Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a promoter element located upstream from the hepatitis B virus X gene

We have analyzed a series of plasmids in which the sequences located upstream from the hepatitis B virus (HBV) X gene were linked to the chloramphenicol acetyl transferase (CAT) gene. Expression of the marker CAT gene in transfected cells clearly demonstrated that sequences preceding the X gene contain an active promoter. RNA mapping by primer extension indicated that the RNA encoded by the X gene promoter initiates at multiple sites spanning nucleotides 1250 to 1350 on the HBV genome. Deletion within the adjacent HBV enhancer element region significantly reduced the activity of the X gene promoter, suggesting that the X gene promoter requires the enhancer element for maximal activity.
Simulation of sub-pixel thermal target detection

Spectral unmixing is commonly used in the solar-reflective spectral regime to find materials down to abundances (‘pixel fill factors’ (PFFs) or ‘target fractions’) of (typically) ∼10%. 12 However, little is known about whether such spectral unmixing applies in the long-wavelength-infrared (LWIR) spectral regime (designated herein as the “thermal” region). The first part of this paper discusses a numerical method to un-mix thermal pixels for target fraction, temperature and emissivity (ε). In the second part, a simulation is performed to detect particular material spectra at the sub-pixel level. The data is assumed to have been reduced to a temperature map and an emissivity data cube (a three-dimensional construct consisting of emissivity versus pixel position in the image plane corresponding to a given spectral interval; referred to herein as a ‘cube’ consisting of ε, x, y). Thus, a hyperspectral emissivity cube is generated and sub-pixel targets are added. The scene is then blurred. Various pre-processing algorithms are then evaluated with respect to the detectability of sub-pixel targets. The result of sharpening a hyperspectral cube increases the number of correctly identified sub-pixel targets compared to attempts at target detection with no pre-processing. In particular, the simple sharpened masking filter generates excellent results. We believe that many sub-pixel target detection algorithms could potentially benefit from sharpening of the spectral data cube.
Regulation of adenosine transport by D‐glucose in human fetal endothelial cells: involvement of nitric oxide, protein kinase C and mitogen‐activated protein kinase

1 The effects of elevated D‐glucose on adenosine transport were investigated in human cultured umbilical vein endothelial cells isolated from normal pregnancies. 2 Elevated D‐glucose resulted in a time‐ (8‐12 h) and concentration‐dependent (half‐maximal at 10 ± 2 mM) inhibition of adenosine transport, which was associated with a reduction in the Vmax for nitrobenzylthioinosine (NBMPR)‐sensitive (es) saturable nucleoside with no significant change in Km. D‐Fructose (25 mM), 2‐deoxy‐D‐glucose (25 mM) or D‐mannitol (20 mM) had no effect on adenosine transport. 3 Adenosine transport was inhibited following incubation of cells with the protein kinase C (PKC) activator phorbol 12‐myristate 13‐acetate (PMA; 100 nM, 30 min to 24 h). D‐Glucose‐induced inhibition of transport was abolished by calphostin C (100 nM, an inhibitor of PKC), and was not further reduced by PMA. 4 Increased PKC activity in the membrane (particulate) fraction of endothelial cells exposed to D‐glucose or PMA was blocked by calphostin C but was unaffected by NG‐nitro‐L‐arginine methyl ester (L‐NAME; 100 μM, an inhibitor of nitric oxide synthase (NOS)) or PD‐98059 (10 μM, an inhibitor of mitogen‐activated protein kinase kinase 1). 5 D‐Glucose and PMA increased endothelial NOS (eNOS) activity, which was prevented by calphostin C or omission of extracellular Ca2+ and unaffected by PD‐98059. 6 Adenosine transport was inhibited by S‐nitroso‐N‐acetyl‐l,D‐penicillamine (SNAP; 100 μM, an NO donor) but was increased in cells incubated with L‐NAME. The effect of SNAP on adenosine transport was abolished by PD‐98059. 7 Phosphorylation of mitogen‐activated protein kinases p44mapk (ERK1) and p42mapk (ERK2) was increased in endothelial cells exposed to elevated D‐glucose (25 mM for 30 min to 24 h) and the NO donor SNAP (100 μM, 30 min). The effect of D‐glucose was blocked by PD‐98059 or L‐NAME, which also prevented the inhibition of adenosine transport mediated by elevated D‐glucose. 8 Our findings provide evidence that D‐glucose inhibits adenosine transport in human fetal endothelial cells by a mechanism that involves activation of PKC, leading to increased NO levels and p42‐p44mapk phosphorylation. Thus, the biological actions of adenosine appear to be altered under conditions of sustained hyperglycaemia.
PHYLOGENETICS OF SPINY POCKET MICE (GENUS LIOMYS): ANALYSIS OF CYTOCHROME b BASED ON MULTIPLE HEURISTIC APPROACHES

Abstract We examined phylogenetic relationships among species of Liomys, including L. adspersus (Panamanian spiny pocket mouse), L. irroratus (Mexican spiny pocket mouse), L. pictus (painted spiny pocket mouse), L. salvini (Salvin's spiny pocket mouse), and L. spectabilis (Jaliscan spiny pocket mouse), several species of Heteromys, as well as representatives of other genera of heteromyids and 2 geomyids by using 1,140 base pairs of the mitochondrial cytochrome-b gene. Gene sequences analyzed under maximum-parsimony (MP), maximum-likelihood (ML), and Bayesian inference optimality criteria converged on essentially identical gene tree topologies. Liomys is paraphyletic relative to Heteromys and this relationship is well supported, with L. adspersus and L. salvini arranged as basal taxa relative to Heteromys. Our gene trees also recovered L. pictus as paraphyletic relative to L. spectabilis and these 2 taxa formed the sister group to L. irroratus. Constraint trees that held the genera Heteromys and Liomys as monophyletic (MP and ML criteria) were significantly longer or less likely (P < 0.009 and 0.046, respectively) than our optimal trees, whereas trees that arranged L. pictus as monophyletic relative to L. spectabilis were not significantly longer (P < 0.101) under the MP criterion, but were significantly less likely under the ML criterion (P < 0.020).
A Comparative Study of Different Sentiment Lexica for Sentiment Analysis of Tweets

We report on interoperability of different sentiment lexica with each other and with the linguistic notions negation and modality for sentiment analysis of tweets in a comprehensive ablation study and in competition results for SemEval 2015. Our approach performed well at the tweet level, but excelled in the presence of ﬁgurative language.
Immunosafety and chronic toxicity evaluation of monomethoxypoly(ethylene glycol)-b-poly(lactic acid) polymer micelles for paclitaxel delivery

Abstract To investigate the physicochemical properties, immunosafety and chronic toxicity of monomethoxypoly(ethylene glycol)-b-poly(lactic acid) (mPEG-PLA), a copolymer used as a carrier for paclitaxel (PTX) delivery. The H-Nuclear Magnetic Resonance (H-NMR), dynamic light scattering and fluorescence probe technique were conducted to determine the physicochemical properties of mPEG-PLA copolymer. PTX-loaded polymeric micelles were characterized regarding their particle size, entrapment efficiency (EE), drug loading (DL), in vitro drug release and hemolysis rate. The complement activation in human serum and mast cells degranulation were performed by ELISA and RBL-2H3 cell line in vitro, respectively. The chronic toxicity study was carried out on beagle dogs. The optimized PTX-loaded mPEG-PLA (40/60) micelles showed a particle size of 37 nm and EE of 98.0% with a DL of 17.0% w/w. Transmission electron microscopy (TEM) analyses showed that mPEG-PLA (40/60) micelles have spherical shape with dense core. In vitro release study showed a sustained release for 24 h, and the hemolysis study revealed that mPEG-PLA (40/60) was a safe nanocarrier for intravenous administration. mPEG-PLA (40/60) showed a lower complement activation ability compared to mPEG-PLA (50/50) and CremophorÂ® EL (Cr EL). Furthermore, the chronic toxicity of PTX-loaded mPEG-PLA (40/60) micelles was significantly lower than those of mPEG-PLA (50/50) and Cr EL.
BodySpeech : A configurable facial and gesture animation system for speaking avatars

Speaking avatars are present in many Human Computer Interaction (HCI) applications. Their importance lies in communicative goals which entail interaction within other avatars in virtual worlds or in marketing where they have become useful in customer push strategies. Generating automatic and plausible animations from speech cues have become a challenge. We present BodySpeech, an automatic system to generate gesture and facial animations driven by speech. Body gestures are aligned with pitch accents and selected based on the strength relation between speech and body gestures. Concurrently, facial animation is generated for lip sync, adding emphatic hints according to intonation strength. Furthermore, we have implemented a tool for animators. This tool enables us to modify the detection of pitch accents and the intonation strength influence on output animations, allowing animators to define the activation of gestural performances.
Structural analysis of processed corneas

Background: Disruption of the microstructure in corneal stroma can lead to the loss of transparency. The lack of a characterization method for the microstructure prevents such scaffolds to be implemented in tissue transplantation. The non-invasive, three-dimensional (3D) rendering multiphoton microscopy (MPM) poses the potential to solve this problem. Methods: MPM images and data analyses were performed with three kinds of samples with known and different quality. Isosurfaces (ISOs) were constructed for the evaluation of void volume and collagen distribution. Results: The differences in the microstructures of these samples were revealed with clear indications and links to their behaviours in rehydration and possible transparency. According to this analysis, the scaffold with the highest void space ratio amongst the three presented the highest successful rates to be thoroughly rehydrated. Conclusions: Such a method can be developed for assessing the quality of tissue engineered corneas, or donated corneas, and be useful as a powerful research tool in cornea related research.
Complexity Theory : Thirty-Five Years of Set Disjointness

The set disjointness problem features k communicating parties and k subsets S1, S2, . , Sk ⊆ {1, 2, . , n}. No single party knows all k subsets, and the objective is to determine with minimal communication whether the k subsets have nonempty intersection. The important special case k = 2 corresponds to two parties trying to determine whether their respective sets intersect. The study of the set disjointness problem spans almost four decades and offers a unique perspective on the remarkable evolution of communication complexity theory. We discuss known results on the communication complexity of set disjointness in the deterministic, nondeterministic, randomized, unbounded-error, and multiparty models, emphasizing the variety of mathematical techniques involved.
XSLT stylesheet generation by example with WYSIWYG editing

XSLT plays an important role in data conversions between different XML representations. However, besides the transformations between XML data representations, conversion to an HTML document is one of the most practical tasks for XSLT, because it allows XML documents to be rendered in a human-readable form using Web browsers. We have developed XSLbyDemo, which is an XSLT stylesheet generation module to be plugged into a commercially available full-fledged HTML authoring tool. The remarkable feature of XSLbyDemo is that users can create an XSLT stylesheet automatically solely on the basis of their knowledge of HTML editing. We briefly explain situations where stylesheets for XML rendering are needed. We then introduce the rule generation method based on the users' operation history recorded behind the WYSIWYG editor, and in particular explain the ways of generalizing the created rules so that the obtained rules can be applied to other documents slightly different from the original one. Finally, we give a practical example of the rules generation by XSLbyDemo, and demonstrate that our method can be used for not only the conversion but also the partitioning of a real-life HTML document into smaller pages represented with Compact HTML to be rendered on Web-enabled cellular phones such as i-mode phones.
Design of a computer code “HPFCODE” to evaluate the influence of the harmonics in the electrical networks

This paper aims to present the design of a computer code (HPFCODE) of the power flow and losses in power systems under the influence of harmonics, using the GUI in MATLAB. After describing the program was run for two networks IEEE 6 nodes and IEEE 14 nodes. The power flow by Newton-Raphson method was calculated as the loss of active and reactive power in the lines, respectively, where the loads are linear and nonlinear (Static Var Compensator (SVC), Thyristor controlled Reactor (TCR), and Unified Power Flow Control (UPFC)).
Impact of comorbidity on lung cancer survival

Lung cancer is associated with smoking and age, both of which are associated with comorbidity. We evaluated the impact of comorbidity on lung cancer survival. Data on 56 comorbidities were abstracted from the records of a cohort of 1,155 patients. Survival effects were evaluated with Cox regression (outcome crude death). The adjusted R2 statistic was used to compare the survival variation explained by predictive variables. No comorbidity was observed in 11.7% of patients, while 54.3% had 3 or more (mean 2.97) comorbidities. In multivariate analysis, 19 comorbidities were associated with survival: HIV/AIDS, tuberculosis, previous metastatic cancer, thyroid/glandular diseases, electrolyte imbalance, anemia, other blood diseases, dementia, neurologic disease, congestive heart failure, COPD, asthma, pulmonary fibrosis, liver disease, gastrointestinal bleeding, renal disease, connective tissue disease, osteoporosis and peripheral vascular disease. Only the latter was protective. Some of the hazards of comorbidities were explained by more directly acting comorbidities and/or receipt of treatment. Stage explained 25.4% of the survival variation. In addition to stage, the 19 comorbidities explained 6.1%, treatments 9.2%, age 3.7% and histology 1.3%. Thirteen uncommon comorbidities (prevalence <6%) affected 21.2% of patients and explained 3.5% of the survival variation. Comorbidity count and the Charlson index were significant predictors but explained only 2.5% and 2.0% of the survival variation, respectively. Comorbidity has a major impact on survival in early‐ and late‐stage disease, and even infrequent deleterious comorbidities are important collectively. Comorbidity count and the Charlson index failed to capture much information. Clinical practice and trials need to consider the effect of comorbidity in lung cancer patients. © 2002 Wiley‐Liss, Inc.
Printer-friendly Version Interactive Discussion Reccap Uncertainty Bgd Printer-friendly Version Interactive Discussion

Biogeosciences Discussions This discussion paper is/has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG if available. Abstract Characterisation of regional carbon budgets and processes (the overall task addressed in this series of articles) is inherently a statistical task. In full form this means that almost all quantities used or produced are realizations or instances of probability distributions. We usually compress the description of these distributions by using some 5 kind of location parameter (e.g. the mean) and some measure of spread or uncertainty (e.g. the standard deviation). Characterising and calculating these uncertainties, and their structure in space and time, is as important as the location parameter but uncertainties are both harder to calculate and harder to interpret. In this paper we describe the various classes of uncertainty that arise in a process like RECCAP and describe 10 how they interact in formal estimation procedures. We also point out the impact these uncertainties will have on the various RECCAP synthesis activities.
A Study of Probabilistic and Algebraic Methods for Semantic Similarity

We study and propose in this article several novel solutions to the task of semantic similarity between two short texts. The proposed solutions are based on the probabilistic method of Latent Dirichlet Allocation (LDA) and on the algebraic method of Latent Semantic Analysis (LSA). Both methods, LDA and LSA, are completely automated methods used to discover latent topics or concepts from large collection of documents. We propose a novel word-to-word similarity measure based on LDA as well as several text-totext similarity measures. We compare these measures with similar, known measures based on LSA. Experiments and results are presented on two data sets: the Microsoft Research Paraphrase corpus and the User Language Paraphrase corpus. We found that the novel word-to-word similarity measure based on LDA is extremely promising.
Religious Leaders’ Attitudes and Beliefs about Genetics Research and the Human Genome Project

Kinh Luan Dinh Phan is a second-year medical student at the University of Michigan Medical School, Ann Arbor. David John Doukas, MD, is Assistant Professor in Family Practice and is Associate Director for Clinical Bioethics at the Program in Society and Medicine, University of Michigan Medical School. Michael D. Fetters, MD, MPH, is an Instructor in Family Practice at the University of Michigan Medical School.
ActivPass: Your Daily Activity is Your Password

This paper explores the feasibility of automatically extracting passwords from a user's daily activity logs, such as her Facebook activity, phone activity etc. As an example, a smartphone might ask the user: "Today morning from whom did you receive an SMS? " In this paper, we observe that infrequent activities (i.e., outliers) can be memorable and unpredictable. Building on this observation, we have developed an end to end system ActivPass and experimented with 70 users. With activity logs from Facebook, browsing history, call logs, and SMSs, the system achieves 95% success (authenticates legitimate users) and is compromised in 5.5% cases (authenticates impostors). While this level of security is obviously inadequate for serious authentication systems, certain practices such as password sharing can immediately be thwarted from the dynamic nature of passwords. With security improvements in the future, activity-based authentication could fill in for the inadequacies in today's password-based systems.
Prevalence of two root canals in human mandibular anterior teeth in an Iranian population.

BACKGROUND Complete debridement and obturation of the root canal system is a key factor in successful endodontic treatment and the operator should therefore have thorough knowledge of the root canal morphology of the teeth. Numerous studies have been carried out to investigate the canal configuration of different tooth types in various populations. AIMS The aim of the present study was to investigate the internal anatomy of mandibular incisors and canines in an Iranian population. MATERIALS AND METHODS A total of 463 mandibular anterior teeth, including 186 centrals, 128 laterals, and 149 canines, were examined. A standard clearing technique was used to make the teeth transparent. India ink was injected into the canals of the teeth and the samples were examined with a magnifying glass. The root canal configurations were categorized according to the Vertucci classification. RESULTS All the incisors in this study had one root, and 12.08% of the canines had two roots. We found a slightly higher prevalence of the second canal in incisors than in canines (36.62% vs. 20.48%). However, the probability of canines having two separate apical foramina was higher than that for incisors (12.08% vs. 0.64%). CONCLUSIONS In view of the high prevalence of two-canaled mandibular anterior teeth found in this study, it would be prudent to assume that any mandibular anterior tooth being treated is two-canaled until a thorough search proves otherwise.
Piezoelectric Energy Harvesting with an Ultrasonic Vibration Source

A piezoelectric energy harvester was developed in this paper. It is actuated by the vibration leakage from the nodal position of a high-power ultrasonic cutting transducer. The harvester was excited at a low displacement amplitude (0.73 µmpp). However, its operation frequency is quite high and reaches the ultrasonic range (24.4 kHz). Compared with another low frequency harvester (66 Hz), both theoretical and experimental results proved that the advantages of this high frequency harvester include (i) high current generation capability (up to 20 mApp compared to 1.3 mApp of the 66 Hz transducer) and (ii) low impedance matching resistance (500 Ω in contrast to 50 kΩ of the 66 Hz transducer). This energy harvester can be applied either in sensing, or vibration controlling, or simply energy harvesting in a high-power ultrasonic system.
Unsupervised lexicon induction for clause-level detection of evaluations

Abstract This article proposes clause-level evaluation detection, which is a fine-grained type of opinion mining, and describes an unsupervised lexicon building method for capturing domain-specific knowledge by leveraging the similar polarities of sentiments between adjacent clauses. The lexical entries to be acquired are called polar atoms, the minimum human-understandable syntactic structures that specify the polarity of clauses. As a hint to obtain candidate polar atoms, we use context coherency, the tendency for the same polarity to appear successively in a context. Using the overall density and precision of coherency in the corpus, the statistical estimation picks up appropriate polar atoms from among the candidates, without any manual tuning of the threshold values. The experimental results show that the precision of polarity assignment with the automatically acquired lexicon was 83 per cent on average, and our method is robust for corpora in diverse domains and for the size of the initial lexicon.
Team RoboSimian: Semi‐autonomous Mobile Manipulation at the 2015 DARPA Robotics Challenge Finals

This paper discusses hardware and software improvements to the RoboSimian system leading up to and during the 2015 DARPA Robotics Challenge (DRC) Finals. Team RoboSimian achieved a 5th place finish by achieving 7 points in 47:59 min. We present an architecture that was structured to be adaptable at the lowest level and repeatable at the highest level. The low‐level adaptability was achieved by leveraging tactile measurements from force torque sensors in the wrist coupled with whole‐body motion primitives. We use the term “behaviors” to conceptualize this low‐level adaptability. Each behavior is a contact‐triggered state machine that enables execution of short‐order manipulation and mobility tasks autonomously. At a high level, we focused on a teach‐and‐repeat style of development by storing executed behaviors and navigation poses in an object/task frame for recall later. This enabled us to perform tasks with high repeatability on competition day while being robust to task differences from practice to execution.