Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-surgical periodontal therapy with systemic antibiotics in patients with untreated chronic periodontitis: a systematic review and meta-analysis.

OBJECTIVE The purpose of this meta-analysis is to evaluate the effectiveness of different systemic antibiotics in combination with scaling and root planing (SRP) when compared to SRP alone in patients with untreated chronic periodontitis. BACKGROUND Although chronic periodontitis is mostly treated without adjunctive systemic antibiotics, some recent meta-analyses have shown clinical benefit for some systemic antibiotics when used as an adjunct to SRP. However, there is a wide variety of systemic antibiotic regimens used today. It remains unclear if the selected type of systemic antibiotic influences the magnitude of clinical benefit. MATERIAL AND METHODS The MEDLINE-PubMed database was searched from their earliest records through May 16, 2013. Several journals were hand searched and some authors were contacted for additional information. Outcome measures analysed were mean bleeding on probing change, mean clinical attachment level gain and mean probing pocket depth reduction. Extracted data were pooled using a random effect model. Weighted mean differences were calculated and heterogeneity was assessed. RESULTS The search yielded 281 abstracts. Ultimately, 95 studies were selected, describing 43 studies meeting the eligibility criteria. Systemic antibiotics showed a significant (p < 0.05) additional pocket depth reduction for moderate (at 3 mo 0.27 mm ± 0.09, at 6 mo 0.23 mm ± 0.10 and at 12 mo 0.25 mm ± 0.27) and deep pockets (at 3 mo 0.62 mm ± 0.17, at 6 mo 0.58 mm ± 0.16 and at 12 mo 0.74 mm ± 0.30). Statistically, no specific type of antibiotic was superior over another. However, when analysing the clinical data for initially moderate pockets or deep pockets, some trends became apparent. CONCLUSION Systemic antibiotics combined with SRP offer additional clinical improvements compared to SRP alone. Although there were no statistically significant differences, there was a trend that for initially moderate and deep pockets, metronidazole or metronidazole combined with amoxicillin, resulted in clinical improvements that were more pronounced over doxycycline or azithromycin. Additionally, there was a trend that the magnitude of the clinical benefit became smaller over time (1 year).
Bullfrog Ghrelin Is Modified by n-Octanoic Acid at Its Third Threonine Residue*

We have identified the amphibian ghrelin from the stomach of the bullfrog. We also examined growth hormone (GH)-releasing activity of this novel peptide in both the rat and bullfrog. The three forms of ghrelin identified, each comprised of 27 or 28 amino acids, possessed 29% sequence identity to the mammalian ghrelins. A unique threonine at amino acid position 3 (Thr3) in bullfrog ghrelin differs from the serine present in the mammalian ghrelins; this Thr3 is acylated by either n-octanoic or n-decanoic acid. The frog ghrelin-28 has a complete structure of GLT (O-n-octanoyl)FLSPADMQKIAERQSQNKLRHGNM; the structure of frog ghrelin-27 was determined to be GLT(O-n-octanoyl)FLSPADMQKIAERQSQNKLRHGN; frog ghelin-27-C10 possessed a structure of GLT(O-n-decanoyl)FLSPADMQKIAERQSQNKLRHGN. Northern blot analysis demonstrated that ghrelin mRNA is predominantly expressed in the stomach. Low levels of gene expression were observed in the heart, lung, small intestine, gall bladder, pancreas, and testes, as revealed by reverse transcription polymerase chain reaction analysis. Bullfrog ghrelin stimulated the secretion of both GH and prolactin in dispersed bullfrog pituitary cells with potency 2–3 orders of magnitude greater than that of rat ghrelin. Bullfrog ghrelin, however, was only minimally effective in elevating plasma GH levels following intravenous injection into rats. These results indicate that although the regulatory mechanism of ghrelin to induce GH secretion is evolutionary conserved, the structural changes in the different ghrelins result in species-specific receptor binding.
Urological complaints in relation to indinavir plasma concentrations in HIV-infected patients.

OBJECTIVE To assess the relationship between indinavir-associated urological complaints and indinavir plasma concentrations. DESIGN Case series, comparing indinavir plasma concentrations in cases with average concentrations in a control group. METHODS Patients taking 800 mg indinavir three times a day (tid), who presented with overt urological complaints (renal colic, flank pain or haematuria) were selected for the study. Plasma indinavir concentrations were measured by means of a standardized high performance liquid chromatography (HPLC) method. Plasma samples taken at 1.5-8 h after the last indinavir ingestion were included for evaluation. Results were compared with the full pharmacokinetic curves of indinavir plasma concentrations from a control group of 14 patients taking 800 mg indinavir tid without urological complaints, and were expressed as concentration ratios. A ratio of 1 indicated a plasma concentration equalling the average concentration in the control population at the same point in time after the ingestion of indinavir. RESULTS Seventeen patients (five women) were enrolled and the indinavir concentrations of 15 patients could be evaluated. Fourteen (93%) patients had a concentration above the mean of the controls, 12 (80%) patients had a concentration above the upper 95% confidence limit, and one (7%) patient had a concentration below the lower 95% confidence limit. The mean indinavir concentration in patients with urological complaints (ratio range 0.55-11.49) was significantly higher than the average concentration and the upper 95% confidence limit of the control group (P < 0.05). The results could not be explained by differences in weight, sex or drug interactions. Two patients had chronic active hepatitis B infection. In six patients with indinavir concentrations above the upper 95% limit, indinavir was reduced to 600 mg tid. Upon repeat measurement after the dose adjustment, their indinavir plasma concentrations fell within the 95% confidence interval around the mean of the control population. All six patients remained asymptomatic and had viral loads of less than 500 copies per ml after a follow-up of 5-16 months. CONCLUSIONS Urological complications occurring during indinavir treatment were associated with elevated indinavir plasma concentrations in 80% of patients in this study. Indinavir plasma concentrations should be monitored upon presentation of urological complaints, on the basis of which dose reductions may be applied if brief interruption and increased hydration are ineffective.
Phosphate homeostasis, parathyroid hormone, and fibroblast growth factor 23 in stages 3 and 4 chronic kidney disease.

AIMS Increased concentrations of parathyroid hormone (PTH) and fibroblast growth factor 23 (FGF23) often coincide with normal serum phosphorus ([P]s) in chronic kidney disease (CKD). We hypothesized that the phosphate concentration ([P]f) in the cortical distal nephron (CDN) determines [PTH] and [FGF23] in this circumstance. METHODS We studied 29 patients with CKD at 4 visits and 28 controls at 1 visit. Assuming GFR = creatinine clearance (Ccr), we examined the following regressions: [P]s on its determinants, EP/Ccr and TRP/Ccr (P excretion and reabsorption per volume of filtrate); [PTH] and [FGF23] on [P]s and EP/Ccr; and TRP/Ccr on [PTH] and [FGF23]. We assumed that EP/Ccr is proportional to [P]f in the CDN. RESULTS In controls, [P]s correlated with TRP/Ccr but not EP/Ccr. [PTH] and [FGF23] were unrelated to [P]s, EP/Ccr, and TRP/Ccr. In CKD, [P]s correlated with EP/Ccr and TRP/Ccr. [PTH] correlated with [P]s at 2 visits and with EP/Ccr at 4; [FGF23] correlated with [P]s and EP/Ccr at all visits. TRP/Ccr correlated with [FGF23] and [PTH] at one visit each. CONCLUSIONS [P]f in the CDN, not [P]s, determined [PTH] in CKD. Because [FGF23] was consistently associated with only one determinant of [P]s, EP/Ccr, we infer that [P]f also determined [FGF23]. In patients with CKD, we speculate that [P]f in the CDN regulates FGF23 synthesis at that site.
Determinants of the Hepatitis C Virus Nonstructural Protein 2 Protease Domain Required for Production of Infectious Virus

ABSTRACT The hepatitis C virus (HCV) nonstructural protein 2 (NS2) is a dimeric multifunctional hydrophobic protein with an essential but poorly understood role in infectious virus production. We investigated the determinants of NS2 function in the HCV life cycle. On the basis of the crystal structure of the postcleavage form of the NS2 protease domain, we mutated conserved features and analyzed the effects of these changes on polyprotein processing, replication, and infectious virus production. We found that mutations around the protease active site inhibit viral RNA replication, likely by preventing NS2-3 cleavage. In contrast, alterations at the dimer interface or in the C-terminal region did not affect replication, NS2 stability, or NS2 protease activity but decreased infectious virus production. A comprehensive deletion and mutagenesis analysis of the C-terminal end of NS2 revealed the importance of its C-terminal leucine residue in infectious particle production. The crystal structure of the NS2 protease domain shows that this C-terminal leucine is locked in the active site, and mutation or deletion of this residue could therefore alter the conformation of NS2 and disrupt potential protein-protein interactions important for infectious particle production. These studies begin to dissect the residues of NS2 involved in its multiple essential roles in the HCV life cycle and suggest NS2 as a viable target for HCV-specific inhibitors.
Contextual Inhibitory Gating of Impulse Traffic in the Intra‐amygdaloid Network

Abstract: New data on the organization of the intra‐amygdaloid circuit is reviewed, beginning with the basolateral (BL) complex, the main input station of the amygdala for sensory afferents, and concluding with the central (CE) nucleus, an important source of projections to brain‐stem structures mediating fear responses. The BL complex is endowed with a highly divergent system of intrinsic glutamatergic connections. Yet, BL projection cells have unusually low firing rates. This apparent contradiction is explained by the presence of powerful inhibitory pressures in the BL amygdala: (1) interneurons that generate large‐amplitude inhibitory synaptic potentials and (2) projection cells that express a Ca2+‐dependent K+ current that can be activated by subthreshold synaptic inputs. Likewise, excitatory projections from the BL amygdala to the CE nucleus are controlled by clusters of GABAergic neurons, termed the intercalated (ITC) cell masses. In response to BL inputs, ITC cells generate feedforward inhibition in CE neurons. However, ITC neurons exhibit properties that allow them to modify the amount of inhibition they generate depending on the distribution of BL activity in space and time. Indeed, ITC cell masses can inhibit each other via lateromedial connections. Moreover, they express an unusual K+ conductance that modifies their response to BL inputs depending on their recent firing history. Thus, inhibitory mechanisms of the amygdala allow for flexible, context‐dependent gating of BL impulses to the CE nucleus.
Activated Mucosal Mast Cells Differentiate Eosinophilic (Allergic) Esophagitis From Gastroesophageal Reflux Disease

Objectives: To evaluate the utility of activated mucosal mast cells (MC) in the differential diagnosis of eosinophilic esophagitis (EE) and gastroesophageal reflux disease (GERD). Methods: Intraepithelial eosinophils and MC were quantified in esophageal biopsies from 25 children with EE, 22 children with GERD and 22 controls. MCs were identified by immunohistochemistry for MC tryptase, whereas MC activation status was evaluated by immunohistochemistry for immunoglobulin E (IgE) and by electron microscopy. Results: Esophageal biopsies from patients with EE showed higher intraepithelial eosinophil counts (55 ± 27.5 vs 6.9 ± 9.7, P < 0.0001) and MC counts (26.3 ± 12.7 vs 7.8 ± 8.9, P < 0.0001) than those from patients with GERD. Almost all EE biopsies (24 of 25 patients; 96%) contained IgE-bearing cells compared with 9 of 22 (41%) GERD biopsies (P < 0.001). GERD biopsies with intraepithelial eosinophil counts >7/high-power field (suggesting an allergic component) contained IgE-bearing cells in 6 of 7 (86%) cases compared to 3 of 15 (20%) cases with eosinophil counts <7/h.p.f (P < 0.01). No intraepithelial eosinophils, MC or IgE-positive cells were present in controls. Electron microscopy confirmed the presence of intraepithelial MC and changes in cytoplasmic granules indicative of MC and eosinophil activation. Conclusions: Intraepithelial MC counts and IgE-bearing cells may help to differentiate EE and GERD and to define a subset of GERD patients in which an allergic component is present. The findings support a role for a MC-mediated hypersensitivity reaction in the pathogenesis of EE.
The hydration structure of guanidinium and thiocyanate ions: Implications for protein stability in aqueous solution

Neutron diffraction experiments were carried out on aqueous solutions containing either guanidinium or thiocyanate ions. The first-order difference method of neutron diffraction and isotopic substitution was applied, and the hydration structures of two of nature's strongest denaturant ions were determined. Each ion is shown to interact weakly with water: Guanidinium has no recognizable hydration shell and is one of the most weakly hydrated cations yet characterized. Hydration of thiocyanate is characterized by a low coordination number involving around one hydrogen-bonded water molecule and approximately two water molecules weakly interacting through “hydration bonds. ” The weak hydration of these denaturant ions strongly supports suggestions that a major contribution to the denaturant effect is the preferential interaction of the denaturant with the protein surface. By contrast, solute species such as many sugars and related polyols that stabilize proteins are strongly hydrated and are thus preferentially retained in the bulk solvent and excluded from the protein surface.
LINE-1 ORF1 Protein Localizes in Stress Granules with Other RNA-Binding Proteins, Including Components of RNA Interference RNA-Induced Silencing Complex

ABSTRACT LINE-1 retrotransposons constitute one-fifth of human DNA and have helped shape our genome. A full-length L1 encodes a 40-kDa RNA-binding protein (ORF1p) and a 150-kDa protein (ORF2p) with endonuclease and reverse transcriptase activities. ORF1p is distinctive in forming large cytoplasmic foci, which we identified as cytoplasmic stress granules. A phylogenetically conserved central region of the protein is critical for wild-type localization and retrotransposition. Yeast two-hybrid screens revealed several RNA-binding proteins that coimmunoprecipitate with ORF1p and colocalize with ORF1p in foci. Two of these proteins, YB-1 and hnRNPA1, were previously reported in stress granules. We identified additional proteins associated with stress granules, including DNA-binding protein A, 9G8, and plasminogen activator inhibitor RNA-binding protein 1 (PAI-RBP1). PAI-RBP1 is a homolog of VIG, a part of the Drosophila melanogaster RNA-induced silencing complex (RISC). Other RISC components, including Ago2 and FMRP, also colocalize with PAI-RBP1 and ORF1p. We suggest that targeting ORF1p, and possibly the L1 RNP, to stress granules is a mechanism for controlling retrotransposition and its associated genetic and cellular damage.
Rapid determination of enzyme activities of recombinant human cytochromes P450, human liver microsomes and hepatocytes

Cytochrome P450 (CYP) substrates that yield fluorescent metabolites were used for rapid screening of drug metabolism activities of 13 recombinant human cytochromes P450, human liver microsomes and human hepatocytes. Reproducible results were obtained using a fluorescent plate reader (CytoFluor) more expediently than those generated using conventional HPLC methods. Typically, results for 96 samples were obtained with the plate reader in less than 10 min as opposed to 15–35 min/sample required by conventional HPLC. The fluorescent substrates used to measure CYP activities were as follows: 3‐cyano‐7‐ethoxycoumarin (CEC) for CYP1A1, CYP1A2, CYP2C9 and CYP2C19; 7‐ethoxyresorufin (7‐ER) for CYP1A1, CYP1A2 and CYP1B1; 3‐[2‐(N,N‐diethyl‐N‐methylammonium)ethyl]‐7‐methoxy‐4‐methylcoumarin (AMMC) for CYP2D6; dibenzylfluorescein (DBF) for CYP3A4, CYP3A5 and CYP2C8; 7‐methoxy‐4‐trifluoromethylcoumarin (7‐MFC) for CYP2E1, CYP2B6 and CYP2C18; and coumarin for CYP2A6. The chemical inhibition and correlation data indicated that the following substrates can be used as specific functional probes for individual cytochrome P450 present in human liver microsomes: coumarin for CYP2A6 (r=0.82), AMMC for CYP2D6 (r=0.83) and DBF for CYP3A4 (r=0.92). The fluorescent plate reader was found to be useful for the rapid assessment of CYP activities (positive control) in both intact cells and subcellular fractions. Copyright © 2003 John Wiley & Sons, Ltd.
Crystals of the urokinase type plasminogen activator variant beta(c)-uPAin complex with small molecule inhibitors open the way towards structure-based drug design.

Urokinase is a serine protease involved in cancer growth and metastasis. Here we present the first urokinase crystal structure in complex with reversible inhibitors at 2.1 and 2.6 A resolution. These inhibitor complex structures have been obtained from crystals of engineered urokinase type plasminogen activator designed to obtain a crystal form open for inhibitor soaking. The mutant C122S loses its flexible A-chain upon activation cleavage and crystallizes in the presence of benzamidine, which was later displaced by the desired inhibitor. This new soakable crystal form turned out to be of great value in the process of structure-based drug design. The evaluated binding mode of amiloride, and UKI-1D revealed a new subsite of the primary specificity pocket of urokinase that will be employed in the future ligand optimisation process.
The Yaa Mutation Promoting Murine Lupus Causes Defective Development of Marginal Zone B Cells1

The accelerated development of systemic lupus erythematosus (SLE) in BXSB male mice is associated with the presence of an as yet unidentified mutant gene, Yaa (Y-linked autoimmune acceleration). In view of a possible role of marginal zone (MZ) B cells in murine SLE, we have explored whether the expression of the Yaa mutation affects the differentiation of MZ and follicular B cells, thereby implicating the acceleration of the disease. In this study, we show that both BXSB and C57BL/6 Yaa mice, including two different substrains of BXSB Yaa males that are protected from SLE, displayed an impaired development of MZ B cells early in life. Studies in bone marrow chimeras revealed that the loss of MZ B cells resulted from a defect intrinsic to B cells expressing the Yaa mutation. The lack of selective expansion of MZ B cells in diseased BXSB Yaa males strongly argues against a major role of MZ B cells in the generation of pathogenic autoantibodies in the BXSB model of SLE. Furthermore, a comparative analysis with mice deficient in CD22 or expressing an IgM anti-trinitrophenyl/DNA transgene suggests that the hyperreactive phenotype of Yaa B cells, as judged by a markedly increased spontaneous IgM secretion, is likely to contribute to the enhanced maturation toward follicular B cells and the block in the MZ B cell generation.
Regulation of G Protein-coupled Receptor Kinases by Calmodulin and Localization of the Calmodulin Binding Domain*

G protein-coupled receptor kinases (GRKs) specifically phosphorylate and regulate the activated form of multiple G protein-coupled receptors. Recent studies have revealed that GRKs are also subject to regulation. In this regard, GRK2 and GRK5 can be phosphorylated and either activated or inhibited, respectively, by protein kinase C. Here we demonstrate that calmodulin, another mediator of calcium signaling, is a potent inhibitor of GRK activity with a selectivity for GRK5 (IC50 ∼50 nm) > GRK6 ≫ GRK2 (IC50 ∼2 μm) ≫ GRK1. Calmodulin inhibition of GRK5 is mediated via a reduced ability of the kinase to bind to both receptor and phospholipid. Interestingly, calmodulin also activates autophosphorylation of GRK5 at sites distinct from the two major autophosphorylation sites on GRK5. Moreover, calmodulin-stimulated autophosphorylation directly inhibits GRK5 interaction with receptor even in the absence of calmodulin. Using glutathione S-transferase-GRK5 fusion proteins either to inhibit calmodulin-stimulated autophosphorylation or to bind directly to calmodulin, we determined that an amino-terminal domain of GRK5 (amino acids 20–39) is sufficient for calmodulin binding. This domain is abundant in basic and hydrophobic residues, characteristics typical of calmodulin binding sites, and is highly conserved in GRK4, GRK5, and GRK6. These studies suggest that calmodulin may serve a general role in mediating calcium-dependent regulation of GRK activity.
Gas uptake and chemical aging of semisolid organic aerosol particles

Organic substances can adopt an amorphous solid or semisolid state, influencing the rate of heterogeneous reactions and multiphase processes in atmospheric aerosols. Here we demonstrate how molecular diffusion in the condensed phase affects the gas uptake and chemical transformation of semisolid organic particles. Flow tube experiments show that the ozone uptake and oxidative aging of amorphous protein is kinetically limited by bulk diffusion. The reactive gas uptake exhibits a pronounced increase with relative humidity, which can be explained by a decrease of viscosity and increase of diffusivity due to hygroscopic water uptake transforming the amorphous organic matrix from a glassy to a semisolid state (moisture-induced phase transition). The reaction rate depends on the condensed phase diffusion coefficients of both the oxidant and the organic reactant molecules, which can be described by a kinetic multilayer flux model but not by the traditional resistor model approach of multiphase chemistry. The chemical lifetime of reactive compounds in atmospheric particles can increase from seconds to days as the rate of diffusion in semisolid phases can decrease by multiple orders of magnitude in response to low temperature or low relative humidity. The findings demonstrate that the occurrence and properties of amorphous semisolid phases challenge traditional views and require advanced formalisms for the description of organic particle formation and transformation in atmospheric models of aerosol effects on air quality, public health, and climate.
Eya‐six are necessary for survival of nephrogenic cord progenitors and inducing nephric duct development before ureteric bud formation

Background: Specification of the metanephric mesenchyme is a central step of kidney development as this mesenchyme promotes nephric duct induction to form a ureteric bud near its caudal end. Before ureteric bud formation, the caudal nephric duct swells to form a pseudostratified epithelial domain that later emerges as the tip of the bud. However, the signals that promote the formation of the transient epithelial domain remain unclear. Here, we investigated the early roles of the mesenchymal factor Six family and its cofactor Eya on the initial induction of nephric duct development.
Analysis of an adaptive observer for sensorless control of PMSM drives

The paper deals with a speed and position estimation method for the sensorless control of permanent magnet synchronous motors. The method is based on a speed-adaptive flux observer augmented with a high-frequency signal injection method at low speeds. The dynamics of the adaptive observer are analyzed by linearizing both the motor model and the observer, and the observer gain is selected to give improved damping and noise suppression. The experimental results are in agreement with the results of the analysis.