Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement of Cytokine Secretion, Intracellular Protein Expression, and mRNA in Resting and Stimulated Peripheral Blood Mononuclear Cells

ABSTRACT Quantitation of cytokine production is a valuable adjunct to standard immunologic assays in defining several pathologic processes. Nevertheless, there is little agreement about which tissues should be assayed, which type of assay should be performed, and which stimulation protocol should be used. As these types of assays enter the clinical arena, there is need for standardization. There is also a need to maximize the amount of information which may be derived from a single sample. We compared secreted interleukin 4 (IL-4), IL-2, IL-6, tumor necrosis factor alpha (TNF-α), and gamma interferon proteins as measured by enzyme-linked immunosorbent assay with intracellular cytokine production (IL-2 and gamma interferon) as detected by flow cytometry and quantitative competitive PCR for IL-2, IL-4, TNF-α, and gamma interferon mRNA and cDNA. Results from unstimulated cells and cells stimulated with phorbol myristate acetate, phytohemagglutinin, and phorbol myristate acetate plus phytohemagglutin were compared. All three methodologies detected significant stimulation of cytokine production. The combination of phytohemagglutinin and phorbol myristate acetate was overall the most-potent stimulus.
Facilitating Change: Roles of the Early Childhood Literacy Coach

This qualitative study sought to explicate the roles Early Childhood Literacy coaches played in a federally-funded project to improve early language and literacy instruction for preschool children. Across three Head Start sites, participants included classroom teachers, literacy coaches, center coordinators, and program coordinators. Structured interviews were conducted and analyzed to understand the roles assumed by coaches who served preschool teachers.
Review of: Saulo de Freitas Araujo: Wundt and the Philosophical Foundations of Psychology: A Reappraisal

In what case do you like reading so much? What about the type of the wundt and the philosophical foundations of psychology a reappraisal book? The needs to read? Well, everybody has their own reason why should read some books. Mostly, it will relate to their necessity to get knowledge from the book and want to read just to get entertainment. Novels, story book, and other entertaining books become so popular this day. Besides, the scientific books will also be the best reason to choose, especially for the students, teachers, doctors, businessman, and other professions who are fond of reading.
Semantic Structuration of Image Annotations: A Data Mining Approach

Image and video data become more and more popular for various applications. A considerable volume of multimedia data has been produced and we need to develop powerful and user-friendly tools in order to efficiently retrieve relevant information. A great challenge is to develop systems supporting multi-criteria information search, taking advantage of semantic querying and visual content-based retrieval. To do that, we must provide a structuration of metadata attached to image or video data. In this paper, we propose to semiautomatically build a concept hierarchy from manual annotations and visual descriptors. The result of our approach is a concept hierarchy that a user can browse in a non-linear fashion.
A Comparison of the Rest Complex Binding Patterns in Embryonic Stem Cells and Epiblast Stem Cells

We detected and characterized the binding sites of the representative Rest complex components Rest, Sin3A, and Lsd1. We compared their binding patterns in mouse embryonic stem (ES) cells and epiblast stem (EpiS) cells. We found few Rest sites unique to the EpiS cells. The ES-unique site features were distinct from those of the common sites, namely, the signal intensities were weaker, and the characteristic gene function categories differed. Our analyses showed that the Rest binding sites do not always overlap with the Sin3A and Lsd1 binding sites. The Sin3A binding pattern differed remarkably between the ES and EpiS cells and was accompanied by significant changes in acetylated-histone patterns in the surrounding regions. A series of transcriptome analyses in the same cell types unexpectedly showed that the putative target gene transcript levels were not dramatically different despite dynamic changes in the Rest complex binding patterns and chromatin statuses, which suggests that Rest is not the sole determinant of repression at its targets. Nevertheless, we identified putative Rest targets with explicitly enhanced transcription upon Rest knock-down in 143 and 60 common and ES-unique Rest target genes, respectively. Among such sites, several genes are involved in ES cell proliferation. In addition, we also found that long, intergenic non-coding RNAs were apparent Rest targets and shared similar features with the protein-coding target genes. Interestingly, such non-coding target genes showed less conservation through evolution than protein-coding targets. As a result of differences in the components and targets of the Rest complex, its functional roles may differ in ES and EpiS cells.
Stemming Effectiveness in Clustering of Arabic Documents

lustering is an important task gives good results with information retrieval (IR), it aims to automatically put similar documents in one cluster. Stemming is an important technique, used as feature selection to reduce many redundant features have the same root in root-based stemming and have the same syntacticalform in light stemming. Stemming has many advantages it reducesthe size of document and increases processing speed and used in many applications as information retrieval (IR). In this paper, we have evaluatedstemmingtechniques in clustering of Arabic language documents and determined the most efficient in pre- processing of Arabic language,whichis more complex than most other languages. Evaluation used three stemming techniques: root-based Stemming, light Stemming and without stemming. K-means, one of famous and widely clustering algorithm, is applied for clustering.Evaluation depends on recall, precision andF-measure methods. From experiments, results show that light stemming achieved best results in terms of recall, precision and F-measure when compared with others stemming. KEYWORDStext clustering, Stemming, light stemming, K-means.
USE OF A STOCHASTIC WEATHER GENERATOR IN A WATERSHED MODEL FOR STREAMFLOW SIMULATION

Hobson, Adam N. (M.S. Civil, Environmental and Architectural Engineering) Use of a Stochastic Weather Generator in a Watershed Model for Streamflow Simulation Thesis directed by Assistant Professor Balaji Rajagopalan Current methods of streamflow forecasting rely on historic climate sequences that are inadequate in length and have statistical relationships that are difficult to fit and condition. Coupling a stochastic weather generator with a deterministic watershed model can provide better streamflow forecasts. This study presents a technique to couple a k-nearest neighbor stochastic weather generator and the Precipitation-Runoff Modeling System (PRMS) watershed model to simulate historic streamflow statistics and provide a framework for forecasting flows. The weather generator uses weather data in the Upper Truckee River Basin on the California and Nevada border (USA) to produce a simulated dataset. The simulated dataset sufficiently preserves the statistics of the historic record of precipitation and maximum and minimum temperature. Simulated weather variables were used as input to PRMS, which adequately simulated modeled historic streamflows. A conditioned forecast based on wet/dry years was used to demonstrate the utility of the forecasting framework.
Subdural grid implantation for intracranial EEG recording: CT and MR appearance.

PURPOSE Subdural grid arrays are used when seizure activity cannot be located by ictal scalp recordings and when functional cortical mapping is required before surgery. This study was performed to determine and compare the CT and MR imaging appearance of subdural EEG grids and to identify the types and frequency of associated complications. METHODS We retrospectively reviewed the medical records and imaging studies of 51 consecutive patients who underwent 54 craniotomies for subdural EEG grid implantation with either stainless steel or platinum alloy contacts between June 1988 and September 1993. Twenty-two patients had both CT and MR examinations, 27 patients had CT only, and five patients had MR imaging only. All studies were assessed for image quality and degradation by the implanted EEG grids, for intra- and extraaxial collections, and for mass effect, with differences of opinion resolved by consensus. RESULTS Subdural EEG grids caused extensive streak artifacts on all CT scans (corresponding directly to grid composition) and mild to moderate magnetic susceptibility artifacts on MR images. Sixteen associated complications were detected among the 54 patients imaged, including four significant extraaxial hematomas, four subfalcine or transtentorial herniations, two tension pneumocephali, two extraaxial CSF collections, two intraparenchymal hemorrhages, and one case each of cerebritis and brain abscess. In all but four cases, the detected complications were not clinically apparent and did not require specific treatment. There were no residual sequelae. CONCLUSION Because of extensive streak artifacts, CT showed only gross complications, such as herniation and grid displacement by extraaxial collections. MR imaging artifacts were more localized, allowing superior evaluation of subdural EEG grid placement and associated complications.
QUALITY ASSESSMENT OF CUSTOMER REVIEWS EXTRACTED FROM WEB PAGES : A REVIEW CLUSTERING APPROACH

The number of customer reviews that a product receives is growing at very fast rate. Customer reviews posted on the websites vary greatly in quality. In this paper, we make an attempt to assess a review based on its quality, to help the customer make a proper buying decision. The quality of customer review is assessed as most significant, more significant, significant and insignificant. A novel and effective web mining technique based on review clustering is proposed for assessing a customer review of a particular product. This is performed in two steps : (1) Cluster the reviews into four groups by applying k-means clustering technique and compute the cluster weights. (2) Assess quality of the given reviews and classify them by considering the cluster weights. Experimentation has been done using publicly available review databases for four different products. The results are analyzed and the efficacy of the proposed method has been demonstrated. Index Terms: Customer reviews, Feature extraction, Feature weights, Cluster weights, Web mining, Clustering technique.
Hybrids in Hollywood: a study of the production and performance of genre-spanning films

Research suggests there are significant market penalties for organizations that do not conform to category boundaries in their product offerings. Yet, organizations continue to span categories despite these risks. In this study, we shed insight into why by examining factors that shape the attractiveness of producing hybrid (i.e. category-spanning) products. In particular, we argue that more ambiguous category schemas encourage hybridization. Moreover, there is potential for exceptional performance advantages for organizations that innovate through hybrids. We use data from the US feature film industry to test and find support for our hypotheses. Copyright 2012 The Author 2012. Published by Oxford University Press on behalf of Associazione ICC. All rights reserved. , Oxford University Press.
Brain networks underlying the clinical effects of long-term subthalamic stimulation for Parkinson's disease: a 4-year follow-up study with rCBF SPECT.

UNLABELLED The motor improvement derived from high-frequency deep brain stimulation (DBS) of the subthalamic nucleus (STN) in Parkinson's disease (PD) is maintained over time after surgery. The aim of the present prospective follow-up study was to assess regional cerebral blood flow (rCBF) changes related to such improvement in the long term. METHODS Ten PD patients with STN-DBS underwent 3 rCBF SPECT studies at rest-once preoperatively in the off-drug condition and the other 2 postoperatively in the off-drug/on-stimulation conditions at 5 +/- 2 and 42 +/- 7 mo. Patients were administered with Unified Parkinson Disease Rating Scale (UPDRS), Hoehn and Yahr (H&Y) scale, and Schwab and England (S&E) scale. Statistical parametric mapping was used to investigate rCBF changes during long-term STN stimulation in comparison with preoperative rCBF and the relationship between rCBF and UPDRS scores was used as a covariate of interest. RESULTS All patients showed a maximum clinical improvement during the first months after surgery and remained rather stable during further follow-up. The effect of STN-DBS from the pre- to the postoperative condition at 5 mo was to produce rCBF increases in the presupplementary motor area (pre-SMA), premotor (PMC), and dorsolateral prefrontal cortices. From the postoperative condition at 5 mo to that at 42 mo, the STN stimulation produced further rCBF increases in these frontal areas, and also in the primary motor/sensory cortices, globus pallidi, ventral lateral thalamic nuclei, cerebellum, pons, and midbrain entailing the substantia nigra (P < 0.0001). A correlation was detected between the improvement in motor scores and the rCBF increase in the pre-SMA and PMC (P < 0.0001). No correlation was present between the daily consumption of levodopa and the rCBF. CONCLUSION Our study suggests that the long-term STN stimulation leads to improvement in neural activity in the frontal motor/associative areas. After an rCBF increase during the first months of stimulation, these regions showed a further increment in the later phase, which was accompanied by an increased activity in subcortical structures. The correlation between motor improvement and rCBF increase in higher order motor cortical areas suggests that even in the long term, as well as in the short term, the STN-DBS achieves its therapeutic benefit by restoring the activity within these cortical regions.
Peak power output, the lactate threshold, and time trial performance in cyclists.

PURPOSE To determine the relationship between maximum workload (W(peak)), the workload at the onset of blood lactate accumulation (W(OBLA)), the lactate threshold (W(LTlog)) and the D(max) lactate threshold, and the average power output obtained during a 90-min (W(90-min)) and a 20-min (W(20-min)) time trial (TT) in a group of well-trained cyclists. METHODS Nine male cyclists (.VO(2max) 62.7 +/- 0.8 mL.kg(-1). min(-1)) who were competing regularly in triathlon or cycle TT were recruited for the study. Each cyclist performed four tests on an SRM isokinetic cycle ergometer over a 2-wk period. The tests comprised 1) a continuous incremental ramp test for determination of maximal oxygen uptake (.VO(2max) (L.min(-1) and mL.kg(-1). min(-1)); 2) a continuous incremental lactate test to measure W(peak), W(OBLA), W(LTlog), and the D(max) lactate threshold; and 3) a 20-min TT and 4) a 90-min TT, both to determine the average power output (in watts). RESULTS The average power output during the 90-min TT (W(90-min)) was significantly (P < 0.01) correlated with W(peak) (r = 0.91), W(LTlog) (r = 0.91), and the D(max) lactate threshold (r = 0.77, P < 0.05). In contrast, W(20-min) was significantly (P < 0.05) related to . VO(2max) (L.min(-1)) (r = 0.69) and W(LTlog) (r = 0.67). The D(max) lactate threshold was not significantly correlated to W(20-min) (r = 0.45). Furthermore, W(OBLA) was not correlated to W(90-min) (r = 0.54) or W(20-min) (r = 0.23). In addition, . VO(2max) (mL.kg(-1). min(-1)) was not significantly related to W(90-min) (r = 0.11) or W(20-min) (r = 0.47). CONCLUSION The results of this study demonstrate that in subelite cyclists the relationship between maximum power output and the power output at the lactate threshold, obtained during an incremental exercise test, may change depending on the length of the TT that is completed.
Experiences of adheres and nonadheres with an application based on the TransTheoretical model with stage tailored and peer-designed text messages

Background: Nowadays people do not engage in the recommend levels of physical activity. Despite that people in general have favourable attitudes towards healthy behaviours, people often encounter difficulties when trying to maintain a workout schedule. Persuasive technology can stimulate individuals to change their behaviour. This qualitative study is aimed to examine experiences of adheres and nonadheres with the Motiapp. The application (Motiapp) is developed to motivate people to keep exercising or to start exercising. The Motiapp is based on the TransTheoretical Model (TTM) and sends daily text messages to exercise. These text messages are tailored to stage of change of the user and are peer-designed. Method: Individual in-depth interviews about their experiences with the Motiapp were conducted with 15 adheres and with 15 nonadheres of the Motiapp. Interviews were audio-recorded, transcribed and analysed both deductively and inductively. Results: The participants adhered to the Motiapp, because the application was easy to use and the participants were curious about the effects of the Motiapp. The participants nonadhered to the Motiapp, because they got no messages anymore, got a new mobile phone or they disliked certain aspects of the Motiapp. Overall, the messages of the Motiapp were experienced positively. Participants indicated that most of the messages were personal, persuasive and relevant. Moreover, the behavioural processes of the TransTheoretical model were helpful to motivate them to exercise. More than half of the participants indicated that the Motiapp had a positive effect, because it was a reminder to exercise. The other participants indicated that the Motiapp had no effect. However, the participants indicated that the messages were a confirmation to their exercise behaviour. The participants would change the time of receiving the messages and would enlarge the Motiapp with an activity tracking system – to track their activities and to share their activities with friends and the messages should include pictures and links to exercise activities. Conclusion: There are no noticeable difference between the adheres and nonadheres. The most reason for nonadherence are unintentionally. Moreover, it seems adherence can be increased by an easily working application. In general the Motiapp was experienced positively. The messages were experienced as personal and a reminder to exercise. Finally, participants would find a more comprehensive application motivating to exercise more.
Large Networks and Graph Limits

The book Large Networks and Graph Limits, xiv + 475 pp., published in late 2012, comprises five parts, the first an illuminating introduction and the last a tantalizing taste of how the scope of the theory developed in its pages might be extended to other combinatorial structures than graphs. The three central parts treat in depth the topics of graph algebras, limits for sequences of dense graphs (this constitutes the most substantial part, occupying nearly half the book) and limits for sequences of bounded degree graphs. Primarily the book is aimed at graduate students and research mathematicians interested in graph theory and its application to networks (for example, the internet and networks in social science, biology, statistical physics and engineering). There are 23 chapters and an appendix, the latter conveniently giving necessary background from areas of mathematics outside mainstream graph theory. A bibliography collects together the extensive research in this area up to 2012, and a subject, author and notation index facilitate navigation of the book. The author maintains a webpage for corrections and supplementary material. Indeed, via the author’s homepage the reader can freely access the many papers he has written with collaborators on the topic of graph homomorphisms and graph limits. The book synthesizes much of the material in these papers, with some revision in
Optimal estimation for global ground‐level fine particulate matter concentrations

We develop an optimal estimation (OE) algorithm based on top‐of‐atmosphere reflectances observed by the MODIS satellite instrument to retrieve near‐surface fine particulate matter (PM2.5). The GEOS‐Chem chemical transport model is used to provide prior information for the Aerosol Optical Depth (AOD) retrieval and to relate total column AOD to PM2.5. We adjust the shape of the GEOS‐Chem relative vertical extinction profiles by comparison with lidar retrievals from the CALIOP satellite instrument. Surface reflectance relationships used in the OE algorithm are indexed by land type. Error quantities needed for this OE algorithm are inferred by comparison with AOD observations taken by a worldwide network of sun photometers (AERONET) and extended globally based upon aerosol speciation and cross correlation for simulated values, and upon land type for observational values. Significant agreement in PM2.5 is found over North America for 2005 (slope = 0.89; r = 0.82; 1‐σ error = 1 µg/m3 + 27%), with improved coverage and correlation relative to previous work for the same region and time period, although certain subregions, such as the San Joaquin Valley of California are better represented by previous estimates. Independently derived error estimates of the OE PM2.5 values at in situ locations over North America (of ±(2.5 µg/m3 + 31%) and Europe of ±(3.5 µg/m3 + 30%) are corroborated by comparison with in situ observations, although globally (error estimates of ±(3.0 µg/m3 + 35%), may be underestimated. Global population‐weighted PM2.5 at 50% relative humidity is estimated as 27.8 µg/m3 at 0.1° × 0.1° resolution.
Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using ᴅ-Amino Acids

Chirality plays a major role in recognition and interaction of biologically important molecules. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first enzyme of the shikimate pathway, which is responsible for the synthesis of aromatic amino acids in bacteria and plants, and a potential target for the development of antibiotics and herbicides. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) displays an unprecedented complexity of allosteric regulation, with three interdependent allosteric binding sites and a ternary allosteric response to combinations of the aromatic amino acids l-Trp, l-Phe and l-Tyr. In order to further investigate the intricacies of this system and identify key residues in the allosteric network of MtuDAH7PS, we studied the interaction of MtuDAH7PS with aromatic amino acids that bear the non-natural d-configuration, and showed that the d-amino acids do not elicit an allosteric response. We investigated the binding mode of d-amino acids using X-ray crystallography, site directed mutagenesis and isothermal titration calorimetry. Key differences in the binding mode were identified: in the Phe site, a hydrogen bond between the amino group of the allosteric ligands to the side chain of Asn175 is not established due to the inverted configuration of the ligands. In the Trp site, d-Trp forms no interaction with the main chain carbonyl group of Thr240 and less favourable interactions with Asn237 when compared to the l-Trp binding mode. Investigation of the MtuDAH7PSN175A variant further supports the hypothesis that the lack of key interactions in the binding mode of the aromatic d-amino acids are responsible for the absence of an allosteric response, which gives further insight into which residues of MtuDAH7PS play a key role in the transduction of the allosteric signal.