Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of non-native aromatic and hydrophobic interactions in the folding of hen egg white lysozyme.

The folding kinetics have been determined for hen egg white lysozyme and two mutants in which Trp-62 and Trp-108 have been individually replaced by tyrosine (Tyr-62-lysozyme and Tyr-108-lysozyme, respectively). An earlier study of wild-type lysozyme [Denton, M. E. , Rothwarf, D. M. , & Scheraga, H. A. (1994) Biochemistry 33, 11225-11236] had indicated that two transient intermediates were formed during the early stages of refolding. Both intermediates were characterized by substantial quenching of tryptophan fluorescence which suggested that, during the refolding process, Trp-62 and/or Trp-108 was involved in a non-native tertiary interaction(s). Both Tyr-108- and Tyr-62-lysozyme fold significantly faster than wild-type lysozyme (7- and 13-fold, respectively). These results indicate that the rate-limiting step in the folding of lysozyme arises not from any inherent slowness in the formation of the native structure but rather as a consequence of the formation of a highly stable intermediate which contains significant non-native structure which must be disrupted prior to, or in concert with, subsequent folding. The data suggest that aromatic and hydrophobic interactions play a pivotal role in the formation of the non-native intermediate. The general role that non-native interactions play in the folding process is discussed.
Are US CEOs Paid More? New International Evidence

This paper challenges the widely accepted stylized fact that CEOs in the United States are paid significantly more than their foreign counterparts. Using CEO pay data across 14 countries with mandated pay disclosures, we show that the US pay premium is economically modest and primarily reflects the performance-based pay demanded by institutional shareholders and independent boards. Indeed, we find no significant difference in either level of CEO pay or the use of equity-based pay between US and non-US firms exposed to international and US capital, product, and labor markets. We also show that US and non-US CEO pay has largely converged in the 2000s. The findings are robust to alternative methods for adjusting the risk of equity-based pay.
Dyad Practice Impacts Self-Directed Practice Behaviors and Motor Learning Outcomes in a Contextual Interference Paradigm

ABSTRACT We studied dyad practice to determine whether and how alternating practice blocks with a partner impacts self-directed practice scheduling, learning, and perceptions of practice. Participants were assigned to be Partner 1 (P1) or 2 (P2). P1s had a blocked, random, or self-directed schedule, while all P2s self-directed practice of 3, differently-timed keystroke-sequences. P2s showed both own error-dependent practice (switching sequences following better performance) and partner-dependent practice, with the partner's schedule impacting sequence selection and switching frequency. A partner's schedule also impacted learning. Random practice resulted in better timing accuracy than blocked practice for both partners in an immediate and delayed retention test. These data give evidence that self-directed practice behaviors and learning outcomes are modulated by a partner's practice schedule.
A Gossip-Based Optimistic Replication for Efficient Delay-Sensitive Streaming Using an Interactive Middleware Support System

Emerging Mobile-Peer-to-Peer (MP2P) systems involve client applications that dynamically demand resources directly from the global environment. While sharing resources the efficiency is substantially degraded as a result of the scarceness of availability of the requested resources in a multiclient support manner. These resources are often aggravated by many factors like the temporal constraints for availability or node flooding by the requested replicated file chunks. Thus replicated file chunks should be efficiently disseminated in order to enable resource availability on-demand by the mobile users. This work considers a cross layered middleware support system for efficient delay-sensitive streaming by using each device's connectivity and social interactions in a cross layered manner. The collaborative streaming is achieved through the epidemically replicated file chunk policy which uses a transition-based approach of a chained model of an infectious disease with susceptible, infected, recovered and death states. The Gossip-based stateful model enforces the mobile nodes whether to host a file chunk or not or, when no longer a chunk is needed, to purge it. The proposed model is thoroughly evaluated through experimental simulation taking measures for the effective throughput E ff as a function of the packet loss parameter in contrast with the effectiveness of the replication Gossip-based policy.
Weak contact equations for mappings into Heisenberg groups

Let k>n be positive integers. We consider mappings from a subset of k-dimensional Euclidean space R^k to the Heisenberg group H^n with a variety of metric properties, each of which imply that the mapping in question satisfies some weak form of the contact equation arising from the sub-Riemannian structure of the Heisenberg group. We illustrate a new geometric technique that shows directly how the weak contact equation greatly restricts the behavior of the mappings. In particular, we provide a new and elementary proof of the fact that the Heisenberg group H^n is purely k-unrectifiable. We also prove that for an open set U in R^k, the rank of the weak derivative of a weakly contact mapping in the Sobolev space W^{1,1}_{loc}(U;R^{2n+1}) is bounded by $n$ almost everywhere, answering a question of Magnani. Finally we prove that if a mapping from U to H^n is s-H\"older continuous, s>1/2, and locally Lipschitz when considered as a mapping into R^{2n+1}, then the mapping cannot be injective. This result is related to a conjecture of Gromov.
Muscle coordination during breaststroke swimming: Comparison between elite swimmers and beginners

ABSTRACT The present study aimed to compare muscle coordination strategies of the upper and lower limb muscles between beginners and elite breaststroke swimmers. Surface electromyography (EMG) of eight muscles was recorded in 16 swimmers (8 elite, 8 beginners) during a 25 m swimming breaststroke at 100% of maximal effort. A decomposition algorithm was used to identify the muscle synergies that represent the temporal and spatial organisation of muscle coordination. Between-groups indices of similarity and lag times were calculated. Individual muscle patterns were moderately to highly similar between groups (between-group indices range: 0.61 to 0.84). Significant differences were found in terms of lag time for pectoralis major (P < 0.05), biceps brachii, rectus femoris and tibialis anterior (P < 0.01), indicating an earlier activation for these muscles in beginners compared to elites (range: −13.2 to −3.8% of the swimming cycle). Three muscle synergies were identified for both beginners and elites. Although their composition was similar between populations, the third synergy exhibited a high within-group variability. Moderate to high indices of similarity were found for the shape of synergy activation coefficients (range: 0.63 to 0.88) but there was a significant backward shift (−8.4% of the swimming cycle) in synergy #2 for beginners compared to elites. This time shift suggested differences in the global arm-to-leg coordination. These results indicate that the synergistic organisation of muscle coordination during breaststroke swimming is not profoundly affected by expertise. However, specific timing adjustments were observed between lower and upper limbs.
Residue Substitutions Near the Redox Center of Bacillus subtilis Spx Affect RNA Polymerase Interaction, Redox Control, and Spx-DNA Contact at a Conserved cis-Acting Element

ABSTRACT Spx, a member of the ArsC protein family, is a regulatory factor that interacts with RNA polymerase (RNAP). It is highly conserved in Gram-positive bacteria and controls transcription on a genome-wide scale in response to oxidative stress. The structural requirements for RNAP interaction and promoter DNA recognition by Spx were examined through mutational analysis. Residues near the CxxC redox disulfide center of Spx functioned in RNAP α subunit interaction and in promoter DNA binding. R60E and C10A mutants were shown previously to confer defects in transcriptional activation, but both were able to interact with RNAP. R92, which is conserved in ArsC-family proteins, is likely involved in redox control of Spx, as the C10A mutation, which blocks disulfide formation, was epistatic to the R92A mutation. The R91A mutation reduced transcriptional activation and repression, suggesting a defect in RNAP interaction, which was confirmed by interaction assays using an epitope-tagged mutant protein. Protein-DNA cross-linking detected contact between RNAP-bound Spx and the AGCA element at −44 that is conserved in Spx-controlled genes. This interaction caused repositioning of the RNAP σA subunit from a −35-like element upstream of the trxB (thioredoxin reductase) promoter to positions −36 and −11 of the core promoter. The study shows that RNAP-bound Spx contacts a conserved upstream promoter sequence element when bound to RNAP.
The use of electrocochleography to monitor the response of Ménière's disease patients to intratympanic steroids

Abstract Conclusions: Intratympanic (IT) dexamethasone provides an alternative for patients with Ménière's disease (MD). A reduction of the endolymphatic hydrops is detected by the EcohG 1 month after the treatment. Objective: The use of intratympanic corticoid injections for MD has become popular due to the lack of reported adverse effects, but the mechanism of action is not well established. This study aimed to evaluate the changes in electrocochleography (EcohG) measurements during IT dexamethasone therapy. Methods: This study included 53 patients with unilateral MD refractory to medical therapy for at least 1 year. Each patient was treated with a fixed protocol of three consecutive weekly injections of a commercial 4 mg/ml dexamethasone preparation. EcohG measurements were performed 1 month before and 1 month after IT steroid therapy. The SP/AP ratio was measured before and after the IT treatment. A Kaplan–Meier analysis was used to evaluate the control of vertigo over a 2-year period. Results: Complete vertigo control (class A) was achieved in 22 patients (41.5%) at the 12-month follow-up and 8 patients (15.1%) at the 24-month follow-up. A significant reduction (p < 0.01) in the SP/AP ratio after the IT steroid treatment was observed.
Image annotation and retrieval based on efficient learning of contextual latent space

Image annotation and retrieval are extremely difficult because of the generic nature of the target images. Generic images contain various miscellaneous objects and scenes. Therefore, desirable annotation results are subjective and underspecified. To overcome this problem, it is important to assume “Weak Labeling” framework, where images are weakly related to multiple words without region information. In this paper, we propose a high speed and high accuracy image annotation and retrieval method based on efficient learning of the contextual latent space. A distance between samples can be defined in the intrinsic feature space for annotation using latent space learning between images and labels. The proposed method is shown to be faster and more accurate than previously published methods.
Structured light for head tracking in radiation therapy

Optical head tracking for robot-guided radiosurgery offers essential advantages. It is based on harmless laser light and it provides a high localization rate. The crucial disadvantage of optical head tracking is given by limited accuracy. The problem is that the registration of surfaces is influenced by the deformable soft tissue. In order to enhance the accuracy of optical head tracking, our research group developed a novel measurement system. By analyzing the measured reflection of a grid of projected laser spots, a point-based reconstruction of the forehead’s surface and optical features are acquired. The latter provide a correlation with the thickness of the soft tissue of the forehead. In future developments, the optical features shall be utilized to compensate for the influence of the soft tissue. In this manner, a highly accurate registration with respect to the rigid skull surface shall be achieved. In this work, the acquisition of point-based surface reconstructions is addressed. In order to establish correspondence between the projected and the captured light information, a method for binary time multiplexing is proposed. The developed method can be used for objects that move slowly. Furthermore, the method provides the basis for a high reconstruction rate. Besides the established point correspondence, the triangulation of surface points also requires the calibration of the extrinsic parameters of the laser scanning system. For this reason, a procedure for the highly accurate calibration of laser rays is proposed. The analysis of the triangulation accuracy revealed a root mean square (RMS) error of 0.1037 mm and 0.1477 mm for the reconstruction of a plane and the surface reconstruction of a stair phantom, respectively. In the case of the reconstruction of the surface of three human foreheads, the analysis revealed RMS errors between 0.1526 mm and 0.1832 mm.
Deprecating the Observer Pattern

Programming interactive systems by means of the observer pattern is hard and error-prone yet is still the implementation standard in many production environments. We present an approach to gradually deprecate observers in favor of reactive programming abstractions. Several library layers help programmers to smoothly migrate existing code from callbacks to a more declarative programming model. Our central high-level API layer embeds an extensible higher-order data-flow DSL into our host language. This embedding is enabled by a continuation passing style transformation.
An asynchronous distributed algorithm for computing a common fixed point of a family of paracontractions

A distributed algorithm is described for finding a common fixed point of a family of m > 1 nonlinear maps Mi : Rn → Rn assuming that each map is a paracontraction. The common fixed point is asynchronously computed in real time by m agents assuming each agent i knows only Mi, the current estimates of the fixed point generated by its neighbors, and nothing more. Each agent recursively updates its estimate of the fixed point at its own event times, by utilizing estimates generated by each of its neighbors. Neighbor relations are characterized by a time-dependent directed graph N(t) whose vertices correspond to agents and whose arcs depict neighbor relations.
Fast Plane Wave 2-D Vector Flow Imaging Using Transverse Oscillation and Directional Beamforming

Several techniques can estimate the 2-D velocity vector in ultrasound. Directional beamforming (DB) estimates blood flow velocities with a higher precision and accuracy than transverse oscillation (TO), but at the cost of a high beamforming load when estimating the flow angle. In this paper, it is proposed to use TO to estimate an initial flow angle, which is then refined in a DB step. Velocity magnitude is estimated along the flow direction using cross correlation. It is shown that the suggested TO-DB method can improve the performance of velocity estimates compared with TO, and with a beamforming load, which is 4.6 times larger than for TO and seven times smaller than for conventional DB. Steered plane wave transmissions are employed for high frame rate imaging, and parabolic flow with a peak velocity of 0.5 m/s is simulated in straight vessels at beam-to-flow angles from 45° to 90°. The TO-DB method estimates the angle with a bias and standard deviation (SD) less than 2°, and the SD of the velocity magnitude is less than 2%. When using only TO, the SD of the angle ranges from 2° to 17° and for the velocity magnitude up to 7%. Bias of the velocity magnitude is within 2% for TO and slightly larger but within 4% for TO-DB. The same trends are observed in measurements although with a slightly larger bias. Simulations of realistic flow in a carotid bifurcation model provide visualization of complex flow, and the spread of velocity magnitude estimates is 7.1 cm/s for TO-DB, while it is 11.8 cm/s using only TO. However, velocities for TO-DB are underestimated at peak systole as indicated by a regression value of 0.97 for TO and 0.85 for TO-DB. An in vivo scanning of the carotid bifurcation is used for vector velocity estimations using TO and TO-DB. The SD of the velocity profile over a cardiac cycle is 4.2% for TO and 3.2% for TO-DB.
Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR

Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR). Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2α and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics.
Three-dimensional reconstruction of an actin bundle

We present the three-dimensional structure of an actin filament bundle from the sperm of Limulus. The bundle is a motile structure which by changing its twist, converts from a coiled to an extended form. The bundle is composed of actin plus two auxiliary proteins of molecular masses 50 and 60 kD. Fraying the bundle with potassium thiocyanate created three classes of filaments: actin, actin plus the 60-kD protein, and actin plus both the auxiliary proteins. We examined these filaments by transmission electron microscopy and scanning transmission electron microscopy (STEM). Three-dimensional reconstructions from electron micrographs allowed us to visualize the actin subunit and the 60- and 50-kD subunits bound to it. The actin subunit appears to be bilobed with dimensions 70 X 40 X 35 A. The inner lobe of the actin subunit, located at 20 A radius, is a prolate ellipsoid, 50 X 25 A; the outer actin lobe, at 30 A radius, is a 35-A-diam spheroid. Attached to the inner lobe of actin is the 60-kD protein, an oblate spheroid, 55 X 40 A, at 50 A radius. The armlike 50-kD protein, at 55 A radius, links the 60-kD protein on one of actin's twin strands to the outer lobe of the actin subunit on the opposite strand. We speculate that the 60-kD protein may be a bundling protein and that the 50-kD protein may be responsible for the change in twist of the filaments which causes extension of the bundle.
ISAR imaging of uniformly rotating targets via parametric matching pursuit

Inverse synthetic aperture radar (ISAR) imaging of maneuvering targets via matching pursuit (MP) can produce high resolution and remove sidelobe effect, providing that the target rotation rate is already known. For non-cooperative uniformly rotating targets, the rotation rate is unknown and should be retrieved together with the ISAR image. In this paper, a computational efficient parametric MP is proposed to simultaneously retrieve the rotation rate and the high-resolution ISAR image. The joint estimation of ISAR image and rotation rate is converted into alternate independent estimations, i.e. alternately estimating the ISAR image and rotation rate in an iterative manner. With the iterations, the rotation rate estimate converges to the true value and meanwhile the clear ISAR image with high resolution and low sidelobes may be obtained. Numerical examples show that the approach is efficient in estimating the real target rotation rate and recovering the high resolution ISAR image.
Generalized Denoising Auto-Encoders as Generative Models

Recent work has shown how denoising and contractive autoencoders implicitly capture the structure of the data-generating density, in the case where the corruption noise is Gaussian, the reconstruction error is the squared error, and the data is continuous-valued. This has led to various proposals for sampling from this implicitly learned density function, using Langevin and Metropolis-Hastings MCMC. However, it remained unclear how to connect the training procedure of regularized auto-encoders to the implicit estimation of the underlying data-generating distribution when the data are discrete, or using other forms of corruption process and reconstruction errors. Another issue is the mathematical justification which is only valid in the limit of small corruption noise. We propose here a different attack on the problem, which deals with all these issues: arbitrary (but noisy enough) corruption, arbitrary reconstruction loss (seen as a log-likelihood), handling both discrete and continuous-valued variables, and removing the bias due to non-infinitesimal corruption noise (or non-infinitesimal contractive penalty).
D-Cell Hypothesis: Pathogenesis of Mesolimbic Dopamine Hyperactivity of Schizophrenia

In the present article, the author proposes a new “D-cell hypothesis” for mesolimbic dopamine (DA) hyperactivity of schizophrenia, of which relevant molecular mechanism has not yet been known. The “D-cell” is defined as “the non-monoaminergic aromatic L-amino acid decarboxylase (AADC)-containing cell”. The D-cell contains AADC but not dopaminergic nor serotonergic. D-cells produce trace amines, and also take up amine precursors and convert them to amines by decarboxylation. The author reported “dopa-decarboxylating neurons specific to the human striatum”, that is, “D-neurons” in the human striatum, and preliminarily the number reduction of D-neurons in the striatum and nucleus accumbens of postmortem brains of patients with schizophrenia. Trace amine-associated receptor, type 1 (TAAR1), a subtype of trace amine receptors, having a large number of ligands, including tyramine, β-phenylethylamine (PEA), and methamphetamine, is a target receptor for the latest neuroleptic discovery. Recent studies have shown that the decreased stimulation of TAAR1 on cell membranes or nerve terminals of DA neurons in the midbrain ventral tegmental area (VTA) increased firing frequency of VTA DA neurons. In brains of schizophrenia, dysfunction of neural stem cells in the subventricular zone of lateral ventricle may cause reduction of the number of D-neurons in the striatum and nucleus accumbens, and may result in decrease of trace amine synthesis. The decrease of stimulation of TAAR1 on terminals of VTA DA neurons caused by trace amine reduction may increase firing frequency of VTA DA neurons, and may finally cause mesolimbic DA hyperactivity. This innovative theory, “D-cell hypothesis” might explain mesolimbic DA hyperactivity in pathogenesis of schizophrenia.