Miracle-dz/UniFAR-FTUs huggingface dataset:
The Putative Assembly Factor CcoH Is Stably Associated with the cbb3-Type Cytochrome Oxidase

ABSTRACT Cytochrome oxidases are perfect model substrates for analyzing the assembly of multisubunit complexes because the need for cofactor incorporation adds an additional level of complexity to their assembly. cbb 3-type cytochrome c oxidases (cbb 3-Cox) consist of the catalytic subunit CcoN, the membrane-bound c-type cytochrome subunits CcoO and CcoP, and the CcoQ subunit, which is required for cbb 3-Cox stability. Biogenesis of cbb 3-Cox proceeds via CcoQP and CcoNO subcomplexes, which assemble into the active cbb 3-Cox. Most bacteria expressing cbb 3-Cox also contain the ccoGHIS genes, which encode putative cbb 3-Cox assembly factors. Their exact function, however, has remained unknown. Here we analyzed the role of CcoH in cbb 3-Cox assembly and showed that CcoH is a single spanning-membrane protein with an N-terminus-out-C-terminus-in (Nout-Cin) topology. In its absence, neither the fully assembled cbb 3-Cox nor the CcoQP or CcoNO subcomplex was detectable. By chemical cross-linking, we demonstrated that CcoH binds primarily via its transmembrane domain to the CcoP subunit of cbb 3-Cox. A second hydrophobic stretch, which is located at the C terminus of CcoH, appears not to be required for contacting CcoP, but deleting it prevents the formation of the active cbb 3-Cox. This suggests that the second hydrophobic domain is required for merging the CcoNO and CcoPQ subcomplexes into the active cbb 3-Cox. Surprisingly, CcoH does not seem to interact only transiently with the cbb 3-Cox but appears to stay tightly associated with the active, fully assembled complex. Thus, CcoH behaves more like a bona fide subunit of the cbb 3-Cox than an assembly factor per se.
Genome Sequence of Rickettsia conorii subsp. caspia, the Agent of Astrakhan Fever

ABSTRACT Rickettsia conorii subsp. caspia is the agent of Astrakhan fever, a spotted fever group rickettsiosis endemic to Astrakhan, Russia. The present study reports the draft genome of Rickettsia conorii subsp. caspia strain A-167.
Genome Sequence of Enterococcus faecium Clinical Isolate LCT-EF128

ABSTRACT Enterococcus faecium, an opportunistic human pathogen that inhabits the gastrointestinal tracts of most mammals, has emerged as an important opportunistic nosocomial pathogen and is a prominent cause of multiresistant nosocomial infections. Here, we report the draft genome sequence of strain LCT-EF128, isolated from clinical specimens.
Comparison of the Poisson's Ratio of Simulated Rigid and Elastic Auxetic Models Using Kinematic and Finite Element Analysis

Materials that possess a negative Poisson's ratio are called Auxetics. They are characterized by the counterintuitive behavior of expanding in tension and contracting in compression. To justify this deformation behavior, there have been developed theoretical modelations like the reentrant and bowtie models. However, the most generalized models are based on geometries that possess rigid trusses and hinging nodes. This does not portrait the reality of the application of these models. In this study, there have been performed simulations, using kinematic analysis to characterize the auxetic behavior of the theoretical rigid/hinging models and finite element analysis to characterize elastic models that represent real bodies. There were determined and compared the Poisson's ratios of the theoretical and elastic reentrant and bowtie. Additionally it was shown that there is a significant difference between the results. In conclusion the theoretical models predict lower values of Poisson's ratio, while the elastic models that simulate a real body show less auxetic behavior.
Interferon-α Therapy in Polycythemia Vera and Essential Thrombocythemia

Essential thrombocythemia (ET) and polycythemia vera (PV) are chronic clonal myeloid disorders that originate from the multipotential hematopoietic stem cell. They are characterized, respectively, by excessive thrombocytosis and erythrocytosis, a high incidence of thrombohemorrhagic events, vasomotor symptoms, and an inherent tendency to undergo leukemic transformation. Current standard therapies to control the excess accumulation of myeloid cells and to provide symptomatic relief carry either a persistent risk of thrombosis, as in the case of phlebotomy, or, in the case of hydroxyurea, the potential for inducing leukemia. None alter the natural history of these diseases. Interferon-alpha has been shown to have potent antiproliferative effects on the hematopoietic stem cells and bone marrow fibroblasts and, as a result, has received much attention as a therapeutic agent for chronic myeloproliferative disorders. The ability of interferon-alpha to induce hematologic and cytogenetic remission in chronic phase chronic granulocytic leukemia has further increased interest in this agent. Interferon-alpha has shown therapeutic activity in PV and ET, as demonstrated in multiple small studies and single-arm trials reviewed in this article. Reported beneficial effects include the ability to control excessive erythrocytosis and thrombocytosis and such disease-related features as vasomotor symptoms, pruritus, and splenomegaly. Recent reports of cytogenetic remission and reversal of bone marrow fibrosis after interferon therapy are of interest. Advantages over current therapeutic standards include lack of known leukemogenic and teratogenic effects and the potential to alter the underlying course of disease. Nevertheless, none of the information available allows definite therapeutic recommendations for the use of interferon-alpha in PV or ET. The available data support the need for randomized controlled trials comparing interferon-alpha with standard therapy.
The σE Pathway Is Involved in Biofilm Formation by Crohn's Disease-Associated Adherent-Invasive Escherichia coli

ABSTRACT Ileal lesions of patients with Crohn's disease are colonized by adherent-invasive Escherichia coli (AIEC) bacteria that are able to adhere to and invade intestinal epithelial cells (IEC), to replicate within macrophages, and to form biofilm. Clinical observations showed that bacterial biofilms were associated with the mucosa of inflammatory bowel disease patients. In the present study, we analyzed the relationship between AIEC colonization of the gut and the formation of biofilm, focusing on the involvement of the σE pathway in the AIEC-IEC interaction. We observed that σE pathway inhibition in AIEC reference strain LF82 led to an impaired ability to adhere to and invade IEC but also induced a large decrease in the abilities to colonize the intestinal mucosa and form biofilm. This indicates that targeting of the σE pathway could be a very potent therapeutic strategy by which to interfere with the ability of AIEC to form biofilm on the gut mucosa of Crohn's disease patients.
Complete Genome Sequence of Streptococcus mutans GS-5, a Serotype c Strain

ABSTRACT Streptococcus mutans, a principal causative agent of dental caries, is considered to be the most cariogenic among all oral streptococci. Of the four S. mutans serotypes (c, e, f, and k), serotype c strains predominate in the oral cavity. Here, we present the complete genome sequence of S. mutans GS-5, a serotype c strain originally isolated from human carious lesions, which is extensively used as a laboratory strain worldwide.
Genome Sequence of Leuconostoc argentinum KCTC 3773

ABSTRACT Leuconostoc argentinum is one of the most prevalent lactic acid bacteria present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of type strain KCTC 3773 of Leuconostoc argentinum (1,720,683 bp, with a G+C content of 42.9%), which consists of 98 large contigs (>100 bp in size).
Visual navigation using a single camera

We assess the usefulness of monocular recursive motion estimation techniques for vehicle navigation in the absence of a model for the environment. For this purpose we extend a recently proposed recursive motion estimator, the Essential filter, to handle scale estimation. We examine experimentally the accuracy with which the motion and position of the vehicle may be computed on an 8000 frame indoors sequence. The issues of sampling time frequency and number of necessary features in the environment are addressed systematically. <<ETX>>
Draft Genome Sequence of Lactobacillus rossiae DSM 15814T

ABSTRACT The draft genome sequence of Lactobacillus rossiae DSM 15814T (CS1, ATCC BAA-88) was determined by a whole-genome shotgun approach. Reads were assembled to a 2.9-Mb draft version. RAST genome annotation evidenced 2,723 predicted coding sequences. Many carbohydrate, amino acid, and amino acid derivative subsystem features were found.
A Type VI Secretion System Effector Protein, VgrG1, from Aeromonas hydrophila That Induces Host Cell Toxicity by ADP Ribosylation of Actin

ABSTRACT We recently delineated the importance of a type VI secretion system (T6SS) gene cluster in the virulence of diarrheal isolate SSU of Aeromonas hydrophila and showed that VasH, a σ54 activator and T6SS component, was involved in the production of its associated effectors, e.g., hemolysin-coregulated protein. To identify additional T6SS effectors and/or secreted proteins, we subjected culture supernatants from deletion mutants of A. hydrophila, namely, a Δact mutant (a T2SS-associated cytotoxic enterotoxin-encoding gene) and a Δact ΔvasH mutant, to 2-dimensional gel electrophoresis and mass spectrometric analysis. Based on these approaches, we identified a member of the VgrG protein family, VgrG1, that contained a vegetative insecticidal protein (VIP-2) domain at its carboxyl-terminal end. Consequently, the vgrG1 gene was cloned in pBI-EGFP and pET-30a vectors to be expressed in HeLa Tet-Off cells and Escherichia coli, respectively. We assessed the ADP-ribosyltransferase (ADPRT) activity of various domains of purified recombinant VgrG1 (rVgrG1) and provided evidence that only the full-length VgrG1, as well as its carboxyl-terminal domain encoding the VIP-2 domain, showed ADPRT activity. Importantly, bacterium-host cell interaction was needed for the T6SS to induce cytotoxicity in eukaryotic cells, and we demonstrated translocation of VgrG1. Furthermore, our data indicated that expression of the genes encoding the full-length VgrG1 and its carboxyl-terminal domain in HeLa Tet-Off cells disrupted the actin cytoskeleton, which was followed by a decrease in cell viability and an increase in apoptosis. Taken together, these findings demonstrated for the first time that VgrG1 of A. hydrophila possessed actin ADPRT activity associated with its VIP-2 domain and that this domain alone was able to induce a rounded phenotype in HeLa Tet-Off cells, followed by apoptosis mediated by caspase 9 activation.
Opening the Black Box: Hierarchical Sampling Optimization for Hand Pose Estimation

Hand pose estimation, formulated as an inverse problem, is typically optimized by an energy function over pose parameters using a ‘black box’ image generation procedure, knowing little about either the relationships between the parameters or the form of the energy function. In this paper, we show significant improvement upon such black box optimization by exploiting high-level knowledge of the parameter structure and using a local surrogate energy function. Our new framework, hierarchical sampling optimization (HSO), consists of a sequence of discriminative predictors organized into a kinematic hierarchy. Each predictor is conditioned on its ancestors, and generates a set of samples over a subset of the pose parameters, with only one selected by the highly-efficient surrogate energy. The selected partial poses are concatenated to generate a full-pose hypothesis. Repeating the same process, several hypotheses are generated and the full energy function selects the best result. Under the same kinematic hierarchy, two methods based on decision forest and convolutional neural network are proposed to generate the samples and two optimization methods are studied when optimizing these samples. Experimental evaluations on three publicly available datasets show that our method is particularly impressive in low-compute scenarios where it significantly outperforms all other state-of-the-art methods.
Bacillus anthracis Acetyltransferases PatA1 and PatA2 Modify the Secondary Cell Wall Polysaccharide and Affect the Assembly of S-Layer Proteins

ABSTRACT The envelope of Bacillus anthracis encompasses a proteinaceous S-layer with two S-layer proteins (Sap and EA1). Protein assembly in the envelope of B. anthracis requires S-layer homology domains (SLH) within S-layer proteins and S-layer-associated proteins (BSLs), which associate with the secondary cell wall polysaccharide (SCWP), an acetylated carbohydrate that is tethered to peptidoglycan. Here, we investigated the contributions of two putative acetyltransferases, PatA1 and PatA2, on SCWP acetylation and S-layer assembly. We show that mutations in patA1 and patA2 affect the chain lengths of B. anthracis vegetative forms and perturb the deposition of the BslO murein hydrolase at cell division septa. The patA1 and patA2 mutants are defective for the assembly of EA1 in the envelope but retain the ability of S-layer formation with Sap. SCWP isolated from the patA1 patA2 mutant lacked acetyl moieties identified in wild-type polysaccharide and failed to associate with the SLH domains of EA1. A model is discussed whereby patA1- and patA2-mediated acetylation of SCWP enables the deposition of EA1 as well as BslO near the septal region of the B. anthracis envelope.
Structure of the Periplasmic Stress Response Protein CpxP

ABSTRACT CpxP is a novel bacterial periplasmic protein with no homologues of known function. In Gram-negative enteric bacteria, CpxP is thought to interact with the two-component sensor kinase, CpxA, to inhibit induction of the Cpx envelope stress response in the absence of protein misfolding. CpxP has also been shown to facilitate DegP-mediated proteolysis of misfolded proteins. Six mutations that negate the ability of CpxP to function as a signaling protein are localized in or near two conserved LTXXQ motifs that define a class of proteins with similarity to CpxP, Pfam PF07813. To gain insight into how these mutations might affect CpxP signaling and/or proteolytic adaptor functions, the crystal structure of CpxP from Escherichia coli was determined to 2.85-Å resolution. The structure revealed an antiparallel dimer of intertwined α-helices with a highly basic concave surface. Each protomer consists of a long, hooked and bent hairpin fold, with the conserved LTXXQ motifs forming two diverging turns at one end. Biochemical studies demonstrated that CpxP maintains a dimeric state but may undergo a slight structural adjustment in response to the inducing cue, alkaline pH. Three of the six previously characterized cpxP loss-of-function mutations, M59T, Q55P, and Q128H, likely result from a destabilization of the protein fold, whereas the R60Q, D61E, and D61V mutations may alter intermolecular interactions.
Tn502 and Tn512 Are res Site Hunters That Provide Evidence of Resolvase-Independent Transposition to Random Sites

ABSTRACT In this study, we report on the transposition behavior of the mercury(II) resistance transposons Tn502 and Tn512, which are members of the Tn5053 family. These transposons exhibit targeted and oriented insertion in the par region of plasmid RP1, since par-encoded components, namely, the ParA resolvase and its cognate res region, are essential for such transposition. Tn502 and, under some circumstances, Tn512 can transpose when par is absent, providing evidence for an alternative, par-independent pathway of transposition. We show that the alternative pathway proceeds by a two-step replicative process involving random target selection and orientation of insertion, leading to the formation of cointegrates as the predominant product of the first stage of transposition. Cointegrates remain unresolved because the transposon-encoded (TniR) recombination system is relatively inefficient, as is the host-encoded (RecA) system. In the presence of the res-ParA recombination system, TniR-mediated (and RecA-mediated) cointegrate resolution is highly efficient, enabling resolution both of cointegrates involving functional transposons (Tn502 and Tn512) and of defective elements (In0 and In2). These findings implicate the target-encoded accessory functions in the second stage of transposition as well as in the first. We also show that the par-independent pathway enables the formation of deletions in the target molecule.
Height-from-Polarisation with Unknown Lighting or Albedo

We present a method for estimating surface height directly from a single polarisation image simply by solving a large, sparse system of linear equations. To do so, we show how to express polarisation constraints as equations that are linear in the unknown height. The local ambiguity in the surface normal azimuth angle is resolved globally when the optimal surface height is reconstructed. Our method is applicable to dielectric objects exhibiting diffuse and specular reflectance, though lighting and albedo must be known. We relax this requirement by showing that either spatially varying albedo or illumination can be estimated from the polarisation image alone using nonlinear methods. In the case of illumination, the estimate can only be made up to a binary ambiguity which we show is a generalised Bas-relief transformation corresponding to the convex/concave ambiguity. We believe that our method is the first passive, monocular shape-from-x technique that enables well-posed height estimation with only a single, uncalibrated illumination condition. We present results on real world data, including in uncontrolled, outdoor illumination.
Down‐regulation of LPS‐induced nitric oxide synthesis of murine macrophages by oral administration of Sho‐saiko‐to

The effect of oral administration of a traditional Chinese herbal medicine, Sho‐saiko‐to (SST), on nitric oxide (NO) synthesis by murine macrophages was examined. SST was orally administered to mice, and NO synthesis of peritoneal exudate cells (PEC) cultured in the presence or absence of lipopolysaccharide (LPS) was measured. NO synthesis of PEC in response to LPS was reduced by oral administration of SST, whereas alkaline phosphatase (ALP) activity expressed by splenic B cells in response to LPS was enhanced. This finding suggests that augmented ALP activity possibly resulted from a decrease in macrophage functions, including NO synthesis. These activities were observed when SST or a low molecular weight fraction of SST was orally administered to mice, suggesting that down‐regulation of macrophage functions depend on low molecular weight substances in SST. Drug Dev. Res. 40:48–55, 1997. © 1997 Wiley‐Liss, Inc.
Contour Code: Robust and efficient multispectral palmprint encoding for human recognition

We propose ‘Contour Code’, a novel representation and binary hash table encoding for multispectral palmprint recognition. We first present a reliable technique for the extraction of a region of interest (ROI) from palm images acquired with non-contact sensors. The Contour Code representation is then derived from the Nonsubsampled Contourlet Transform. A uniscale pyramidal filter is convolved with the ROI followed by the application of a directional filter bank. The dominant directional subband establishes the orientation at each pixel and the index corresponding to this subband is encoded in the Contour Code representation. Unlike existing representations which extract orientation features directly from the palm images, the Contour Code uses a two stage filtering to extract robust orientation features. The Contour Code is binarized into an efficient hash table structure that only requires indexing and summation operations for simultaneous one-to-many matching with an embedded score level fusion of multiple bands. We quantitatively evaluate the accuracy of the ROI extraction by comparison with a manually produced ground truth. Multispectral palmprint verification results on the PolyU and CASIA databases show that the Contour Code achieves an EER reduction upto 50%, compared to state-of-the-art methods.
Pattern of Local Gravitational Force (PLGF): A Novel Local Image Descriptor

This paper presents a novel local image descriptor called Pattern of Local Gravitational Force (<italic>PLGF</italic>). It is inspired by Law of Universal Gravitation. <italic>PLGF</italic> is a hybrid descriptor, which is a combination of two feature components: one is the Pattern of Local Gravitational Force Magnitude (<italic>PLGFM</italic>), and another is Pattern of Local Gravitational Force Angle (<italic>PLGFA</italic>). <italic>PLGFM</italic> encodes the local gravitational force magnitude, and <italic>PLGFA</italic> encodes the local gravitational force angle that the center pixel exerts on all other pixels within a local neighborhood. We propose a novel noise resistance and the edge-preserving binary pattern called neighbors to center difference binary pattern (<italic>NCDBP</italic>) for gravitational force magnitude encoding. Finally, the histograms of the two components are concatenated to construct the <italic>PLGF</italic> descriptor. Experimental results on the existing face recognition databases, texture database, and biomedical image database show that <italic>PLGF</italic> is an effective image descriptor, and it outperforms other widely used existing descriptors. Even if in complicated variations like noise, and illumination with smaller databases, a combination of <italic>PLGF</italic> and convolutional neural network (CNN) performs consistently better than other state-of-the-art techniques.
Isolation of Highly Persistent Mutants of Salmonella enterica Serovar Typhimurium Reveals a New Toxin-Antitoxin Module

ABSTRACT Bacterial persistence is characterized by the ability of a subpopulation within bacterial cultures to survive exposure to antibiotics and other lethal treatments. The surviving persisters are not the result of genetic changes but represent epigenetic variants that are in a physiological state where growth is inhibited. Since characterization of persisters has been performed mainly in Escherichia coli K-12, we sought to identify mechanisms of persistence in the pathogen Salmonella enterica serovar Typhimurium. Isolation of new highly persistent mutants revealed that the shpAB locus (Salmonella high persistence) imparted a 3- to 4-order-of-magnitude increase in survival after ampicillin exposure throughout its growth phase and protected the population against exposure to multiple antibiotics. Genetic characterization revealed that shpAB is a newly discovered toxin-antitoxin (TA) module. The high-persistence phenotype was attributed to a nonsense mutation in the 3′ end of the shpB gene encoding an antitoxin protein. Characteristic of other TA modules, shpAB is autoregulated, and high persistence depends on the Lon protease.
Genome Sequence and Comparative Pathogenomics Analysis of a Salmonella enterica Serovar Typhi Strain Associated with a Typhoid Carrier in Malaysia

ABSTRACT Salmonella enterica serovar Typhi is a human pathogen that causes typhoid fever predominantly in developing countries. In this article, we describe the whole genome sequence of the S. Typhi strain CR0044 isolated from a typhoid fever carrier in Kelantan, Malaysia. These data will further enhance the understanding of its host persistence and adaptive mechanism.