Structural and Serological Characterization of Yet Another New O Antigen, O86, in Clinical Strains.

Bacteria from the genus are facultative human pathogens, primarily attacking the urinary tract and wounds. A total of 85 O serogroups have been identified so far among these bacilli. Bprz 86 was isolated from the fistula of a patient in Łódź, Poland.

Electron delocalization in defect-containing graphene and its influence on tetrel bond formation.

Using the advanced analyses of electron density and fermionic potential, we show how electron delocalization influences the ability of defect-containing graphene to form tetrel bonds. The C atoms of a vacancy defect can produce one nonpolar interaction, alongside a peculiar polar C⋯C bond. The latter stems from the presence of a localized electron pair on a vacancy defect C atom and the local depletion of electron localization on another C atom.

[Peculiarities of CI processor fitting in children with auditory neuropathy spectrum disorders].

The peculiarities of cochlear implant (CI) processor fitting in children with auditory neuropathy spectrum disorders (ANSD) were investigated. At the 1-st fitting of the CI processor a standard protocol of parameters was used in all patients, including patients with cochlear nerve hypoplasia. After the initial fitting session, the behavioral tonal thresholds with CI in 55% of patients were 30-35 dB, in 32.

DFT potentials from a chemical perspective: Anatomy of electron (de)localization in molecules and crystals.

We introduce a fermionic potential, , as a comprehensive measure of electron (de)localization in atomic-molecular systems. Unlike other common descriptors as ELF, LOL, etc., it characterizes all physical effects responsible for (de)localization of electrons, namely: an exchange hole depth, its tendency to change, a sensitivity of an exchange correlation hidden in a pair density and kinetic potential to local variations in electron density.

Structural and Serological Characterization of the O Antigen of Clinical Isolates Classified into a New Serogroup, O84.

Two closely related smooth strains, Kr1 and Ks20, were isolated from wound and skin samples, respectively, of two infected patients in central Poland. Serological tests, using the rabbit Kr1-specific antiserum, revealed that both strains presented the same O serotype. Their O antigens are unique among the O serotypes, which had been described earlier, as they were not recognized in an enzyme-linked immunosorbent assay (ELISA) by a set of O1-O83 antisera.

Depletion of COPI in cancer cells: the role of reactive oxygen species in the induction of lipid accumulation, noncanonical lipophagy and apoptosis.

The coatomer protein complex 1 (COPI) is a multisubunit complex that coats intracellular vesicles and is involved in intracellular protein trafficking. Recently we and others found that depletion of COPI complex subunits zeta (COPZ1) and delta (ARCN1) preferentially kills tumor cells relative to normal cells. Here we delineate the specific cellular effects and sequence of events of COPI complex depletion in tumor cells.

Keto-enol tautomerism from the electron delocalization perspective.

The equilibrium between keto and enol forms in acetylacetone and its derivatives is studied using electron delocalization indices and delocalization tensor density. We demonstrate how electron delocalization governs the equilibrium between keto and enol forms. The less stable enols have more distinct double and single bond character in the CCC fragment, while electron delocalization in this fragment is more pronounced in more stable enols.

Metallo-β-Lactamases: Influence of the Active Site Structure on the Mechanisms of Antibiotic Resistance and Inhibition.

The review focuses on bacterial metallo-β-lactamases (MβLs) responsible for the inactivation of β-lactams and associated antibiotic resistance. The diversity of the active site structure in the members of different MβL subclasses explains different mechanisms of antibiotic hydrolysis and should be taken into account when searching for potential MβL inhibitors. The review describes the features of the antibiotic inactivation mechanisms by various MβLs studied by X-ray crystallography, NMR, kinetic measurements, and molecular modeling.

The explicit role of electron exchange in the hydrogen bonded molecular complexes.

We applied a set of advanced bonding descriptors to establish the hidden electron density features and binding energy characteristics of intermolecular DH∙∙∙A hydrogen bonds (OH∙∙∙O, NH∙∙∙O and SH∙∙∙O) in 150 isolated and solvated molecular complexes. The exchange-correlation and Pauli potentials as well as corresponding local one-electron forces allowed us to explicitly ascertain how electron exchange defines the bonding picture in the proximity of the H-bond critical point. The electron density features of DH∙∙∙A interaction are governed by alterations in the electron localization in the H-bond region displaying itself in the exchange hole.

The unique structure of bacterial polysaccharides - Immunochemical studies on the O-antigen of Proteus penneri 4034-85 clinical strain classified into a new O83 Proteus serogroup.

The serological classification scheme of the opportunistic Proteus bacilli includes a number of Proteus penneri strains. The tested P. penneri 4034-85 strain turned out to be serologically distinguished in ELISA and Western blotting.

Revealing electronic features governing hydrolysis of cephalosporins in the active site of the L1 metallo-β-lactamase.

The QM/MM simulations followed by electron density feature analysis are carried out to deepen the understanding of the reaction mechanism of cephalosporin hydrolysis in the active site of the L1 metallo-β-lactamase. The differences in reactivity of ten similar cephalosporin compounds are explained by using an extended set of bonding descriptors. The limiting step of the reaction is characterized by the proton transfer to the nitrogen atom of the cephalosporin thiazine ring accompanied with formation of the C[double bond, length as m-dash]C double bond in its N-C-C fragment.

Structural and serological characterization of the O82 antigen of a Proteus mirabilis strain isolated from a patient in Poland.

P. mirabilis strains Kro 45 and Kwy 46 were isolated from the pus and the muscular fluid, respectively, of a hospitalized 61-year-old female in Łódź, Poland. Both strains demonstrated a good swarming ability on a solid medium, and the Dienes test for differentiation of swarming strains indicated their identity.

NETWORK CLASSIFICATION WITH APPLICATIONS TO BRAIN CONNECTOMICS.

While statistical analysis of a single network has received a lot of attention in recent years, with a focus on social networks, analysis of a sample of networks presents its own challenges which require a different set of analytic tools. Here we study the problem of classification of networks with labeled nodes, motivated by applications in neuroimaging. Brain networks are constructed from imaging data to represent functional connectivity between regions of the brain, and previous work has shown the potential of such networks to distinguish between various brain disorders, giving rise to a network classification problem.

Solving the enigma of weak fluorine contacts in the solid state: a periodic DFT study of fluorinated organic crystals.

The nature and strength of weak interactions with organic fluorine in the solid state are revealed by periodic density functional theory (periodic DFT) calculations coupled with experimental data on the structure and sublimation thermodynamics of crystalline organofluorine compounds. To minimize other intermolecular interactions, several sets of crystals of perfluorinated and partially fluorinated organic molecules are considered. This allows us to establish the theoretical levels providing an adequate description of the metric and electron-density parameters of the C-F⋯F-C interactions and the sublimation enthalpy of crystalline perfluorinated compounds.

Basic Units of Inter-Individual Variation in Resting State Connectomes.

Resting state functional connectomes are massive and complex. It is an open question, however, whether connectomes differ across individuals in a correspondingly massive number of ways, or whether most differences take a small number of characteristic forms. We systematically investigated this question and found clear evidence of low-rank structure in which a modest number of connectomic components, around 50-150, account for a sizable portion of inter-individual connectomic variation.

Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac.

Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level.

Steroid Sulfates from Ophiuroids (Brittle Stars): Action on Some Factors of Innate and Adaptive Immunity.

The action of seven polyhydroxylated sterol mono- and disulfates (1-7), isolated from ophiuroids, on innate and adaptive immunity was examined in in vitro and in vivo experiments. At least, three of them (1, 2 and 4) increased the functional activities of neutrophils, including levels of oxygen-dependent metabolism, adhesive and phagocytic properties, and induced the expression of pro-inflammatory cytokines TNF-α and IL-8. Compound 4 was the most active for enhancing the production of antibody forming cells in the mouse spleen.

ESTIMATING HETEROGENEOUS GRAPHICAL MODELS FOR DISCRETE DATA WITH AN APPLICATION TO ROLL CALL VOTING.

We consider the problem of jointly estimating a collection of graphical models for discrete data, corresponding to several categories that share some common structure. An example for such a setting is voting records of legislators on different issues, such as defense, energy, and healthcare. We develop a Markov graphical model to characterize the heterogeneous dependence structures arising from such data.

Graphical Models for Ordinal Data.

A graphical model for ordinal variables is considered, where it is assumed that the data are generated by discretizing the marginal distributions of a latent multivariate Gaussian distribution. The relationships between these ordinal variables are then described by the underlying Gaussian graphical model and can be inferred by estimating the corresponding concentration matrix. Direct estimation of the model is computationally expensive, but an approximate EM-like algorithm is developed to provide an accurate estimate of the parameters at a fraction of the computational cost.

Identification of novel genes that regulate androgen receptor signaling and growth of androgen-deprived prostate cancer cells.

Prostate cancer progression to castration refractory disease is associated with anomalous transcriptional activity of the androgen receptor (AR) in an androgen-depleted milieu. To identify novel gene products whose downregulation transactivates AR in prostate cancer cells, we performed a screen of enzymatically-generated shRNA lenti-libraries selecting for transduced LNCaP cells with elevated expression of a fluorescent reporter gene under the control of an AR-responsive promoter. The shRNAs present in selected populations were analyzed using high-throughput sequencing to identify target genes.

Classification of a Proteus penneri clinical isolate with a unique O-antigen structure to a new Proteus serogroup, O80.

Proteus penneri is an opportunistic pathogen, which may cause severe diseases, most frequently urinary tract infections in immunocompromised patients. P. penneri Br 114 exhibiting a good swarming growth ability as an S-form strain was isolated from a wound of a patient in Łódź, Poland.

[A role of neuroprotective therapy in the rehabilitation of children with sensorineural hearing loss, IV degrees, after cochlear implanta-tion].

Objective: To study clinical/psychological characteristics in children with sensorineural hearing loss, IV degrees, before and after the cochlear implantation (CI) and to assess the dynamics of speech development during the rehabilitation using the neuroprotective drug cerebrolysin.

Material And Methods: Authors examined 93 patients, aged from 5 to 8 years. The main group (n=46) received cerebrolysin, the control group was not treated with this drug.

A sparse Ising model with covariates.

There has been a lot of work fitting Ising models to multivariate binary data in order to understand the conditional dependency relationships between the variables. However, additional covariates are frequently recorded together with the binary data, and may influence the dependence relationships. Motivated by such a dataset on genomic instability collected from tumor samples of several types, we propose a sparse covariate dependent Ising model to study both the conditional dependency within the binary data and its relationship with the additional covariates.

Structure and gene cluster of the O-antigen of Escherichia coli O36.

The O-polysaccharide (O-antigen) of Escherichia coli O36 was isolated from the lipopolysaccharide and studied by sugar analyses and Smith degradation along with (1)H and (13)C NMR spectroscopy. The following structure of the branched pentasaccharide repeating unit was established, which is unique among the known structures of bacterial polysaccharides: The O-antigen gene cluster of E. coli O36 has been sequenced.

[Steroidal compounds from the Pacific starfish Mithrodia clavigera and their toxic properties against human melanoma cells].

The new sulfated polyhydroxysteroid has been isolated from the Pacific starfish Mithrodia clavigera, collected from Maldives Islands and named as mitrotriol (I, Na-salt of (20S)-3beta,6alpha,20-trihydroxy-5alpha-cholest-9(11)-ene 3-O-sulfate). In addition six previously known compounds, including glycosides: echinasteroside B, granulatoside A, linckoside K, forbeside L and thornasterol sulfate A and cholesterol sulfate were isolated and identified. The structure of mitrotriol was elucidated by spectroscopic methods (mainly 2D NMR: 1H, 13C, DEPT, COSY-45, NOESY, HSQC and HMBC) and mass-spectrometry.