Miracle-dz/UniFAR-FTUs huggingface dataset:
The Staphylococcus aureus AirSR Two-Component System Mediates Reactive Oxygen Species Resistance via Transcriptional Regulation of Staphyloxanthin Production

ABSTRACT Staphylococcus aureus is an important opportunistic pathogen and is the etiological agent of many hospital- and community-acquired infections. The golden pigment, staphyloxanthin, of S. aureus colonies distinguishes it from other staphylococci and related Gram-positive cocci. Staphyloxanthin is the product of a series of biosynthetic steps that produce a unique membrane-embedded C30 golden carotenoid and is an important antioxidant. We observed that a strain with an inducible airR overexpression cassette had noticeably increased staphyloxanthin production compared to the wild-type strain under aerobic culturing conditions. Further analysis revealed that depletion or overproduction of the AirR response regulator resulted in a corresponding decrease or increase in staphyloxanthin production and susceptibility to killing by hydrogen peroxide, respectively. Furthermore, the genetic elimination of staphyloxanthin during AirR overproduction abolished the protective phenotype of increased staphyloxanthin production in a whole-blood survival assay. Promoter reporter and gel shift assays determined that the AirR response regulator is a direct positive regulator of the staphyloxanthin-biosynthetic operon, crtOPQMN, but is epistatic to alternative sigma factor B. Taken together, these data indicate that AirSR positively regulates the staphyloxanthin-biosynthetic operon crtOPQMN, promoting survival of S. aureus in the presence of oxidants.
Episodic and working memory deficits in alcoholic Korsakoff patients: the continuity theory revisited.

BACKGROUND The exact nature of episodic and working memory impairments in alcoholic Korsakoff patients (KS) remains unclear, as does the specificity of these neuropsychological deficits compared with those of non-Korsakoff alcoholics (AL). The goals of the present study were therefore to (1) specify the nature of episodic and working memory impairments in KS, (2) determine the specificity of the KS neuropsychological profile compared with the AL profile, and (3) observe the distribution of individual performances within the 2 patient groups. METHODS We investigated episodic memory (encoding and retrieval abilities, contextual memory and state of consciousness associated with memories), the slave systems of working memory (phonological loop, visuospatial sketchpad and episodic buffer) and executive functions (inhibition, flexibility, updating and integration abilities) in 14 strictly selected KS, 40 AL and 55 control subjects (CS). RESULTS Compared with CS, KS displayed impairments of episodic memory encoding and retrieval, contextual memory, recollection, the slave systems of working memory and executive functions. Although episodic memory was more severely impaired in KS than in AL, the single specificity of the KS profile was a disproportionately large encoding deficit. Apart from organizational and updating abilities, the slave systems of working memory and inhibition, flexibility and integration abilities were impaired to the same extent in both alcoholic groups. However, some KS were unable to complete the most difficult executive tasks. There was only a partial overlap of individual performances by KS and AL for episodic memory and a total mixture of the 2 groups for working memory. CONCLUSIONS Korsakoff's syndrome encompasses impairments of the different episodic and working memory components. AL and KS displayed similar profiles of episodic and working memory deficits, in accordance with neuroimaging investigations showing similar patterns of brain damage in both alcoholic groups.
A preliminary study on the effects of barnstars on Wikipedia editing

This paper presents a preliminary study into the awarding of barnstars among Wikipedia editors to better understand their motivations in contributing to Wikipedia articles. We crawled the talk pages of all active Wikipedia editors and retrieved 21,299 barnstars that were awarded among 14,074 editors. In particular, we found that editors do not award and receive barnstars in equal (or similar) quantities. Also, editors were more active in editing articles before awarding or receiving barnstars.
Silicon Neurons that Inhibit to Synchronize

We present a network of silicon neurons that achieve robust synchrony using mutual inhibition. Synchrony strongly influences neuronal spike timing within many brain regions, potentially playing a crucial role in computation. Yet it has been largely ignored in neuromorphic systems, which use mixed analog and digital circuits to model neurobiology in silicon. Our neurons synchronize by using shunting inhibition (conductance-based) with a synaptic rise-time. Synaptic rise-time promotes synchrony by delaying the effect of inhibition, providing an opportune period for neurons to spike together. Shunting inhibition, through its voltage dependence, inhibits neurons that are late more strongly (delaying the spike further), pushing them into phase (in the next cycle). We fabricated a chip with 256 inhibitory neurons and 1,024 excitatory neurons in 0.25mum CMOS. We show that synchronized inhibitory neurons (population of 256) spike with a period that is proportional to the synaptic rise-time. We use these neurons to entrain the excitatory neurons, implementing a form of object binding
2 FACE SKETCH SYNTHESIS USING THE MULTISCALE MARKOV RANDOM FIELDS MODEL

In this paper, we propose a novel face photo-sketch synthesis and recognition method using a multiscale Markov Random Fields (MRF) model. Our system has three components: (1) given a face photo, synthesizing a sketch drawing; (2) given a face sketch drawing, synthesizing a photo; (3) searching for face photos in the database based on a query sketch drawn by an artist. It has useful applications for both digital entertainment and law enforcement. We assume that faces to be studied are in a frontal pose, with normal lighting and neutral expression, and have no occlusions. To synthesize sketch/photo images, the face region is divided into overlapping patches for learning. The size of the patches decides the scale of local face structures to be learnt. From a training set which contains photo-sketch pairs, the joint photo-sketch model is learnt at multiple scales using a multiscale MRF model. By transforming a face photo to a sketch (or transforming a sketch to a photo), the difference between photos and sketches is significantly reduced, thus allowing effective matching between the two in face sketch recognition. After the photo-sketch transformation, in principle, most of the proposed face photo recognition approaches can be applied to face sketch recognition in a straightforward way. Extensive experiments are conducted on a face sketch database including 606 faces, which can be downloaded at our website (http://mmlab.ie.cuhk.edu.hk/facesketch.html).
Mutiny at the white-hole district

The white-hole sector of Kruskal's solution is almost never used in physical applications. However, it might contain the solution to many of the problems associated with gravitational collapse and evaporation. This essay tries to draw attention to some bouncing geometries that make a democratic use of the black- and white-hole sectors. We will argue that these types of behaviour could be perfectly natural in some approaches to the next physical level beyond classical general relativity.
Robust heartbeat detection from in-home ballistocardiogram signals of older adults using a bed sensor

We propose a simple and robust method to detect heartbeats using the ballistocardiogram (BCG) signal that is produced by a hydraulic bed sensor placed under the mattress. The proposed method is found beneficial especially when the BCG signal does not display consistent J-peaks, which can often be the case for overnight, in-home monitoring, especially with frail seniors. Heartbeat detection is based on the short-time energy of the BCG signal. Compared with previous methods that rely on the J-peaks observed from the BCG amplitude, we are able to achieve considerable improvement even when significant distortions are present. Test results are included for different BCG waveform patterns from older adults.
Toward Perception-Driven Urban Environment Modeling for Automated Road Vehicles

Automated driving is a widely discussed topic nowadays. Impressive demonstrations have shown the potentials of vehicle automation. However, many projects in the context of automated driving use a priori data in order to compensate insufficiencies in perceiving and understanding the vehicle's environment. Additionally, in terms of functional safety and redundancy, it is not yet known whether such localization-and map-based approaches are really path breaking. This is the reason why we focus on on-board perception also of the stationary urban environment. While object tracking is a commonly used approach, the combination of grid-based and object-based representations for environment perception is still a research topic. The sufficient perception of lanes and drivable areas is an unsolved issue in urban environment. Several perception modules have to collaborate for a suitable representation of the vehicles' surroundings. In this paper, we present the latest contributions of the project Stadtpilot to a perception-driven modeling of urban environments. We propose a lane detection approach which is based on a grid-based representation of different environmental features. Our approach is able to detect multi-lane structures and it is capable to deal with complex lane structures which are typical of urban roads. The extracted features are stabilized by a tracking module. Additionally, we incorporate a free-space representation which data is not derived implicitly from detected targets, but based on an explicit ground representation. Extensions of our dynamic classification module focus on the start/stop behavior of other road users in order to enhance the completeness of track list (mobile objects) and grid (stationary environment). The presented algorithms run in real-time on a standard PC and are evaluated with real sensor data.
Distributed Suffix Tree Overlay for Peer-to-Peer Search

Establishing an appropriate semantic overlay on peer-to-peer (P2P) networks to obtain both semantic ability and scalability is a challenge. Current DHT-based P2P networks are limited in their ability to support a semantic search. This paper proposes the distributed suffix tree (DST) overlay as the intermediate layer between the DHT overlay and the semantic overlay to support the search of a keyword sequence. Its time cost is sublinear with the length of the keyword sequence. Analysis and experiments show that the DST-based search is fast, load-balanced, and useful in realizing an accurate content search on P2P networks.
Proteomic Analyses Reveal Common Promiscuous Patterns of Cell Surface Proteins on Human Embryonic Stem Cells and Sperms

Background It has long been proposed that early embryos and reproductive organs exhibit similar gene expression profiles. However, whether this similarity is propagated to the protein level remains largely unknown. We have previously characterised the promiscuous expression pattern of cell surface proteins on mouse embryonic stem (mES) cells. As cell surface proteins also play critical functions in human embryonic stem (hES) cells and germ cells, it is important to reveal whether a promiscuous pattern of cell surface proteins also exists for these cells. Methods and Principal Findings Surface proteins of hES cells and human mature sperms (hSperms) were purified by biotin labelling and subjected to proteomic analyses. More than 1000 transmembrane or secreted cell surface proteins were identified on the two cell types, respectively. Proteins from both cell types covered a large variety of functional categories including signal transduction, adhesion and transporting. Moreover, both cell types promiscuously expressed a wide variety of tissue specific surface proteins, and some surface proteins were heterogeneously expressed. Conclusions/Significance Our findings indicate that the promiscuous expression of functional and tissue specific cell surface proteins may be a common pattern in embryonic stem cells and germ cells. The conservation of gene expression patterns between early embryonic cells and reproductive cells is propagated to the protein level. These results have deep implications for the cell surface signature characterisation of pluripotent stem cells and germ cells and may lead the way to a new area of study, i.e., the functional significance of promiscuous gene expression in pluripotent and germ cells.
A Massively Parallel Approach to Real-Time Bearing Fault Detection Using Sub-Band Analysis on an FPGA-Based Multicore System

The fact that rolling element bearing faults have an amplitude-modulating effect on their characteristic frequencies calls for sub-band analysis to determine an optimal sub-band signal that contains intrinsic information about bearing faults. In this regard, it is significant to accurately assess the presence of a bearing's abnormal symptoms. Hence, a bearing abnormality index (BAI) that properly quantifies how much information a sub-band signal contains about bearing faults is presented. Additionally, to facilitate real-time sub-band analysis based on the BAI, a massively parallel approach is introduced, where the approach involves the use of the multicore system. Likewise, the multicore system supports high-performance computing by exploiting 128 processing elements operating at 200 MHz in a Xilinx Virtex-7 field-programmable gate array (FPGA) device.
Can user-level probing detect and diagnose common home-WLAN pathologies

Common Wireless LAN (WLAN) pathologies include low signal-to-noise ratio, congestion, hidden terminals or interference from non-802.11 devices and phenomena. Prior work has focused on the detection and diagnosis of such problems using layer-2 information from 802.11 devices and special purpose access points and monitors, which may not be generally available. Here, we investigate a user-level approach: is it possible to detect and diagnose 802.11 pathologies with strictly user-level active probing, without any cooperation from, and without any visibility in, layer-2 devices? In this paper, we present preliminary but promising results indicating that such diagnostics are feasible.
Isolation and Characterization of a Genetically Tractable Photoautotrophic Fe(II)-Oxidizing Bacterium, Rhodopseudomonas palustris Strain TIE-1

ABSTRACT We report the isolation and characterization of a phototrophic ferrous iron [Fe(II)]-oxidizing bacterium named TIE-1 that differs from other Fe(II)-oxidizing phototrophs in that it is genetically tractable. Under anaerobic conditions, TIE-1 grows photoautotrophically with Fe(II), H2, or thiosulfate as the electron donor and photoheterotrophically with a variety of organic carbon sources. TIE-1 also grows chemoheterotrophically in the dark. This isolate appears to be a new strain of the purple nonsulfur bacterial species Rhodopseudomonas palustris, based on physiological and phylogenetic analysis. Fe(II) oxidation is optimal at pH 6.5 to 6.9. The mineral products of Fe(II) oxidation are pH dependent: below pH 7.0 goethite (α-FeOOH) forms, and above pH 7.2 magnetite (Fe3O4) forms. TIE-1 forms colonies on agar plates and is sensitive to a variety of antibiotics. A hyperactive mariner transposon is capable of random insertion into the chromosome with a transposition frequency of ∼10−5. To identify components involved in phototrophic Fe(II) oxidation, mutants of TIE-1 were generated by transposon mutagenesis and screened for defects in Fe(II) oxidation in a cell suspension assay. Among approximately 12,000 mutants screened, 6 were identified that are specifically impaired in Fe(II) oxidation. Five of these mutants have independent disruptions in a gene that is predicted to encode an integral membrane protein that appears to be part of an ABC transport system; the sixth mutant has an insertion in a gene that is a homolog of CobS, an enzyme involved in cobalamin (vitamin B12) biosynthesis.
Simultaneous registration of gnomonic projections and central perspectives

An innovative methodology that combines central perspectives and panoramic gnomonic projections into an integrated bundle block adjustment is discussed. The use of both kinds of images generates metric products with a superior level of detail (image resolution) compared with conventional central perspectives alone, whilst achieving the accuracy of the latter. The entire methodology is intended as a low‐cost solution to improving the ground sampling distance over that achievable with single exposures by conventional modern terrestrial cameras. Very high‐resolution close‐range images can be automatically generated and oriented with a rigorous multi‐step procedure that integrates both types of images within a unified least squares adjustment. The advantages and disadvantages of the proposed approach are analysed from both theoretical and practical points of view and illustrated through a series of examples.
Recombinant Salmonella Bacteria Vectoring HIV/AIDS Vaccines

HIV/AIDS is an important public health problem globally. An affordable, easy-to-deliver and protective HIV vaccine is therefore required to curb the pandemic from spreading further. Recombinant Salmonella bacteria can be harnessed to vector HIV antigens or DNA vaccines to the immune system for induction of specific protective immunity. These are capable of activating the innate, humoral and cellular immune responses at both mucosal and systemic compartments. Several studies have already demonstrated the utility of live recombinant Salmonella in delivering expressed foreign antigens as well as DNA vaccines to the host immune system. This review gives an overview of the studies in which recombinant Salmonella bacteria were used to vector HIV/AIDS antigens and DNA vaccines. Most of the recombinant Salmonella-based HIV/AIDS vaccines developed so far have only been tested in animals (mainly mice) and are yet to reach human trials.
Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands

Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T = VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0–7.0 (optimum pH 5.0–5.5) and at 6–30°C (optimum 20–26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (≤0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1ω5c, C18:1ω5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9–10 double bonds) and C30:1/C32:1 (ω-1) hydroxy fatty acids. The G + C content of the DNA is 58.5–59.0 mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov.
Internalizing Conservation through Our Own Microbes

This is the peer reviewed version of the following article: BA Sikes (2012) Internalizing Conservation through our own Microbes. Conservation Biology, 26(2): 198. http://dx.doi.org/10.1111/j.1523-1739.2012. 01834.x, which has been published in final form at http://doi.org/10.1111/j.1523-1739.2012. 01834.x. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
Ecosystem specific yield for estimating evapotranspiration and groundwater exchange from diel surface water variation

The White method, routinely used to estimate phreatophyte transpiration from diel groundwater variation, also provides measures of total evapotranspiration (ET) and groundwater fluxes in surface waters. Such applications remain rare, however, and critically require accurate representation of stage‐dependent variation in specific yield (Sy). High‐resolution stage data from three Florida swamps were used to evaluate different relationships between Sy and stage (ecosystem specific yield, ESY). A discretized form, ESYD, assumes constant Sy near unity for inundated conditions, applying soil Sy for belowground stage and open water Sy (Sy,OW ≈ 1.0) for aboveground stage. A mixture approach, ESYM, applies a stage‐dependent interpolation between Sy,Soil and Sy,OW using stage‐area relationships and assumes rapid lateral equilibration between inundated and non‐inundated wetland areas. Finally, an empirical formulation, ESYRR, uses measured ratios of rain to rise to estimate stage‐specific Sy. All formulations yielded reasonable ET rates (ET ≈ PET) at high stage; ESYD markedly overestimated ET (ET/PET > 3) at intermediate stage, whereas ESYM and ESYRR maintained ET/PET near 1.0. Estimated groundwater fluxes using ESYM and ESYRR correlated well with Darcy‐estimated flows, but were larger, likely due to uncertainties in Darcy parameters. Well transects across wetlands documented equal water elevation and diel variation across inundated and non‐inundated areas, verifying rapid equilibration that reduces Sy and explaining overestimation by ESYD. However, equilibration area varied within and among wetlands, explaining observed differences between ESYM and ESYRR, and suggesting ESYRR may be preferred. Stage histograms followed the shape of ESYRR, highlighting reciprocal influences of ESY on stage stability. Copyright © 2012 John Wiley & Sons, Ltd.