Miracle-dz/UniFAR-FTUs huggingface dataset:
KINARI-Mutagen Case Study: 1CRN Crambin

Figure 1: Protein 1CRN, Crambin, is a 46 amino acid protein composed of two alpha helices and a short anti-parallel beta sheet (1(a)). When rigidity analysis is performed on the non-mutated form of Crambin, the majority of the atoms in the proteins core are part of a single large rigid cluster (shown in purple))(1(b)). KINARI-Mutagen was used to generate several in-silico mutants of crambin. When excision was performed on residue 3, the size of the largest rigid cluster decreased(1(c)).
Utilizing reflection properties of surfaces to improve mobile robot localization

A main difficulty that arises in the context of probabilistic localization is the design of an appropriate observation model, i.e., determining the likelihood of a sensor measurement given the pose of the robot and a map of the environment. Many successful approaches to localization rely on data provided by range sensors, e.g., laser range scanners. When using such data one normally has to deal with erroneous maximum-range readings that occur due to poor-reflecting surfaces. In general, these readings cannot be distinguished from readings obtained when no obstacle is within the measurement range of the sensor. Therefore, existing localization techniques treat these readings alike in the observation model. In this paper, we present a novel approach that explicitly considers the reflection properties of surfaces and thus the expectation of valid range measurements. In addition to the expected range measurement, we compute the probability of reflectance for a beam given the relative pose of the robot to the obstacle taking into account the angle of incidence of the beam. We estimate the reflection properties of surfaces using data collected with a mobile robot equipped with a laser range scanner. As we demonstrate in experiments carried out with a real robot, our technique leads to significantly improved localization results compared to a state-of-the-art observation model.
Vanadate Impedes Adipogenesis in Mesenchymal Stem Cells Derived from Different Depots within Bone

Glucocorticoid-induced osteoporosis (GIO) is associated with an increase in bone marrow adiposity, which skews the differentiation of mesenchymal stem cell (MSC) progenitors away from osteoblastogenesis and toward adipogenesis. We have previously found that vanadate, a non-specific protein tyrosine phosphatase inhibitor, prevents GIO in rats, but it was unclear whether vanadate directly influenced adipogenesis in bone-derived MSCs. For the present study, we investigated the effect of vanadate on adipogenesis in primary rat MSCs derived from bone marrow (bmMSCs) and from the proximal end of the femur (pfMSCs). By passage 3 after isolation, both cell populations expressed the MSC cell surface markers CD90 and CD106, but not the hematopoietic marker CD45. However, although variable, expression of the fibroblast marker CD26 was higher in pfMSCs than in bmMSCs. Differentiation studies using osteogenic and adipogenic induction media (OM and AM, respectively) demonstrated that pfMSCs rapidly accumulated lipid droplets within 1 week of exposure to AM, while bmMSCs isolated from the same femur only formed lipid droplets after 3 weeks of AM treatment. Conversely, pfMSCs exposed to OM produced mineralized extracellular matrix (ECM) after 3 weeks, compared to 1 week for OM-treated bmMSCs. Vanadate (10 μM) added to AM resulted in a significant reduction in AM-induced intracellular lipid accumulation and expression of adipogenic gene markers (PPARγ2, aP2, adipsin) in both pfMSCs and bmMSCs. Pharmacological concentrations of glucocorticoids (1 μM) alone did not induce lipid accumulation in either bmMSCs or pfMSCs, but resulted in significant cell death in pfMSCs. Our findings demonstrate the existence of at least two fundamentally different MSC depots within the femur and highlights the presence of MSCs capable of rapid adipogenesis within the proximal femur, an area prone to osteoporotic fractures. In addition, our results suggest that the increased bone marrow adiposity observed in GIO may not be solely due to direct effect of glucocorticoids on bone-derived MSCs, and that an increase in femur lipid content may also arise from increased adipogenesis in MSCs residing outside of the bone marrow niche.
Pulling chromatin fibers: computer simulations of direct physical micromanipulations.

A low-resolution molecular model, which combines the known mechanical properties of protein-free DNA with the accumulating picture of chromatosome structure, has been developed to account for the stretching of single chromatin fibers by an imposed external force. Force-extension characteristics of sets of chains accumulated by Monte Carlo sampling are consistent with recently observed findings in the non-destructive regime (<20 pN imposed force), where the structure of the chromatosome remains intact. The correspondence between simulation and the relaxation phase of the experiment limits the equilibrium entry-exit angle of linker DNA on the chromatosome to W=50(+/-10) degrees and the effective DNA linker length to L(eff)=40(+/-5) bp. The computed force-extension characteristics are relatively insensitive to other parameters of the model, precluding their accurate estimation. The introduction of an attractive potential between closely spaced nucleosomes reproduces the added initial resistance of single fibers to extension at high salt conditions. The consideration of elastic linkers also improves the fitting of assorted classical measurements of unstressed chromatin structure in solution. The overall picture of chromatin that emerges is an irregular, fluctuating, three-dimensional, zig-zag structure with intact, mechanically stable chromatosome units and deformable linkers. The modeled fiber undergoes large-scale configurational rearrangements without significant perturbation of the constituent chromatosome beads, collapsing into a highly condensed form in response to small (<2kT) inter-nucleosomal attractions.
Integrated active contours for texture segmentation

We address the issue of textured image segmentation in the context of the Gabor feature space of images. Gabor filters tuned to a set of orientations, scales and frequencies are applied to the images to create the Gabor feature space. A two-dimensional Riemannian manifold of local features is extracted via the Beltrami framework. The metric of this surface provides a good indicator of texture changes and is used, therefore, in a Beltrami-based diffusion mechanism and in a geodesic active contours algorithm for texture segmentation. The performance of the proposed algorithm is compared with that of the edgeless active contours algorithm applied for texture segmentation. Moreover, an integrated approach, extending the geodesic and edgeless active contours approaches to texture segmentation, is presented. We show that combining boundary and region information yields more robust and accurate texture segmentation results.
Re-evaluating Multicast Streaming Using Large-Scale Network Simulation

Internet-based media streaming services are replacing more traditional broadcast services, resulting in increased demand for network resources. Multicast techniques may be used to improve bandwidth utilisation by servicing one or more clients with each network stream. In this paper, we re-evaluate the performance of the existing multicast Patching technique. In particular, we build on theoriginal server-centric performance evaluation to examine the effect of Patching on an entire network. We also propose a novel approach to the implementation ofPatching using standardised transport control (RTSP) and multicast control (MLD) protocols. Our results highlight how network distance from the origin servereffects the improvements gained by using Patching.
Antidotes for Anthrax Anecdotes

Two experiments, conducted approximately 6 weeks apart, examined the conjoint effects of participant rationality, as assessed by the Rational- Experiential Inventory, and base-rate information on apprehension about a threat. Experiment 1 predicted and found that high-rationality individuals who first received context-expanding information about a relatively likely hazard (traffic deaths) manifested less apprehension in response to a subsequent news story about a less likely threat (anthrax death) than did highs who read only the anthrax-death story. It was further predicted and found that among low-rationality individuals this relationship was reversed. Experiment 1 was conducted when the anthrax threat was perceived to be quite serious. The interaction was not found in Experiment 2, after national attention to anthrax decreased. Findings are discussed in terms of how high- and low- rationality individuals process threat-related information and how they respond to changes in the perceived seriousness of threat.
Video‐enhanced microscopy with a computer frame memory

Video‐enhanced microscopy combined with the use of a computer frame memory extends considerably the useful range of our video enhanced contrast (AVEC) methods for polarizing, double‐beam interference and differential interference contrast microscopy. Increased visual contrast is achieved by two stages of amplifications: the first optical, by using high bias retardation settings, and the second electronic. These steps are followed by a reduction of background brightness by means of a clamp voltage applied to a DC restoration circuit of the video camera. One of the limitations of the AVEC method alone is the inevitable appearance under high gain conditions of a pattern of mottle due to inaccessible dirt and defects in the lenses even of high quality. This limitation has been circumvented by storing the mottle pattern in the frame memory (frame store) and continuously subtracting it from each succeeding frame to clear the image. A major gain in image quality has resulted. In polarizing microscopy, the frame memory can be used also to subtract the image at one compensator setting from that at the equivalent setting of opposite sign, thus removing from the final image not only most of the mottle pattern but also the contrast due to the bright‐field contrast. In the polarizing microscope, these manipulations of the raw video image make it possible to observe and measure the birefringence of various organelles and elements such as microtubules, intermediate filaments and bundles of as few as a half dozen actin filaments. Since scattered light is also removed from the image, features hidden from view in the unprocessed image become visible. In differential interference microscopy, the AVEC method makes visible (i.e. detectable) many linear elements and particles that are an order of magnitude smaller than the resolution limit and not visible in the optical image. Such features are inflated by diffraction, however, to Airy disk size.
Fast Exact Max-Kernel Search

The wide applicability of kernels makes the problem of max-kernel search ubiquitous and more general than the usual similarity search in metric spaces. We focus on solving this problem efficiently. We begin by characterizing the inherent hardness of the max-kernel search problem with a novel notion of directional concentration. Following that, we present a method to use an $O(n \log n)$ algorithm to index any set of objects (points in $\Real^\dims$ or abstract objects) directly in the Hilbert space without any explicit feature representations of the objects in this space. We present the first provably $O(\log n)$ algorithm for exact max-kernel search using this index. Empirical results for a variety of data sets as well as abstract objects demonstrate up to 4 orders of magnitude speedup in some cases. Extensions for approximate max-kernel search are also presented.
Children’s strategies for coping : links with social anxiety and depressive symptoms

Cognitive and behavioural theories of social anxiety and depression provide clear explanations for the links between these conditions and the strategies children use to cope with peer conflict situations. However, empirical research in the area has left several unresolved issues, warranting further investigation if we are to understand more fully the links between coping and emotional adjustment. This programme of research was designed to develop a comprehensive measure of children‟s coping, particularly in the context of peer stressors, and to examine the links between specific coping strategies and social anxiety and depression over time. In a series of seven studies, reported in four papers, a total of 833 primary and secondary school children completed measures of social anxiety, depression, coping, and a sociometric survey, as well as measures of goals and appraisals. In Paper 1, seven distinct coping strategies were revealed across several interpersonal situations that were related to children‟s feelings in distinct ways, and that meaningfully mapped onto differences between a mainstream school sample and a sample of pupils with emotional and behavioural difficulties. In Paper 2, six of the seven coping subscales identified in Paper 1 were confirmed and these specific ways of coping were differentially associated with social anxiety and depression. Generally, social anxiety and depression were longitudinally associated with distinctive profiles of coping strategies over a period of 9 months. In Paper 3, coping was found to have these differential associations with social anxiety and depression across a range of peer conflict situations, and there was also evidence of mediating effects of children‟s appraisals and goals. Finally, in Paper 4, coping was found to be predictive of changes in depression over one year, but associations between coping and emotional adjustment did not hold up over a two-year period. These findings are discussed in relation to the existing coping literature and theories of social anxiety and depression.
Color Perception

Colour has been studied for centuries, but remains incompletely understood. Digital technology has recently sparked a burgeoning inter-disciplinary interest in colour. Graphic artists prefer to create their images on computers even though colours seen on display look different when printed; galleries now digitally archive valuable work. The fundamental problem that arises is that colour reproduction is not simply a matter of reproducing identical physical phenomenona, but is rather a matter of creating perceptual equivalencies. The fact that colour is a quality of perception rather than a "physical quality" brings up a host of interesting questions and makes it of common interest to both artists and scholars. This interdisciplinary volume - the ninth in the Vancouver Studies in Cognitive Science series - brings together chapters by psychologists, philosophers, computer scientists and artists to explore the nature of human colour perception, and hopes to further our understanding of colour by encouraging interdisciplinary interaction.
Fast Uncertainty Sampling for Labeling Large E-mail Corpora

One of the biggest challenges in building effective anti-spam solutions is designing systems to defend against the everevolving bag of tricks spammers use to defeat them. Because of this, spam filters that work well today may not work well tomorrow. The adversarial nature of the spam problem makes large, up-to-date, and diverse e-mail corpora critical for the development and evaluation of new anti-spam filtering technologies. Gathering large collections of messages can actually be quite easy, especially in the context of a large, corporate or ISP environment. The challenge is not necessarily in collecting enough mail, however, but in collecting a representative distribution of mail types as seen “in the wild” and in then accurately labeling the hundreds of thousands or millions of accumulated messages as spam or non-spam. In the field of machine learning Uncertainty Sampling is a well-known Active Learning algorithm which uses a collaborative model to minimize the human effort required to label large datasets. While conventional Uncertainty Sampling has been shown to be very effective, it is also computationally very expensive since the learner must reclassify all the unlabeled instances during each learning iteration. We propose a new algorithm, Approximate Uncertainty Sampling (AUS), which is nearly as efficacious as Uncertainty Sampling, but has substantially lower computational complexity. The reduced computational cost allows Approximate Uncertainty Sampling to be applied to labeling larger datasets and also makes it possible to update the learned model more frequently. Approximate Uncertainty Sampling encourages the building of larger, more topical, and more realistic example e-mail corpora for evaluating new anti-spam filters. While we focus on the binary labeling of large volumes of e-mail messages, as with Uncertainty Sampling, Approximate Uncertainty Sampling can be used with a wide range of underlying classification algorithms for a variety of categorization tasks.
Enhancing Performance of Protein Name Recognizers Using Collocation

Named entity recognition is a fundamental task in biological relationship mining. This paper employs protein collocates extracted from a biological corpus to enhance the performance of protein name recognizers. Yapex and KeX are taken as examples. The precision of Yapex is increased from 70.90% to 81.94% at the low expense of recall rate (i.e., only decrease 2.39%) when collocates are incorporated. We also integrate the results proposed by Yapex and KeX, and employs collocates to filter the merged results. Because the candidates suggested by these two systems may be inconsistent, i.e., overlap in partial, one of them is considered as a basis. The experiments show that Yapex-based integration is better than KeX-based integration.
Effects of salmon lice infection on the behaviour of sea trout in the marine phase

Salmon lice Lepeophtheirus salmonis Kroyer may affect survival and growth of anadromous salmonids through physiological stress and/or behavioural changes. Using acoustic telemetry tracking, we investigated the behaviour of 30 infected sea trout Salmo trutta throughout the summer in a fjord with very high salmon lice infection pressure. Most of the tracked sea trout adopted a movement pattern expected to suppress salmon lice infestation, as they showed a strong preference for fresh or brackish water, spending most of the time close to a river outlet or even migrating into the river. Highly infested sea trout preferred shallower depths, associated with lower salinity. The fish lost to predation stayed further away from the river outlet than non- predated fish, and were likely subjected to a stronger infection pressure. Half of the tracked group were treated with a salmon lice prophylaxis, emamectin benzoate. The effect of treatment on infestation was monitored in a separate group held in a sea cage and found to be moderate; the mortality in this group was associated with infestation by motile lice stages. In contrast, treatment was not found to have an effect on tracked fish behaviour. It is likely that some physiological and behavioural responses to high salmon lice infection pressure may be present even after a prophy- laxis treatment, in particular when the treatment is given after exposure to salmon lice infection. We conclude that increased salmon lice infection pressure associated with altered salmon farming practice may have the potential to influence the marine behaviour and growth of sea trout.
Terrain mapping for off-road Autonomous Ground Vehicles using rational B-Spline surfaces and stereo vision

Autonomous Ground Vehicles designed for extreme environments (e.g mining, constructions, defense, exploration applications) require a reliable estimation of terrain traversability, in terms of both terrain slope and obstacles presence. In this paper we present a new technique to build, in real time and only from a 3D points cloud, a dense terrain elevation map able to: 1) provide slope estimation; 2) provide a reference for segmenting points into terrain's inliers and outliers, to be then used for obstacles detection. The points cloud is first smartly sampled into a 2.5 grid map, then samples are fitted into a rational B-Spline surface by means of re-weighted least square fitting and equalization. To meet an extensive range of extreme off-road scenarios, no assumptions on vehicle pose are made and no road infrastructure or a-priori knowledge about terrain appearance and shape is required. The algorithm runs in real time; it has been tested on one of VisLab's AGVs using a modified SGM-based stereo system as 3D data source.
Microwave application for the detection of biodiesel-glycerine and biodiesel-water interfaces in the biodiesel production

In biodiesel industry there is a need to detect interfacing layer between biodiesel and glycerine after the transesterification and interfacing layer between water and biodiesel after the washing process. The detection of these two interfaces is important for separation process. In this work, a simple, low cost, and accurate microwave reflection type system for production of coconut biodiesel has been applied for the detection these interfaces. A module that works at 10.7 GHz, consisting of a microwave generator and a detecting diode, is used to measure the microwave reflection coefficient at various positions through the tank. The experimental results show the ability of the system to detect the level or height of these interfaces at the accuracy of 0.1 mm.
Effect of multi-users and multipaths on the performance of an adaptive serial acquisition scheme for DS/CDMA systems

In this work, we studied the effect of multi-user and multipath, on the performance of a serial acquisition search system, using adaptive threshold with constant false alarm rate, in Rayleigh fading channels. Since the received signal levels in mobile communications are unknown and location varying, the acquisition schemes for pseudo-noise (PN) sequences with fixed thresholds may cause too many false alarms and/or low probability of detection. Therefore, adaptively varying threshold schemes are proposed through the use of a constant false alarm rate (CFAR) algorithms. We propose the use of cell-averaging (CA), greatest-of (GO), smallest-of (SO) and order-statistics (OS) CFAR processors for PN code acquisition in DS/CDMA systems. From simulation results, we observe that the CA-CFAR detector gives good performances in this environment, followed by the SO-CFAR detector. The OS-CF AR outperforms the GO-CFAR which gives the worst results. All studied CFAR detectors are sensible to multi-user and multipath effect.