method

In this research, polypropylene (PP) nanocomposite films were prepared by melt intercalation method and their properties have been evaluated. To facilitate the formation of either intercalated or exfoliated nanocomposites, ethylene vinyl acetate copolymer (EVA) was used as a compatibiliser. Morphology of composites was determined by X-ray Diffraction (XRD) and transmission electron microscopy (TEM). XRD and TEM analyses confirmed that increasing of EVA content leads to achievement of intercalated nanocomposites. Furthermore, differential scanning calorimetry (DSC) measurement indicated a decrease in crystallinity, melting point and crystallization temperature. Also, permeability tests showed that gas barrier properties of PP/EVA nanocomposite films against oxygen can be significantly improved by increasing of organoclay content even at low concentration. Tension test showed that organoclay exhibits a considerable increase in Young's modulus and stress at break of nanocomposite films.
Ultrafast Mid-infrared Fibre Lasers

Laser light has enabled some of the most important scientific discoveries and innovations, and research in newer types of lasers continues to reveal more applications. Mid-infrared light, which interacts strongly with naturally occurring molecules, holds many promises in sensing and medical technologies and their applications are now beginning to appear. This surging development will strongly benefit with the availability of field-usable, compact and robust sources of mid-infrared light. The fibre lasers have the extreme potential to achieve this; however their performance in terms of generating ultrafast pulses of mid-infrared light has not yet been demonstrated. Here we explore the potential fluoride fibre lasers have in the ultrafast pulsed regime. We have demonstrated this via the production of nanosecond, to picosecond, and finally femtosecond pulses from fluoride fibre lasers using a variety of methods. These demonstrations reveal that fluoride fibres lasers are strong candidates to be an ultrafast mid-infrared source, with applications ranging from frequency comb based molecular sensing to next generation laser scalpels.
Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.

Shotgun metagenomics creates millions of fragments of short DNA reads, which are meaningless unless analyzed appropriately. The Metagenomics RAST server (MG-RAST) is a web-based, open source system that offers a unique suite of tools for analyzing these data sets. After de-replication and quality control, fragments are mapped against a comprehensive nonredundant database (NR). Phylogenetic and metabolic reconstructions are computed from the set of hits against the NR. The resulting data are made available for browsing, download, and most importantly, comparison against a comprehensive collection of public metagenomes. A submitted metagenome is visible only to the user, unless the user makes it public or shares with other registered users. Public metagenomes are available to all.
Bayesian Networks 2014-2015 Assignment II – Learning Bayesian Networks 1

The purpose of this assignment is to test and possibly expand your knowledge about learning Bayesian networks from data, by exploring various issues such as comparison of learning algorithms, dealing with missing data and evaluation of the networks learnt. Recall that learning Bayesian networks involves both structure learning, i.e., learning the graph topology from data, and parameter learning, i.e., learning the actual, local probability distributions from data. There are basically two approaches to structure learning: (i) search-and-score structure learning, and (ii) constraint-based structure learning. Recent approaches are also based on the combination of these two classes of algorithms. Search-and-score algorithms search for a Bayesian network structure that fits the data best (in some sense). They start with an initial network structure (often a graph without arcs or a complete graph), and then traverse the search space of network structures by in each step either removing an arc, adding an arc, or reversing an arc. Read the paper by Castello and Kočka [1] for a good overview of the principles and difficulties associated with this learning method. Recent search-and-score-algorithms take Markov equivalence into account, i.e., they search in the space of equivalence classes of Bayesian networks and the scoring method they use give the same score for equivalent networks. Bayesian networks with different graph topologies that are included in the same Markov equivalence class represent exactly the same conditionalindependence information by d-separation. Examples of search-and-score algorithms are K2 and inclusion-driven learning, usually based on hill-climbing (greedy) search. Constraint-based algorithms carry out a conditional (in)dependence analysis on the data. Based on this analysis an undirected graph is generated (to be interpreted as a Markov network). Using additional independence tests, this network is converted into a Bayesian network. Constraint-based learning algorithms allow for the easy incorporation of background knowledge, i.e., prior knowledge on dependences or independences that hold for the domain under consideration. Examples of constraint-based learning algorithms are PC, NPC, growshrink, and incremental association. A good paper discussing the difficulties with constraintbased methods is the paper by Chickering and Meek [2]. For the underlying theory, consult the book “Bayesian Artificial Intelligence” [3] and the two papers referred to above, which can be downloaded from the course assignments webpage. You may consult more specialised books, if required. In the following Sections 2, 3 and 4 you will find descriptions of the software, datasets and the tasks that you need to perform in order to complete this assignment.
Calmodulin-like Protein Increases Filopodia-dependent Cell Motility via Up-regulation of Myosin-10*

Human calmodulin-like protein (CLP) is an epithelial-specific protein that is expressed during cell differentiation but down-regulated in primary cancers and transformed cell lines. Using stably transfected and inducible HeLa cell lines, we found that CLP expression did not alter the proliferation rate and colony-forming potential of these cells. However, remarkable phenotypic changes were observed in CLP-expressing compared with control cells. Soft agar colonies of CLP-expressing cells had rough boundaries, with peripheral cells migrating away from the colony. Cells expressing CLP displayed a striking increase in the number and length of myosin-10-positive filopodia and showed increased mobility in a wound healing assay. This increase in wound healing capacity was prevented by small interference RNA-mediated down-regulation of myosin-10. Fluorescence microscopy and Western blotting revealed that CLP expression results in up-regulation of its target protein, myosin-10. This up-regulation occurs at the protein level by stabilization of myosin-10. Thus, CLP functions by increasing the stability of myosin-10, leading to enhanced myosin-10 function and a subsequent increase in filopodial dynamics and cell migration. In stratified epithelia, CLP may be required during terminal differentiation to increase myosin-10 function as cells migrate toward the upper layers and establish new adhesive contacts.
A low-power integrated circuit for analog spike detection and sorting in neural prosthesis systems

Since the proof of viability of prosthetic devices directly controlled by neurons, there is a huge increase in the interest on integrated multichannel recording systems to register neural signals with implanted chronic electrodes. One of the bottlenecks in such compact systems is the limited rate of data transmission by the wireless link, requiring some sort of data compression/reduction. We propose an analog low power integrated system for action potential (AP) detection and sorting that reduces the output data rate ~100 times. In this system, AP detection is performed by a double threshold method that reduces the probability of false detections while AP sorting is based on the measurement of peak and trough amplitudes and peak width. The circuit has been implemented in 0.35 - mum CMOS technology with power consumption of 70 muW per channel including the pre-amplifier. The system was tested with real recorded traces: compared to standard AP sorting techniques, the proposed simple AP sorter was able to correctly assign to single units over 90% of detected APs.
Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration

Autophagy is a regulated lysosomal degradation process that involves autophagosome formation and transport. Although recent evidence indicates that basal levels of autophagy protect against neurodegeneration, the exact mechanism whereby this occurs is not known. By using conditional knockout mutant mice, we report that neuronal autophagy is particularly important for the maintenance of local homeostasis of axon terminals and protection against axonal degeneration. We show that specific ablation of an essential autophagy gene, Atg7, in Purkinje cells initially causes cell-autonomous, progressive dystrophy (manifested by axonal swellings) and degeneration of the axon terminals. Consistent with suppression of autophagy, no autophagosomes are observed in these dystrophic swellings, which is in contrast to accumulation of autophagosomes in the axonal dystrophic swellings under pathological conditions. Axonal dystrophy of mutant Purkinje cells proceeds with little sign of dendritic or spine atrophy, indicating that axon terminals are much more vulnerable to autophagy impairment than dendrites. This early pathological event in the axons is followed by cell-autonomous Purkinje cell death and mouse behavioral deficits. Furthermore, ultrastructural analyses of mutant Purkinje cells reveal an accumulation of aberrant membrane structures in the axonal dystrophic swellings. Finally, we observe double-membrane vacuole-like structures in wild-type Purkinje cell axons, whereas these structures are abolished in mutant Purkinje cell axons. Thus, we conclude that the autophagy protein Atg7 is required for membrane trafficking and turnover in the axons. Our study implicates impairment of axonal autophagy as a possible mechanism for axonopathy associated with neurodegeneration.
Nanostructured diffractive optical elements on SiNX membrane for UV-visible regime applications

Silicon nitride (SiNX) film is a commonly used material in silicon technology. In addition, it has excellent optical properties. It is transparent in both the UV and visible range, with a high refractive index of about 1.7~2. Owing to its superior mechanical and optical properties, we used a silicon nitride membrane as an optical phase element. We will fabricate nano-structured diffractive optical elements, such as wave-plate, polarizer, and polarized beam splitter on SiNXHY membrane by e-beam lithography for the UV-visible regime applications. The SiNXHY membranes were made from SiNXHY films deposited by an plasma enhanced chemical vapor deposition (PECVD) as an alternative method for low stress membrane fabrication used in UV-visible transmittance. The stress of silicon nitride film showed a change from compressive to tensile with increasing working pressure during film deposition. The UV-visible transmittance of the free standing membrane was measured, which showed that UV light is transparent at wavelength as short as 240nm. We will show the feasibility to fabricate nano-structured diffractive optical elements on the SiNXHY membrane combined with microoptoelectromechanical systems (MOEMS) technology for the application in the UV-visible regimes.
Twelve tips for developing effective mentors

Mentoring is often identified as a crucial step in achieving career success. However, not all medical trainees or educators recognize the value of a mentoring relationship. Since medical educators rarely receive training on the mentoring process, they are often ill equipped to face challenges when taking on major mentoring responsibilities. This article is based on half-day workshops presented at the 11th Ottawa International Conference on Medical Education in Barcelona on 5 July 2004 and the annual meeting of the Association of American Medical Colleges in Boston on 10 November 2004 as well as a review of literature. Thirteen medical faculty participated in the former and 30 in the latter. Most participants held leadership positions at their institutions and mentored trainees as well as supervised mentoring programs. The workshops reviewed skills of mentoring and strategies for designing effective mentoring programs. Participants engaged in brainstorming and interactive discussions to: (a) review different types of mentoring programs; (b) discuss measures of success and failure of mentoring relationships and programs; and (c) examine the influence of gender and cultural differences on mentoring. Participants were also asked to develop an implementation plan for a mentoring program for medical students and faculty. They had to identify student and faculty mentoring needs, and describe methods to recruit mentors as well as institutional reward systems to encourage and support mentoring.
Performance analysis of low bit rate H.26L video encoder

A new video encoder proposal, H.26L, is compared against H.263 and H.263+. In the comparison, both computational complexity and compression performance are analyzed. Moreover, the trade-off possibilities between the complexity and compression performance within H.26L are presented. Experimental comparisons with H.263 and H.263+ show that H.26L reduces the output bit rate about 30% with the same quality. The computation time increases about three times compared to H.263 and leads into the encoding speed of 3-6 fps for QCIF sequences on a 400 MHz Pentium III processor. Realtime operation can be achieved by applying additional, algorithmic and platform-specific optimizations.
PicAChoo: a tool for customizable feature extraction utilizing characteristics of textual data

Although documents have hundreds of thousands of unique words, only a small number of words are significantly useful for intelligent services. For this reason, feature extraction has become an important issue to be addressed in various fields, such as information retrieval, text mining, pattern recognition, etc. Numerous supporting tools for feature extraction are available, but most of them deal with text as a simple literal. Unfortunately, text is not just a literal, but a semantically significant unit including linguistic characteristics. So, we need customized extraction methods that consider the characteristics of source documents. PicAChoo stands for 'Pick And Choose', and it provides an environment which enables feature extraction methods using the structure of sentences and the part-of-speech information of words. Moreover, we suggest dynamic composition of different extraction methods without hard-coding.
Feasibility and Preliminary Efficacy of a Web-Based Smoking Cessation Intervention for HIV-Infected Smokers: A Randomized Controlled Trial

Objective:To evaluate the feasibility and preliminary efficacy of a Web-based tobacco treatment for persons living with HIV (PLWH). Design:Prospective, randomized controlled trial. Setting:HIV-care center in the Bronx, New York. Subjects:Eligibility criteria included HIV infection, current tobacco usage, interest in quitting, and access to a computer with internet. One hundred thirty-eight subjects enrolled, and 134 completed the study. Intervention:Positively Smoke Free on the Web (PSFW), an 8-session, 7-week targeted tobacco treatment program for PLWH, was compared with standard care (brief advice to quit and self-help brochure). All subjects were offered nicotine patches. Main Outcome Measures:The main feasibility outcomes were number of sessions logged into, number of Web pages visited, number of interactive clicks, and total time logged in. The main efficacy outcome was biochemically verified, 7-day point prevalence abstinence 3 months after intervention. Results:PSFW subjects logged into a mean of 5.5 of 8 sessions and 26.2 of 41 pages. They executed a mean of 10 interactive clicks during a mean total of 59.8 minutes logged in. Most required reminder phone calls to complete the sessions. Educational level, anxiety score, and home access of the Web site were associated with Web site usage. Ten percent of the PSFW group vs. 4.3% of controls achieved the abstinence end point. Among those who completed all 8 sessions, 17.9% were abstinent, and among women completers, 30.8% were abstinent. Conclusions:Web-based treatment is a feasible strategy for PLWH smokers, and preliminary findings suggest therapeutic efficacy.
Mining complex relationships in the SDSS SkyServer spatial database

We describe the process of mining complex relationships in spatial databases using the maximal participation index (maxPI), which has a property of discovering low support and high confidence rules. Complex relationships are defined as those involving two or more of: multifeature co-location, self-co-location, one-to many relationships, self-exclusion and multifeature exclusion. We report our results of mining complex relationships in data extracted from the Sloan Digital Sky Survey (SDSS) database.
The galactic dynamo effect due to Parker-shearing instability of magnetic flux tubes I. General formalism and the linear approximation

In this paper we investigate the idea of Hanasz & Lesch 1993 that the galactic dynamo effect is due to the Parker instability of magnetic flux tubes. In addition to the former ap- proach,wetakeintoaccountmoregeneralphysicalconditionsin this paper, by incorporating cosmic rays and differential forces due to the axisymmetric differential rotation and the density waves as well. We present the theory of slender magnetic flux tube dy- namics in the thin flux tube approximation and the Lagrange description. This is the application of the formalism obtained for solar magnetic flux tubes by Spruit (1981), to the galactic conditions.WeperformalinearstabilityanalysisfortheParker- shearing instability of magnetic flux tubes in galactic discs and then calculate the dynamo coefcients. We present a number of new effects which are very essen- tial for cosmological and contemporary evolution of galactic magnetic elds. First of all we demonstrate that a very strong dynamo-effect is possible in the limit of weak magnetic elds inpresenceofcosmicrays.Second,weshowthatthedifferential force resulting from axisymmetric differential rotation and the linear density waves causes that the -effect is essentially mag- nied in galactic arms and switched off in the interarm regions. Moreover, we predict a non-uniform magnetic eld in spiral arms and well aligned one in interarm regions. These properties are well conrmed by recent observational results by Beck & Hoernes (1996)
Factors That Influence Blood Pressure in 3- to 5-Year-Old Children: A Pilot Study

While incident elevations in blood pressure (BP) are apparent in preschool years, factors influencing BP in this population have received little attention. The purposes of this pilot study were to determine the feasibility of collecting data from preschoolers and their mothers and to determine effect sizes of relationships between BP and sex, race, birth status, body mass index (BMI), waist circumference (WC), geographic location, serum C-reactive protein (CRP), and salivary cortisol (morning, afternoon). A hypothesis-generating correlational design was used; 56 children, aged 3–5 years, were enrolled from six rural and urban Head Start programs in a southeastern state. On Day 1 of data collection, mothers completed demographic questionnaires and children had blood drawn by finger stick. On Day 2, children gave saliva samples for cortisol, were measured for height by stadiometer, weight by digital scales, and WC by tape measure and had their BP measured by Dinamap. Incident elevations in BP were found in 30% of children (17/56), the majority of which were of systolic BP; 65% of those with elevations were of normal weight. Data collection was feasible with few problems. Small-to-medium effect sizes were noted for BP status (normal, prehypertensive, and hypertensive) and cortisol p.m. and birth status (parent-reported prematurity or term); small effect sizes were seen for BP status and BMI, race, sex, and geographic location. CRP and cortisol had medium- and small-to-medium effect sizes, respectively, with diastolic blood pressure. Studies with larger, more diverse samples need to be conducted to test hypotheses posited from these estimated effect sizes.