Miracle-dz/UniFAR-FTUs huggingface dataset:
Mexican blind cavefish use mouth suction to detect obstacles

Fish commonly use their lateral line system to detect moving bodies such as prey and predators. A remarkable case is the Mexican blind cavefish Astyanax fasciatus, which evolved the ability to detect non-moving obstacles. The swimming body of A. fasciatus generates fluid disturbances, the alteration of which by an obstacle can be sensed by the fish's lateral line system. It is generally accepted that these alterations can provide information on the distance to the obstacle. We observed that A. fasciatus swimming in an unfamiliar environment open and close their mouths at high frequency (0.7–4.5 Hz) in order to generate suction flows. We hypothesized that repeated mouth suction generates a hydrodynamic velocity field, which is altered by an obstacle, inducing pressure gradients in the neuromasts of the lateral line and corresponding strong lateral line stimuli. We observed that the frequency and rate of mouth-opening events varied with the fish's distance to obstacles, a hallmark of pulse-based navigation mechanisms such as echolocation. We formulated a mathematical model of this hitherto unrecognized mechanism of obstacle detection and parameterized it experimentally. This model suggests that suction flows induce lateral line stimuli that are weakly dependent on the fish's speed, and may be an order of magnitude stronger than the correspondent stimuli induced by the fish's gliding body. We illustrate that A. fasciatus can navigate non-visually using a combination of two deeply ancestral and highly conserved mechanisms of ray-finned fishes: the mechanism of sensing water motion by the lateral line system and the mechanism of generating water motion by mouth suction.
Opportunistic Geocast in Disruption-Tolerant Networks

Disruption-tolerant networks (DTNs) have gained great attractions recently by addressing intermittent network connectivity suffered due to short radio transmission range, high node mobility, sporadic node densities, etc. Data communication across DTN is achieved over store-carry-forward (SCF) paradigm by exploiting temporary wireless links and connections opportunistically arising from mobility nature of nodes. In the literature, multi-copy-based routing approaches are widely considered to overcome mobility randomness and subsequently the uncertainty of future network states, while routing information such as mobility statistics and context is employed to control the number of message copies. However, none of the existing approaches can be directly implemented for recent emerging geocast services. This is because instead of specifying any particular node as the destination in advance, the message generated by a geocast service falls into a certain geographical area addressed by the location descriptions. As a result, this paper introduces a novel opportunistic geocasting message delivery scheme for DTNs. To improve the efficiency, the expected visiting rate to the destined region of a message is proposed for an intermediate node to choose a next-hop with larger visiting likelihood. Simulation results demonstrate the enhanced delivery performance offered by the proposed opportunistic geocasting message delivery scheme.
On Fusion of Effective Retrieval Strategies in the Same Information Retrieval System

Prior efforts have shown that under certain situations, retrieval effectiveness may be improved via the use of data fusion techniques. Although these improvements have been observed from the fusion of result sets from several distinct information retrieval systems, it has often been thought that fusing different document retrieval strategies in a single information retrieval system will lead to similar improvements. In this study, we show that this is not the case. We hold constant systemic differences such as parsing, stemming, phrase processing, and relevance feedback, and fuse result sets generated from highly effective retrieval strategies in the same information retrieval system. From this, we show that data fusion of highly effective retrieval strategies alone shows little or no improvement in retrieval effectiveness. Furthermore, we present a detailed analysis of the performance of modern data fusion approaches, and demonstrate the reasons why they do not perform well when applied to this problem. Detailed results and analyses are included to support our conclusions.
Modeled structure of the 75‐kDa neurotrophin receptor

Motifs in ligand‐binding domains of the neurotrophin (NTR) and lymphotoxin (TNFR‐I) receptors define a family of receptors that mediates programmed cell death. We have explored relationships of architecture and function in this family through a molecular model of NTR, also called p75NGFR or LANR. Modeling by homology took advantage of four modular subdomains in the crystal structure of TNFR‐1 that also occur in NTR. Hypothetical complexes between the model and a ligand structure (for nerve growth factor, NGF) were then examined using docking software. NTR appears to bind in the dimer interface of NGF, making two sets of contacts. NTR subdomains III and IV provide the ligand‐contact surfaces, in contrast to TNFR, in which subdomains II and III contact TNF‐β. NTR subdomain II appears to have been evolutionarily modified, potentially contributing to an interface between receptor subunits. These and other specific predictions of the model will require experimental confirmation.
Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin

Bacteriorhodopsin, a light activated protein that creates a proton gradient in halobacteria, has long served as a simple model of proton pumps. Within bacteriorhodopsin, several key sites undergo protonation changes during the photocycle, moving protons from the higher pH cytoplasm to the lower pH extracellular side. The mechanism underlying the long-range proton translocation between the central (the retinal Schiff base SB216, D85 and D212) and exit clusters (E194 and E204) remains elusive. To obtain a dynamic view of the key factors controlling proton translocation, a systematic study using molecular dynamics simulation was performed for eight bacteriorhodopsin models varying in retinal isomer and protonation of the SB216, D85, D212 and E204. The side-chain orientation of R82 is determined primarily by the protonation states of the residues in the EC. The side-chain reorientation of R82 modulates the hydrogen-bond network and consequently possible pathways of proton transfer. Quantum mechanical intrinsic reaction coordinate calculations of proton-transfer in the methyl guanidinium-hydronium-hydroxide model system show that proton transfer via a guanidinium group requires an initial geometry permitting proton donation and acceptance by the same amine. In all the models, R82 can form proton wires with both the CC and the EC connected by the same amine. Alternatively, rare proton wires for proton transfer from the CC to the EC without involving R82 were found in an O’ state where the proton on D85 is transferred to D212.
DeskTOP, a system based on virtual spaces to support and to promote collaborative learning (poster session)

provides a coordination mechanism to help to maintain an interaction order among the participants and to make it more efficient. The collaborative virtual environments have become a good alternative to construct collaborative learning systems. In this paper we present DeskTOP, a collaborative virtual environment implemented on the Web to support and to promote collaborative learning in university courses. This environment is designed mainly from the perspective of the desk and room metaphors. It makes use of design patterns in its architecture, promote the creation of customized collaborative learning environments and support a communication, collaboration and social interaction between lecturer and students through a shared virtual space. 2.2 Metaphors used in DeskTOP design The DeskTOP system uses the hall and collaboration rooms metaphors, as metaphors of place [3]; and the desk metaphor, as metaphor of interface [9]. The hall metaphor establishes a virtual environment which promotes public casual and informal interaction among its users. The collaboration rooms metaphor helps to represent shared environments within which the user can work in group. Through this metaphor, a common area is created for private interaction which provides users with working tools. Figure 2.1 represents the idea of these two metaphors.
An Improvement of Robust Biometrics-Based Authentication and Key Agreement Scheme for Multi-Server Environments Using Smart Cards

In multi-server environments, user authentication is a very important issue because it provides the authorization that enables users to access their data and services; furthermore, remote user authentication schemes for multi-server environments have solved the problem that has arisen from user’s management of different identities and passwords. For this reason, numerous user authentication schemes that are designed for multi-server environments have been proposed over recent years. In 2015, Lu et al. improved upon Mishra et al.’s scheme, claiming that their remote user authentication scheme is more secure and practical; however, we found that Lu et al.’s scheme is still insecure and incorrect. In this paper, we demonstrate that Lu et al.’s scheme is vulnerable to outsider attack and user impersonation attack, and we propose a new biometrics-based scheme for authentication and key agreement that can be used in multi-server environments; then, we show that our proposed scheme is more secure and supports the required security properties.
Area and Speed Oriented Implementations of Asynchronous Logic Operating under Strong Constraints

Asynchronous circuit implementations operating under strong constraints (DIMS, Direct Logic, some of NCL gates, etc.) are attractive due to: 1) regularity, 2) combined implementation of the functional and completion detection logics, what simplifies the design process, 3) circuit output latency is based on the actual gate delays of the unbounded nature, 4) absence of additional synchronization chains (even of a local nature). However, the area and speed penalty is rather high. In contrast to the state-of-the-art approaches, where simple (NAND, NOR, etc.) 2 input gates are used, we propose a synthesis method based on complex nodes, i.e., nodes implementing any function of an arbitrary number of inputs. Synchronous synthesis procedures may be freely adopted for this purpose. Numerous experiments on standard benchmarks were performed and the efficiency of the proposed complex gate based method is clearly shown. DIMS and Direct Logic based asynchronous designs are considered in the paper.
Making an SCI fabric dynamically fault tolerant

In this paper we present a method for dynamic fault tolerant routing for SCI networks implemented on Dolphin Interconnect Solutions hardware. By dynamic fault tolerance, we mean that the interconnection network reroutes affected packets around a fault, while the rest of the network is fully functional. To the best of our knowledge this is the first reported case of dynamic fault tolerant routing available on commercial off the shelf interconnection network technology without duplicating hardware resources. The development is focused around a 2-D torus topology, and is compatible with the existing hardware, and software stack. We look into the existing mechanisms for routing in SCI. We describe how to make the nodes that detect the faulty component do routing decisions, and what changes are needed in the existing routing to enable support for local rerouting. The new routing algorithm is tested on clusters with real hardware. Our tests show that distributed databases like MySQL can run uninterruptedly while the network reacts to faults. The solution is now part of Dolphin Interconnect Solutions SCI driver, and hardware development to further decrease the reaction time is underway.
A Navigation-Field-Based Semi-Autonomous Nonholonomic Vehicle-Parking Assistant

We present a closed-loop approach to solve the semi-autonomous nonholonomic vehicle-parking assistant problem. The method allows for a priori unknown and potentially high vehicle speeds and dynamic environment variations. The computationally low-cost, memory-efficient algorithm respects constraints on the steering angle and its first two derivatives, allowing for comfortable, safe, and smooth steering motions. A parking situation is captured by an arrangement of precalculated vector fields of feasible nonholonomic paths, by which the vehicle is controlled toward a desired goal configuration inside a parking bay. Using standard onboard environment perception sensors, the system adapts to changes in the environment and avoids collisions whenever possible, without aborting a parking procedure.
Mechanical Behavior of Multilayered Nanoscale Metal‐Ceramic Composites

Single and multilayered structures at nano‐length scale are very attractive materials due to their high strength, toughness, and wear resistance relative to conventional laminated composites. In this study, single layered Al, SiC, and multilayered Al/SiC composites were synthesized by DC/RF magnetron sputtering. The microstructure of the multilayered structures was characterized by scanning electron microscopy (SEM). The elastic and plastic behavior of single and multilayered materials was investigated by nanoindentation and tensile testing. For nanoindentation, an analytical model was employed to subtract the contribution of the Si substrate, in order to extract the true modulus of the films. Finite element simulations were employed to confirm the analytical predictions and to investigate the anisotropic elastic behavior of the multilayered composite. It was concluded that while indentation provides reasonable Young's modulus and hardness values in monolithic layers, it does not provide the true modulus of the multilayered materials because of their inherent anisotropy.
Tree Representations via Ordinal Machines

We study sets of reals computable by ordinal Turing machines with a tape of length the ordinals that are steered by a standard Turing program. The machines halt at some ordinal time or diverge. We construct tree representations for ordinal semi-decidable sets of reals from ordinal computations. The aim is to generalize uniformization results to classes of sets which are semi-decidable by computations with input-dependent bounds on the halting time. We further briefly examine the jump structure and nondeterminism.
Preface to the special issue on covert contrasts

We were delighted that Professor Martin Ball invited us to guest edit this special edition of Clinical Linguistics & Phonetics on ‘Covert Contrasts’ in child speech. Although the idea of covert contrasts is not new, there has been renewed interest in the topic recently due to new developments in the methodologies used to uncover these types of contrasts in child speech. These developments are highly significant, in our opinion, because they provide for the first time the potential to identify reliably the presence, and therefore also the prevalence, of covert contrasts in child speech. In this Introduction we briefly define the meaning of the term covert contrasts, outline the importance of the phenomenon, and explain why it is pertinent to bring together research papers on this topic within a special edition at this time. First, what ismeant by the term covert contrast? In essence, these contrasts involve sounds that the child produces differently (acoustically or articulatorily) but are heard and transcribed by listeners with the same phonetic symbol. In the field of child speech, a frequently used methodology for a variety of research and clinical purposes involves transcription-based data, which show extensive neutralisation of phonological contrasts. However, closer examination of neutralised contrasts using an alternative methodology – namely instrumental techniques such as acoustic analysis, electropalatography (EPG), or ultrasound – has provided convincing evidence that children do sometimes produce acoustic or articulatory contrasts that listeners hear as neutralised. These subtle differences in the production of contrasts are called covert because listeners do not readily detect them and therefore they pass unnoticed and unrecorded in transcribed data. Kornfeld (1971) summed up the phenomenon when he said ‘adults do not always perceive distinctions that childrenmake’ (p. 462) and that ‘adults are biased to hear children’s speech in terms of their own (adult) distinctions’ (p. 462). Although covert contrasts were described nearly 50 years ago, there are surprisingly few research papers that report instrumental data on this topic. This small literature has nevertheless been influential in shaping our understanding of the nature of both typical and atypical speech acquisition as well as informing interventions for children with speech disorders. Taking some illustrative examples, researchers have found evidence that the presence of covert contrasts in children’s speech is a positive sign of progress towards their production of an overt adult-like contrast. The presence of covert contrasts in children’s speech has also lent support for the view that speech acquisition is a gradual process and that children can be making significant steps in phonetic mastery of the sound system that may not be captured fully in transcription data. In a recent review of evidence about the underlying nature of children’s phoneme errors, it has been argued that ‘apparent substitutions are actually cases of
Minimum bit error probability of large randomly spread MC-CDMA systems in multipath Rayleigh fading

We address bit error probability of the optimum multiuser detector for multi-carrier code division multiple access in frequency-selective fading channels. We use the replica method, a tool from statistical physics, to calculate the bit error probability in the large system limit for randomly assigned spreading sequences. The analysis allows for binary input symbols with biased probabilities and, therefore, can be used to analyze iterative multiuser decoders.
Evaluation of coronary band temperatures in healthy horses.

OBJECTIVE To measure coronary band temperature (CBT) in healthy horses fed high-fructan or low-carbohydrate diets and to analyze the association of CBT with diet, time of day, and ambient temperature. ANIMALS 6 healthy horses. PROCEDURES Horses were fed 3 diets (treatment 1, 1 g of fructan/kg fed daily in the morning; treatment 2, 1 g of fructan/kg fed daily in the afternoon; and treatment 3, a low-carbohydrate [7.2%] diet) in a 3 × 3 Latin square study design. For each horse, the CBT of all 4 limbs as well as rectal and ambient temperatures were recorded by use of infrared thermometry and standard thermometers hourly from 8 am to 10 pm for 4 consecutive days after the initiation of each diet. Each horse received each diet, and there was a 10-day washout period between each diet change. Data were analyzed by use of a mixed linear model. RESULTS 4,320 CBTs were obtained from the 6 horses. The CBT ranged from 9.6° to 35.5°C. Coronary band temperature followed a diurnal pattern and was positively associated with ambient temperature but was not associated with diet. CONCLUSIONS AND CLINICAL RELEVANCE CBT of healthy horses varied significantly during the day and among limbs. These results should be considered whenever increased CBT is used as an indication of incipient laminitis or in other clinical investigations.
QuickSync: Improving Synchronization Efficiency for Mobile Cloud Storage Services

Mobile cloud storage services have gained phenomenal success in recent few years. In this paper, we identify, analyze, and address the synchronization (sync) inefficiency problem of modern mobile cloud storage services. Our measurement results demonstrate that existing commercial sync services fail to make full use of available bandwidth, and generate a large amount of unnecessary sync traffic in certain circumstances even though the incremental sync is implemented. For example, a minor document editing process in Dropbox may result in sync traffic 10 times that of the modification. These issues are caused by the inherent limitations of the sync protocol and the distributed architecture. Based on our findings, we propose QuickSync, a system with three novel techniques to improve the sync efficiency for mobile cloud storage services, and build the system on two commercial sync services. Our experimental results using representative workloads show that QuickSync is able to reduce up to 73.1 percent sync time in our experiment settings.
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks

MOTIVATION Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks, the informal goal is to group together related nodes. For the case of protein-protein interaction networks, such groups are expected to form clusters of functionally orthologous proteins. Construction of such clusters for networks from different species may prove useful in determining evolutionary relationships, in predicting the functions of proteins with unknown functions and in verifying those with estimated functions. RESULTS A central informal objective in constructing clusters of orthologous proteins is to guarantee that each cluster is composed of members with high homological similarity, usually determined via sequence similarities, and that the interactions of the proteins involved in the same cluster are conserved across the input networks. We provide a formal definition of the global many-to-many alignment of multiple protein-protein interaction networks that captures this informal objective. We show the computational intractability of the suggested definition. We provide a heuristic method based on backbone extraction and merge strategy (BEAMS) for the problem. We finally show, through experiments based on biological significance tests, that the proposed BEAMS algorithm performs better than the state-of-the-art approaches. Furthermore, the computational burden of the BEAMS algorithm in terms of execution speed and memory requirements is more reasonable than the competing algorithms. AVAILABILITY AND IMPLEMENTATION Supplementary material including code implementations in LEDA C++, experimental data and the results are available at http://webprs.khas. edu.tr/~cesim/BEAMS.tar. gz.
Value-at-Risk Prediction: A Comparison of Alternative Strategies

Given the growing need for managing financial risk, risk prediction plays an increasing role in banking and finance. In this study we compare the out-of-sample performance of existing methods and some new models for predicting value-at-risk (VaR) in a univariate context. Using more than 30 years of the daily return data on the NASDAQ Composite Index, we find that most approaches perform inadequately, although several models are acceptable under current regulatory assessment rules for model adequacy. A hybrid method, combining a heavy-tailed generalized autoregressive conditionally heteroskedastic (GARCH) filter with an extreme value theory-based approach, performs best overall, closely followed by a variant on a filtered historical simulation, and a new model based on heteroskedastic mixture distributions. Conditional autoregressive VaR (CAViaR) models perform inadequately, though an extension to a particular CAViaR model is shown to outperform the others. Copyright 2006, Oxford University Press.