Miracle-dz/UniFAR-FTUs huggingface dataset:
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, http://www.guidetopharmacology.org) provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. Developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), this resource, and its earlier incarnation as IUPHAR-DB, is described in our 2014 publication. This update incorporates changes over the intervening seven database releases. The unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. Most information comes from journal articles, but we now also index kinase cross-screening panels. Targets are specified by UniProtKB IDs. Small molecules are defined by PubChem Compound Identifiers (CIDs); ligand capture also includes peptides and clinical antibodies. We have extended the capture of ligands and targets linked via published quantitative binding data (e.g. Ki, IC50 or Kd). The resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. The database also provides an expanded substrate for the biennially published compendium, the Concise Guide to PHARMACOLOGY. This article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options.
Sexual selection on male development time in the parasitoid wasp Nasonia vitripennis

Mating systems are shaped by a species’ ecology, which sets the stage for sexual selection. Males of the gregarious parasitoid wasp Nasonia vitripennis compete to mate virgin females at the natal site, before females disperse. Males could increase their fitness by being larger and monopolizing female emergence sites or by emerging earlier pre‐empting access to females. We consider sexual selection on male body size and development time in Nasonia, and a potential trade‐off between the two traits. We explored sex‐specific patterns of larval and pupal development, finding that smaller wasps developed slower than their host‐mates. Using competition experiments between brothers, we found that earlier eclosing males mated more females independently of absolute and relative body size. Our data explain the lack of relationship between fitness and body size in male Nasonia and reinforce the importance of protandry in mating systems where access to mates is time‐limited.
Development of a Recombinant Nucleoprotein-Based Enzyme-Linked Immunosorbent Assay for Quantification of Antibodies against Porcine Reproductive and Respiratory Syndrome Virus

ABSTRACT A rapid, inexpensive enzyme-linked immunosorbent assay (ELISA) to quantitate antibodies to porcine respiratory and reproductive syndrome virus (PRRSV) in serum was developed using a recombinant PRRSV nucleoprotein (rN). The sensitivity (85.3%) and specificity (81.7%) of the Kansas State University ELISA were good, correlating well (82.4%) with the IDEXX HerdChek ELISA.
Design Patterns Reuse for Real Time Embedded Software Development

This article describes software reuse components using C language on IBM-Rational Rose Real Time (RRRT)environment. In it a software development process becomes refined by means of a design pattern reuse. Its main contribution meets definition of a process for construction of a Data Logger Platform. Use of design pattern in an Integrated Computer Aided Software Engineering Environment allows definition of an industrial process aimed for future systematic reuse. Direction lines from Rational Unified Process (RUP) had recently helped undergraduate and graduate students from the Brazilian Aeronautics Institute of Technology (ITA) to create a fertile scene for practical applications of design pattern concepts. A Computer Software Component was constructed with attributes and generic methods in order to make possible its reuse. As a result of this process, members of ITA Software Engineering Research Group had generated a quality report previously improved to carry out classroom work, and proposed a specific data management design pattern for input and output.
Resonant-coherent excitation of channeled ions.

A first-principles calculation of the resonant-coherent excitation of planar-channeled hydrogeni is presented. The interplay between coherent interaction with the periodic crystal lattice potenti inelastic electron-electron collisions is shown to be crucial in both intraionic transitions and ele loss from the ion. The magnitude of resonant-coherent excitation is predicted to oscillate wi amplitude of the oscillations of the ion trajectory. Good agreement is found with experiments.
Ketone-Based Metabolic Therapy: Is Increased NAD+ a Primary Mechanism?

The ketogenic diet’s (KD) anticonvulsant effects have been well-documented for nearly a century, including in randomized controlled trials. Some patients become seizure-free and some remain so after diet cessation. Many recent studies have explored its expanded therapeutic potential in diverse neurological disorders, yet no mechanism(s) of action have been established. The diet’s high fat, low carbohydrate composition reduces glucose utilization and promotes the production of ketone bodies. Ketone bodies are a more efficient energy source than glucose and improve mitochondrial function and biogenesis. Cellular energy production depends on the metabolic coenzyme nicotinamide adenine dinucleotide (NAD), a marker for mitochondrial and cellular health. Furthermore, NAD activates downstream signaling pathways (such as the sirtuin enzymes) associated with major benefits such as longevity and reduced inflammation; thus, increasing NAD is a coveted therapeutic endpoint. Based on differential NAD+ utilization during glucose- vs. ketone body-based acetyl-CoA generation for entry into the tricarboxylic cycle, we propose that a KD will increase the NAD+/NADH ratio. When rats were fed ad libitum KD, significant increases in hippocampal NAD+/NADH ratio and blood ketone bodies were detected already at 2 days and remained elevated at 3 weeks, indicating an early and persistent metabolic shift. Based on diverse published literature and these initial data we suggest that increased NAD during ketolytic metabolism may be a primary mechanism behind the beneficial effects of this metabolic therapy in a variety of brain disorders and in promoting health and longevity.
History, ocean channels, and distance determine phylogeographic patterns in three widespread Philippine fruit bats (Pteropodidae)

The comparative phylogeography of widespread, codistributed species provides unique insights into regional biodiversity and diversification patterns. I used partial DNA sequences of the mitochondrial genes ND2 and cyt b to investigate phylogeographic structure in three widespread Philippine fruit bats. Ptenochirus jagori is endemic to the oceanic region of the Philippines and is most abundant in lowland primary forest. Macroglossus minimus and Cynopterus brachyotis are most common in disturbed and open habitats and are not endemic. In all three, genetic differentiation is present at multiple spatial scales and is associated to some degree with Pleistocene landbridge island groups. In P. jagori and C. brachyotis, genetic distance is correlated with geographic distance; in C. brachyotis and M. minimus, it is correlated with the sea‐crossing distance between islands. P. jagori has the least overall genetic structure of these three species, whereas C. brachyotis and M. minimus have more geographic association among haplotypes, suggesting that phylogeographic patterns are linked to ecology and habitat preference. However, contrary to expectation, the two widespread, disturbed habitat species have more structure than the endemic species. Mismatch distributions suggest rapid changes in effective population size in C. brachyotis and P. jagori, whereas M. minimus appears to be demographically more stable. Geologic and geographic history are important in structuring variation, and phylogeographic patterns are the result of dynamic long‐term processes rather than simply reflecting current conditions.
Feature Combination in Kernel Space for Distance Based Image Hashing

The paper presents a novel feature based indexing scheme for image collections. The scheme presents the extension of distance based hashing to kernel space for generating the indexing structure based on similarity in kernel space. The objective of the scheme is to incorporate multiple features for defining the image indexing space using the concept of multiple kernel learning. However, the indexing problems are defined with unique learning objective; therefore, a novel application of genetic algorithm is presented for the optimization task. The extensive evaluation of the proposed concept is performed for developing word based document indexing application of Devanagari, Bengali, and English scripts. In addition, the efficacy of the proposed concept is shown by experimental evaluations on handwritten digits and natural image collection.
Theory of melt fracture instabilities in the capillary flow of polymer melts

We present a model for the flow of a polymer melt through a capillary with nonlinear slip boundary conditions at the wall of the capillary. The model consists of the linearized Navier-Stokes equations coupled to a Maxwell constitutive relation for the viscoelasticity and a phase-field model for a first-order transition between stick and slip flow at the boundary. Specializing to the case of a two-dimensional capillary, we perform a linear stability analysis about the steady-state solutions and predict in which parameter regimes the steady-state becomes unstable. A numerical study of the model shows regions of steady flow, as well as regimes with periodic oscillations, spatially uniform but temporally chaotic oscillations, and more complicated spatiotemporal behavior. We show that the oscillations can account for the sharkskin texturing and defect structures seen in the extrusion of polymer melts. @S1063-651X~97! 10401-9#
Evidence of persistent executive function deficits in cannabis dependence after one month of abstinence.

461 • Revista Brasileira de Psiquiatria 2010 • vol 32 • no 4 • dez2010 References 1. Lavretsky H. The Russian concept of schizophrenia: a review of the literature. Schizophr Bull. 1998;24(4):537-57. 2. Jenkins R, Klein J, Parker C. Mental health in post-communist countries. BMJ. 2005;331(7510):173-4. 3. Jargin SV. Overdiagnosis of schizophrenia: A view from Russia. Asian J Psychiatr. 2009;2(3):119. 4. Jenkins R, McDaid D, Nikiforov A, Potasheva A, Watkins J, Lancashire S, Samyshkin Y, Huxley P, Atun R. Mental health care reforms in Europe: Rehabilitation and social inclusion of people with mental illness in Russia. Psychiatr Serv. 2010;61(3):222-4. 5. Fulford KW, Smirnov AY, Snow E. Concepts of disease and the abuse of psychiatry in the USSR. Br J Psychiatry. 1993;162:801-10.
Integration of Planning with Recognition for Responsive Interaction Using Classical Planners

Interaction between multiple agents requires some form of coordination and a level of mutual awareness. When computers and robots interact with people, they need to recognize human plans and react appropriately. Plan and goal recognition techniques have focused on identifying an agent's task given a sufficiently long action sequence. However, by the time the plan and/or goal are recognized, it may be too late for computing an interactive response. We propose an integration of planning with probabilistic recognition where each method uses intermediate results from the other as a guiding heuristic for recognition of the plan/goal in-progress as well as the interactive response. We show that, like the used recognition method, these interaction problems can be compiled into classical planning problems and solved using off-the-shelf methods. In addition to the methodology, this paper introduces problem categories for different forms of interaction, an evaluation metric for the benefits from the interaction, and extensions to the recognition algorithm that make its intermediate results more practical while the plan is in progress.
Distinct Roles of Rock (Rho-Kinase) and Mlck in Spatial Regulation of Mlc Phosphorylation for Assembly of Stress Fibers and Focal Adhesions in 3t3 Fibroblasts

ROCK (Rho-kinase), an effector molecule of RhoA, phosphorylates the myosin binding subunit (MBS) of myosin phosphatase and inhibits the phosphatase activity. This inhibition increases phosphorylation of myosin light chain (MLC) of myosin II, which is suggested to induce RhoA-mediated assembly of stress fibers and focal adhesions. ROCK is also known to directly phosphorylate MLC in vitro; however, the physiological significance of this MLC kinase activity is unknown. It is also not clear whether MLC phosphorylation alone is sufficient for the assembly of stress fibers and focal adhesions. We have developed two reagents with opposing effects on myosin phosphatase. One is an antibody against MBS that is able to inhibit myosin phosphatase activity. The other is a truncation mutant of MBS that constitutively activates myosin phosphatase. Through microinjection of these two reagents followed by immunofluorescence with a specific antibody against phosphorylated MLC, we have found that MLC phosphorylation is both necessary and sufficient for the assembly of stress fibers and focal adhesions in 3T3 fibroblasts. The assembly of stress fibers in the center of cells requires ROCK activity in addition to the inhibition of myosin phosphatase, suggesting that ROCK not only inhibits myosin phosphatase but also phosphorylates MLC directly in the center of cells. At the cell periphery, on the other hand, MLCK but not ROCK appears to be the kinase responsible for phosphorylating MLC. These results suggest that ROCK and MLCK play distinct roles in spatial regulation of MLC phosphorylation.
Generation of electronic program guide for RF fed TV channels by recognizing the channel logo using fuzzy multifactor analysis

This paper presents a novel method for providing the Electronic Program Guide (EPG) for the Radio Frequency (RF) fed cable TV users by recognizing the channel logo and then extracting the EPG from their website. The prototype is developed in X86 platform and then ported on a real time DSP platform and performs with nearly 100% accuracy.
Minimum Face-Spanning Subgraphs of Plane Graphs

A plane graph is a planar graph with a fixed embedding. Let G =( V,E )b e an edge weighted connected plane graph, where V and E are the set of vertices and edges, respectively. Let F be the set of faces of G. For each edge e ∈ E, let w(e) ≥ 0b e the weight of the edge e of G. A face-spanning subgraph of G is a connected subgraph H induced by a set of edges S ⊆ E such that the vertex set of H contains at least one vertex from the boundary of each face f ∈ F of G. A minimum face-spanning subgraph H of G is a face-spanning subgraph of G, where e∈S w(e) is minimum. In this paper we consider the problem of finding a minimum face-spanning subgraph of a plane graph and deal with the following problem which we call “the face-spanning subgraph problem”: “Is there any face-spanning subgraph H of G such that e∈S w(e) ≤ b, for a positive real number b? ”. We prove that the face-spanning subgraph problem of a plane graph is NP-complete, which implies that it is unlikely to have a polynomial time algorithm for finding a minimum face-spanning subgraph of a plane graph. In this paper, we consider a variation of the face-spanning subgraph problem called “minimum-vertex face-spanning subgraph problem” where the objective is to minimize the number of vertices instead of edge cost and we prove that the minimum-vertex face-spanning subgraph problem is also NP-complete. We also present approximation algorithms for both the problems. We calculate the approximation ratios and time complexities for both the algorithms. In this paper, we also present a linear time algorithm for finding a minimal face-spanning subgraph of a plane graph. We calculate the upper bound and lower bound on the number of vertices for a minimal face-spanning subgraph. We show that the upper bound and the lower bound are tight. Note that the graphs being dealt with in the paper are all undirected.
Micropatterned Coatings for Guided Tissue Regeneration in Dental Implantology

Dento-alveolar trauma and congenital absences are the most important causes of edentulism that are not associated with bacteria. However, the World Health Organization reports show that dental caries and periodontitis, two conditions of bacterial origin, are the most frequent oral diseases in humans [1]. These conditions might be avoided if an adequate oral preventive health policy is implemented, including preventive and educational measures that, regardless of the population s socioeconomic factors, have shown their effectiveness. Despite these facts, tooth extraction1, defined as the surgical removal of a tooth, is currently the most frequent surgical procedure in the world [1].
Nonclinical models for antituberculosis drug development: a landscape analysis.

BACKGROUND Several nonclinical drug-development tools (DDTs) have been used for antituberculosis drug development over several decades. The role of the DDTs used for evaluating the efficacy of antituberculosis drug combinations and the gaps in the evidence base for which new tools or approaches are needed are as yet undefined. METHODS We performed a landscape analysis based on a comprehensive literature review to create evidence based guidelines. RESULTS There are 3 important questions that a DDT should answer with regard to antituberculosis drugs: What combination(s) of drugs will be most effective? What dose(s) and schedule(s) of each drug should be administered? and What duration(s) of treatment will be efficacious? Four DDTs were identified as having a track record to answer these questions: in vitro susceptibility tests, the hollow fiber system model of tuberculosis, mice, and guinea pigs. No single nonclinical in vitro or animal model recapitulates all aspects of human tuberculosis. Therefore, a combination of models is recommended for drug development. Gaps identified include the need for standardization of nonclinical model experiments, evaluation of animal models with pathology more similar to that in humans, and identification of experimental quantitative output in the DDTs that correlates with sterilizing effect in humans. CONCLUSIONS There is a need for formal quantitative analyses of how well DDTs forecast clinical outcomes.
The Endocannabinoid 2-Arachidonoylglycerol Is Responsible for the Slow Self-Inhibition in Neocortical Interneurons

In the CNS, endocannabinoids are identified mainly as two endogenous lipids: anandamide, the ethanolamide of arachidonic acid, and 2-arachidonoylglycerol (2-AG). Endocannabinoids are known to inhibit transmitter release from presynaptic terminals; however we have recently demonstrated that they are also involved in slow self-inhibition (SSI) of layer V low-threshold spiking (LTS) interneurons in rat somatosensory cortex. SSI is induced by repetitive firing in LTS cells, which can express either cholecystokinin or somatostatin. SSI is triggered by an endocannabinoid-dependent activation of a prolonged somatodendritic K+ conductance and associated hyperpolarization in the same cell. The synthesis of both endocannabinoids is dependent on elevated [Ca2+]i such as occurs during sustained neuronal activity. To establish whether 2-AG mediates autocrine LTS-SSI, we blocked its biosynthesis from phospholipase C (PLC) and diacylglycerol lipases (DAGLs). Current-clamp recordings from LTS interneurons in acute neocortical slices showed that inclusion of DAGL inhibitors in the whole-cell pipette prevented the long-lasting hyperpolarization triggered by LTS cell repetitive firing. Similarly, extracellular applications of a PLC inhibitor prevented SSI in LTS interneurons. Moreover, metabotropic glutamate receptor-dependent activation of PLC produced a long-lasting hyperpolarization which was prevented by the CB1 antagonist AM251, as well as by PLC and DAGL inhibitors. The loss of SSI in the presence of intracellular DAGL blockers confirms that endocannabinoid production occurs in the same interneuron undergoing the persistent hyperpolarization. Since DAGLs produce no endocannabinoid other than 2-AG, these results identify this compound as the autocrine mediator responsible for the postsynaptic slow self-inhibition of neocortical LTS interneurons.
Valuing evaluation: methodologies to bridge research and practice

The potential disconnect between research and practice in software engineering (SE) means that the uptake of research outcomes has at times been limited. In this paper we seek to identify research approaches that are rigorous in terms of method but that are also relevant to software engineering practitioners. After considering the correspondence of several approaches to software systems research and practice we recommend a framework for applying grounded theory in SE research, as a means of delivering both robust and useful outcomes.