Miracle-dz/UniFAR-FTUs huggingface dataset:
The Moraxella catarrhalis Autotransporter McaP Is a Conserved Surface Protein That Mediates Adherence to Human Epithelial Cells through Its N-Terminal Passenger Domain

ABSTRACT The protein McaP was previously shown to be an adhesin expressed by the Moraxella catarrhalis strain O35E, which also displays esterase and phospholipase B activities (J. M. Timpe et al., Infect. Immun. 71:4341-4350, 2003). In the present study, sequence analysis suggests that McaP is a conventional autotransporter protein that contains a 12-stranded β-barrel transporter module (amino acids [aa] 383 to 650) linked to a surface-exposed passenger domain exhibiting lipolytic activity (aa 62 to 330). An in-frame deletion removing most of this predicted N-terminal passenger domain was engineered, and Escherichia coli expressing the truncated McaP protein exhibited greatly reduced adherence to A549 human lung epithelial cells compared to E. coli expressing wild-type McaP. Site-directed mutagenesis of a serine residue at position 62 of McaP, predicted to be important for the lipolytic activity of the protein, resulted in loss of hydrolysis of p-nitrophenyl ester of caproate. E. coli expressing this mutated McaP, however, adhered to A549 monolayers at levels greater than recombinant bacteria expressing the wild-type adhesin. These results indicate that the predicted passenger domain of McaP is involved in both the binding and the lipolytic activity of the molecule and demonstrate that the adhesive properties of McaP do not require its lipolytic activity. Sequence analysis of mcaP from eight Moraxella catarrhalis strains revealed that the gene product is highly conserved at the amino acid level (98 to 100% identity), and Western blot analysis demonstrated that a panel of 16 isolates all express McaP. Flow cytometry experiments using antibodies raised against various portions of McaP indicated that its predicted passenger domain as well as transporter module contain surface-exposed epitopes. In addition to binding to the surface of intact bacteria, these antibodies were found to decrease adherence of M. catarrhalis to A549 human lung cells by up to 47% and to reduce binding of recombinant E. coli expressing McaP by 98%. These results suggest that McaP should be considered as a potential vaccine antigen.
Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family

Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family James M. Aramini,* Yuanpeng J. Huang, G.V. T. Swapna, John R. Cort, P.K. Rajan, Rong Xiao, Ritu Shastry, Thomas B. Acton, Jinfeng Liu, Burkhard Rost, Michael A. Kennedy, and Gaetano T. Montelione* 1 Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854 2Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854 3 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 4Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 5Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854
Domain-Independent Shallow Sentence Ordering

We present a shallow approach to the sentence ordering problem. The employed features are based on discourse entities, shallow syntactic analysis, and temporal precedence relations retrieved from VerbOcean. We show that these relatively simple features perform well in a machine learning algorithm on datasets containing sequences of events, and that the resulting models achieve optimal performance with small amounts of training data. The model does not yet perform well on datasets describing the consequences of events, such as the destructions after an earthquake.
A Novel Prioritization Technique for Solving Markov Decision Processes

We address the problem of computing an optimal value function for Markov decision processes. Since finding this function quickly and accurately requires substantial computation effort, techniques that accelerate fundamental algorithms have been a main focus of research. Among them prioritization solvers suggest solutions to the problem of ordering backup operations. Prioritization techniques for ordering the sequence of backup operations reduce the number of needed backups considerably, but involve significant overhead. This paper provides a new way to order backups, based on a mapping of states space into a metric space. Empirical evaluation verifies that our method achieves the best balance between the number of backups executed and the effort required to prioritized backups, showing order of magnitude improvement in runtime over number of benchmarks.
Clinical characteristics of first-admitted patients with ICD-10 schizotypal disorder

Background The clinical picture of schizotypal disorders is rarely comprehensively described. Aims To describe psychopathological profiles of patients with ICD-10 schizotypal disorder. Method A total of 151 first-admitted patients (with affective and somatic disorders excluded) were given a comprehensive psychopathological evaluation, including the Bonn Scale for the Assessment of Basic Symptoms. Patients with schizotypal disorder (n=50) were compared with those with psychosis (n=51) and those outside the schizophrenia spectrum (other diagnoses, n=50) on a number of psychopathological scales. Results Patients with schizotypal disorder scored intermediately between patients with psychosis and other diagnoses on scales related to positive and negative symptoms, disorders of emotional contact and formal thought disorder, but had the same scores as patients with schizophrenia for subtle aberrations of subjective experience. Schizotypal criteria were not normally distributed with an excess of patients between 2 and 6 criteria. Family history of schizophrenia was equally elevated among those with schizotypal disorder and those with psychosis. Conclusions ICD-10 schizotypy represents a milder, less psychotic, variant of schizophrenia but there is no clear-cut division between the two disorders.
A small-size software defined cognitive radio prototype

A small-size software defined cognitive radio equipment that consists of a hardware platform and a software platform have been introduced. The hardware platform consists of a multiband/tunable RF unit with multiple switching circuits, signal processing unit consists of FPGA and CPU boards. The software platform consists of several managers that manage spectrum sensing and reconfiguration of communication systems and is worked on the Linux. The developed cognitive radio prototype combined by hardware and software platforms senses the signal level (RSSI) over 400 MHz-6 GHz bands and moreover identifies the system by using reconfiguration of software packages and checks RSSI, BER, connectivity, and so on. The software packages can configure specified wireless communication systems and consist of physical layer, MAC/DLC layer, IP layer, and application layer part of the systems. This paper also describes the sensing time and reconfiguration time.
Analysis of a window-based flow control mechanism based on TCP Vegas in heterogeneous network environment

Another version of TCP called TCP Vegas has been proposed and studied in the literature. It can achieve better performance than the current TCP Reno. In our previous studies, steady-state behavior of a window-based flow control mechanism based on TCP Vegas has been analyzed for a simple network topology. In this paper, we extend our analysis to a generic network topology where multiple bottleneck links exist. We first derive equilibrium values of a window size of a TCP connection and the number of packets waiting in a router's buffer in steady state. We also derive throughput of each TCP connection in steady state, and investigate the effect of control parameters of TCP Vegas on fairness among TCP connections. We then present several numerical examples, showing how control parameters of TCP Vegas should be configured for achieving both stability and better transient performance.
The continuous differential Ant-Stigmergy Algorithm applied to dynamic optimization problems

Many real-world problems are dynamic, requiring an optimization algorithm which is able to continuously track a changing optimum over time. In this paper, we present an ant-colony based algorithm for solving optimization problems with continuous variables, labeled Continuous Differential Ant-Stigmergy Algorithm (CDASA). The CDASA is applied to dynamic optimization problems without any modification to the algorithm. The performance of the CDASA is evaluated on the set of benchmark problems provided for the IEEE Competition on Evolutionary Computation for Dynamic Optimization Problems (ECDOP-Competition-2012).
CDD: a curated Entrez database of conserved domain alignments

The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi. nlm.nih. gov/entrez/query.fcgi? db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi. nlm.nih. gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein-protein queries submitted to BLAST(R) at http://www.ncbi. nlm.nih. gov/BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.
Comparative Researches of Semen Arecae and Charred Semen Arecae on Gastrointestinal Motility, Motilin, Substance P, and CCK in Chronically Stressed Rats

Aims To compare the effects of Semen Arecae (SA) and Charred Semen Arecae (CSA) on gastrointestinal motility, motilin, substance P (SP), and cholecystokinin (CCK) in chronically stressed rats. Methods Rats were randomly divided into control group and stress group. Rats in stress group were randomly exposed to a variety of unpredictable stimulations for 21 days. Then, the rats were treated orally with distilled water, SA, CSA, and mosapride for 7 days. Gastric residue rate and intestinal propulsion rate were evaluated. Serum levels of motilin and SP were measured by enzyme-linked immunosorbent assay (ELISA). CCK mRNA was quantified by using quantitative real-time PCR (qRT-PCR). Results Both SA and CSA improved the intestinal propulsion and reduced the gastric residue in chronically stressed rats. Furthermore, the serum levels of motilin and SP were significantly higher and the CCK mRNA expressions in intestine and hypothalamus were downregulated in SA and CSA groups. Furthermore, it was found that CSA is more effective. Conclusion Both SA and CSA enhanced gastrointestinal motility and increased serum levels of motilin and SP in chronically stressed rats via downregulating CCK mRNA expressions in intestine and hypothalamus. Importantly, CSA possessed more effective promoting effects.
A review of the biological and potential therapeutic actions of Harpagophytum procumbens

Harpagophytum procumbens (Hp), commonly known as Devil's Claw is a perennial plant which thrives in arid conditions. For centuries, it has been used as a traditional treatment for a variety of illnesses, including fevers, skin complaints, arthritis and diseases of the digestive tract as well as an appetite stimulant. Since its introduction to Europe in the early twentieth century, it has become a popular antiinflammatory and analgesic preparation amongst herbalists for supportive or adjuvant treatment of degenerative joint diseases, tendonitis, headache, backache and menstrual pain. The validity of Hp as an effective antiinflammatory and analgesic preparation, particularly in the relief of arthritic symptoms, has been investigated in numerous animal, clinical and in vitro studies. Although some contradictory evidence exists, the majority of animal studies appear to indicate Hp as an effective antiinflammatory and analgesic preparation in the treatment of acute and subacute inflammation. Clinical trials support Hp as a beneficial treatment for the alleviation of pain and improvement of mobility in a variety of musculoskeletal conditions. Analysis of the in vitro and ex vivo studies that currently exist, indicate that Hp has significant effects on numerous proinflammatory markers. However, the exact mechanism(s) by which Hp may reduce inflammation remain to be elucidated. Copyright © 2006 John Wiley & Sons, Ltd.
Subretinal electronic chips can restore useful visual functions in blind retinitis pigmentosa patients

Retinitis pigmentosa leads to progressive loss of retinal photoreceptors causing blindness. We developed an active subretinal electronic device being implanted in 11 volunteers suffering from a hereditary retinal disease in an end-stage. The active part of the implant consists of a chip carrying a microphotodiode array (MPDA) with 1500 light sensitive pixels and of a 4 x 4 matrix of electrodes for direct retinal stimulation and assessment of the tissue-electrode interface. The direct stimulation of the retina was performed by single electrodes or patterns formed by the 4x4 matrix leading to percepts described as well defined dots. Stimulation by simple patterns could be reliable recognized and described in tested subjects. Five of the eleven patients could use the subretinal MPDA to perceive and localize light sources or large bright objects. In two subjects spatial resolution up to 0.32 cycles/deg and 0.22 cycles/deg was achieved. In the subject, whose subretinal implant has been placed directly under the macula a visual acuity of 20/1000 could be measured by a standard test, as well as letters and words recognition. For the first time we could show that subretinal implants can restore useful visual functions in blind patients with hereditary retinal diseases.
Coordinated Robot Navigation via Hierarchical Clustering

We introduce the use of hierarchical clustering for relaxed deterministic coordination and control of multiple robots. Traditionally, an unsupervised learning method, hierarchical clustering offers a formalism for identifying and representing spatially cohesive and segregated robot groups at different resolutions by relating the continuous space of configurations to the combinatorial space of trees. We formalize and exploit this relation, developing computationally effective reactive algorithms for navigating through the combinatorial space in concert with geometric realizations for a particular choice of the hierarchical clustering method. These constructions yield computationally effective vector field planners for both hierarchically invariant as well as transitional navigation in the configuration space. We apply these methods to the centralized coordination and control of n perfectly sensed and actuated Euclidean spheres in a d-dimensional ambient space (for arbitrary n and d). Given a desired configuration supporting a desired hierarchy, we construct a hybrid controller that is quadratic in n and algebraic in d and prove that its execution brings all but a measure zero set of initial configurations to the desired goal, with the guarantee of no collisions along the way.
First Results from NuSTAR Observations of Mkn 421

Mkn 421 is a nearby active galactic nucleus dominated at all wavelengths by a very broad nonthermal continuum thought to arise from a relativistic jet seen at a small angle to the line of sight. Its spectral energy distribution peaks in the X-ray and TeV γ-ray bands, where the energy output is dominated by cooling of high-energy electrons in the jet. In order to study the electron distribution and its evolution, we carried out a dedicated multi-wavelength campaign, including extensive observations by the recently launched highly sensitive hard X-ray telescope NuSTAR, between December 2012 and May 2013. Here we present some initial results based on NuSTAR data from January through March 2013, as well as calibration observations conducted in 2012. Although the observations cover some of the faintest hard X-ray flux states ever observed for Mkn 421, the sensitivity is high enough to resolve intra-day spectral variability. We find that in this low state the dominant flux variations are smooth on timescales of hours, with typical intra-hour variations of ≲ 5%. We do not find evidence for either a cutoff in the hard X-ray spectrum, or a rise towards a high-energy component, but rather that at low flux the spectrum assumes a power law shape with a photon index of approximately 3. The spectrum is found to harden with increasing brightness.
The Proper Motion, Parallax, and Origin of the Isolated Neutron Star RX J185635–3754

The isolated neutron star RX J185635-3754 is the closest known neutron star to the Sun. Based on Hubble Space Telescope Wide Field Planetary Camera 2 observations over a 3 yr baseline, I report its proper motion (332 ± 1 mas yr-1 at a position angle of 100.°3 ± 0.°1) and parallax (16.5 ± 2.3 mas, 61 pc). This proper motion brings the neutron star from the general vicinity of the Sco-Cen OB association. For an assumed neutron star radial velocity between -55 and -60 km s-1, the runaway O star ζ Oph, the Upper Sco OB association, and the neutron star come into spatial coincidence between 0.9 × 106 and 1.0 × 106 yr ago. RX J185635-3754 may be the remnant of the original primary of the ζ Oph system. If so, the space velocity suggests that the neutron star received a kick of about 200 km s-1 at birth.
Converting Russian Treebank SynTagRus into Praguian PDT Style

In this paper, we report a work in progress on transforming syntactic structures from the SynTagRus corpus into tectogrammatical trees in the Prague Dependency Treebank (PDT) style. SynTagRus (Russian) and PDT (Czech) are both dependency treebanks sharing lots of common features and facing similar linguistic challenges due to the close relatedness of the two languages. While in PDT the tectogrammatical representation exists, sentences in SynTagRus are annotated on syntactic level only.
Fitting the Modified-Power-Lognormal to the Sum of Independent Lognormals Distribution

We propose a new method for calculating a tight approximation to the distribution of the sum of independent lognormal random variables. We make use of a three-parameter modified-power-lognormal distribution function as the approximating distribution. We use theoretical results from our previous work on the tails of the distribution of the sum of lognormals to match the slope of the modified-power-lognormal function at both tails. This would not have been possible with many of the recently-proposed distribution functions, which do not behave properly in the tails. We then also use moment-matching to find the best curve match. Our method is mostly closed-form, requiring only one simple numerical integral. We compare our method with those in literature in terms of complexity and accuracy. We conclude that our method is more accurate than the simple (closed-form) methods, and much simpler to understand and implement than the more accurate methods which rely heavily on numerical integration.
An efficient thermal estimation scheme for microprocessors

In recent years, thermal management, which improves the reliability, performance, power leakage, etc. of modern microprocessors, has been the subject of numerous computer architecture and system software studies. To determine the detailed thermal distribution of a microprocessor is among the critical tasks for thermal management. However, because thermal modeling tools require considerable computation time and memory to simulate fine-grain thermal information, they may be unsuitable for dynamic thermal management and hardware implementation. This study proposes a novel model based on reduced resistance-capacitance (RC) networks for efficiently calculating the temperature of a microprocessor. The proposed model is compared with two existing thermal simulation tools, namely, HotSpot [1] and Temptor [2]. The experiment studies show that the results generated using the proposed model differ from those of the existing tools by only 0.5 to 1.5%. However, the suggested model can increase computation speeds by 5 to 9 times and 98 to 161 times that of Temptor and HotSpot, respectively. For the memory usage, the proposed model consumes merely 0.45% of the space used by the existing tools.
On crowdsourced interactive live streaming: a Twitch.tv-based measurement study

Empowered by today's rich tools for media generation and collaborative production, the multimedia service paradigm is shifting from the conventional single source, to multi-source, to many sources, and now toward crowdsource. Such crowdsourced live streaming platforms as Twitch.tv allow general users to broadcast their content to massive viewers, thereby greatly expanding the content and user bases. The resources available for these non-professional broadcasters however are limited and unstable, which potentially impair the streaming quality and viewers' experience. The diverse live interactions among the broadcasters and viewers can further aggravate the problem. In this paper, we present an initial investigation on the modern crowdsourced live streaming systems. Taking Twitch as a representative, we outline their inside architecture using both crawled data and captured traffic of local broadcasters/viewers. Closely examining the access data collected in a two-month period, we reveal that the view patterns are determined by both events and broadcasters' sources. Our measurements explore the unique source- and event-driven views, showing that the current delay strategy on the viewer's side substantially impacts the viewers' interactive experience, and there is significant disparity between the long broadcast latency and the short live messaging latency. On the broadcaster's side, the dynamic uploading capacity is a critical challenge, which noticeably affects the smoothness of live streaming for viewers.