Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure-based Insights into the Catalytic Power and Conformational Dexterity of Peroxiredoxins

Peroxiredoxins (Prxs), some of nature's dominant peroxidases, use a conserved Cys residue to reduce peroxides. They are highly expressed in organisms from all kingdoms, and in eukaryotes, they participate in hydrogen peroxide signaling. Seventy-two Prx structures have been determined that cover much of the diversity of the family. We review here the current knowledge and show that Prxs can be effectively classified by a structural= evolutionary organization into six subfamilies followed by specification of a 1-Cys or 2-Cys mechanism, and for 2-Cys Prxs, the structural location of the resolving Cys. We visualize the varied catalytic structural transitions and highlight how they differ depending on the location of the resolving Cys. We also review new insights into the question of how Prxs are such effective catalysts; the enzyme activates not only the conserved Cys thiolate but also the peroxide substrate. Moreover, the hydrogen-bonding network created by the four residues conserved in all Prx active sites stabilizes the transition state of the peroxidatic S N 2 displacement reaction. Strict conservation of the peroxidatic active site along with the variation in structural transitions provides a fascinating picture of how the diverse Prxs function to break down peroxide substrates rapidly. P eroxiredoxins (Prxs) are now recognized as the family of peroxidases that is broadly important in both antioxidant protection and cellular signaling pathways (84). Much ongoing work is elucidating the role of Prxs throughout biology, and many excellent reviews (25) have been published summarizing our current understanding of various aspects of Prxs, including covalent modifications (2) and signaling (28), and their importance in systems such as mitochondria (16), plants (22), yeast (18), and Caenorhabditis elegans (63). As for all enzymes, function flows directly from structure, and in this case, structural knowledge makes critical contributions to illuminating Prx function in both its antioxidant and cellular signaling roles. The goal of this review is to survey and organize the current structural information known about the Prxs; since our previous review published in 2007 (42), the number of known Prx structures has doubled. This review does not simply provide an up-to-date reference guide, pointing readers to the original publications for additional insights, but also presents essential principles of Prx function that can be derived from these structures.
A Polyhedral Study of Binary Polynomial Programs

We study the polyhedral convex hull of a mixed-integer set 𝒮 defined by a collection of multilinear equations over the unit hypercube. Such sets appear frequently in the factorable reformulation of mixed-integer nonlinear optimization problems. In particular, the set 𝒮 represents the feasible region of a linearized unconstrained binary polynomial optimization problem. We define an equivalent hypergraph representation of the mixed-integer set 𝒮, which enables us to derive several families of facet-defining inequalities, structural properties, and lifting operations for its convex hull in the space of the original variables. Our theoretical developments extend several well-known results from the Boolean quadric polytope and the cut polytope literature, paving a way for devising novel optimization algorithms for nonconvex problems containing multilinear sub-expressions.
Dual Presentation and Linear Basis of Temperley-lieb Algebra

The braid groups map homomorphically into the Temperley-Lieb algebras. Recently, Zinno showed that the homomorphic images of the simple elements arising from the dual presentation of the braid groups form a basis for the vector space underlying the Temperley-Lieb algebras. We give a simple geometric proof of his theorem, using a new presentation of the Temperley-Lieb algebras that corresponds to the dual presentation of the braid groups.
Rapid Sampling of Molecular Motions with Prior Information Constraints

Proteins are active, flexible machines that perform a range of different functions. Innovative experimental approaches may now provide limited partial information about conformational changes along motion pathways of proteins. There is therefore a need for computational approaches that can efficiently incorporate prior information into motion prediction schemes. In this paper, we present PathRover, a general setup designed for the integration of prior information into the motion planning algorithm of rapidly exploring random trees (RRT). Each suggested motion pathway comprises a sequence of low-energy clash-free conformations that satisfy an arbitrary number of prior information constraints. These constraints can be derived from experimental data or from expert intuition about the motion. The incorporation of prior information is very straightforward and significantly narrows down the vast search in the typically high-dimensional conformational space, leading to dramatic reduction in running time. To allow the use of state-of-the-art energy functions and conformational sampling, we have integrated this framework into Rosetta, an accurate protocol for diverse types of structural modeling. The suggested framework can serve as an effective complementary tool for molecular dynamics, Normal Mode Analysis, and other prevalent techniques for predicting motion in proteins. We applied our framework to three different model systems. We show that a limited set of experimentally motivated constraints may effectively bias the simulations toward diverse predicates in an outright fashion, from distance constraints to enforcement of loop closure. In particular, our analysis sheds light on mechanisms of protein domain swapping and on the role of different residues in the motion.
Identifying Objective EEG Based Markers of Linear Vection in Depth

This proof-of-concept study investigated whether a time-frequency EEG approach could be used to examine vection (i.e., illusions of self-motion). In the main experiment, we compared the event-related spectral perturbation (ERSP) data of 10 observers during and directly after repeated exposures to two different types of optic flow display (each was 35° wide by 29° high and provided 20 s of motion stimulation). Displays consisted of either a vection display (which simulated constant velocity forward self-motion in depth) or a control display (a spatially scrambled version of the vection display). ERSP data were decomposed using time-frequency Principal Components Analysis (t–f PCA). We found an increase in 10 Hz alpha activity, peaking some 14 s after display motion commenced, which was positively associated with stronger vection ratings. This followed decreases in beta activity, and was also followed by a decrease in delta activity; these decreases in EEG amplitudes were negatively related to the intensity of the vection experience. After display motion ceased, a series of increases in the alpha band also correlated with vection intensity, and appear to reflect vection- and/or motion-aftereffects, as well as later cognitive preparation for reporting the strength of the vection experience. Overall, these findings provide support for the notion that EEG can be used to provide objective markers of changes in both vection status (i.e., “vection/no vection”) and vection strength.
Design of Joint Sparse Graph for OFDM System

Low density signature orthogonal frequency division multiplexing (LDS-OFDM) and low density parity-check (LDPC) codes are multiple access and forward error correction (FEC) techniques, respectively. Both of them can be expressed by a bipartite graph. In this paper, we construct a joint sparse graph combining the single graphs of LDS-OFDM and LDPC codes, namely joint sparse graph for OFDM (JSG-OFDM). Based on the graph model, a low complexity approach for joint multiuser detection and FEC decoding (JMUDD) is presented. The iterative structure of JSG-OFDM receiver is illustrated and its extrinsic information transfer (EXIT) chart is researched. Furthermore, design guidelines for the joint sparse graph are derived through the EXIT chart analysis. By offline optimization of the joint sparse graph, numerical results show that the JSG-OFDM brings about 1.5-1.8 dB performance improvement at bit error rate (BER) of 10-5 over similar well-known systems such as group-orthogonal multi-carrier code division multiple access (GO-MC-CDMA), LDS-OFDM, and turbo structured LDS-OFDM.
Internal structure and drainage conduits in a cold Svalbard glacier

A combination of speleological exploration and highresolution radar survey was applied to investigate the englacial and subglacial drainage system of Longyearbreen, a cold glacier in Svalbard. Direct observations were compiled with remotely-sensed data in a 3D visualization of the glacier system using Petrel software package. In addition, a radar survey covering the entire glacier provided information on changes in the glacier thermal regime over time. Previous studies assumed that, in cold glaciers, no englacial and subglacial drainage systems form because cold ice acts as a barrier to water flow (Hodgkins 1997; see also the classical model of the evolution of the englacial meltwater system of Shreve 1972). However, the meltwater conduits present in Longyearbreen show that englacial and subglacial drainage channels indeed can develop in an un-crevassed, cold glacier, and we suggest that they formed through the cut-and-closure process as in the conceptual model of Gulley (2009). In the view of the present global temperature rise, investigating whether meltwater may reach the bed through a cold surface layer is vital for the understanding of glacier dynamics and stability. Valley glaciers in Spitsbergen such as Longyearbreen are potentially important contributors to the near-future sea level rise (Meier et al. 2007).
A scoring system for bruise patterns: a tool for identifying abuse

Aims: To determine whether abused and non-abused children differ in the extent and pattern of bruising, and whether any differences which exist are sufficiently great to develop a score to assist in the diagnosis of abuse. Methods: Total length of bruising in 12 areas of the body was determined in 133 physically abused and 189 control children aged 1–14 years. Results: Our method of recording bruises by site, maximum dimension, and shape was easy to use. There were clear differences between cases and controls in the total length of bruises. These differences were at their greatest in the head and neck and were less notable in the limbs. A scoring system was developed using logistic regression analysis using total lengths of bruising in five regions of the body. Good discrimination between the two sets of children was achieved using this score; by including a variable that indicates whether a bruise had a recognisable shape the discrimination could be made even better. Given a prior probability of abuse the score can be used to give posterior odds of abuse, given a particular bruising pattern. Conclusions: The scoring system provides a measure that discriminates between abused and non-abused children, which should be straightforward to implement, though the results must be interpreted carefully. We do not see this score as replacing the complex qualitative analysis of the diagnosis of abuse. This clearly includes history as well as examination, but rather as the beginning of the development of an important aid in this process.
What Role Does Error Orientation Play in the Relationship Between Error Management Climate and Innovative Behavior

Through theoretical analysis on the effect mechanism of error management climate and error orientation on innovative behavior, it’s find that the positive error management climate can not only has a positive influence on employee’s innovative behavior on organizational level also positively affect error orientation on personal level; positive error orientation can directly promote innovative behavior, meanwhile, it can serve as an intermediary role between error management climate and innovative behavior.
Parallel 'Go with the winners' algorithms in the LogP model

The authors parallelize the 'Go with the winners' algorithm of Aldous and Vazirani (1994) and analyze the resulting parallel algorithm in the LogP-model. The main issues in the analysis are load imbalances and communication delays. The result of the analysis is a practical algorithm which, under reasonable assumptions, achieves linear speedup. Finally, they analyze the algorithm for a concrete application: generating models of amorphous chemical structures.
Indoor C-band polarimetric observations of a mature wheat canopy

Ground based facilities allow for tightly controlled experiments which are very useful to identify the suitability and limitations, as well as the development of observational techniques. In this work, we report on the use of an indoor anechoic chamber, part of the GB-SAR facility, for polarimetric interferometry studies of vegetation. We give a brief description of the system, pointing out a few differences with common airborne I and spaceborne systems, present results of single polarisation interferometry using the H/V basis. These results show that for large angles of incidence, the height difference between the VV-VV and HH-HH interferograms can be used as an estimate of crop height. The use of coherence optimisation (both constrained and unconstrained) is also investigated. These techniques find polarisation states that allow for the accurate estimation of crop height. Some concluding remarks on the issues and prospects of ground based systems for this kind of work are also presented.
KOCL: Power Self- Awareness for Arbitrary FPGA-SoC-Accelerated OpenCL Applications

<italic>Editor’s note:</italic> Being aware of its own power consumption is essential for any system under power constraints, i.e. all systems with moderate or high complexity. This paper describes a tool that provides this power awareness for applications written in OpenCL and implemented on FPGAs. <italic>—Axel Jantsch, TU Wien</italic>
Optimal control of dispersive tubular chemical reactors: Part I

Abstract This paper, the first of a series of two, deals with the determination of optimal steady-state jacket fluid temperature profiles for dispersive tubular chemical reactors, ranging from plug flow to perfectly mixed reactors. According to Pontryagin's minimum principle, the optimal control is of the bang-bang type for the proposed terminal cost criterion. The bang-bang switching position is numerically optimised, by means of a weighted shooting-type procedure for the determination of the reactor profiles, ensuring the Danckwerts boundary conditions are satisfied. Following this procedure the impact of dispersion on the optimised profiles is illustrated. In the second paper, the performance of the obtained optimal control laws will be compared with that of practically more feasible controls. Furthermore, the transient behaviour will be assessed.
Metallic coatings for high-temperature oxidation resistance

Abstract: This chapter reviews metallic coatings with the ability to thermally grow a protective layer of chromia or alumina, together with the coating techniques. First generation coatings are developed using chemical vapour deposition techniques (CVD); adding small amounts of reactive elements (e.g., Ce, Y, La) or adding noble elements such as Pt can further enhance performance. Second-generation coatings of the alumina-forming M–Cr–Al–Y overlay type bring the advantages that composition can be tailored to specific environments and to match the composition of matrix alloy, in order to minimize the interdiffusion between coatings and matrix.
Complex Gangliosides at the Neuromuscular Junction Are Membrane Receptors for Autoantibodies and Botulinum Neurotoxin But Redundant for Normal Synaptic Function

One specialization of vertebrate presynaptic neuronal membranes is their multifold enrichment in complex gangliosides, suggesting that these sialoglycolipids may play a major functional role in synaptic transmission. We tested this hypothesis directly by studying neuromuscular synapses of mice lacking complex gangliosides attributable to deletion of the gene coding for β1,4 GalNAc-transferase (GM2/GD2 synthase), which catalyzes an early step in ganglioside synthesis. Our studies show that complex gangliosides are surprisingly redundant for regulated neurotransmitter release under normal physiological conditions. In contrast, we show that they are membrane receptors for both the paralytic botulinum neurotoxin type-A and human neuropathy-associated anti-ganglioside autoantibodies that arise through molecular mimicry with microbial structures. These data prove the critical importance of complex gangliosides in mediating pathophysiological events at the neuromuscular synapse.
The enumerative geometry of rational and elliptic curves in projective space

We study the geometry of varieties parametrizing degree d rational and elliptic curves in P^n intersecting fixed general linear spaces and tangent to a fixed hyperplane H with fixed multiplicities along fixed general linear subspaces of H. As an application, we derive recursive formulas for the number of such curves when the number is finite. These recursive formulas require as ``seed data'' only one input: there is one line in P^1 through two points. These numbers can be seen as top intersection products of various cycles on the Hilbert scheme of degree d rational or elliptic curves in P^n, or on certain components of $\mbar_0(P^n,d)$ or $\mbar_1(P^n,d)$, and as such give information about the Chow ring (and hence the topology) of these objects. The formula can also be interpreted as an equality in the Chow ring (not necessarily at the top level) of the appropriate Hilbert scheme or space of stable maps. In particular, this gives an algorithm for counting rational and elliptic curves in P^n intersecting various fixed general linear spaces. (The genus 0 numbers were found earlier by Kontsevich-Manin, and the genus 1 numbers were found for n=2 by Ran and Caporaso-Harris, and independently by Getzler for n=3.)
Bayesian Approach To Derivative Pricing And Model Uncertainty

A fluid supply device such as a fuel pump has an impeller 24 on which vanes and vane grooves are arranged alternately on its outer circumference. All adjacent groove angles, each of which is defined by the adjacent two vane grooves, are different from each other. Among the arrangement of the vane grooves, a sum Sm of the angles of the vane grooves which are adjacent in succession in the number of m=n/k (k=2, 3 and 4) is determined. If the number n/k is not an integer, at least (n/k)+1 between n/k and (n/k)+1 is set as m. The sum Sm is determined n-times by shifting the vane groove, from which the sum is determined each time, in the circumferential direction one by one. The arrangement in which the sum Sm of each time satisfies the following relation is adopted: (360/k)-10</=Sm</=(360/k)+10.
Ultrasound detection of pneumothorax with minimally trained sonographers: a preliminary study.

BACKGROUND Prompt recognition and treatment of a tension pneumothorax is critical to reducing mortality in both military and civilian settings. Physician assistants, Special Operations Forces (SOF) and conventional force Medics are often the first medical providers to care for combat trauma patients with penetrating chest trauma and frequently have limited diagnostic capabilities available to them due to mission constraints. The purpose of this study is to examine the potential for non-physician providers to determine the absence or presence of a pneumothorax in a porcine model, with the use of a portable ultrasound machine, after receiving minimal training. METHODS Physician assistants, SOF and conventional force Medics, veterinary technicians, and food service inspectors, all naive to ultrasound, were recruited for this study. Participants underwent a brief presentation on detection of a pneumothorax by ultrasound and were then asked to perform a thoracic ultrasound examination on euthanized, ventilated swine. Some of the swine were induced with a pneumothorax prior to these examinations, and all participants were blinded to the absence or presence of a pneumothorax. RESULTS Twenty-two participants examined a total of 44 hemithoraces. A total of 21 out of 22 pneumothoraces were correctly identified with one false-negative. All 22 normal hemithoraces were correctly identified for a sensitivity of 95.4% (95% CI 0.75-0.99), and a specificity of 100% (95% CI 0.81-1.00), with PPV of 100%, NPV of 95.6%. CONCLUSIONS Non-physician healthcare providers can accurately detect a pneumothorax with portable ultrasound after receiving minimal focused training.
A new data compression algorithm for sources with memory based on error correcting codes

A new fixed-length asymptotically optimal scheme for lossless compression of stationary ergodic tree sources with memory is proposed. Our scheme is based on the concatenation of the Burrows-Wheeler block sorting transform with the syndrome former of a linear error correcting code. Low-density parity-check (LDPC) codes together with belief propagation decoding lead to linear compression and decompression times, and to natural universal implementation of the algorithm.
Characterizing Anomalous Behaviors and Revising Robotic Controllers

This paper is concerned with revising autonomous robotic controllers. A proof of concept of the proposed machine learning-based approach is presented, aimed at characterizing and avoiding the wobbling phenomenon incurred by a Braitenberg controller. Based on the global assessment of a few trajectories by the expert, the goal is to identify erroneous sub-behaviors. The success criterion is to be able to identify as soon as possible (early alarm) such behaviors when they occur, in order e.g. to trigger an emergency controller.
Finding a Maximum Independent Set in a Sparse Random Graph

We consider the problem of finding a maximum independent set in a random graph. The random graph $G$, which contains $n$ vertices, is modeled as follows. Every edge is included independently with probability $\frac{d}{n}$, where $d$ is some sufficiently large constant. Thereafter, for some constant $\alpha$, a subset $I$ of $\alpha n$ vertices is chosen at random, and all edges within this subset are removed. In this model, the planted independent set $I$ is a good approximation for the maximum independent set $I_{max}$, but both $I \setminus I_{max}$ and $I_{max} \setminus I$ are likely to be nonempty. We present a polynomial time algorithm that with high probability (over the random choice of random graph $G$ and without being given the planted independent set $I$) finds the maximum independent set in $G$ when $\alpha \geq \sqrt{c_0 /d}$, where $c_0$ is some sufficiently large constant independent of $d$.