Miracle-dz/UniFAR-FTUs huggingface dataset:
Activation of the bacteriophage Mu lys promoter by Mu C protein requires the sigma 70 subunit of Escherichia coli RNA polymerase

Bacteriophage Mu C protein, a product of the middle operon, is required for activation of the four Mu late promoters. To address its mechanism of action, we overproduced the approximately 16.5-kilodalton C protein from a plasmid containing the C gene under the control of a phage T7 promoter and ribosome-binding site. A protein fraction highly enriched for Escherichia coli RNA polymerase (E sigma 70) and made from the overproducing strain was able to activate transcription in vitro from both the tac promoter (Ptac) and a Mu late promoter, Plys. The behavior of Plys was similar in vivo and in vitro; under both conditions, transcription was C dependent and the RNA 5' ends were identical. When anti-sigma 70 antibody was added to C-dependent transcription reactions containing both Ptac and Plys templates, transcription from both promoters was inhibited; transcription was restored by the addition of excess E sigma 70. This result suggests that C-dependent activation of Plys requires sigma 70. Further supporting evidence was provided by a reconstitution experiment in which an E sigma 70-depleted fraction containing C was unable to activate transcription from Plys unless both purified sigma 70 and core polymerase were added. These results strongly suggest that C is not a new sigma factor but acts as an activator for E sigma 70-dependent transcription.
Neuronal activity in the superior colliculus related to saccade initiation during coordinated gaze–reach movements

One must be quick and precise when foveating targets to be reached, because the eyes have to guide the hand trajectory by visual feedback, and we may miss a rapidly moving target if our grasping is not fast and accurate enough. To this end, our brains developed mechanisms coordinating gaze and hand movements to optimize the way in which we foveate and reach. One of these mechanisms is the facilitation of the primary saccade – proven in humans and confirmed here in monkeys – which allows the generation of short‐latency gaze movements when reaching towards visual targets. Here we tested whether the neuronal activity in the superior colliculus (SC) accounts for this mechanism; alternatively, cortical saccade‐related areas could play a major role in the fast initiation of saccades during such elaborated behaviours bypassing the SC. Upon presentation of a target, neurons located at the rostral pole of the SC started the saccade‐related pause in their activity earlier in tasks involving coordinated gaze–reach movements than in tasks in which the saccades were made in isolation. In the same tasks neurons located at the caudal SC reached peak firing rates earlier in coordinated gaze–reach movements than with isolated saccades, confirming the tight coupling between their burst activity latencies and the saccadic reaction times. In sum, our results extend the role of the SC in saccade initiation to coordinated gaze–reach movements, identifying its activity as an important part of the distributed neural system for eye–hand coordination.
Protein prenylation in an insect cell‐free protein synthesis system and identification of products by mass spectrometry

To evaluate the ability of an insect cell‐free protein synthesis system to carry out proper protein prenylation, several CAIX (X indicates any C‐terminal amino acid) sequences were introduced into the C‐terminus of truncated human gelsolin (tGelsolin). Tryptic digests of these mutant proteins were analyzed by MALDI‐TOF MS and MALDI‐quadrupole‐IT‐TOF MS. The results indicated that the insect cell‐free protein synthesis system possesses both farnesyltransferase (FTase) and geranylgeranyltransferase (GGTase) I, as is the case of the rabbit reticulocyte lysate system. The C‐terminal amino acid sequence requirements for protein prenylation in this system showed high similarity to those observed in rat prenyltransferases. In the case of rhoC, which is a natural geranylgeranylated protein, it was found that it could serve as a substrate for both prenyltransferases in the presence of either farnesyl or geranylgeranyl pyrophosphate, whereas geranylgeranylation was only observed when both prenyl pyrophosphates were added to the in vitro translation reaction mixture. Thus, a combination of the cell‐free protein synthesis system with MS is an effective strategy to analyze protein prenylation.
An Analytical Model of the IEEE 802.3ah MAC Protocol for EPON-based Access Systems

Ethernet Passive Optical Networks (EPON) access systems are considered as an alternative to ADSL for high speed access to the Internet. Supported by the Ethernet First Mile Alliance and the IEEE, the MPCP protocol has been adopted as the standardized MAC protocol for EPONs. Moreover, the IPACT dynamic bandwidth allocation mechanism has been proposed for hierarchical multiplexing. Today, IPACT is considered as interesting complement to MPCP for dynamic bandwidth allocation over EPONs. In this paper, we propose an original analytical model of the MPCP+IPACT protocol. Numerical results obtained from this model are commented and compared to computer simulations.
On energy efficiency of the nearest-neighbor cooperative communication in heterogeneous networks

In this paper, we consider a two-dimensional heterogeneous cellular network scenario consisting of one base station (BS) and some mobile stations (MSs) whose locations follow a Poisson point process (PPP). The MSs are equipped with multiple radio access interfaces including a cellular access interface and at least one short-range communication interface. We propose a nearest-neighbor cooperation communication (NNCC) scheme by exploiting the short-range communication between a MS and its nearest neighbor to collaborate on their uplink transmissions. In the proposed cooperation scheme, a MS and its nearest neighbor first exchange data by the short-range communication. Upon successful decoding of the data from each other, they proceed to send their own data, as well as the data received from the other to the BS respectively in orthogonal time slots. The energy efficiency analysis for the proposed scheme is presented based on the characteristics of the PPP and the Rayleigh fading channel. Numerical results show that the NNCC scheme significantly improves the energy efficiency compared to the conventional non-cooperative uplink transmissions.
A 2.3GHz single-ended energy recovery rectifier with stepped-impedance resonator for improved efficiency of outphasing amplifier

This paper proposes an energy recovery rectifier suitable for the use in outphasing and/or linear amplification with nonlinear components (LINC) transmitters. The proposed application oriented rectifier consists of a high-efficiency resistive rectifier and a stepped-impedance resonator (SIR) which stores the energy in order to reduce load sensitivity of the circuit. The rectifier is designed including harmonic frequency control to improve conversion efficiency and to provide a resistive input impedance at the fundamental frequency. The proposed rectifier has been implemented in hybrid technology. The fabricated circuit provides peak RF-to-DC efficiency of 73.5% at 2.3 GHz and more than 60% over a dynamic range of 8 dB. Furthermore, measurements show good agreement with simulation results.
Chlamydia muridarum Infection of Macrophages Elicits Bactericidal Nitric Oxide Production via Reactive Oxygen Species and Cathepsin B

ABSTRACT The ability of certain species of Chlamydia to inhibit the biogenesis of phagolysosomes permits their survival and replication within macrophages. The survival of macrophage-adapted chlamydiae correlates with the multiplicity of infection (MOI), and optimal chlamydial growth occurs in macrophages infected at an MOI of ≤1. In this study, we examined the replicative capacity of Chlamydia muridarum in the RAW 264.7 murine macrophage cell line at different MOIs. C. muridarum productively infected these macrophages at low MOIs but yielded few viable elementary bodies (EBs) when macrophages were infected at a moderate (10) or high (100) MOI. While high MOIs caused cytotoxicity and irreversible host cell death, macrophages infected at a moderate MOI did not show signs of cytotoxicity until late in the infectious cycle. Inhibition of host protein synthesis rescued C. muridarum in macrophages infected at a moderate MOI, implying that chlamydial growth was blocked by activated defense mechanisms. Conditioned medium from these macrophages was antichlamydial and contained elevated levels of interleukin 1β (IL-1β), IL-6, IL-10, and beta interferon (IFN-β). Macrophage activation depended on Toll-like receptor 2 (TLR2) signaling, and cytokine production required live, transcriptionally active chlamydiae. A hydroxyl radical scavenger and inhibitors of inducible nitric oxide synthase (iNOS) and cathepsin B also reversed chlamydial killing. High levels of reactive oxygen species (ROS) led to an increase in cathepsin B activity, and pharmacological inhibition of ROS and cathepsin B reduced iNOS expression. Our data demonstrate that MOI-dependent TLR2 activation of macrophages results in iNOS induction via a novel ROS- and cathepsin-dependent mechanism to facilitate C. muridarum clearance.
Measuring Social Capital in Five Communities

This article develops an empirically grounded definition of social capital. Drawing on the work of Coleman and Putnam and others, the article discusses social capital in terms of participation in networks, reciprocity, trust, social norms, the commons, and social agency. Potential items to measure these elements were developed in an empirical study. A questionnaire containing 68 potential items was administered to approximately 1,200 adults in five Australian communities: two rural communities, two outer metropolitan areas, and one inner-city area of Sydney. The responses were subjected to extensive statistical analysis involving a hierarchical factor analysis, which identified a single general underlying factor and eight orthogonal specific factors, accounting for 49% of the variance. Three of the specific factors identified were community participation, agency, and trust. The five communities differed significantly in terms of the general and specific factors.
Semantic web applications and tools for life sciences SWAT4LS - 2010

SWAT4LS (Semantic Web Applications and Tools for Life Sciences) is a workshop that aims at providing a venue to critically discuss benefits and limits of Semantic Web technologies and tools in the Life Sciences. The third edition of SWAT4LS was held in Berlin on December 10 th , 2010. The workshop was attended by about 70 people, with a worldwide attendance. Keynotes were given by Prof. Jonas Almeida: Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS), and Prof. Christopher Baker: A renaissance for the point mutation: from legacy data to semantic web service. The workshop was preceded by two days of tutorials whose topics have been: Semantic Web meets Cloud Computing, Interoperable Semantic Web Services, D2RQ, Query Federation with SWObjects. The workshop also hosted the 7 th Berlin Semantic Web Meetup, which focused on Semantic Health Care and Life Sciences. These proceedings include 13 full papers, 4 demo papers and 18 poster papers. The presentations and tutorials have been made available on Nature Precedings
Indoor Localization of Mobile Devices for Wireless Networks Monitoring System Based on Pedestrian Dead Reckoning

This project presents the implementation of a localization system for mobile phones based on Pedestrian Dead Reckoning, assisted by Map-Matching when Activity Classification indicates the opportunity. All computations are performed in the cloud by analyzing samples of acceleration and heading readings collected from every phone's sensors. The system was designed to cope with activities performed with the phone in hand as well as with activities performed with the phone in pocket, permanently offering a comparison for the two cases. Because the step counting method of distance estimation for Pedestrian Dead Reckoning isn't reliable for walking with the phone in pocket, a new method of estimating speed was introduced, which is based on a regression algorithm using features extracted from acceleration. Also, this thesis presents how adapting an algorithm to best fit a cloud platform's characteristics can have beneficial effects on resource consumption.
EM algorithm for sequence estimation over Gauss-Markov ISI channels

This paper presents a new algorithm, based on an EM (expectation-maximization) formulation, for ML (maximum likelihood) sequence estimation over unknown ISI (inter-symbol interference) channels with random channel coefficients which have a Gauss-Markov fast time-varying distribution. By using the EM formulation to marginalize over the channel coefficient distribution, maximum-likelihood estimates of the transmitted sequence are obtained. This EM algorithm is shown to perform better, in terms of BER, than existing algorithms which perform jointly-optimal sequence and channel estimation, or which do not take into account fast time-varying channel effects.
Intrinsically backdrivable hydraulic servovalve for interactive robot control

There has been consistent trials to make a hydraulic actuator to be effective in interactive robot applications that require high power and durability. However, conventional strategies to obtain this goal, such as force/torque servo control or adding elastic components, suffer from complexity, sensor problems, and reduced system robustness. In this paper, we show that introducing backdrivability to hydraulic system may be an ultimate solution to constructing interactive hydraulic robot systems, by analyzing the advantages of backdrivability for this application. Moreover, we show that the backdrivability of valve-controlled hydraulic system can be achieved by adding a load pressure feedback mechanism on the spool of the servovalve, using the similarity of its dynamics structure to that of a flexible joint robot. Finally, we show that the derived backdrivable servovalve dynamics is actually the dynamics of the pressure control valve, and we report experiments that verify the analyzed advantages of backdrivability.
Image Classification Using Mathematical Morphology

Holding stand for surgical instruments which has a comb bar having receiving recesses for instrument shafts. To secure or release simultaneously all of the instrument shafts in the associated receiving recesses, a locking bar is allocated to the comb bar, which locking bar is arranged adjacent and parallel to the comb bar and can be moved relative to the comb bar in the longitudinal direction and, at each receiving recess of the comb bar, has a locking lug which, as a result of the displacement, can be pushed over the instrument shaft or removed from the latter, which instrument shaft is located in the receiving recess.
Genome-wide analysis of copy number changes and loss of heterozygosity in myelodysplastic syndrome with del(5q) using high-density single nucleotide polymorphism arrays

This study shows a clear distinction between 5q- syndrome and other cases of myelodysplastic syndrome with del(5q) with regards to both copy number changes and the presence of large uniparental disomy, consistent with the different clinical behavior of patients with these two disorders. See related perspective on page 967. Background We undertook a genome wide single nucleotide polymorphism analysis of a spectrum of patients with myelodysplastic syndrome del(5q) in order to investigate whether additional genomic abnormalities occur. Single nucleotide polymorphism array analysis has been shown to detect not only gene deletions but also regions of uniparental disomy that can pinpoint particular regions for mutation analysis. Design and Methods We studied 42 cases of myelodysplastic syndrome with del(5q), comprising 21 patients with 5q- syndrome and 21 with del(5q) (not 5q- syndrome), and 45 healthy controls by genome wide single nucleotide polymorphism analysis with the 50K Affymetrix single nucleotide polymorphism arrays. Results The del(5q) was characterized in all cases. The commonly deleted region of the 5q- syndrome extends between the genes SH3TC2 (proximal boundary) and GLRA1 (distal boundary) and measures 2.9 Mb. Copy number changes in addition to the del(5q) were observed in 10 of 21 patients with del(5q) myelodysplastic syndrome but in none of the patients with the 5q- syndrome. A total of 63 regions of uniparental disomy greater than 2 Mb were detected in 40 of 42 patients, dispersed on 18/23 chromosomes. In the 5q- syndrome group 31 regions of uniparental disomy were identified in 19 of 21 patients, the largest one being 7.6 Mb. All 21 patients with del(5q) myelodysplastic syndrome had uniparental disomy; in total 32 regions of uniparental disomy were identified in the 21 patients, including six regions of uniparental disomy > 10 Mb. Eight recurrent regions of uniparental disomy were observed among the 42 patients. For eight patients we had T-cell DNA as a germline control and four recurrent regions of uniparental disomy were identified that were present only in the neutrophil and not T-cell DNA. One small region of uniparental disomy at 10p12.31-p12.2 was observed in four patients with the 5q- syndrome. Conclusions This study shows that regions of uniparental disomy greater than 2 Mb are found in the 5q-syndrome and del(5q) myelodysplastic syndrome, although large regions of uniparental disomy (>10 Mb) are only found in the latter group. The recurrent regions of uniparental disomy may indicate the position of novel leukemia-associated genes.
Evidence of Lévy walk foraging patterns in human hunter–gatherers

Significance Lévy walks are a random walk search strategy used by a wide variety of organisms when searching for heterogeneously distributed food. This type of search involves mostly short move steps (defined as the distance traveled before pausing or changing direction) combined with rarer longer move steps. Here, we show that the Hadza, hunter–gatherers from northern Tanzania, perform Lévy walks when foraging for a wide variety of food items, suggesting that Lévy walks are an important movement pattern for the most cognitively complex foragers on Earth. Our results suggest that scale-invariant, superdiffusive movement profiles are a fundamental feature of human landscape use, regardless of the physical or cultural environment, and may have played an important role in the evolution of human mobility. When searching for food, many organisms adopt a superdiffusive, scale-free movement pattern called a Lévy walk, which is considered optimal when foraging for heterogeneously located resources with little prior knowledge of distribution patterns [Viswanathan GM, da Luz MGE, Raposo EP, Stanley HE (2011) The Physics of Foraging: An Introduction to Random Searches and Biological Encounters]. Although memory of food locations and higher cognition may limit the benefits of random walk strategies, no studies to date have fully explored search patterns in human foraging. Here, we show that human hunter–gatherers, the Hadza of northern Tanzania, perform Lévy walks in nearly one-half of all foraging bouts. Lévy walks occur when searching for a wide variety of foods from animal prey to underground tubers, suggesting that, even in the most cognitively complex forager on Earth, such patterns are essential to understanding elementary foraging mechanisms. This movement pattern may be fundamental to how humans experience and interact with the world across a wide range of ecological contexts, and it may be adaptive to food distribution patterns on the landscape, which previous studies suggested for organisms with more limited cognition. Additionally, Lévy walks may have become common early in our genus when hunting and gathering arose as a major foraging strategy, playing an important role in the evolution of human mobility.
LGA: a method for finding 3D similarities in protein structures

We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl. gov/local/lga. Data generated by LGA can be successfully used in a scoring function to rank the level of similarity between two structures and to allow structure classification when many proteins are being analyzed. LGA also allows the clustering of similar fragments of protein structures.
The use of dynamic reliability scoring in speech recognition

Typically, along a recognizer’s search path, some acoustic units are modeled more reliably than others, due to differences in their acoustic-phonetic features and many other factors. This paper presents a dynamic reliability scoring scheme which can help adjust the partial path scores while the recognizer searches through the composed lexical and acoustic-phonetic network. The reliability models are trained on the acoustic scores of the correct arc and its immediate competing arcs extending the current partial path. During recognition, if, according to the trained reliability models, an arc can be more easily distinguished from the competing alternatives, that arc is more likely to be in the right path, and the partial path score can be adjusted accordingly on the ﬂy to have a more accurate path hypothesis. We have applied this reliability scoring mechanism in two weather related domains, JUPITER [6] (for English) and PANDA (a predecessor of MUXING [5] for Mandarin Chinese). We get 9.8% word error rate (WER) reduction in the JUPITER domain and 12.4% WER reduction in the PANDA domain, thus demonstrating the effectiveness of this approach.
Cellular proteomic characterization using Active Shape and Non-Gaussinan stochastic texture models

This paper presents a method for the systematical extraction cellular parameters from imaging proteomic datasets in a way suitable for subsequent biological modeling and simulation. This was achieved by capturing the spatial boundaries of cell structures as well as the distribution of its constituents. The model uses the Active Shape Models to parameterize the shape of cellular structures and the Non-Gaussian Texture Model to parameterize spatial distribution of sub-cellular material. Results show the model can extract then generate faithful representations of cellular shapes and textures for a variety of cell types and protein expressions and hence could offer a natural spatial framework for current research on simulating and predicting sub-cellular processes.
IS_SUM: A Multi-Document Summarizer based on Document Index Graphic and Lexical Chains

IS_SUM is a summarizer developed at Institute of Software (IS) of Chinese Academy of Sciences for DUC 2005. We adopt a new way for clustering and summarizing documents by integrating Document Index Graphic (DIG) [7] with Lexical Chains [5]. Our results show the benefit of integrating DIG with Lexical Chains.