Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure-Function Analysis of HscC, theEscherichia coli Member of a Novel Subfamily of Specialized Hsp70 Chaperones*

Hsp70 chaperones assist protein folding processes through nucleotide-controlled cycles of substrate binding and release. In our effort to understand the structure-function relationship within the Hsp70 family of proteins, we characterized the Escherichia coli member of a novel Hsp70 subfamily, HscC, and identified considerable differences to the well studied E. colihomologue, DnaK, which together suggest that HscC is a specialized chaperone. The basal ATPase cycle of HscC hadk cat and K m values that were 8- and 10,000-fold higher than for DnaK. The HscC ATPase was not affected by the nucleotide exchange factor of DnaK GrpE and stimulated 8-fold by DjlC, a DnaJ protein with a putative transmembrane domain, but not by other DnaJ proteins tested. Substrate binding dynamics and substrate specificity differed significantly between HscC and DnaK. These differences are explicable by distinct structural variations. HscC does not have general chaperone activity because it did not assist refolding of a denatured model substrate. In vivo, HscC failed to complement temperature sensitivity of ΔdnaKcells. Deletion of hscC caused a slow growth phenotype that was suppressed after several generations. Triple knock-outs of allE. coli genes encoding Hsp70 proteins (ΔdnaKΔhscA ΔhscC) were viable, indicating that Hsp70 proteins are not strictly essential for viability. An extensive search for ΔhscC phenotypes revealed a hypersensitivity to Cd2+ ions and UV irradiation, suggesting roles of HscC in the cellular response to these stress treatments. Together our data show that the Hsp70 structure exhibits an astonishing degree of adaptive variations to accommodate requirements of a specialized function.
A Fast Multimodal Ectopic Beat Detection Method Applied for Blood Pressure Estimation Based on Pulse Wave Velocity Measurements in Wearable Sensors

Automatic detection of ectopic beats has become a thoroughly researched topic, with literature providing manifold proposals typically incorporating morphological analysis of the electrocardiogram (ECG). Although being well understood, its utilization is often neglected, especially in practical monitoring situations like online evaluation of signals acquired in wearable sensors. Continuous blood pressure estimation based on pulse wave velocity considerations is a prominent example, which depends on careful fiducial point extraction and is therefore seriously affected during periods of increased occurring extrasystoles. In the scope of this work, a novel ectopic beat discriminator with low computational complexity has been developed, which takes advantage of multimodal features derived from ECG and pulse wave relating measurements, thereby providing additional information on the underlying cardiac activity. Moreover, the blood pressure estimations’ vulnerability towards ectopic beats is closely examined on records drawn from the Physionet database as well as signals recorded in a small field study conducted in a geriatric facility for the elderly. It turns out that a reliable extrasystole identification is essential to unsupervised blood pressure estimation, having a significant impact on the overall accuracy. The proposed method further convinces by its applicability to battery driven hardware systems with limited processing power and is a favorable choice when access to multimodal signal features is given anyway.
Nanoencapsulation Enhances the Post-Emergence Herbicidal Activity of Atrazine against Mustard Plants

Poly(epsilon-caprolactone) (PCL) nanocapsules have been recently developed as a modified release system for atrazine, an herbicide that can have harmful effects in the environment. Here, the post-emergence herbicidal activity of PCL nanocapsules containing atrazine was evaluated using mustard (Brassica juncea) as target plant species model. Characterization of atrazine-loaded PCL nanocapsules by nanoparticle tracking analysis indicated a concentration of 7.5 x 1012 particles mL-1 and an average size distribution of 240.7 nm. The treatment of mustard plants with nanocapsules carrying atrazine at 1 mg mL-1 resulted in a decrease of net photosynthesis and PSII maximum quantum yield, and an increase of leaf lipid peroxidation, leading to shoot growth inhibition and the development of severe symptoms. Time course analysis until 72 h after treatments showed that nanoencapsulation of atrazine enhanced the herbicidal activity in comparison with a commercial atrazine formulation. In contrast to the commercial formulation, ten-fold dilution of the atrazine-containing nanocapsules did not compromise the herbicidal activity. No effects were observed when plants were treated with nanocapsules without herbicide compared to control leaves sprayed with water. Overall, these results demonstrated that atrazine-containing PCL nanocapsules provide very effective post-emergence herbicidal activity. More importantly, the use of nanoencapsulated atrazine enables the application of lower dosages of the herbicide, without any loss of efficiency, which could provide environmental benefits.
A Low-Power Nonvolatile Switching Element Based on Copper-Tungsten Oxide Solid Electrolyte

We describe the materials aspects and electrical characteristics of W-(Cu/WO3)-Cu switching elements. These materials are compatible with back-end-of-line processing in CMOS integrated circuits where both tungsten and copper already play a significant role. Devices based on Cu/WO3 solid electrolytes formed by photodiffusion of copper into tungsten oxide switch via the electrochemical formation of a conducting filament within the high resistance electrolyte film. They are able to switch reversibly between widely spaced nonvolatile resistance states at low voltage (<1 V) and current (<10 muA). Electrical characterization revealed that devices consisting of plasma-grown oxides have a variable initial threshold voltage and poor retention, whereas devices based on deposited oxide exhibit a stable switching threshold and good retention, even at elevated operating temperature (>125 degC). This difference in behavior was attributed to the observation that the copper tends to oxidize in the plasma-grown oxide whereas the copper in the deposited oxide exists in an unbound state and is, therefore, more able to participate in the switching process
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation

MOTIVATION We describe an extension of the pathway-based enrichment approach for analyzing microarray data via a robust test for transcriptional variance. The use of a variance test is intended to identify additional patterns of transcriptional regulation in which many genes in a pathway are up- and down-regulated. Such patterns may be indicative of the reciprocal regulation of pathway activators and inhibitors or of the differential regulation of separate biological sub-processes and should extend the number of detectable patterns of transcriptional modulation. RESULTS We validated this new statistical approach on a microarray experiment that captures the temporal transcriptional profile of muscle differentiation in mouse C2C12 cells. Comparisons of the transcriptional state of myoblasts and differentiated myotubes via a robust variance test implicated several novel pathways in muscle cell differentiation previously overlooked by a standard enrichment analysis. Specifically, pathways involved in cell structure, calcium-mediated signaling and muscle-specific signaling were identified as differentially modulated based on their increased transcriptional variance. These biologically relevant results validate this approach and demonstrate the flexible nature of pathway-based methods of data analysis. AVAILABILITY The software is available as Supplementary Material.
Intra- and Interspecies Regulation of Gene Expression by Actinobacillus actinomycetemcomitansLuxS

ABSTRACT The cell density-dependent control of gene expression is employed by many bacteria for regulating a variety of physiological functions, including the generation of bioluminescence, sporulation, formation of biofilms, and the expression of virulence factors. Although periodontal organisms do not appear to secrete acyl-homoserine lactone signals, several species, e.g., Porphyromonas gingivalis,Prevotella intermedia, and Fusobacterium nucleatum, have recently been shown to secrete a signal related to the autoinducer II (AI-2) of the signal system 2 pathway inVibrio harveyi. Here, we report that the periodontal pathogen Actinobacillus actinomycetemcomitans expresses a homolog of V. harveyi luxS and secretes an AI-2-like signal. Cell-free conditioned medium from A. actinomycetemcomitans or from a recombinant Escherichia coli strain (E. coli AIS) expressing A. actinomycetemcomitans luxS induced luminescence in V. harveyi BB170 >200-fold over controls. AI-2 levels peaked in mid-exponential-phase cultures of A. actinomycetemcomitans and were significantly reduced in late-log- and stationary-phase cultures. Incubation of early-log-phaseA. actinomycetemcomitans cells with conditioned medium from A. actinomycetemcomitans or from E. coli AIS resulted in a threefold induction of leukotoxic activity and a concomitant increase in leukotoxin polypeptide. In contrast, no increase in leukotoxin expression occurred when cells were exposed to sterile medium or to conditioned broth from E. coli AIS−, a recombinant strain in whichluxS was insertionally inactivated. A. actinomycetemcomitans AI-2 also induced expression ofafuA, encoding a periplasmic iron transport protein, approximately eightfold, suggesting that LuxS-dependent signaling may play a role in the regulation of iron acquisition by A. actinomycetemcomitans. Finally, A. actinomycetemcomitans AI-2 added in transcomplemented a luxS knockout mutation in P. gingivalis by modulating the expression of theluxS-regulated genes uvrB andhasF in this organism. Together, these results suggest that LuxS-dependent signaling may modulate aspects of virulence and the uptake of iron by A. actinomycetemcomitans and induce responses in other periodontal organisms in mixed-species oral biofilm.
Three-dimensional reconstruction of refractive index distribution in optical phase elements by interferometric and photoelastic tomography

The paper gives a review of interferometric and photoelastic tomography with focus on their necessary modification when applied to 3D refractive index determination in micro-objects. Specifically the influence of diffraction phenomenon and radial run-out occurring during measurement are analyzed. The analysis are confirmed by results of measurements of 3D refractive index distribution in a multimode and single mode fibres.
Morphological Transformation from Galaxy Harassment

Galaxy morphologies in clusters have undergone a remarkable transition over the past several billion yr. Distant clusters at z ~ 0.4 are filled with small spiral galaxies, many of which are disturbed and show evidence of multiple bursts of star formation. This population is absent from nearby clusters, where spheroidals comprise the faint end of the luminosity function. Our numerical simulations follow the evolution of disk galaxies in a rich cluster resulting from encounters with brighter galaxies and the cluster's tidal field, or "galaxy harassment. " After a bursting transient phase, they undergo a complete morphological transformation from "disks" to "spheroidals. " We examine the remnants and find support for our theory in detailed comparisons of the photometry and kinematics of the spheroidal galaxies in clusters. Our model naturally accounts for the intermediate-age stellar population seen in these spheroidals, as well as for the trend in the dwarf-to-giant ratio with cluster richness. The final shapes are typically prolate and are flattened primarily by velocity anisotropy. Their mass-to-light ratios are in the range 3-8, in good agreement with observations.
Alternative proteolytic processing of the arterivirus replicase ORF1a polyprotein: evidence that NSP2 acts as a cofactor for the NSP4 serine protease

The C-terminal half of the replicase ORF1a polyprotein of the arterivirus equine arteritis virus is processed by a chymotrypsinlike serine protease (SP) (E. J. Snijder et al., J. Biol. Chem. 271:4864-4871, 1996) located in nonstructural protein 4 (nsp4). Three probable SP cleavage sites had previously been identified in the ORF1a protein. Their proteolysis explained the main processing products generated from the C-terminal part of the ORF1a protein in infected cells (E. J. Snijder et al., J. Virol. 68:5755-5764, 1994). By using sequence comparison, ORF1a expression systems, and site-directed mutagenesis, we have now identified two additional SP cleavage sites: Glu-1430 / Gly and Glu-1452 / Ser. This means that the ORF1a protein can be cleaved into eight processing end products: nsp1 to nsp8. By microsequence analysis of the nsp5 and nsp7 N termini, we have now formally confirmed the specificity of the SP for Glu / (Gly/Ser) substrates. Importantly, our studies revealed that the C-terminal half of the ORF1a protein (nsp3-8) can be processed by the SP following two alternative pathways, which appear to be mutually exclusive. In the majority of the nsp3-8 precursors the SP cleaves the nsp4/5 site, yielding nsp3-4 and nsp5-8. Subsequently, the latter product is cleaved at the nsp7/8 site only, whereas the newly identified nsp5/6 and nsp6/7 sites appear to be inaccessible to the protease. In the alternative proteolytic cascade, which is used at a low but significant level in infected cells, it is the nsp4/5 site which remains uncleaved, while the nsp5/6 and nsp6/7 sites are processed to yield a set of previously unnoticed processing products. Coexpression studies revealed that nsp3-8 has to interact with cleaved nsp2 to allow processing of the nsp4/5 junction, the first step of the major processing pathway. When the nsp2 cofactor is absent, the nsp4/5 site cannot be processed and nsp3-8 is processed following the alternative, minor pathway.
Roles of clinical and subclinical reactivated herpes simplex virus type 2 infection and human immunodeficiency virus type 1 (HIV-1)-induced immunosuppression on genital and plasma HIV-1 levels.

BACKGROUND Few longitudinal studies have described the interactions between reactivation of herpes simplex virus type 2 (HSV-2) infection (hereafter, "HSV-2 reactivation") and genital and systemic replication of human immunodeficiency virus type 1 (HIV-1). METHODS Women in Burkina Faso who were seropositive for both HIV-1 and HSV-2 were enrolled in a randomized placebo-controlled trial of therapy to suppress reactivation of HSV-2 infection (hereafter, "HSV suppressive therapy"). During the baseline phase, 6 enriched cervicovaginal lavage specimens were obtained over 12 weeks to detect and quantify the HIV-1 RNA and HSV-2 DNA loads. RESULTS Women with genital ulcer disease (GUD) detected at least once were more likely than women in whom GUD was not detected (risk ratio [RR], 1.23; 95% confidence interval [CI], 1.09-1.37) to have genital HIV-1 RNA detected during >or=1 visit. Similarly, women with genital HSV-2 DNA detected during >or=1 clinic visit were more likely than women in whom genital HSV-2 DNA was not detected (RR, 1.17; 95% CI, 1.01-1.34) to have genital HIV-1 RNA detected at least once. In addition, the mean genital HIV-1 RNA loads for women with GUD detected during >or=1 visit and women with HSV-2 genital shedding detected during >or=1 visit were greater than that for women in whom genital HSV-2 DNA or GUD was never detected. The plasma HIV-1 RNA load was increased among women for whom >or=1 visit revealed GUD (+0.25 log(10) copies/mL; 95% CI, -0.05-0.55) or genital HSV-2 DNA (+0.40 log(10) copies/mL; 95% CI, 0.15-0.66), compared with women who did not experience GUD or HSV-2 genital shedding, respectively. The association of HSV-2 reactivations on HIV-1 replication tended to be stronger in patients with a higher CD4(+) cell count (i.e., >500 cells/microL). The contribution of HSV-2 to HIV-1 replication among women with CD4(+) cell count of <or=500 cells/microL was reduced because almost all experienced HIV-1 genital shedding. CONCLUSIONS Both clinical and subclinical HSV-2 reactivations play a role in increasing the rate of HIV-1 replication. HSV suppressive therapy is a promising tool for HIV control. Initiation of such therapy when the CD4(+) cell count is >500 cells/microL deserves further investigation. CLINICAL TRIALS REGISTRATION The ANRS 1285 Study is registered with the National Institutes of Health (registration number NCT00158509).
Cortical Function in Children Receiving Bilateral Cochlear Implants Simultaneously or After a Period of Interimplant Delay

Hypothesis: Children using bilateral cochlear implants (CIs) develop normal patterns of cortical activity when interimplant delays are minimized. Background: It is not clear whether bilateral CIs can promote normally functioning bilateral auditory pathways in children. Methods: Cortical responses were recorded from 64 cephalic sites in 2 normal hearing participants and 8 children with 3 to 4 years of bilateral CI experience (age at first CI, 0.9-4.1 yr; age at second CI, 1.1-9.7 yr; interimplant delay, 0-5.8 yr). Results: Beamformer analyses on the dominant positive peak in CI users and P1 in normal hearers revealed that stimuli delivered from the left side evoked responses lateralized to right auditory cortex in the 2 participants with normal hearing and the 3 children receiving bilateral CIs with minimal interimplant delay at young ages. These 5 participants showed a shift in cortical lateralization away from the right cortical hemisphere when stimuli were moved to the right. In contrast, 4 of 5 children receiving bilateral CIs after longer delays and at older ages showed abnormal ipsilateral parietal activity in response to left stimuli and lateralization to the left cortical hemisphere in response to both right and left stimuli. The fifth child in this group showed abnormal lateralization to the ipsilateral cortex in response to both right and left stimuli. Conclusion: The data suggest that, after 3 to 4 years of bilateral CI use, normal-like patterns of bilateral cortical activity are promoted in children receiving bilateral CI with minimal interimplant delays and young ages but are not present in older children who had longer interimplant delays.
Efficiently decodable non-adaptive group testing

We consider the following "efficiently decodable" non-adaptive group testing problem. There is an unknown string <i>x</i> ∈ {0, 1}<i><sup>n</sup></i> with at most <i>d</i> ones in it. We are allowed to test any subset <i>S</i> ⊆ [<i>n</i>] of the indices. The answer to the test tells whether <i>x</i><sub><i>i</i></sub> = 0 for all <i>i</i> ∈ <i>S</i> or not. The objective is to design as few tests as possible (say, <i>t</i> tests) such that <i>x</i> can be identified as fast as possible (say, poly(<i>t</i>)-time). Efficiently decodable non-adaptive group testing has applications in many areas, including data stream algorithms and data forensics. A non-adaptive group testing strategy can be represented by a <i>t</i> x <i>n</i> matrix, which is the stacking of all the characteristic vectors of the tests. It is well-known that if this matrix is <i>d</i>-disjunct, then any test outcome corresponds uniquely to an unknown input string. Furthermore, we know how to construct <i>d</i>-disjunct matrices with <i>t</i> = <i>O</i>(<i>d</i><sup>2</sup> log <i>n</i>) efficiently. However, these matrices so far only allow for a "decoding" time of <i>O</i>(<i>nt</i>), which can be exponentially larger than poly(<i>t</i>) for relatively small values of <i>d</i>. This paper presents a randomness efficient construction of <i>d</i>-disjunct matrices with <i>t</i> = <i>O</i>(<i>d</i><sup>2</sup> log <i>n</i>) that can be decoded in time poly(<i>d</i>) · <i>t</i> log<sup>2</sup> <i>t</i> + <i>O</i>(<i>t</i><sup>2</sup>). To the best of our knowledge, this is the first result that achieves an efficient decoding time and matches the best known <i>O</i>(<i>d</i><sup>2</sup> log <i>n</i>) bound on the number of tests. We also derandomize the construction, which results in a polynomial time deterministic construction of such matrices when <i>d</i> = <i>O</i>(log <i>n</i> / log log <i>n</i>). A crucial building block in our construction is the notion of (<i>d</i>, <i>l</i>)-list disjunct matrices, which represent the more general "list group testing" problem whose goal is to output less than <i>d</i> + <i>l</i> positions in <i>x</i>, including all the (at most <i>d</i>) positions that have a one in them. List disjunct matrices turn out to be interesting objects in their own right and were also considered independently by [Cheraghchi, FCT 2009]. We present connections between list disjunct matrices, expanders, dispersers and disjunct matrices. List disjunct matrices have applications in constructing (<i>d</i>, <i>l</i>)-sparsity separator structures [Ganguly, ISAAC 2008] and in constructing tolerant testers for Reed-Solomon codes in the data stream model.
A Low-cost Ultrasonic 3D Measurement Device for Calibration for Cartesian and Non-Cartesian Machines

The major obstacles to the widespread adoption of 3D measurement systems are accuracy, speed of process and the cost. At present, high accuracy for measuring 3D position has been achieved, and there have been real advances in reducing measurement time, but the cost of such systems remains high. A high-accuracy and high-resolution ultrasonic distance measurement system has been achieved in this project by creating multi-frequency continuous wave frequency modulation (MFCWFM) system. The low-cost system measures dynamic distance (displacements of an ultrasound transmitter) and fixed distance (distances between receivers). The instantaneous distance between the transmitter and each receiver can be precisely determined. New geometric algorithms for transmitter 3D position and receiver positing have also been developed in the current research to improve the measurement system‟s practicability. These algorithms allow the ultrasound receivers to be arbitrarily placed and located by self-calibration following a simple procedure. After the development and testing of the new 3D measurement system, further studies have also been carried out on the system, considering the two major external disturbances: air temperature drifting and ultrasound echo interference. Novel methods have been successfully developed and tested to minimize measurement errors and evaluation of speed of sound. All the enabling research described in the thesis means that it is now possible to build and implement a measurement system at reasonable cost for industrial exploitation. This will have the necessary performance to provide ultrasonic 3D position measurements in real time for monitoring position.