Miracle-dz/UniFAR-FTUs huggingface dataset:
Enzyme Selectivity Fine‐Tuned through Dynamic Control of a Loop

Abstract Allostery has been revealed as an essential property of all proteins. For enzymes, shifting of the structural equilibrium distribution at one site can have substantial impacts on protein dynamics and selectivity. Promising sites of remotely shifting such a distribution by changing the dynamics would be at flexible loops because relatively large changes may be achieved with minimal modification of the protein. A ligand‐selective change of binding affinity to the active site of cyclophilin is presented involving tuning of the dynamics of a highly flexible loop. Binding affinity is increased upon substitution of double Gly to Ala at the hinge regions of the loop. Quenching of the motional amplitudes of the loop slightly rearranges the active site. In particular, key residues for binding Phe60 and His126 adopt a more fixed orientation in the bound protein. Our system may serve as a model system for studying the effects of various time scales of loop motion on protein function tuned by mutations.
Spectral correspondence method for fingerprint minutia matching

This paper presents a spectral correspondence method for fingerprint matching. Minutia matching is formulated as recovering the dense sub-block in the corresponding matrix. And then the spectral correspondence method is used for searching the dense sub-block. First, we propose the pairwise adjacency matrix (PAM), whose diagonal elements represent similarities of minutia structures and other elements represent pairwise compatibilities between local minutia structure pair. Second, correct minutia pairs are likely to establish both large similarities and large compatibilities among each other and they form a dense sub-block. Then minutia matching is formulated as recovering the dense sub-block in the PAM. It gives a clear mathematical meaning for “optimal matching minutia pairs”. Third, we recover the dense sub-block based on spectral correspondence method, by using the principal eigenvector of PAM and imposing the one-to-one mapping constraints. Proposed method has stronger description ability and better robustness. Experiments conducted on FVC database demonstrate the effectiveness and the efficiency.
Therapeutic potential of human amniotic membrane-derived mesenchymal stem cells in APP transgenic mice

Growing evidence indicates that the presence of extensive oxidative stress plays an essential role in the initiation and progression of Alzheimer's disease (AD). Amyloid-β (Aβ) aggregation is involved in the elevation of oxidative stress, contributing to mitochondrial dysfunction and lipid peroxidation. In the present study, human placenta amniotic membrane-derived mesenchymal stem cells (hAMMSCs) were intravenously injected into C57BL/6J-APP transgenic mice. hAMMSCs significantly ameliorated spatial learning and memory function, and were associated with a decreased amount of amyloid plaques of the brain. The correlation of oxidative stress with Aβ levels was lower in the hAMMSCs-injected group than in the phosphate-buffered saline (PBS)-injected group, as indicated by the increased level of antioxidative enzymes and the decreased level of lipid peroxidation product. The glutathione (GSH) level and ratio of GSH to glutathione disulfide were higher in the hAMMSC group than in the PBS group. The superoxide dismutase activity and malonaldehyde level were improved significantly as the level of Aβ decreased, but there was no such trend in the PBS group. As a result, our findings represent evidence that hAMMSC treatment might improve the pathology of AD and memory function through the regulation of oxidative stress.
Shape representation and classification through Height functions and Local Binary Pattern - a decision level fusion approach

In this paper, we propose a combined classifier model based on Height functions (HF) and Local Binary Pattern (LBP) to classify shapes accurately. The height functions are insensitive to geometric transformations and nonlinear deformations and LBP is capable of capturing the region information. We propose to integrate these two techniques for accurate shape classification. The Dynamic Programming (DP) in case of HF and the Earth Movers Distance (EMD) metric in case of LBP were respectively employed to obtain similarity values and hence fused to classify given query shape based on minimum similarity value. The experiments are conducted on publicly available shape datasets namely MPEG-7, Kimia-99, Kimia-216, Myth and Tools-2D and the results are presented by means of Bull's eye score and precision-recall metric. The comparative study is also provided with the well known approaches to exhibit the retrieval accuracy of the proposed approach. The proposed approach shows better results compared to other algorithms.
DIDS (distributed intrusion detection system)—motivation, architecture, and an early prototype

Intrusion detection is the problem of identifying unauthorized use, misuse, and abuse of computer systems by both system insiders and external penetrators. The proliferation of heterogeneous computer networks provides additional implications for the intrusion detection problem. Namely, the increased connectivity of computer systems gives greater access to outsiders, and makes it easier for intruders to avoid detection. IDS’s are based on the belief that an intruder’s behavior will be noticeably different from that of a legitimate user. We are designing and implementing a prototype Distributed Intrusion Detection System (DIDS) that combines distributed monitoring and data reduction (through individual host and LAN monitors) with centralized data analysis (through the DIDS director) to monitor a heterogeneous network of computers. This approach is unique among current IDS’s. A main problem considered in this paper is the Network-user Identification problem, which is concerned with tracking a user moving across the network, possibly with a new user-id on each computer. Initial system prototypes have provided quite favorable results on this problem and the detection of attacks on a network. This paper provides an overview of the motivation behind DIDS, the system architecture and capabilities, and a discussion of the early prototype.
Type 6 Secretion Dynamics Within and Between Bacterial Cells

Time-lapse video records a bacterial protein transportation machine in action. The bacterial type 6 secretion system (T6SS) functions as a virulence factor capable of attacking both eukaryotic and prokaryotic target cells by a process that involves protein transport through a contractile bacteriophage tail-like structure. The T6SS apparatus is composed, in part, of an exterior sheath wrapped around an interior tube. Here, we report that in living cells the cytoplasmic adenosine triphosphatase called ClpV specifically recognizes the contracted T6SS sheath structure, causing its disassembly within seconds. ClpV imaging allowed spatial and temporal documentation of cell-cell interactions (termed T6SS dueling) that likely mark the location of repeated T6SS-mediated protein translocation events between bacterial cells.
Automated synthesis of streaming C applications to process networks in hardware

The demand for embedded computing power is continuously increasing and FPGAs are becoming very interesting computing platforms, as they provide huge amounts of customizable parallelism. However, programming them is challenging, let alone from a high level language. In [1], the ESPAM methodology was already presented to quickly obtain realizations on FPGAs from sequential C code. The realization consists of a network of processors and IP cores. In this approach, a problem was that the IP cores had to be provided manually. In this paper, we present an extension on the ESPAM methodology by incorporating the industrial high level synthesis tool PICO from Synfora Inc. In this way, we realize the automated generation of efficient hardware implementations on FPGAs from a single sequential C input specification of a streaming application. We demonstrate our approach for the Sobel and QR applications.
On the Achievable Rate and Average Sum Capacity of Spread Spectrum Underlay CR Networks

In this paper, we investigate the achievable rate and the average sum capacity of an underlay cognitive radio (CR) (also known as a secondary) system. We consider single user (SU) and multiple users (MU) secondary systems that deploy spread spectrum as the signaling technique which utilizes the whole available spectrum. The objective is to maximize the achievable rate and the average sum capacity of the SU and MU secondary systems, respectively, by allocating the optimum power to the secondary transmitter(s) (STs), such that the instantaneous (aggregate) interference power from STs is below a certain threshold at the primary receiver (PR), to guarantee the quality of service (QoS) of the primary system. Numerical and Monte-Carlo Simulation results show that the achievable rate of the SU system and the average sum capacity of the MU system can be enhanced significantly compared to other signaling techniques, because of the fact that in spread spectrum the signal's power is spread over a wider bandwidth, which gives the secondary system more freedom to allocate power to enhance the data rate.
How much parallelism is there in irregular applications?

Irregular programs are programs organized around pointer-based data structures such as trees and graphs. Recent investigations by the Galois project have shown that many irregular programs have a generalized form of data-parallelism called amorphous data-parallelism. However, in many programs, amorphous data-parallelism cannot be uncovered using static techniques, and its exploitation requires runtime strategies such as optimistic parallel execution. This raises a natural question: how much amorphous data-parallelism actually exists in irregular programs? In this paper, we describe the design and implementation of a tool called ParaMeter that produces parallelism profiles for irregular programs. Parallelism profiles are an abstract measure of the amount of amorphous data-parallelism at different points in the execution of an algorithm, independent of implementation-dependent details such as the number of cores, cache sizes, load-balancing, etc. ParaMeter can also generate constrained parallelism profiles for a fixed number of cores. We show parallelism profiles for seven irregular applications, and explain how these profiles provide insight into the behavior of these applications.
Structural, elastic and electronic properties of 2H- and 4H-SiC

The structural, five different elastic constants and electronic properties of 2H- and 4H-Silicon carbide (SiC) are investigated by using density functional theory (DFT). The total energies of primitive cells of 2H- and 4H-SiC phases are close to each other and moreover satisfy the condition E2H >E4H . Thus, the 4H-SiC structure appears to be more stable than the 2H- one. The analysis of elastic properties also indicates that the 4H-SiC polytype is stiffer than the 2H structures. The electronic energy bands, the total density of states (DOS) are calculated. The fully relaxed and isotropic bulk modulus is also estimated. The implication of the comparison of our results with the existing experimental and theoretical studies is made.
Changing base without losing space

We describe a simple, but powerful local encoding technique, implying two surprising results: 1. We show how to represent a vector of n values from some alphabet S using ceiling(n * log2 |S|) bits, such that reading or writing any entry takes O(1) time. This demonstrates, for instance, an "equivalence" between decimal and binary computers, and has been a central toy problem in the field of succinct data structures. Previous solutions required space of n * log2 |S| + n/logO(1) n bits for constant access. 2. Given a stream of n bits arriving online (for any n, not known in advance), we can output a *prefix-free* encoding that uses n + log2 n + O(loglog n) bits. The encoding and decoding algorithms only require O(log n) bits of memory, and run in constant time per word. This result is interesting in cryptographic applications, as prefix-free codes are the simplest counter-measure to extensions attacks on hash functions, message authentication codes and pseudorandom functions. Our result refutes a conjecture of [Maurer, Sjodin 2005] on the hardness of online prefix-free encodings.
Myocardial Alterations in Senescent Mice and Effect of Exercise Training: A Strain Rate Imaging Study

Background—Aging is accompanied by an alteration in myocardial contractility. However, its noninvasive detection is difficult. The effect of chronic exercise on this decrease is unknown. Murine models of senescence are increasingly used to test therapies in aging. We tested whether strain rate imaging detected left ventricular (LV) systolic dysfunction in aging mice and was able to assess a potential improvement after exercise. Methods and Results—Young (3 weeks), adult (2 to 3 months), and old (6 to 18 months) C57BL6 male mice underwent echocardiograms with strain rate imaging, either in sedentary conditions or before, 2 weeks and 4 weeks after chronic swimming. Hemodynamic parameters of LV function including maximal and end-systolic elastance were obtained before euthanizing. LV fibrosis was measured using Sirius red staining. Conventional echocardiography was unable to detect LV systolic dysfunction in old mice, whereas both systolic strain rate and load-independent hemodynamic parameters such as preload recruitable stroke work and end-systolic elastance were significantly decreased. Both strain rate and load-independent hemodynamic parameters normalized after 4 weeks of exercise. Both endocardial and epicardial fibrosis were increased in the LV of aging mice. Endocardial fibrosis decreased in exercised aged mice. Conclusions—Strain rate noninvasively detects LV systolic dysfunction associated with aging in mice, whereas conventional echocardiography does not. Chronic exercise normalizes LV systolic function and decreases fibrosis in old mice. Strain rate imaging in mice may be a useful tool to monitor the effect of new therapeutic strategies preventing the myocardial dysfunction associated with aging.
Lanthanide luminescence for biomedical analyses and imaging.

Keywords: Time-Resolved Fluorescence ; Resonance Energy-Transfer ; Near-Infrared Luminescence ; Double-Stranded Dna ; Prostate-Specific Antigen ; Photoinduced Electron-Transfer ; Europium-Tetracycline Complex ; Sybr-Green-I ; Terbium Complexes ; Optical Probes Reference EPFL-ARTICLE-149396doi:10.1021/cr900362eView record in Web of Science Record created on 2010-06-17, modified on 2017-05-12
Mapping dynamic programming algorithms on graphics processing units

The Graphics Processing Unit (GPU) is a highly parallel, many-core streaming architecture that can execute hundreds of threads concurrently. The data parallel architecture of the GPU is suitable to perform computation intensive applications. In recent years, the use of GPUs for general purpose computation has increased and a large set of problems can be tackled by mapping onto GPUs. The programming model CUDA enables to design C like programs with some extensions which leverages programmers to efficiently use the graphics API. Alignment is the fundamental operation used to compare biological sequences and in this way to identify regions of similarity that are eventually consequences of structural, functional, or evolutionary relationships. Multiple sequence alignment is an important tool for the simultaneous alignment of three or more sequences. Efficient heuristics exist to cope with this problem. In the thesis, progressive alignment methods and their parallel implementation by GPUs are studied. More specifically, the dynamic programming algorithms of profile-profile and profile-sequence alignment are mapped onto GPU. Wavefront and matrix-matrix product techniques are discussed which can deal well with the data dependencies. The performance of these methods is analyzed. Simulations show that one order of magnitude of speed-up over the serial version can be achieved. ClustalW is the most widely used progressive sequence alignment method which aligns more closely related sequences first and then gradually adds more divergent sequences. It consists of three stages: distance matrix calculation, guide tree compilation, and progressive alignment. In this work, the efficient mapping of the alignment stage onto GPU by using a combination of wavefront and matrix-matrix product techniques has been studied. In the hidden Markov model, the Viterbi algorithm is used to find the most probable sequence of hidden states that has generated the observation. In the thesis, the parallelism exhibited by the compute intensive tasks is studied and a parallel solution based on the matrix-matrix product method onto GPU is devised. Moreover, the opportunity to use optimized BLAS library provided by CUDA is explored. Finally, the performance by fixing the number of states and changing the number of observations and vice versa is portrayed. At the end, general principles and guidelines for GPU programming of matrixmatrix product algorithms are discussed.
Cliques in Steiner systems

A partial Steiner (k,l)-system is a k-uniform hypergraph with the property that every l-element subset of V is contained in at most one edge of . In this paper we show that for given k,l and t there exists a partial Steiner (k,l)-system such that whenever an l-element subset from every edge is chosen, the resulting l-uniform hypergraph contains a clique of size t. As the main result of this note, we establish asymptotic lower and upper bounds on the size of such cliques with respect to the order of Steiner systems.
Use of insertional inactivation to facilitate studies of biological properties of pneumococcal surface protein A (PspA)

PspA is a cell surface protein of Streptococcus pneumoniae that is present on a number of clinical isolates as well as the nonencapsulated laboratory strain Rx1. In a previous report we have shown that mAbs directed against PspA can protect mice from at least some of the pneumococcal strains bearing this protein. In our present report we have produced insertional inactivation mutants that lack PspA and have used these mutants to demonstrate that PspA can play a role in pneumococcal virulence and that anti-PspA immunity can lead to protection against pneumococcal infection. PspA- mutants were obtained using derivatives of plasmid pVA891 carrying chromosomal fragments from Rx1. From one of the mutants, we cloned a 550 bp fragment of the pneumococcal gene into pVA891 and transferred this chimeric plasmid, designated pKSD300, into Escherichia coli. After transformation of pKSD300 into Rx1, PspA production is not detected. In colony hybridization experiments, the 550 bp fragment hybridizes specifically to pneumococcal isolates in a pattern consistent with the hypothesis that the fragment is a portion of the pspA structural gene that is different from the portions coding for the antigenic determinants detected by mAbs Xi64 or Xi126. When X-linked immunodeficient (xid) CBA/N mice were immunized with wild-type Rx1, they were resistant to challenge with type 3 strain WU2. However, when these mice were immunized with a PspA- mutant of Rx1, they failed to survive the subsequent challenge, indicating that immunity to PspA can contribute to the resistance to pneumococcal infection. Using pKSD300 we insertionally inactivated pspA in D39, a virulent strain of S. pneumoniae. When injected intravenously there was a 10-fold greater reduction of the mutant pneumococci in the blood, as compared to the wild-type D39.
The insulin-dependent glucose transporter isoform 4 is expressed in bovine blastocysts.

We have investigated the expression of two glucose transporter isoforms, Glut1 and 4, in 14- and 16-day-old bovine blastocysts (d14, d16) using RT-PCR, competitive RT-PCR and in situ hybridization. The blastocysts were grown in vivo or had been produced in vitro. Glut1 mRNA was detected in all blastocysts studied, Glut4 in all d14 blastocysts, but only in a few d16 blastocysts. Glut4 mRNA was localized in trophoblast and endoderm cells. Glut1 mRNA increased from d14 to d16 while Glut4 transcription was down-regulated in d16 blastocysts. The mRNA amounts varied between 0.8 to 23 pg and 3.9 to 65 fg per 100 ng embryonic RNA for Glut1 and Glut4, respectively, displaying a 100- to 1500-fold lower expression of Glut4 compared with Glut1 during blastocyst elongation. This is the first report on the expression of the insulin-sensitive Glut4 isoform in mammalian preimplantation embryos.
Flocking of multi-agent systems with a dynamic virtual leader

This paper considers the flocking problem of a group of autonomous agents moving in Euclidean space with a virtual leader. We investigate the dynamic properties of the group for the case where the state of the virtual leader may be time-varying and the topology of the neighbouring relations between agents is dynamic. To track such a leader, we introduce a set of switching control laws that enable the entire group to generate the desired stable flocking motion. The control law acting on each agent relies on the state information of its neighbouring agents and the external reference signal (or ‘virtual leader’). Then we prove that, if the acceleration of the virtual leader is known, then each agent can follow the virtual leader, and the convergence rate of the centre of mass (CoM) can be estimated; if the acceleration is unknown, then the velocities of all agents asymptotically approach the velocity of the CoM, thus the flocking motion can be obtained. However, in this case, the final velocity of the group may not be equal to the desired velocity. Numerical simulations are worked out to illustrate our theoretical results.
Longitudinal Analysis of the Absence of Intraoperative Neural Response Telemetry in Children using Cochlear Implants

Abstract Introduction Currently the cochlear implant allows access to sounds in individuals with profound hearing loss. The objective methods used to verify the integrity of the cochlear device and the electrophysiologic response of users have noted these improvements. Objective To establish whether the evoked compound action potential of the auditory nerve can appear after electrical stimulation when it is absent intraoperatively. Methods The clinical records of children implanted with the Nucleus Freedom (Cochlear Ltd., Australia) (CI24RE) cochlear implant between January 2009 and January 2010 with at least 6 months of use were evaluated. The neural response telemetry (NRT) thresholds of electrodes 1, 6, 11, 16, and 22 during surgery and after at least 3 months of implant use were analyzed and correlated with etiology, length of auditory deprivation, and chronological age. These data were compared between a group of children exhibiting responses in all of the tested electrodes and a group of children who had at least one absent response. Results The sample was composed of clinical records of 51 children. From these, 21% (11) showed no NRT in at least one of the tested electrodes. After an average of 4.9 months of stimulation, the number of individuals exhibiting absent responses decreased from 21 to 11% (n = 6). Conclusion It is feasible that absent responses present after a period of electrical stimulation. In our sample, 45% (n = 5) of the patients with intraoperative absence exhibited a positive response after an average of 4.9 months of continued electrical stimulation.