Miracle-dz/UniFAR-FTUs huggingface dataset:
HDL and CER-001 Inverse-Dose Dependent Inhibition of Atherosclerotic Plaque Formation in apoE-/- Mice: Evidence of ABCA1 Down-Regulation

Objective CER-001 is a novel engineered HDL-mimetic comprised of recombinant human apoA-I and charged phospholipids that was designed to mimic the beneficial properties of nascent pre-ß HDL. In this study, we have evaluated the dose-dependent regulation of ABCA1 expression in vitro and in vivo in the presence of CER-001 and native HDL (HDL3). Methods and Results CER-001 induced cholesterol efflux from J774 macrophages in a dose-dependent manner similar to natural HDL. A strong down-regulation of the ATP-binding cassette A1 (ABCA1) transporter mRNA (- 50%) as well as the ABCA1 membrane protein expression (- 50%) was observed at higher doses of CER-001 and HDL3 compared to non-lipidated apoA-I. In vivo, in an apoE-/- mouse “flow cessation model,” in which the left carotid artery was ligatured to induce local inflammation, the inhibition of atherosclerotic plaque burden progression in response to a dose-range of every-other-day CER-001 or HDL in the presence of a high-fat diet for two weeks was assessed. We observed a U-shaped dose-response curve: inhibition of the plaque total cholesterol content increased with increasing doses of CER-001 or HDL3 up to a maximum inhibition (- 51%) at 5 mg/kg; however, as the dose was increased above this threshold, a progressively less pronounced inhibition of progression was observed, reaching a complete absence of inhibition of progression at doses of 20 mg/kg and over. ABCA1 protein expression in the same atherosclerotic plaque was decreased by-45% and-68% at 50 mg/kg for CER-001 and HDL respectively. Conversely, a-12% and 0% decrease in ABCA1 protein expression was observed at the 5 mg/kg dose for CER-001 and HDL respectively. Conclusions These data demonstrate that high doses of HDL and CER-001 are less effective at slowing progression of atherosclerotic plaque in apoE-/- mice compared to lower doses, following a U-shaped dose-response curve. A potential mechanism for this phenomenon is supported by the observation that high doses of HDL and CER-001 induce a rapid and strong down-regulation of ABCA1 both in vitro and in vivo. In conclusion, maximally efficient HDL- or CER-001-mediated cholesterol removal from atherosclerotic plaque is achieved by maximizing macrophage-mediated efflux from the plaque while minimizing dose-dependent down-regulation of ABCA1 expression. These observations may help define the optimal dose of HDL mimetics for testing in clinical trials of atherosclerotic burden regression.
Teaching Expository Comprehension Skills in Early Childhood Classrooms

Purpose: This pilot project implemented and evaluated a theme-based unit designed to teach expository comprehension skills to young children in four preschool classrooms. Method: The program and the unit were collaborative efforts of speech-language pathologists (SLPs) and early childhood educators. Within topically related units, 71 children ages 4:1 to 5:0 engaged in first-hand experiences related to narrative texts, adapted expository texts, and mapping tasks within large group, small group, and class routine contexts. Data sources consisted of expository compare/contrast and problem/solution tasks, classroom observations, teacher and parent interviews, and parent surveys. Results: During instruction most of the 71 participating children made gains in both the compare/contrast and problem/solution tasks. They spontaneously applied problem/solution strategies in noninstructional settings. Teachers and parents reported that children were motivated by and engaged in the playful but systematic instruction. Discussion: Although there were limitations in the study, results suggest that preschool children are able to benefit from expository instruction that is explicit, purposeful, and focused on topics of natural interest to young children. The study should be replicated with refined measures and a more diverse population.
Pain management in the 21st century: utilization of pharmacogenomics and therapeutic drug monitoring

Introduction: Anesthesiologists and pain management physicians recognize that the key to clinical success is the ability to effectively control pain and related symptoms in patients without causing excess side effects from prescribed medications. The use of opioids for pain management is broadly accepted by regulatory bodies, professional organizations (i.e., the WHO) and physicians, as is the wide range of patient responses to these medications. Pharmacogenomics and therapeutic drug monitoring are two underutilized tools which can be implemented to best predict and monitor which opioid and dose may be the most appropriate for an individual patient. Areas covered: This review summarizes and discusses evidence for the use of genetic analysis to guide the selection and modification of opioid therapy along with the use of therapeutic drug monitoring to objectively check therapeutic outcomes and compliance. The reader will gain an understanding of the most notable genetic polymorphisms that can affect a patient's response to commonly prescribed opioids, along with the clinical benefits of genotyping and performing therapeutic drug monitoring. Expert opinion: In the end, the authors strongly believe that objective tools such as pharmacogenomics and therapeutic drug monitoring provide added benefit (minimizing adverse effects, while maximizing efficacy) and will ultimately advance the practice of pain management by incorporating these tools into the standard of care.
Local density fluctuations, hyperuniformity, and order metrics.

Questions concerning the properties and quantification of density fluctuations in point patterns continue to provide many theoretical challenges. The purpose of this paper is to characterize certain fundamental aspects of local density fluctuations associated with general point patterns in any space dimension d. Our specific objectives are to study the variance in the number of points contained within a regularly shaped window Omega of arbitrary size, and to further illuminate our understanding of hyperuniform systems, i.e., point patterns that do not possess infinite-wavelength fluctuations. For large windows, hyperuniform systems are characterized by a local variance that grows only as the surface area (rather than the volume) of the window. We derive two formulations for the number variance: (i) an ensemble-average formulation, which is valid for statistically homogeneous systems, and (ii) a volume-average formulation, applicable to a single realization of a general point pattern in the large-system limit. The ensemble-average formulation (which includes both real-space and Fourier representations) enables us to show that a homogeneous point pattern in a hyperuniform state is at a "critical point" of a type with appropriate scaling laws and critical exponents, but one in which the direct correlation function (rather than the pair correlation function) is long ranged. We also prove that the non-negativity of the local number variance does not add a new realizability condition on the pair correlation. The volume-average formulation is superior for certain computational purposes, including optimization studies in which it is desired to find the particular point pattern with an extremal or targeted value of the variance. We prove that the simple periodic linear array yields the global minimum value of the average variance among all infinite one-dimensional hyperuniform patterns. We also evaluate the variance for common infinite periodic lattices as well as certain nonperiodic point patterns in one, two, and three dimensions for spherical windows, enabling us to rank-order the spatial patterns. Our results suggest that the local variance may serve as a useful order metric for general point patterns. Contrary to the conjecture that the lattices associated with the densest packing of congruent spheres have the smallest variance regardless of the space dimension, we show that for d=3, the body-centered cubic lattice has a smaller variance than the face-centered cubic lattice. Finally, for certain hyperuniform disordered point patterns, we evaluate the direct correlation function, structure factor, and associated critical exponents exactly.
Neuroglian, Gliotactin, and the Na+/K+ ATPase are essential for septate junction function in Drosophila

One essential function of epithelia is to form a barrier between the apical and basolateral surfaces of the epithelium. In vertebrate epithelia, the tight junction is the primary barrier to paracellular flow across epithelia, whereas in invertebrate epithelia, the septate junction (SJ) provides this function. In this study, we identify new proteins that are required for a functional paracellular barrier in Drosophila. In addition to the previously known components Coracle (COR) and Neurexin (NRX), we show that four other proteins, Gliotactin, Neuroglian (NRG), and both the α and β subunits of the Na+/K+ ATPase, are required for formation of the paracellular barrier. In contrast to previous reports, we demonstrate that the Na pump is not localized basolaterally in epithelial cells, but instead is concentrated at the SJ. Data from immunoprecipitation and somatic mosaic studies suggest that COR, NRX, NRG, and the Na+/K+ ATPase form an interdependent complex. Furthermore, the observation that NRG, a Drosophila homologue of vertebrate neurofascin, is an SJ component is consistent with the notion that the invertebrate SJ is homologous to the vertebrate paranodal SJ. These findings have implications not only for invertebrate epithelia and barrier functions, but also for understanding of neuron–glial interactions in the mammalian nervous system.
Safety and Efficacy of Banaba–Moringa oleifera–Green Coffee Bean Extracts and Vitamin D3 in a Sustained Release Weight Management Supplement

This 60‐day, 30‐subject pilot study examined a novel combination of ingredients in a unique sustained release (Carbopol matrix) tablet consumed twice daily. The product was composed of extracts of banaba leaf, green coffee bean, and Moringa oleifera leaf and vitamin D3. Safety was assessed using a 45‐measurement blood chemistry panel, an 86‐item self‐reported Quality of Life Inventory, bone mineral density, and cardiovascular changes. Efficacy was assessed by calculating a body composition improvement index (BCI) based on changes in dual energy X‐ray absorptiometry measured fat mass (FM) and fat‐free mass (FFM) as well as between the study group (SG) and a historical placebo group. No changes occurred in any blood chemistry measurements. Positive changes were found in the Quality of Life (QOL) inventory composite scores. No adverse effects were observed. Decreases occurred in FM (p = 0.004) and increases in FFM (p = 0.009). Relative to the historical placebo group, the SG lost more FM (p < 0.0001), gained more FFM (p = <0.0001), and had a negative BCI of −2.7 lb. compared with a positive BCI in the SG of 3.4 lb. , a 6.1 discordance (p = 0.0009). The data support the safety and efficacy of this unique product and demonstrate importance of using changes in body composition versus scale weight and BMI. © 2016 The Authors Phytotherapy Research Published by John Wiley & Sons Ltd
The utility of a single sputum specimen in the diagnosis of tuberculosis. Comparison between HIV-infected and non-HIV-infected patients.

STUDY OBJECTIVES (1) To assess the utility of a single sputum specimen in the evaluation of HIV-infected patients who are suspected of having tuberculosis (TB). (2) To identify radiographic findings that discriminate between HIV-infected patients with TB and those with pneumonia of other causes. DESIGN Retrospective cohort analysis. PATIENTS All patients evaluated at Harborview Medical Center, Seattle, between January 1986 and July 1994 in whom culture of respiratory secretions grew Mycobacterium tuberculosis or Mycobacterium avium-complex. Patients who were coinfected with HIV formed the primary study group. Their chest radiographs were then compared with those of a matched group of patients with pneumonia of other causes. MEASUREMENTS AND RESULTS We identified 164 patients with TB, 20 of whom were HIV infected. The initial sputum specimen grew M tuberculosis in all HIV-infected patients and 99% of non-HIV-infected patients. Seventy percent of HIV-infected and 71% of non-HIV-infected patients had at least one positive smear. Most of these patients tested positive on their initial smear, and no significant difference was found between HIV-positive and HIV-negative patients (79% and 90%, respectively [p = 0.34]). The addition of a second sputum smear identified all HIV-infected patients and all but one in non-HIV-infected patients who were ultimately determined to be smear positive. A total of 27 HIV-infected patients had a positive acid-fast bacilli sputum smear during the study period, 14 of which were attributable to TB (specificity = 52%). The only radiographic findings that discriminated between HIV-infected patients with TB and those with pneumonia of other causes were the presence of cavitation or a miliary pattern (p = 0.014). CONCLUSIONS A single sputum specimen was sufficient to establish the diagnosis in all HIV-infected patients with pulmonary TB. A single negative sputum smear made the diagnosis of TB significantly less likely. However, a minimum of two smears were necessary to achieve an acceptable early diagnostic yield. The presenting chest radiograph failed to discriminate between HIV-infected patients with TB and pneumonia of other causes in most cases.
Word Senses

What is the meaning of a word? Unless one believes that we are born with an innate set of meanings waiting to find their corresponding expression in language, another option is that we learn the meaning of a word by observing how it is used by the language community we are born in. Some usages find their way into dictionaries and become established word senses. In order to understand what constitutes a word sense, we can look at the criteria lexicographers use when they decide that a word usage is a word sense and record it in a dictionary for future generations.
SeqCluSum: Combining Sequential Clustering and Contextual Importance Measuring to Summarize Developing Events over Time

Unexpected events such as accidents, natural disasters and terrorist attacks represent an information situation where it is essential to give users access to important and non-redundant information as fast as possible. In this paper, we introduce SeqCluSum, a temporal summarization system which combines sequential clustering to cluster sentences and a contextual importance measurement to weight the created clusters and thereby to identify important sentences. We participated with this system in the TREC Temporal Summarization track where systems have to generate extractive summaries for developing events by publishing sentencelength updates extracted from web documents. Results show that our approach is very well suited for this task by achieving best results. We furthermore point out several improvement possibilities to show how the system can further be enhanced.
CollectiveTeach: Crowdsourcing Lesson Plans

Lack of quality textbooks and good educational resources is a well-known problem in developing regions. In this paper, we describe the design of CollectiveTeach, a web platform that aims to integrate rich educational content into an inquiry-based framework, viz. the 5E learning model, for generating web-annotated lesson plans for school and college teachers in developing countries. Given the wealth of educational resources on the Web, CollectiveTeach helps teachers to author new lesson plans through a simple web interface allowing them to easily search, select, order and collect educational content relevant to the topics they wish to teach. This paper describes our experiences building two versions of the Col-lectiveTeach platform. The initial platform was tested via a user study with a cohort of 19 teachers in Ghana and the learnings of this user study were incorporated in a second, improved version of CollectiveTeach; the current prototype of CollectiveTeach was evaluated using human experts for computer science subjects covered in standard undergraduate curriculum.
Space- and time-efficient deterministic algorithms for biased quantiles over data streams

Skew is prevalent in data streams, and should be taken into account by algorithms that analyze the data. The problem of finding "biased quantiles"—that is, approximate quantiles which must be more accurate for more extreme values—is a framework for summarizing such skewed data on data streams. We present the first deterministic algorithms for answering biased quantiles queries accurately with small—sublinear in the input size—space and time bounds in one pass. The space bound is near-optimal, and the amortized update cost is close to constant, making it practical for handling high speed network data streams. We not only demonstrate theoretical properties of the algorithm, but also show it uses less space than existing methods in many practical settings, and is fast to maintain.
Design of Efficient Adaptive Neuro-Fuzzy Controller Based on Supervisory Learning Capable for Speed and Torque Control of BLDC Motor

Brushless DC (BLDC) motors have been widely used in many field of drives for their high power/weight, high torque, high efficiency, long operating life, noiseless operation, high speed ranges and ease of control. In this paper, a Neuro-Fuzzy Controller (NFC) based on supervisory learning is presented for the speed and torque control of BLDC motors to enhance high control performance of the drive under transient and steady state conditions. This designed controller is combination of Neural Networks (NNs) and Fuzzy Logic (FL), therefore has parallel processing and learning abilities of NNs and inference capacity of FL. For improvement the performance of leaning algorithm and thereupon increase efficiency of drive, instead of usual Error Back Propagation (EBP) learning technique, a fuzzy based supervisory learning algorithm is employed. The proposed controller has simple structure and also due to its modest fuzzy rule in rule-base is relatively easy for implementation. This controller has high accuracy, suitable performance, high robustness and high tracking efficiency. In order to demonstrate the NFC ability to tracking reference speed and torque and also test of robustness and rejection ability of controller against undesired disturbances or suddenly changes in speed and torque, these designs are simulated with MATLAB/SIMULINK. In some cases, results are compared with that of a conventional PID controller and other designs. Streszczenie. W artykule zaprezentowane uklad sterowania bezszczotkowym silnikiem DC z wykorzystaniem sterownika Neuro-Fuzzy. Dla poprawienia efektywności uczenia sieci zamiast wstecznej propagacji bledu zaproponowano algorytm wykorzystujący logike rozmytą. Sterownik okazal sie byc dokladny, odporny i o duzej efektywności śledzenia zmian. Porownano mozliwości kontrolera z konwencjonalnym sterownikiem PID. (Projekt skutecznego sterownika silnika bezszczotkowego DC z wykorzystaniem sieci neuronowych i logiki rozmytej)
Insights into Structural and Mechanistic Features of Viral IRES Elements

Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements.
Timing and Lattice Attacks on a Remote ECDSA OpenSSL Server: How Practical Are They Really?

In 2011, B.B. Brumley and N.Tuveri found a remote timing attack on OpenSSL’s ECDSA implementation for binary curves. We will study if the title of their paper was indeed relevant (Remote Timing Attacks are Still Practical). We improved on their lattice attack using the Embedding Strategy that reduces the Closest Vector Problem to the Shortest Vector Problem so as to avoid using Babai’s procedures to solve the CVP and rely on the better experimental results of LLL. We will detail (along with publishing the source code of the tools we used) our attempts to reproduce their experiments from a remote machine located on the same network with the server, and see that such attacks are not trivial and far from being practical. Finally we will see other attacks and countermeasures.
FLORIN - A System to Support (Near) Real-Time Applications on User Generated Content on Daily News

In this paper, we propose a system, FLORIN, which provides support for near real-time applications on user generated content on daily news. FLORIN continuously crawls news outlets for articles and user comments accompanying them. It attaches the articles and comments to daily event stories. It identifies the opinionated content in user comments and performs named entity recognition on news articles. All these pieces of information are organized hierarchically and exportable to other applications. Multiple applications can be built on this data. We have implemented a sentiment analysis system that runs on top of it.
Bone-marrow transplantation in a patient with sickle-cell anemia.

SICKLE-CELL anemia affects 1 in 600 of the U.S. black population and accounts for 80,000 deaths annually throughout the world.1 , 2 Current therapy is designed to prevent sickle-cell crises, but supportive care remains the only treatment available once they occur. Attempts to alter the expression of hemoglobin genes in β-thalassemia and sickle-cell anemia with the use of azacytidine have produced only transient effects.3 This report describes the conversion of sickle-cell anemia to sickle-cell trait by marrow transplantation (done for treatment of leukemia) in a child with both sickle-cell anemia and acute myeloblastic leukemia. It raises the possibility of using marrow transplantation .
Advances in noise robust digit recognition using hybrid exemplar-based techniques

Expressing noisy speech spectra as a linear combination of speech and noise exemplars has been shown to be a powerful tool to achieve noise robust ASR. Such a model has been used both to do feature enhancement (FE) and to directly provide noise robust speech state probabilities using a method called sparse classification (SC). The goal of this work is threefold: First, we integrate various SC advances recently proposed in literature, second, we improve upon the results obtained with FE through retraining and multi-condition training of the acoustic models used in the recognizer and finally, we propose the use of a single hybrid SC-FE system. In our experiments on AURORA-2 we obtain an impressive 3% and 5% average WER on matched and on mismatched noise types, respectively.