Miracle-dz/UniFAR-FTUs huggingface dataset:
Enzymes and genes of taurine and isethionate dissimilation in Paracoccus denitrificans.

Growth of the alpha-proteobacterium Paracoccus denitrificans NKNIS with taurine or isethionate as sole source of carbon involves sulfoacetaldehyde acetyltransferase (Xsc), which is presumably encoded by an xsc gene in subgroup 3, none of whose gene products has been characterized. The genome of the alpha-proteobacterium Rhodobacter sphaeroides 2.4. 1 was interpreted to contain a nine-gene cluster encoding the inducible dissimilation of taurine, and this deduced pathway included a regulator, a tripartite ATP-independent transporter, taurine dehydrogenase (TDH; presumably TauXY) as well as Xsc (subgroup 3), a hypothetical protein and phosphate acetyltransferase (Pta). A similar cluster was found in P. denitrificans NKNIS, in contrast to an analogous cluster encoding an ATP-binding cassette transporter in Paracoccus pantotrophus. Inducible TDH, Xsc and Pta were found in extracts of taurine-grown cells of strain NKNIS. TDH oxidized taurine to sulfoacetaldehyde and ammonium ion with cytochrome c as electron acceptor. Whereas Xsc and Pta were soluble enzymes, TDH was located in the particulate fraction, where inducible proteins with the expected masses of TauXY (14 and 50 kDa, respectively) were detected by SDS-PAGE. Xsc and Pta were separated by anion-exchange chromatography. Xsc was effectively pure; the molecular mass of the subunit (64 kDa) and the N-terminal amino acid sequence confirmed the identification of the xsc gene. Inducible isethionate dehydrogenase (IDH), Xsc and Pta were assayed in extracts of isethionate-grown cells of strain NKNIS. IDH was located in the particulate fraction, oxidized isethionate to sulfoacetaldehyde with cytochrome c as electron acceptor and correlated with the expression of a 62 kDa protein. Strain NKNIS excreted sulfite and sulfate during growth with a sulfonate and no sulfite dehydrogenase was detected. There is considerable biochemical, genetic and regulatory complexity in the degradation of these simple molecules.
Visual assessment of a real-time system design: a case study on a CNC controller

We describe our experiments on a real-time system design, focusing on design alternatives such as scheduling jitter, sensor-to-output latency, intertask communication schemes and the system utilization. The prime objective of these experiments was to evaluate a real-time design produced using the period calibration method (Gerber et al., 1995) and thus identify the limitations of the method. We chose a computerized numerical control (CNC) machine as our target real-time system and built a realistic controller and a plant simulator. Our results were extracted from a controlled series of more than a hundred test controllers obtained by varying four test variables. This study unveils many interesting facts: average sensor-to-output latency is one of the most dominating factors in determining control quality; the effect of scheduling jitter appears only when the average sensor-to-output latency is sufficiently small; and loop processing periods are another dominating factor of performance. Based on these results, we propose a new communication scheme and a new objective function for the period calibration method.
Infants' Perseverative Search Errors Are Induced by Pragmatic Misinterpretation

Having repeatedly retrieved an object from a location, human infants tend to search the same place even when they observe the object being hidden at another location. This perseverative error is usually explained by infants' inability to inhibit a previously rewarded search response or to recall the new location. We show that the tendency to commit this error is substantially reduced (from 81 to 41%) when the object is hidden in front of 10-month-old infants without the experimenter using the communicative cues that normally accompany object hiding in this task. We suggest that this improvement is due to an interpretive bias that normally helps infants learn from demonstrations but misleads them in the context of a hiding game. Our finding provides an alternative theoretical perspective on the nature of infants' perseverative search errors.
Identifying relevant social media content: leveraging information diversity and user cognition

As users turn to large scale social media systems like Twitter for topic-based content exploration, they quickly face the issue that there may be hundreds of thousands of items matching any given topic they might query. Given the scale of the potential result sets, how does one identify the 'best' or 'right' set of items? We explore a solution that aligns characteristics of the information space, including specific content attributes and the information diversity of the results set, with measurements of human information processing, including engagement and recognition memory. Using Twitter as a test bed, we propose a greedy iterative clustering technique for selecting a set of items on a given topic that matches a specified level of diversity. In a user study, we show that our proposed method yields sets of items that were, on balance, more engaging, better remembered, and rated as more interesting and informative compared to baseline techniques. Additionally, diversity indeed seemed to be important to participants in the study in the consumption of content. However as a rather surprising result, we also observe that content was perceived to be more relevant when it was highly homogeneous or highly heterogeneous. In this light, implications for the selection and evaluation of topic-centric item sets in social media contexts are discussed.
Concept Recognition and the TREC Genomics Tasks

We applied concept recognition techniques to the Genomics track primary and secondary tasks. For the primary task, we developed a foundational information retrieval system which incorporated Entrez Gene entries and UMLS concepts for query expansion via phrasal and term boosting representations of synonyms. For the secondary task, we evaluated three conceptual features—mouse strain names, indexed MeSH terms, and normalized citations—in addition to two surface linguistic features—BOW and bigrams. Our final feature set yielded consistently high F-measures.
Eye Movements on Brain Maps

This report shows that eye movement artifact, either in the form of up-down or side to side movements, can be clearly demonstrated on brain maps by carefully adjusting the gain in order to delineate the distribution of activity on the anterior regions. Clearly circumscribed activity then appears above (up-down) or to the side (side-side) of each eye.
CXCR3 Internalization Following T Cell-Endothelial Cell Contact: Preferential Role of IFN-Inducible T Cell α Chemoattractant (CXCL11)1

Chemokine receptors are rapidly desensitized and internalized following ligand binding, a process that attenuates receptor-mediated responses. However, the physiological settings in which this process occurs are not clear. Therefore, we examined the fate of CXCR3, a chemokine receptor preferentially expressed on activated T cells following contact with endothelial cells. By immunofluorescence microscopy and flow cytometry, we found that CXCR3 was rapidly internalized when T cells were incubated with IFN-γ-activated human saphenous vein endothelial cells (HSVEC), but not with resting HSVEC. Similar results were obtained using human CXCR3-transfected murine 300-19 B cells. CXCR3 down-regulation was significantly more pronounced when T cells were in contact with HSVEC than with their supernatants, suggesting that CXCR3 ligands were efficiently displayed on the surface of HSVEC. Using neutralizing mAbs to IFN-induced protein-10 (CXCL10), monokine induced by IFN-γ (CXCL9), and IFN-inducible T cell α chemoattractant (I-TAC; CXCL11), we found that even though I-TAC was secreted from IFN-γ-activated HSVEC to lower levels than IFN-induced protein-10 or the monokine induced by IFN-γ, it was the principal chemokine responsible for CXCR3 internalization. This correlated with studies using recombinant chemokines, which revealed that I-TAC was the most potent inducer of CXCR3 down-regulation and of transendothelial migration. Known inhibitors of chemokine-induced chemotaxis, such as pertussis toxin or wortmannin, did not reduce ligand-induced internalization, suggesting that a distinct signal transduction pathway mediates internalization. Our data demonstrate that I-TAC is the physiological inducer of CXCR3 internalization and suggest that chemokine receptor internalization occurs in physiological settings, such as leukocyte contact with an activated endothelium.
A New Variant of the Diffie-Hellman Key-Exchange Protocol Based on Block Triangular Matrix Groups

Efficient authenticated key exchange is the most important part of a security system that employs cryptographic techniques in World Wide Web-based applications. In this paper, an ECC (Elliptic Curve Cryptography) version of Hughespsilas key-exchange protocol is proposed based on the matrix-based ECC by Climent et al. The basic security of the proposed scheme is based on the ECDLP (Elliptic Curve Discrete Logarithm Problem) and the DLP defined over a cyclic subgroup generated by a 2times2 block matrix consisting of two matrices with entries in an optimal extension field and one matrix whose entries are points of an elliptic curve. Analysis indicates that besides several desirable security properties this system can, by means of linear combination of elliptic curve points, get larger key spaces flexibly without having to increase the underlying elliptic curve and save the computational requirements inherent to the regeneration and revalidation of elliptic curves.
OLEAR: Optimal Localized Energy Aware Routing in Mobile Ad Hoc Networks

We consider the problem of localized energy aware routing in mobile ad hoc networks. In localized routing algorithms, each node forwards a message based on the position of itself, its neighbors and the destination. The objective of energy aware routing algorithms is to minimize the total power for routing a message from source to destination or to maximize the total number of routing tasks that a node can perform before its battery power depletes. In this paper we propose a new localized energy aware routing algorithm called OLEAR. The algorithm shows a high packet delivery rate with low packet forwarding and battery power consumption. In addition, it ensures a good energy distribution among the nodes and packets reach their destinations using smaller number of hops. All these properties make our algorithm suitable for routing in any energy constrained environment. We compare the performance of OLEAR with existing energy and non energy aware localized algorithms. Simulation experiments show that OLEAR presents comparable energy consumption and distribution to other energy aware algorithms and better packet delivery rates.
Fast Primitives for Irregular Computations on the NEC SX-4

Modern science and engineering disciplines make extensive use of computer simulations. As these simulations increase in size and detail, the computational costs of naive algorithms can easily become prohibitive. Fortunately, sophisticated modeling techniques have been developed in many areas that that vary model resolution as needed coupled with sparse and adaptive algorithms that vary computational effort in time and space as needed. For example, adaptive spatial decompositions are used with fast n-body techniques such as FMA or PM in cosmological simulations, and adaptive unstructured meshing and sparse linear system solvers are used in computational fluid dynamics. The computations that result from these techniques are called irregular, reflecting the a priori unpredictability in the reference pattern and distribution of work.
A New Variable Step Size LMS Adaptive Filtering Algorithm

Focus on the inconsistency between the convergence rate and the steady state error in LMS algorithm, this paper proposed a new variable step size LMS(VSS-LMS) algorithm, by constructing a nonlinear function between the step factor μ and the error signal e(n). The algorithm which modified the weight vector appropriately achieving the optimal by adjusting the step size parameters, could improve the convergence rate and steady-state error performance effectively. The simulation analysis showed that, this algorithm had faster convergence rate speed and smaller steady-state maladjustment compared with the basic LMS algorithm and parts of the similar variable step size algorithm, it fatherly validated this algorithm was superior to existing algorithms.
Combining genetic and demographic information to prioritize conservation efforts for anadromous alewife and blueback herring

A major challenge in conservation biology is the need to broadly prioritize conservation efforts when demographic data are limited. One method to address this challenge is to use population genetic data to define groups of populations linked by migration and then use demographic information from monitored populations to draw inferences about the status of unmonitored populations within those groups. We applied this method to anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), species for which long‐term demographic data are limited. Recent decades have seen dramatic declines in these species, which are an important ecological component of coastal ecosystems and once represented an important fishery resource. Results show that most populations comprise genetically distinguishable units, which are nested geographically within genetically distinct clusters or stocks. We identified three distinct stocks in alewife and four stocks in blueback herring. Analysis of available time series data for spawning adult abundance and body size indicate declines across the US ranges of both species, with the most severe declines having occurred for populations belonging to the Southern New England and the Mid‐Atlantic Stocks. While all alewife and blueback herring populations deserve conservation attention, those belonging to these genetic stocks warrant the highest conservation prioritization.
“Topological Significance” Analysis of Gene Expression and Proteomic Profiles from Prostate Cancer Cells Reveals Key Mechanisms of Androgen Response

Background The problem of prostate cancer progression to androgen independence has been extensively studied. Several studies systematically analyzed gene expression profiles in the context of biological networks and pathways, uncovering novel aspects of prostate cancer. Despite significant research efforts, the mechanisms underlying tumor progression are poorly understood. We applied a novel approach to reconstruct system-wide molecular events following stimulation of LNCaP prostate cancer cells with synthetic androgen and to identify potential mechanisms of androgen-independent progression of prostate cancer. Methodology/Principal Findings We have performed concurrent measurements of gene expression and protein levels following the treatment using microarrays and iTRAQ proteomics. Sets of up-regulated genes and proteins were analyzed using our novel concept of “topological significance”. This method combines high-throughput molecular data with the global network of protein interactions to identify nodes which occupy significant network positions with respect to differentially expressed genes or proteins. Our analysis identified the network of growth factor regulation of cell cycle as the main response module for androgen treatment in LNCap cells. We show that the majority of signaling nodes in this network occupy significant positions with respect to the observed gene expression and proteomic profiles elicited by androgen stimulus. Our results further indicate that growth factor signaling probably represents a “second phase” response, not directly dependent on the initial androgen stimulus. Conclusions/Significance We conclude that in prostate cancer cells the proliferative signals are likely to be transmitted from multiple growth factor receptors by a multitude of signaling pathways converging on several key regulators of cell proliferation such as c-Myc, Cyclin D and CREB1. Moreover, these pathways are not isolated but constitute an interconnected network module containing many alternative routes from inputs to outputs. If the whole network is involved, a precisely formulated combination therapy may be required to fight the tumor growth effectively.
A biomechanical study of the recovery in spinal stability of flexion/extension and torsion after the resection of different posterior lumbar structures in a sheep model

Posterior lumbar structures are vital for spinal stability, and many researchers thought that laminectomy and facetectomy would lead to severe spinal instability. However, because living organisms have compensatory repair capacities, their long-term condition after injuries may change over time. To study the changes in the lumbar biomechanical stability of flexion/extension and torsion at different time points after the resection of various posterior structures, as well as to assess the capacity for self-healing, sheep that had undergone laminectomy or facetectomy were used as an experimental animal model. The injured sheep models included three groups: laminectomy only, laminectomy plus left total facetectomy, and laminectomy plus bilateral facetectomy. Eight nonoperative sheep were used as the control group. At 0, 6, 12, 24, and 36 weeks after injury, the lumbar specimens were harvested for biomechanical testing using the Instron 8874 servohydraulic biomechanical testing system. The changes in the injured lumbar spine were also analyzed through radiological examination. The lumbar stability in flexion/extension and torsion was severely decreased after the three types of surgery. After 6 weeks, the flexion/extension mechanical parameters recovered substantially; each parameter had returned to normal levels by 12 weeks and exceeded the intact group by 24 and 36 weeks. Torsional stiffness also recovered gradually over time. All injury groups demonstrated decreased intervertebral space and degeneration or even fusion in the small joints of the surgical segment or in adjacent segments. These results indicate that the body has the ability to repair the mechanical instability to a certain extent.
Complete Genome Sequence of Corynebacterium kutscheri DSM 20755, a Corynebacterial Type Strain with Remarkably Low G+C Content of Chromosomal DNA

ABSTRACT The complete genome sequence of the type strain Corynebacterium kutscheri DSM 20755 comprises 2,354,065 bp and 2,047 protein-coding genes. The mean G+C content of the chromosomal DNA is 46.46%, which is the lowest value detected so far in a member of the genus Corynebacterium.
Genome profiles in maternal blood during early onset preeclampsia and towards term

Abstract Aims: Inflammatory processes are present during preeclampsia and in normal pregnancy. Maternal inflammatory reactions may change towards term. Our objective was to evaluate genome signaling in blood during preeclampsia and towards term using microarrays. Methods: RNA microarrays (Illumina) were conducted on blood from preeclamptic pregnancies delivered preterm, normal pregnancies at term and normal pregnancies at gestational week 31. Two statistical methods (Q-value cut-off 1%) identified data structures in the three groups and retrieved activated genes along a time axis and a diseased-healthy axis. Signaling genes were localized within known pathways and gene sets, and genes associated with inflammation were identified. Results: Early onset preeclampsia and term pregnancies both showed distinct expression patterns when compared to normal pregnancy at gestational week 31. In preeclampsia, 19 genes were differentially expressed, including a down-regulation of CC-chemokine receptor 3 (CCR3). Among the 183 differentially expressed genes towards term, tumor necrosis factor superfamily member 15 (TNFSF15) was up-regulated and interferon-γ receptor 2 (IFNGR2) and CXC-chemokine receptor type 4 (CXCR4) were down-regulated. Seven of the genes were similarly changed during preeclampsia and towards term. Conclusions: A possible type 1 immune response was identified both during preeclampsia and towards term. In pre-eclampsia a premature activation of leucocytes might be present.
Adaptive fuzzy sliding mode controller for linear systems with mismatched time-varying uncertainties

A new design approach for an adaptive fuzzy sliding mode controller (AFSMC) for linear systems with mismatched time-varying uncertainties is presented. The coefficient matrix of the sliding function can be designed to satisfy a sliding coefficient matching condition provided time-varying uncertainties are bounded. With the sliding coefficient matching condition satisfied, an AFSMC is proposed to stabilize the uncertain system. The parameters of output fuzzy sets in the fuzzy mechanism are on-line adapted to improve the performance of the fuzzy sliding mode control system. The bounds of uncertainties are not required to be known in advance for the AFSMC. Stability of the fuzzy control system is guaranteed and the system is shown to be invariant on the sliding surface. Moreover, chattering around the sliding surface in sliding mode control can be reduced by the proposed design approach. Simulation results are included to illustrate the effectiveness of the proposed AFSMC.
Automated generation of test programs from closed specifications of classes and test cases

Most research on automated specification-based software testing has focused on the automated generation of test cases. Before a software system can be tested, it must be set up according to the input requirements of the test cases. This setup process is usually performed manually, especially when testing complex data structures and databases. After the system is properly set up, a test execution tool runs the system according to the test cases and pre-recorded test scripts to obtain the outputs, which are evaluated by a test evaluation tool. This paper complements the current research on automated specification-based testing by proposing a scheme that combines the setup process, test execution, and test validation into a single test program for testing the behavior of object-oriented classes. The test program can be generated automatically given the desired test cases and closed specifications of the classes. With closed specifications, every class method is defined in terms of other methods which are, in turn, defined in their own class specifications. The core of the test program generator is a partial-order planner which plans the sequence of instructions required in the test program. The planner is, in turn, implemented as a tree-search algorithm. It makes function calls to the Omega Calculator library, which solves the constraints given in the test cases. A first-cut implementation of the planner has been completed, which is able to handle simple arithmetics and existential quantifications in the class specifications. A soundness and completeness proof sketch of the planner is also provided in this paper.