Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 Integrase-DNA Recognition Mechanisms

Integration of a reverse transcribed DNA copy of the HIV viral genome into the host chromosome is essential for virus replication. This process is catalyzed by the virally encoded protein integrase. The catalytic activities, which involve DNA cutting and joining steps, have been recapitulated in vitro using recombinant integrase and synthetic DNA substrates. Biochemical and biophysical studies of these model reactions have been pivotal in advancing our understanding of mechanistic details for how IN interacts with viral and target DNAs, and are the focus of the present review.
Effect of Vagus Nerve Stimulation on Serotonergic and Noradrenergic Transmission

Vagus nerve stimulation (VNS) is an antiepileptic treatment, which has recently shown promise as an antidepressant. Yet, its antidepressant mechanisms of action are unknown. Serotonergic [5-hydroxytryptamine (5-HT, serotonin)] and noradrenergic [norepinephrine (NE)] systems are involved in the pathophysiology of depression and in the mechanisms of action of antidepressants. The present study analyzes 5-HT and NE neuronal firing rates in their brainstem nuclei: the dorsal raphe nucleus (DRN) and locus coeruleus (LC), respectively. The basal firing rates in the DRN and LC were significantly increased after long-term treatments with VNS. After short-term VNS treatments, firing rates were significantly higher for LC (at 1 h and 3 days). As changes in their firing rate may have been due to altered autoreceptor sensitivities, the responses of autoreceptors to the acute administration of their respective agonists were assessed. However, no significant difference was seen in the DRN. No significant differences in dose response curves for 5-HT1A somatodendritic and α2-adrenergic autoreceptors were noticed between long-term VNS and controls. VNS appears to have a novel mechanism of antidepressant action, enabling its effectiveness in treatment-resistant depression. LC firing rates significantly increase earlier than the DRN basal firing. As the LC has an excitatory influence on DRN, it is possible that the increased DRN firing rate is secondary to an initial increased LC firing rate from VNS.
Nearest neighbor classification using bottom-k sketches

Bottom-k sketches are an alternative to k×minwise sketches when using hashing to estimate the similarity of documents represented by shingles (or set similarity in general) in large-scale machine learning. They are faster to compute and have nicer theoretical properties. In the case of k×minwise hashing, the bias introduced by not truly random hash function is independent of the number k of hashes, while this bias decreases with increasing k when employing bottom-k. In practice, bottom-k sketches can expedite classification systems if the trained classifiers are applied to many data points with a lot of features (i.e., to many documents encoded by a large number of shingles on average). An advantage of b-bit k×minwise hashing is that it can be efficiently incorporated into machine learning methods relying on scalar products, such as support vector machines (SVMs). Still, experimental results indicate that a nearest neighbors classifier with bottom-k sketches can be preferable to using a linear SVM and b-bit k×minwise hashing if the amount of training data is low or the number of features is high.
The perception of /l/ vocalization by listeners with speech therapy as children *

To determine the strength of F3 as an acoustic cue for perceiving vocalization – a cross-linguistic process whereby a historical instance of /l/ is realized as a [w]-like sound (Knowles 1987) – of syllable-final /l/, a forced choice identification task was administered to listeners of English (American and New Zealand). A 15-step continuum was synthesized, with endpoints from syllable-final /l/ to vocalized /l/. However, post-task interviews revealed potential interactions from nonnormal language development in participants. Normally developing participants (who had not undergone speech therapy) demonstrated categorical perception. Two participants who had undergone speech therapy as children demonstrated persistent difficulty in perceiving vocalized /l/, but post-hoc analysis suggests that categorization was learned as the experiment progressed. This paper considers the potential implications of these results.
Pre-processing Closed Captions for Machine Translation

We describe an approach to Machine Translation of transcribed speech, as found in closed captions. We discuss how the colloquial nature and input format peculiarities of closed captions are dealt with in a pre-processing pipeline that prepares the input for effective processing by a core MT system. In particular, we describe components for proper name recognition and input segmentation. We evaluate the contribution of such modules to the system performance. The described methods have been implemented on an MT system for translating English closed captions to Spanish and Portuguese.
Eye Blink Detection

Nowadays, people spend more time in front of electronic screens like computers, laptops, TV screens, mobile phones or tablets which cause eye blink frequency to decrease. Each blink spreads the tears on the eye cornea to mois- ture and disinfect the eye. Reduced blink rate causes eye redness and dryness also known as Dry Eye, which belongs to the major symptoms of the Computer Vision Syndrome. The goal of this work is to design eye blink detector which can be used in dry eye prevention system. We have analyzed available tech- niques for blink detection and designed our own solutions based on histogram backprojection and optical flow methods. We have tested our algorithms on different datasets under various lighting conditions. Inner movement detection method based on optical flow performs better than the histogram based ones. We achieve higher recognition rate and much lower false positive rate than the-state-of-the-art technique presented by Divjak and Bischof.
Improving Corpus Comparability for Bilingual Lexicon Extraction from Comparable Corpora

Previous work on bilingual lexicon extraction from comparable corpora aimed at finding a good representation for the usage patterns of source and target words and at comparing these patterns efficiently. In this paper, we try to work it out in another way: improving the quality of the comparable corpus from which the bilingual lexicon has to be extracted. To do so, we propose a measure of comparability and a strategy to improve the quality of a given corpus through an iterative construction process. Our approach, being general, can be used with any existing bilingual lexicon extraction method. We show here that it leads to a significant improvement over standard bilingual lexicon extraction methods.
Oligomerization of a MutS Mismatch Repair Protein from Thermus aquaticus *

The MutS DNA mismatch protein recognizes heteroduplex DNAs containing mispaired or unpaired bases. We have examined the oligomerization of a MutS protein from Thermus aquaticus that binds to heteroduplex DNAs at elevated temperatures. Analytical gel filtration, cross-linking of MutS protein with disuccinimidyl suberate, light scattering, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry establish that the Taq protein is largely a dimer in free solution. Analytical equilibrium sedimentation showed that the oligomerization ofTaq MutS involves a dimer-tetramer equilibrium in which dimer predominates at concentrations below 10 μm. The ΔG 0 2–4 for the dimer to tetramer transition is approximately −6.9 ± 0.1 kcal/mol of tetramer. Analytical gel filtration of native complexes and gel mobility shift assays of an maltose-binding protein-MutS fusion protein bound to a short, 37-base pair heteroduplex DNA reveal that the protein binds to DNA as a dimer with no change in oligomerization upon DNA binding.
Spatial Reasoning for Real-time Robotic Manipulation

Presented in this paper is an approach to real-time spatial reasoning for manipulative robotic tasks. When a service robot is requested to manipulate an object, it should determine the directions along which it can access and remove the object. The potential accessible directions for the object are retrieved from the object database. Then, spatial reasoning with the surrounding environment and the gripper geometry is invoked to verify the directions. The verification process mainly utilizes the visibility test of the commodity graphics hardware. Then, the directions along which both of the object and gripper are translated without colliding with the surrounding obstacles are computed using Minkowski sum and cube map of the graphics hardware. The access and removal directions are passed to the potential field path planning algorithm to determine the robot arm's full path for accessing, removing and delivering the object. The experimental results show the feasibility of using graphics hardware for manipulative robotic tasks and further its performance gain in real-time manipulation
Tumor Necrosis Factor Alpha: A Link between Neuroinflammation and Excitotoxicity

Tumor necrosis factor alpha (TNF-α) is a proinflammatory cytokine that exerts both homeostatic and pathophysiological roles in the central nervous system. In pathological conditions, microglia release large amounts of TNF-α; this de novo production of TNF-α is an important component of the so-called neuroinflammatory response that is associated with several neurological disorders. In addition, TNF-α can potentiate glutamate-mediated cytotoxicity by two complementary mechanisms: indirectly, by inhibiting glutamate transport on astrocytes, and directly, by rapidly triggering the surface expression of Ca+2 permeable-AMPA receptors and NMDA receptors, while decreasing inhibitory GABAA receptors on neurons. Thus, the net effect of TNF-α is to alter the balance of excitation and inhibition resulting in a higher synaptic excitatory/inhibitory ratio. This review summarizes the current knowledge of the cellular and molecular mechanisms by which TNF-α links the neuroinflammatory and excitotoxic processes that occur in several neurodegenerative diseases, but with a special emphasis on amyotrophic lateral sclerosis (ALS). As microglial activation and upregulation of TNF-α expression is a common feature of several CNS diseases, as well as chronic opioid exposure and neuropathic pain, modulating TNF-α signaling may represent a valuable target for intervention.
Video-based characters: creating new human performances from a multi-view video database

We present a method to synthesize plausible video sequences of humans according to user-defined body motions and viewpoints. We first capture a small database of multi-view video sequences of an actor performing various basic motions. This database needs to be captured only once and serves as the input to our synthesis algorithm. We then apply a marker-less model-based performance capture approach to the entire database to obtain pose and geometry of the actor in each database frame. To create novel video sequences of the actor from the database, a user animates a 3D human skeleton with novel motion and viewpoints. Our technique then synthesizes a realistic video sequence of the actor performing the specified motion based only on the initial database. The first key component of our approach is a new efficient retrieval strategy to find appropriate spatio-temporally coherent database frames from which to synthesize target video frames. The second key component is a warping-based texture synthesis approach that uses the retrieved most-similar database frames to synthesize spatio-temporally coherent target video frames. For instance, this enables us to easily create video sequences of actors performing dangerous stunts without them being placed in harm's way. We show through a variety of result videos and a user study that we can synthesize realistic videos of people, even if the target motions and camera views are different from the database content.
Konrad-zuse-zentrum F ¨ Ur Informationstechnik Berlin Branching Rules Revisited Branching Rules Revisited

Mixed integer programs are commonly solved with linear programming based branch-and-bound algorithms. The success of the algorithm strongly depends on the strategy used to select the variable to branch on. We present a new generalization called reliability branching of to-day's state-of-the-art strong branching and pseudocost branching branching strategies for linear programming based branch-and-bound algorithms. After reviewing commonly used branching strategies and performing extensive computational studies we compare different parameter settings and show the superiority of our proposed new strategy.
Stem Cells Are Not Proarrhythmic: Letting the Genie out of the Bottle

Ischemic heart disease remains a leading cause of mortality worldwide. Myocardial infarction (MI) accounts for more than half of cardiovascular-related deaths.1 With rising numbers of surviving MI patients and an aging population, congestive heart failure has become a major health concern, with symptomatic patients having a poorer prognosis.2 Despite substantial advances in medical and device strategies for congestive heart failure, there remains a growing unmet clinical need. Accordingly, various novel therapies have been explored in recent years, with the potential offered by stem cells (SCs) arguably garnering the most attention.3,4 Cardiac SC therapy has emerged as a promising option to repair ischemic/dysfunctional myocardium through a variety of potential mechanisms (Figure 1). 5–7 Continuing debates over unresolved mechanistic issues and the rapid transition toward clinical application, with already-demonstrated modest but tangible benefits for cardiac structure and function, underscore the fact that the field is still in its infancy.8–10 As with other emerging therapies, safety concerns have arisen in relation to potential hazards of SC therapy.11 Figure 1. Postulated mechanisms for beneficial effects of cardiac SC therapy. SC therapy has been shown to increase cardiac performance. Both direct and indirect mechanisms (as listed in the Figure) have been proposed to explain this benefit. However, as illustrated by the schematic balance, the weight of currently available evidence suggests that indirect mechanisms are more important. Among the most contentious issues, the risk of proarrhythmia has sparked debate and generated lingering doubts, which run the risk of paralyzing a potentially revolutionary opportunity.12–15 Although findings that have raised concerns about proarrhythmic potential of SC transplants cannot be discounted, we contend that the available data are encouraging rather than damning. Here, we highlight experimental and clinical data on SC-related arrhythmogenesis, discuss possible confounding issues, and argue that SC therapy, rather …
Conditional Rényi Entropies

There is no generally accepted definition of conditional Rényi entropy. The (unconditional) Rényi entropy depends on a parameter α, which for the case of min-entropy takes the value ∞. Even for this particular case, there are several proposals for the definition of conditional entropy. This paper describes three general definitions of conditional Rényi entropy that were found or suggested in the literature. Their properties are studied and their values, as a function of α, are compared. The particular case of min-entropy is widely used in cryptography as a security parameter; this case is studied in some detail.
Scheduling algorithms for optimal robot cell coordination - a comparison

Flexibility is the keyword in the modern industrial world. Automatic generation of collision- and blocking free, time optimal schedules for industrial robot cells is thus motivated. While a lot of attention has been paid to the control of industrial systems, as well as to the development of general optimization algorithms, there is still a need to properly combine these two research areas. This paper discusses two scheduling algorithms, designed for industrial robot cells, in terms of performance. A novel heuristic to an A*-based algorithm, operating on discrete event systems, is proposed and benchmarked against the well-known MILP algorithm
Safety profile of topical VEGF neutralization at the cornea.

PURPOSE Bevacizumab eyedrops inhibit corneal neovascularization. The purpose of this study was to analyze the safety profile of VEGF-A neutralization at the ocular surface. METHODS Bevacizumab eyedrops (5 mg/mL) and an antimurine VEGF-A antibody (250 microg/mL) were applied to normal murine corneas five times a day for 7 and 14 days. Subsequently, corneas were analyzed for morphologic changes by light and electron microscopy. In a mouse model of corneal epithelial abrasion, the effects of topically applied anti-VEGF antibodies on epithelial wound healing were analyzed: the treatment group received bevacizumab (5 mg/mL) or the antimurine VEGF-A antibody (250 microg/mL) as eyedrops, and the control group received an equal volume of saline solution. After 12, 18, and 24 hours, corneas were photographed in vivo with and without fluorescein staining for morphometry. Afterwards the mice were killed, and eyes were removed for histology, immunohistochemistry with Ki67/DAPI, and electron microscopy. The effect of midterm anti-VEGF therapy on corneal nerve density was assessed by staining corneas treated with an FITC-conjugated anti-neurofilament antibody and morphometric analysis. RESULTS Murine corneas treated with two different types of anti-VEGF antibody eyedrops did not show obvious corneal morphologic changes at the light and electron microscopic levels. Furthermore, anti-VEGF antibody eyedrops had no significant impact on the wound healing process after corneal epithelial injury or on normal murine corneal nerve fiber density. CONCLUSIONS Topical neutralization of VEGF-A at the corneal surface does not have significant side effects on normal corneal epithelial wound healing, normal corneal integrity, or normal nerve fiber density. Therefore, anti-VEGF eyedrops seem to be a relatively safe option to treat corneal neovascularization.
Book Review: Made in the Philippines: Gendered Discourses and the Making of Migrants

and public officials fail to acknowledge immigrant and ethnic groups, less formal links may be established with ‘mediators’ for these groups. In their comparison of Amsterdam, Liege and Zurich, Meindert Fennema and Jean Tillie explore a similar issue, namely how local policies to alleviate social deprivation may lead to a greater and more dense network of immigrant organizations, particularly when such organizations have the opportunity to participate in the formulation and implementation of the policy. The most comprehensive attempt to order and interpret the wealth of MPMC data is made by Michael Alexander, who presents a typology of local migrant policies. He distinguishes five basic policy types nonpolicy, guestworker, assimilationist, pIuralist and intercultural that are differentiated over a broad spectrum of local issues. With a preliminary categorization of 26 cities, before zooming in on Rome, Tel Aviv, Amsterdam and Birmingham, the author critically illustrates the potential value of the typology. Margarida Marques and Rui Santos explore the interrelation between activation and mobilization processes in one suburb of Lisbon. They argue that the MPMC framework requires far more refined levels of analysis to adequately assess these empirical practices, and develop the typology to anchor their point. In the closing chapter, Rinus Penninx and Martin Martiniello evaluate the MPMC project, outlining its implications for research and policy development. While several conferences and numerous publications have developed within the MPMC, this book provides a summary consideration of the central issues. The volume does have its limitations. The title suggests a primary focus upon the concept of citizenship, but it is the subtitle that more aptly covers the topics under consideration. The views concerning citizenship remain largely implicit throughout the volume. One then wonders to what extent the volume may be relevant for academics outside the European continent. Or even, as the editors point out, for those outside the wealthier, hierarchical welfare states of northern Europe.
Microsatellite Instability of Endothelial Cell Growth and Apoptosis Genes Within Plexiform Lesions in Primary Pulmonary Hypertension

Abstract— Primary pulmonary hypertension (PPH) is a frequently fatal disease whose pathobiology is poorly understood. Monoclonal endothelial cell growth is present within plexiform lesions of patients with PPH but not secondary PH because of congenital heart malformations. We hypothesized that endothelial cells within PPH plexiform lesions harbor mutations permissive for clonal cell growth. We found that endothelial cells in PPH plexiform lesions demonstrated microsatellite instability within the human MutS Homolog 2 gene (10 of 20 lesions) and displayed microsatellite site mutations and reduced protein expression of transforming growth factor-&bgr; receptor type II (6 of 19 lesions) and Bax (4 of 19 lesions). These results suggest that, in PPH, proliferated endothelial cells have genetic alterations associated with microsatellite instability and concomitant perturbation of growth and apoptosis gene expression akin to neoplasia. The full text of this article is available at http://www.circresaha. org.
Endoscopic ultrasound for differential diagnosis of focal pancreatic lesions, confirmed by surgery.

BACKGROUND Endoscopic ultrasound is increasingly used for evaluation of pancreatic cancer. The potential of sonographic morphology to differentiate histology type and biological behaviour of pancreatic lesions is doubtful. METHODS We prospectively studied 115 patients with focal pancreatic lesions on endoscopic ultrasound. Morphology was assessed using Olympus UM3/20/200 echoendoscopes. Histologic confirmation of diagnosis was obtained in all patients. RESULTS Endoscopic ultrasound correctly diagnosed 18/34 benign and 77/81 malignant lesions. Sensitivity, specificity, accuracy, PPV and NPV for diagnosing malignancy were 95%, 53%, 83%, 83% and 82%, respectively. Endosonographic diagnosis of the lesions (% correct) were: pancreatic cancer, 84 (63.3%); chronic pancreatitis, 14 (71.4%); ampullary cancer, 9 (77.8%); cystadenoma, 5 (80%); ampullary adenoma, 2 (50%); acute pancreatitis, 1 (0). In 13 patients of chronic pancreatitis, diagnosed as cancer, diagnosis was based on absence of sonographic features of chronic pancreatitis (7) or suspected involvement of adjacent structures (6). In 3 patients malignancy was missed owing to features of chronic pancreatitis. Non-suspected neuroendocrine tumours were misjudged in all 10 cases using morphologic criteria as pancreatic cancer (8), cystadenoma and chronic pancreatitis. Accuracy for prediction of metastatic lymph nodes and an advanced pancreatic cancer stage (TxN1 or T3Nx) was 61% and 75%, respectively. On retrospective analysis, a lesion >2 cm, vessel ingrowth, absence of cystic spaces and absence of diffuse pancreatitis were associated with pancreatic cancer. CONCLUSIONS While overall sensitivity was high, specificity of endoscopic ultrasound for diagnosis of malignancy was low, especially in presence of chronic pancreatitis. In addition, endosonography had only a limited potential to predict the histological type of lesions.