Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrasound-guided nerve blocks of the pelvic limb in dogs.

OBJECTIVES To evaluate the efficacy of ultrasound-guidance in nerve blockade of the sciatic and saphenous nerves in dogs and to determine if this technique could allow lower anaesthetic doses to be used with predictable onset and duration of effect. STUDY DESIGN Prospective randomized (for dose and leg) blinded experimental crossover trial with 10 day washout period. ANIMALS Six healthy female Hound dogs aged 12.3 +/- 0.5 (mean +/- SD) months and weighing 18.7 +/- 0.8 (mean +/- SD) kg. METHODS An ultrasound-guided, perineural injection was used with saline at 0.2 mL kg(-1) (Sal) or bupivacaine 0.5% at 0.05 (low dose; LD), 0.1 (medium dose; MD), or 0.2 (high dose; HD) mL kg(-1), divided 2/3 at the sciatic nerve and 1/3 at the saphenous nerve. Blocks were performed using dexmedetomidine sedation with atipamezole reversal immediately after completion of the injections. Motor/proprioceptive and sensory functions were scored using a 0-8 and a 0-2 scale, respectively. Clinically relevant blocks were defined as a motor score > or =2 and sensory score > or =1. Nonparametric methods were used for statistical analysis. RESULTS No adverse effects were noted. There was a significant difference between the treatments with bupivacaine and the saline control, but not between the three bupivacaine treatments. Success rates of clinically relevant sciatic and saphenous blocks were both 67% (CI 95% 0.22-0.96). Onset and duration of the blocks were variable; 20-160 and 20-540 minutes, respectively. CONCLUSION AND CLINICAL RELEVANCE None of the bupivacaine doses was significantly superior, though there was a tendency for a better block with the high bupivacaine dose. Either the technique or the doses used need further modification before this method will be useful in clinical practice.
Metamorphic Runtime Checking of Non-Testable Programs

Challenges arise in assuring the quality of applications that do not have test oracles, i.e., for which it is difficult or impossible to know what the correct output should be for arbitrary input. Recently, metamorphic testing [7] has been shown to be a simple yet effective technique in addressing the quality assurance of these so-called “non-testable programs” [51]. In metamorphic testing, existing test case input is modified to produce new test cases in such a manner that, when given the new input, the function should produce an output that can easily be computed based on the original output. That is, if input x produces output f (x), then we create input x’ such that we can predict f (x’ ) based on f (x); if the application does not produce the expected output, then a defect must exist, and either f (x) or f (x’ ) (or both) is wrong. Previously we have presented an approach called “Automated Metamorphic System Testing” [37], in which metamorphic testing is conducted automatically as the program executes. In the approach, metamorphic properties of the entire application are specified, and then checked after execution is complete. Here, we improve upon that work by presenting a technique in which the metamorphic properties of individual functions are used, allowing for the specification of more complex properties and enabling finer-grained runtime checking. Our goal is to demonstrate that such an approach will be more effective than one based on specifying metamorphic properties at the system level, and is also feasible for use in the deployment environment. This technique, called Metamorphic Runtime Checking, is a system testing approach in which the metamorphic properties of individual functions are automatically checked during the program’s execution. The tester is able to easily specify the functions’ properties so that metamorphic testing can be conducted in a running application, allowing the tests to execute using real input data and in the context of real system states, without affecting those states. We also describe an implementation framework called Columbus, and present the results of empirical studies that demonstrate that checking Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. FSE 2009 Amsterdam, The Netherlands Copyright 200X ACM X-XXXXX-XX-X/XX/XX . $5.00. the metamorphic properties of individual functions increases the effectiveness of the approach in detecting defects, with minimal performance impact.
Fine-grained visual categorization via multi-stage metric learning

Fine-grained visual categorization (FGVC) is to categorize objects into subordinate classes instead of basic classes. One major challenge in FGVC is the co-occurrence of two issues: 1) many subordinate classes are highly correlated and are difficult to distinguish, and 2) there exists the large intra-class variation (e.g., due to object pose). This paper proposes to explicitly address the above two issues via distance metric learning (DML). DML addresses the first issue by learning an embedding so that data points from the same class will be pulled together while those from different classes should be pushed apart from each other; and it addresses the second issue by allowing the flexibility that only a portion of the neighbors (not all data points) from the same class need to be pulled together. However, feature representation of an image is often high dimensional, and DML is known to have difficulty in dealing with high dimensional feature vectors since it would require O(d2) for storage and O(d3) for optimization. To this end, we proposed a multi-stage metric learning framework that divides the large-scale high dimensional learning problem to a series of simple subproblems, achieving O(d) computational complexity. The empirical study with FVGC benchmark datasets verifies that our method is both effective and efficient compared to the state-of-the-art FGVC approaches.
Game-Theoretic Approach to Capacity and Stability Evaluations of Decentralized Adaptive Route Selections in Wireless Ad Hoc Networks

A game-theoretic analysis is applied to the evaluation of capacity and stability of a wireless ad hoc network in which each source node independently chooses a route to the destination node so as to enhance throughput. First, the throughput of individual multihop transmission with rate adaptation is evaluated. Observations from this evaluation indicate that the optimal number of hops in terms of the achievable end-to-end throughput depends on the received signal-to-noise ratio. Next, the decentralized adaptive route selection problem in which each source node competes for resources over arbitrary topologies is defined as a game. Numerical results reveal that in some cases this game has no Nash equilibria; i.e., each rational source node cannot determine a unique route. The occurrence of such cases depends on both the transmit power and spatial arrangement of the nodes. Then, the obtained network throughput under the equilibrium conditions is compared to the capacity under centralized scheduling. Numerical results reveal that when the transmit power is low, decentralized adaptive route selection may attain throughput near the capacity.
Occupational therapy with people with depression: Using nominal group technique to collate clinician opinion

Abstract Aims. This aim of this study was to obtain a consensus from clinicians regarding occupational therapy for people with depression, for the assessments and practices they use that are not currently supported by research evidence directly related to functional performance. The study also aimed to discover how many of these assessments and practices were currently supported by research evidence. Methods. Following a previously reported systematic review of assessments and practices used in occupational therapy for people with depression, a modified nominal group technique was used to discover which assessments and practices occupational therapists currently utilize. Three online surveys gathered initial data on therapeutic options (survey 1), which were then ranked (survey 2) and re-ranked (survey 3) to gain the final consensus. Twelve therapists completed the first survey, whilst 10 clinicians completed both the second and third surveys. Major findings. Only 30% of the assessments and practices identified by the clinicians were supported by research evidence. A consensus was obtained on a total of 35 other assessments and interventions. These included both occupational-therapy-specific and generic assessments and interventions. Principle conclusion. Very few of the assessments and interventions identified were supported by research evidence directly related to functional performance. While a large number of options were generated, the majority of these were not occupational therapy specific.
Elongation Factor P and Modifying Enzyme PoxA Are Necessary for Virulence of Shigella flexneri

ABSTRACT Elongation factor P (EF-P) is a universally conserved bacterial translation factor. In many bacteria, EF-P is posttranslationally modified by PoxA, which covalently attaches a β-lysine to a conserved lysine residue of EF-P. Here we show that both EF-P and PoxA are necessary for virulence of the human diarrheal pathogen Shigella flexneri. Loss of either EF-P or PoxA leads to an impaired ability of S. flexneri to invade epithelial cells and form plaques in an epithelial cell monolayer. Proteomic analysis of efp and poxA deletion mutants revealed decreased levels of several virulence effector proteins, including IpaA, -B, and -C and IcsA. Additionally, mRNA levels of virB and virF, which encode master virulence regulators, were decreased in the efp mutant. The reduction in virF transcription was at least partially due to decreased levels of CpxA, which activates virF through the response regulator CpxR. The role of CpxAR in reduced synthesis of VirF and its downstream effectors was indicated by restoration of invasion when a mutation resulting in constitutively activated CpxR was introduced into the efp mutant. Thus, modified EF-P is required for appropriate synthesis of proteins involved in the virulence of this bacterial pathogen.
Deep Poisson Factor Modeling

We propose a new deep architecture for topic modeling, based on Poisson Factor Analysis (PFA) modules. The model is composed of a Poisson distribution to model observed vectors of counts, as well as a deep hierarchy of hidden binary units. Rather than using logistic functions to characterize the probability that a latent binary unit is on, we employ a Bernoulli-Poisson link, which allows PFA modules to be used repeatedly in the deep architecture. We also describe an approach to build discriminative topic models, by adapting PFA modules. We derive efficient inference via MCMC and stochastic variational methods, that scale with the number of non-zeros in the data and binary units, yielding significant efficiency, relative to models based on logistic links. Experiments on several corpora demonstrate the advantages of our model when compared to related deep models.
Example-Based Approach For Real-Time Rigged Character Animation

We present a system that allows users to generate animations for 3D rigged geometry easily and quickly us- ing just a regular consumer Microsoft Kinect. The interactive system allows diverse meshes to be animated through the interaction of human body. Traditionally, creating expressive and convincing animation is a challenging and laborious. Our system is a real-time performance-based puppetry application for any rigged object, which makes the animation generation more playful. This paper describes the system in full, explaining the generation procedures, highlighting the technical contributions, and demonstrating many examples.
Learning Algorithms for Second-Price Auctions with Reserve

Second-price auctions with reserve play a critical role in the revenue of modern search engine and popular online sites since the revenue of these companies often directly depends on the outcome of such auctions. The choice of the reserve price is the main mechanism through which the auction revenue can be influenced in these electronic markets. We cast the problem of selecting the reserve price to optimize revenue as a learning problem and present a full theoretical analysis dealing with the complex properties of the corresponding loss function. We further give novel algorithms for solving this problem and report the results of several experiments in both synthetic and real-world data demonstrating their effectiveness.
Principles for Echo Position Determination Using Airborne Ultrasound

Different approaches for determining the position of the reflection point of a transmitted ultrasound signal are investigated assuming a specular environment. Two different principles are outlined: one based on the evaluation of time of flight (TOF) differences at multiple receivers, the second on the evaluation of the directional characteristics of the ultrasound transducer itself. Experimental results are discussed as well as advantages that are gained by combining both methods.
Does the cellular labile iron pool participate in the oxidation of 2′,7′-dichlorodihydrofluorescein?

The fluorogenic probe 2′,7′-dichlorodihydrofluorescein diacetate (H2DCF-DA) is widely used for the estimation of oxidative stress in cells. It is known that 2′,7′-dichlorodihydrofluorescein (H2DCF), product of intracellular hydrolysis of H2DCF-DA, is oxidized to the fluorescent compound, DCF, mainly by hydrogen peroxide (H2O2) in the presence of catalysts. The present study was aimed at answering the question whether the labile iron pool (LIP) may contribute to the oxidation of H2DCF in cellular systems. The membrane-permeable lipophilic iron chelator salicylaldehyde isonicotinoyl hydrazone (SIH) was found to inhibit oxidation of the probe by H2O2 dependent on ferrous ions but not by peroxidase or superoxide dismutase in defined in vitro systems. When applied to cells, the probe inhibited considerably oxidation of H2DCF in V79 Chinese hamster fibroblasts and two murine lymphoma L5178Y(LY) sublines (LY-R, LY-S) differing in LIP level, the extent of inhibition being greater in the LY-R line of higher LIP level. These results demonstrate that LIP is a significant factor determining the rate of intracellular H2DCF oxidation.
Developmental extinction of major histocompatibility complex class II gene expression in plasmocytes is mediated by silencing of the transactivator gene CIITA

Constitutive major histocompatibility complex (MHC) class II gene expression is tightly restricted to antigen presenting cells and is under developmental control. Cells of the B cell lineage acquire the capacity to express MHC class II genes early during ontogeny and lose this property during terminal differentiation into plasma cells. Cell fusion experiments have suggested that the extinction of MHC class II expression in plasma cells is due to a dominant repression, but the underlying mechanisms are not understood. CIITA was recently identified as an MHC class II transactivator that is essential for MHC class II expression in B lymphocytes. We show here that inactivation of MHC class II genes in plasmocytes is associated with silencing of the CIITA gene. Moreover, experimentally induced expression of CIITA in plasmocytes leads to reexpression of MHC class II molecules to the same level as that observed on B lymphocytes. We therefore conclude that the loss of MHC class II expression observed upon terminal differentiation of B lymphocytes into plasmocytes results from silencing of the transactivator gene CIITA.
RNA-Dependent Synthesis of Mammalian mRNA: Identification of Chimeric Intermediate and Putative End Product

Our initial understanding of the flow of protein-encoding genetic information, DNA to RNA to protein, a process defined as the “central dogma of molecular biology”, was eventually amended to account for the information back-flow from RNA to DNA (reverse transcription), and for its “side-flow” from RNA to RNA (RNA-dependent RNA synthesis, RdRs). These processes, both potentially leading to protein production, were described only in viral systems, and although putative RNA-dependent RNA polymerase (RdRp) was shown to be present, and RdRs to occur, in most, if not all, mammalian cells, its function was presumed to be restricted to regulatory. Here we report the occurrence of protein-encoding RNA to RNA information transfer in mammalian cells. We describe below the detection, by next generation sequencing (NGS), of a chimeric doublestranded/pinhead intermediate containing both sense and antisense globin RNA strands covalently joined in a predicted and uniquely defined manner, whose cleavage at the pinhead would result in the generation of an endproduct containing the intact coding region of the original mRNA. We also describe the identification of the putative end product of RNA-dependent globin mRNA amplification. It is heavily modified, uniformly truncated at both untranslated regions (UTRs), terminates with the OH group at the 5’ end, consistent with a cleavagegenerated 5’ terminus, and its massive cellular amount is unprecedented for a conventional mRNA transcription product. It also translates in a cell-free system into polypeptides indistinguishable from the translation product of conventional globin mRNA. The physiological significance of the mammalian mRNA amplification, which might operate during terminal differentiation and in the production of highly abundant rapidly generated proteins such as some collagens or other components of extracellular matrix, with every genome-originated mRNA molecule acting as a potential template, as well as possible implications, including physiologically occurring intracellular PCR process, iPCR, are discussed in the paper.
Pathways of ligand clearance in acetylcholinesterase by multiple copy sampling.

The clearance of seven different ligands from the deeply buried active-site of Torpedo californica acetylcholinesterase is investigated by combining multiple copy sampling molecular dynamics simulations, with the analysis of protein-ligand interactions, protein motion and the electrostatic potential sampled by the ligand copies along their journey outwards. The considered ligands are the cations ammonium, methylammonium, and tetramethylammonium, the hydrophobic methane and neopentane, and the anionic product acetate and its neutral form, acetic acid. We find that the pathways explored by the different ligands vary with ligand size and chemical properties. Very small ligands, such as ammonium and methane, exit through several routes. One involves the main exit through the mouth of the enzyme gorge, another is through the so-called back door near Trp84, and a third uses a side door at a direction of approximately 45 degrees to the main exit. The larger polar ligands, methylammonium and acetic acid, leave through the main exit, but the bulkiest, tetramethylammonium and neopentane, as well as the smaller acetate ion, remain trapped in the enzyme gorge during the time of the simulations. The pattern of protein-ligand contacts during the diffusion process is highly non-random and differs for different ligands. A majority is made with aromatic side-chains, but classical H-bonds are also formed. In the case of acetate, but not acetic acid, the anionic and neutral form, respectively, of one of the reaction products, specific electrostatic interactions with protein groups, seem to slow ligand motion and interfere with protein flexibility; protonation of the acetate ion is therefore suggested to facilitate clearance. The Poisson-Boltzmann formalism is used to compute the electrostatic potential of the thermally fluctuating acetylcholinesterase protein at positions actually visited by the diffusing ligand copies. Ligands of different charge and size are shown to sample somewhat different electrostatic potentials during their migration, because they explore different microscopic routes. The potential along the clearance route of a cation such as methylammonium displays two clear minima at the active and peripheral anionic site. We find moreover that the electrostatic energy barrier that the cation needs to overcome when moving between these two sites is small in both directions, being of the order of the ligand kinetic energy. The peripheral site thus appears to play a role in trapping inbound cationic ligands as well as in cation clearance, and hence in product release.
Spherical blend skinning: a real-time deformation of articulated models

Skin deformation based on an underlying skeleton is a common method to animate believable organic models. The most widely used skeletal animation algorithm, linear blend skinning, is also known as skeleton subspace deformation, vertex blending, or enveloping. It runs in real-time even on a low-end hardware but it is also notorious for its failures, such as the collapsing-joints artifacts. We present a new algorithm which removes these shortcomings while maintaining almost the same time and memory complexity as the linear blend skinning. Unlike other approaches, our method works with exactly the same input data as the popular linear version. This minimizes the cost of upgrade from linear to spherical blend skinning in many existing applications: the data structures and models need no change at all. The paper discusses also theoretical properties of rotation interpolation, essential to spherical blend skinning.
AFM probes fabricated with masked–maskless combined anisotropic etching and p+ surface doping

The paper presents a newly developed high-yield micro-fabrication technology for single-crystalline silicon atomic force microscope (AFM) probes. Both the tips and the cantilevers are simultaneously formed by a masked–maskless combined anisotropic etching process. Compared to a conventional tip-to-cantilever sequential fabrication scheme, this tip-and-cantilever simultaneous formation can effectively increase fabrication yield by avoiding the tips damaged during the following processed photolithographic steps for defining the cantilevers. By heavy boron doping at the surface, the conductive AFM probe provides an electrical path to the electric ground of the AFM that helps to eliminate the electrostatic accumulation of charges and, therefore, eliminate undesirable electrostatic forces between the probes and the samples. A fabrication yield as high as 90% has been obtained for the AFM probes for 4 inch wafers. The tips after oxidation-sharpening treatment generally have a radius of 10–30 nm. The cantilever spring constant can be well controlled in the range of 0.025–40 N m−1. High-quality sample scanning results with the formed AFM probes are obtained with a slightly better resolution than that from commercial probes without surface conductive treatment.