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Biomedical subjects

R Orlando

Publications and source records attributed to R Orlando.

At least 19 recordsLinked to original sources
PubMed2006

Vibrational spectrum of katoite Ca3Al2[(OH)4]3: a periodic ab initio study.

The vibrational spectrum of the Si-free katoite hydrogarnet (116 atoms in the unit cell) has been calculated at the periodic ab initio quantum mechanical level with the CRYSTAL program, by using a Gaussian type basis set and the hybrid B3LYP Hamiltonian. The harmonic frequencies at the Gamma point have been obtained by diagonalizing the mass-weighted Hessian matrix, that is evaluated by numerical differentiation of the analytical first derivatives of the energy with respect to the atomic Cartesian coordinates. The parameters controlling the numerical differentiation, as well as the numerical integration of the exchange-correlation functional for the self-consistent field (SCF) calculation, are shown to affect the obtained frequencies by less than 3 cm-1. Before diagonalization, the dynamical matrix is transformed to a block diagonal form according to the irreducible representations of the point group, so that the 345 vibrational modes are automatically classified by symmetry. Various tools are adopted (graphical representation, isotopic substitution, "freezing" part of the unit cell) that permit a complete classification of normal modes and, in particular, an analysis of the modes in terms of simple models (octahedra modes, Ca modes, H stretching, bending, rotations). The harmonic OH stretching band (48 modes) is quite narrow (20 cm-1), indicating that the interaction among OH groups is very weak. As the OH stretching modes are known to be totally separable from the other modes and strongly anharmonic, the one-dimensional Schroedinger equation for the anharmonic oscillator is solved numerically for the two extreme situations, corresponding to the vibration of one decoupled OH and of all 48 OH groups moving in phase. The anharmonic frequencies are 3682 and 3673 cm-1, respectively, in good agreement with IR experiments (a single band at 3661 cm-1 with a width at half band height of 33 cm-1) and confirming that the interaction between OH groups is extremely weak.

Journal Article↗
PubMed2006

Severe reactivation of hepatitis B virus infection in a patient with hairy cell leukemia: Should lamivudine prophylaxis be recommended to HBsAg-negative, anti-HBc-positive patients?

The reverse seroconversion to hepatitis B virus infection has been sporadically described in onco-haematological patients receiving cytotoxic therapy or allogeneic bone marrow transplantation and can be associated with the development of acute icteric hepatitis. We present a male HBsAg-negative, anti-HBc-positive patient with Hairy Cell Leukemia who developed acute B hepatitis more than 1 year after the last course of 2-CdA and 6 months after splenectomy, while the patient was receiving therapy with alphaIFNr. The acute B hepatitis promptly responded to lamivudine therapy followed by viral clearance.

Aged↗
PubMed2005

Analysis of the SAGES outcomes initiative cholecystectomy registry.

BACKGROUND: In 1999, the Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) introduced the SAGES Outcomes Initiative as a method for its members to use for tracking their own outcomes. This report provides a descriptive analysis of the cholecystectomy database. METHODS: The SAGES Outcome Initiative database was accessed for all gallbladder cases from September 1999 to February 2005. The data from the preoperative, intraoperative, and postoperative entries were summarized. These data are purely descriptive, and no statistical analysis was performed. RESULTS: The gallbladder registry contained 3,285 cases, with 2,005 follow-up cases. Most patients were employed women with some comorbidities who had elective surgery under general anesthesia. Most of the operating surgeons were attending surgeons and surgical assistants. Most of the patients had biliary colic, and symptoms were improved for more than 95% of the patients. More than 90% of the cases were managed laparoscopically, with a conversion rate of 3%. Biliary imaging was used in the vast majority of cases, with most shown to be normal. Intraoperative gallbladder perforation was common, with bile duct injury occurring in 0.25% of cases. The most frequently cited postoperative event was wound infection, with most complications classified as class 1. More than 95% of the patients were able to return to work. CONCLUSIONS: The SAGES Outcomes Initiative database demonstrates that most participating SAGES members perform laparoscopic cholecystectomies themselves using intraoperative cholangiograms. Adverse outcomes are few, with most patients able to return to normal activity. Importantly, there were relatively few missing data points, implying that when surgeons enter data, the information is relatively complete.

Cholangiography↗
PubMed2005

Vibration frequencies of Ca3Fe2Si3O12 andradite: an ab initio study with the CRYSTAL code.

The vibrational spectrum of Ca3Fe2Si3O12 andradite is calculated at the Gamma point by using the periodic ab initio CRYSTAL program that adopts an all-electron Gaussian-type basis set and the B3LYP Hamiltonian. The full set of frequencies (17 IR active, 25 Raman active, and 55 inactive modes) is calculated. The effect of the basis set on the calculated frequencies is discussed. The modes are characterized by direct inspection of the eigenvectors and isotopic substitution. The present calculations permit us to clarify some of the assignment problems raised by experiments. The mean absolute differences of the various modes with respect to the available experimental IR and Raman data are as small as 9 and 5 cm(-1), respectively.

Journal Article↗
PubMed2005

The Trypanosoma cruzi proteome.

To complement the sequencing of the three kinetoplastid genomes reported in this issue, we have undertaken a whole-organism, proteomic analysis of the four life-cycle stages of Trypanosoma cruzi. Peptides mapping to 2784 proteins in 1168 protein groups from the annotated T. cruzi genome were identified across the four life-cycle stages. Protein products were identified from >1000 genes annotated as "hypothetical" in the sequenced genome, including members of a newly defined gene family annotated as mucin-associated surface proteins. The four parasite stages appear to use distinct energy sources, including histidine for stages present in the insect vectors and fatty acids by intracellular amastigotes.

Adaptation, Physiological↗
PubMed2004

Calculation of the vibration frequencies of alpha-quartz: the effect of Hamiltonian and basis set.

The central-zone vibrational spectrum of alpha-quartz (SiO2) is calculated by building the Hessian matrix numerically from the analytical gradients of the energy with respect to the atomic coordinates. The nonanalytical part is obtained with a finite field supercell approach for the high-frequency dielectric constant and a Wannier function scheme for the evaluation of Born charges. The results obtained with four different Hamiltonians, namely Hartree-Fock, DFT in its local (LDA) and nonlocal gradient corrected (PBE) approximation, and hybrid B3LYP, are discussed, showing that B3LYP performs far better than LDA and PBE, which in turn provide better results than HF, as the mean absolute difference from experimental frequencies is 6, 18, 21, and 44 cm(-1), respectively, when a split valence basis set containing two sets of polarization functions is used. For the LDA results, comparison is possible with previous calculations based on the Density Functional Perturbation Theory and usage of a plane-wave basis set. The effects associated with the use of basis sets of increasing size are also investigated. It turns out that a split valence plus a single set of d polarization functions provides frequencies that differ from the ones obtained with a double set of d functions and a set of f functions on all atoms by on average less than 5 cm(-1).

Journal Article↗
PubMed2004

The katoite hydrogarnet Si-free Ca3Al2([OH]4)3: a periodic Hartree-Fock and B3-LYP study.

The structure of the Si-free katoite hydrogarnet (116 atoms in the unit cell) has been investigated at the periodic ab initio quantum mechanical level with the CRYSTAL program, by using a Gaussian type basis set and both the HF and the hybrid B3-LYP Hamiltonians. The structure has been fully optimized at various pressures in the 0-46 GPa range; the modifications of the structure, and in particular of the (OH)4 group, as a function of pressure are analyzed. At the B3-LYP level and P greater than 15 GPa, a O-H...O interaction of increasing strength appears, with important modifications in the local geometry of the tetrahedral site. The calculated omega01(O-H) fundamental vibrational frequency at zero pressure is in excellent agreement with experiment (3674 and 3663 cm(-1), respectively); the omega01(O-H) stretching frequency remains essentially constant in the 0-15 GPa interval, whereas it dramatically decreases at higher pressures with a corresponding anharmonicity increase, as a consequence of the formation of a strong hydrogen bond. The hydration energy of grossular and the formation energy of Si-free katoite have also been computed, and the B3-LYP results are in quite good agreement with experiment.

Journal Article↗
PubMed2004

The calculation of the vibrational frequencies of crystalline compounds and its implementation in the CRYSTAL code.

The problem of numerical accuracy in the calculation of vibrational frequencies of crystalline compounds from the hessian matrix is discussed with reference to alpha-quartz (SiO(2)) as a case study and to the specific implementation in the CRYSTAL code. The Hessian matrix is obtained by numerical differentiation of the analytical gradient of the energy with respect to the atomic positions. The process of calculating vibrational frequencies involves two steps: the determination of the equilibrium geometry, and the calculation of the frequencies themselves. The parameters controlling the truncation of the Coulomb and exchange series in Hartree-Fock, the quality of the grid used for the numerical integration of the Exchange-correlation potential in Density Functional Theory, the SCF convergence criteria, the parameters controlling the convergence of the optimization process as well as those controlling the accuracy of the numerical calculation of the Hessian matrix can influence the obtained vibrational frequencies to some extent. The effect of all these parameters is discussed and documented. It is concluded that with relatively economical computational conditions the uncertainty related to these parameters is smaller than 2-4 cm(-1). In the case of the Local Density Approximation scheme, comparison is possible with recent calculations performed with a Density Functional Perturbation Theory method and a plane-wave basis set.

Journal Article↗
PubMed2004

Bile leakage and resultant bile peritonitis during or after diagnostic laparoscopy: an unpredictable event.

Bile peritonitis secondary to bile leakage is a rare complication of laparoscopy-guided liver biopsy. We report two cases of bile peritonitis occurring, respectively, during and 6 days after liver biopsy in patients with an initial diagnosis of intrahepatic cholestasis associated with chronic pancreatitis. In both cases, bile leakage was first managed by compression with a palpating probe and, at onset or worsening of symptoms, by suture during laparotomy. However, while the first patient progressed uneventfully during the postoperative period, the second died 13 days after laparotomy. In the latter patient, bile leakage was associated with bleeding from the biopsy site with consequently diminished peritoneal irritation and delayed onset of symptoms. In this patient, pancreatic carcinoma, of which evidence was found at autopsy, may also have contributed to the fatal outcome. In conclusion, bile leakage and secondary peritonitis may also occur in the absence of dilation of the biliary tree and may be fatal, especially if not recognized and treated early.

Adult↗
PubMed2002

Impairment of albumin and whole body postprandial protein synthesis in compensated liver cirrhosis.

To investigate the anabolic effects of feeding in cirrhosis, we measured albumin fractional synthesis rate (FSR) and whole body protein synthesis in six nondiabetic patients with stable liver cirrhosis (three in the Child-Pugh classification Class A, three in Class B) and in seven normal control subjects, before and after administration of a 4-h mixed meal. Leucine tracer precursor-product relationships and whole body kinetics were employed at steady state. Basal levels of postabsorptive albumin concentration and FSR, whole body leucine rate of appearance, oxidation, and nonoxidative leucine disposal (NOLD, approximately equal to protein synthesis) were similar in the two groups. However, after the meal, in the patients neither albumin FSR (from 8.5 +/- 1.5 to 8.8 +/- 1.8 %/day) nor NOLD (from 1.69 +/- 0.22 to 1.55 +/- 0.26 micromol x kg(-1) x min(-1)) changed (P = nonsignificant vs. basal), whereas they increased in control subjects (albumin FSR: from 10.9 +/- 1.5 to 15.9 +/- 1.9 %/day, P < 0.002; NOLD: from 1.80 +/- 0.14 to 2.10 +/- 0.19 micromol x kg(-1) x min(-1), P = 0.032). Thus mixed meal ingestion did not stimulate either albumin FSR or whole body protein synthesis in compensated liver cirrhosis. The mechanism(s) maintaining normoalbuminemia at this disease stage need to be further investigated.

Adult↗
PubMed2001

Agenesis of the gallbladder associated with Gilbert's syndrome.

A case of gallbladder agenesis associated with Gilbert's syndrome in a 52-year-old man with a striking family history of cholelithiasis is reported. The diagnosis of Gilbert's syndrome was made 30 years earlier, whereas the anomaly of the gallbladder was manifested when the patient, at the age of 34 years, started complaining of abdominal symptoms suggestive of biliary tract disease. Diagnostic confirmation was accomplished by magnetic resonance cholangiography, thus avoiding laparotomy, whereas conventional hepatobiliary imaging studies and laparoscopy could not achieve a definite diagnosis. No other malformations were detected. To our knowledge, this is the first report of an association between gallbladder agenesis and Gilbert's syndrome. Such association may be incidental or could represent the occurrence of a concomitant metabolic error in adults with isolated agenesis of the gallbladder.

Adult↗
PubMed2001

Bladder injury during diagnostic laparoscopy. A case report.

We report the case of a bladder injury that was incurred during diagnostic laparoscopy in a 19-year-old man with hepatomegaly, neuropsychiatric disturbances, and urinary retention whose final diagnosis was Wilson's disease. In order to define the nature of his hepatomegaly, the patient underwent laparoscopy. However, the lack of recognition of urinary retention by the operator and the absence of cooperation by the patient caused bladder injury during the insertion of the Veress needle, resulting in the leakage of a yellow fluid consistent with urine. Since the injury was small, it was managed with antibiotics and bladder drainage, alone and deemed not to require surgical repair. We also discuss potential risk factors and describe some approaches that can help to avoid this laparoscopic complication.

Adult↗
PubMed2001

Limited acid hydrolysis as a means of fragmenting proteins isolated upon ProteinChip array surfaces.

ProteinChip array technology enables protein purification, protein profiling, and biomarker discovery on a convenient biochip platform. Traditional proteomic approaches towards protein identification rely upon the generation of peptides through the use of specific proteases. However, for a variety of reasons, the digestion of proteins bound to planar arrays by specific proteases, such as trypsin, has proven to be difficult, at times providing little or no protein digestion at all. Additionally, should more than one protein be present on the array surface, the digestion product consists of peptides from different proteins, adding another dimension of complexity to database mining approaches. These factors have driven our group to explore alternative means of on-chip protein digestion. In this article, we describe an approach to generate peptide maps by limited acid hydrolysis. Depending upon the adsorbed protein, this method requires between 500 femtomole to 5 picomole of protein for on-chip hydrolysis. Besides generating several internal peptide fragments, limited acid hydrolysis also has the advantage of generating peptide ladders from the N- or C-terminus of the protein. From these ladders, partial primary sequence of the protein can be directly derived when analyzed by a simple laser desorption/ionization mass spectrometer. Furthermore, tandem mass spectrometry can be performed on several internal peptide fragments, thus facilitating the identification of several proteins within a mixture. Based upon the preliminary results of this work, we continue to explore the possibility of using limited acid hydrolysis to identify unknown proteins captured on ProteinChip array surfaces.

Acids↗
PubMed2001

On-target endoglycosidase digestion matrix-assisted laser desorption/ionization mass spectrometry of glycopeptides.

The digestion of glycopeptides with endoglycosidases can be used in the process of their structural characterization, and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is often used to analyze the products of these digestions. In the currently accepted protocol for the endoglycosidase digestion of glycopeptides on the MALDI target, the target must be incubated at 37 degrees C, and an hour or more is needed for digestion. We have modified the procedure so that the process can be performed at room temperature in 5 to 15 min, and digestions are performed in the presence of a MALDI matrix. The endoglycosidases used for digestion were endoglycosidase H and peptide-N-glycosidase F. Glycopeptides from asialofetuin and endopolygalacturonase (EPG) II were used as standards because their glycan structures have been previously characterized. Glycopeptides with unknown glycan structures were also digested, including glycopeptides from pectate lyase, EPG I, and pectin methylesterase from Aspergillus niger.

Amidohydrolases↗
PubMed2001

Role of apolipoprotein E receptors in regulating the differential in vivo neurotrophic effects of apolipoprotein E.

Apolipoprotein E (apoE) is known to bind to at least five receptors, including the low-density lipoprotein (LDL) receptor-related protein (LRP), very low density LDL receptor (VLDL-R), LDL-R, apoE receptor 2 (apoER2), and megalin/gp330. In this context, the main objective of the present study was to better understand the contributions of LRP and LDL-R to the in vivo neurotrophic effects of apoE. For this purpose, apoE-deficient and receptor-associated protein (RAP)-deficient mice were infused with recombinant apoE3, RAP, or saline. Infusion of apoE3 into apoE-deficient mice resulted in amelioration of degenerative alterations of pyramidal neurons, but had no effect on somatostatin-producing interneurons. In contrast, infusion of apoE3 into RAP-deficient mice resulted in amelioration of degenerative alterations of somatostatin-producing interneurons. LRP and LDL-R levels were significantly reduced in RAP-deficient mice, but significantly increased in the apoE-deficient mice. In contrast, levels of apoE were reduced in the RAP-deficient mice compared to wildtype controls, suggesting that neurotrophic effects of apoE3 in the RAP-deficient mice were related to a combined deficit in endogenous apoE and selected apoE receptors. Furthermore, in apoE-deficient mice, infusion of apoE3 had a neurotrophic effect on somatostatin-producing interneurons only when combined with RAP, suggesting that increased expression of apoE receptors in apoE-deficient mice prevented apoE from rescuing somatostatin-producing neurons. This study supports the contention that some of the in vivo neurotrophic effects of apoE are mediated by LRP and LDL-R and that a critical balance between levels of apoE and its receptors is necessary for the differential neurotrophic effects to appear.

Animals↗
PubMed2001

Prognostic value of serum biological markers in patients with hepatocellular carcinoma.

PURPOSE: Prognosis of patients with hepatocellular carcinoma (HCC) is assessed by using indexes based on clinical and instrumental parameters. The Cancer of the Liver Italian Program (CLIP) staging system combines the Child-Pugh classification with tumor size, portal invasion, and alpha-fetoprotein and predicts the outcome of HCC patients more precisely than the Okuda staging system. Serum levels of a number of biological variables have been found to be increased in patients with HCC and are associated with different outcomes. Our aims in this study were to test the prognostic role of the serum levels of soluble intercellular adhesion molecule-1 (sICAM-1), soluble interleukin-2 receptor (sIL-2R), interleukin 6 (IL-6), and anti-p53 and to assess whether the addition of any of the above serum markers could further improve the predictive ability of the CLIP score. EXPERIMENTAL DESIGN: Serum levels of sICAM-1, sIL-2R, IL-6, and anti-p53 were assayed in 80 patients with HCC and correlated with their outcomes. Nonparametric procedures were applied to test correlations between serum sICAM-1, sIL-2R, IL-6, anti-p53, and other prognostic factors. For survival analyses, the product-limit method, log-rank test, and Cox proportional hazards model were applied. RESULTS: Only serum levels of sIL-2R correlated with survival, which was longer for patients with lower values (< or =950 units/ml). However, with multivariate analysis sIL-2R did not confirm its predictive role when tested with the CLIP score as a covariate, with a hazard of death of 1.51 (95% confidence interval, 0.76-3.01). CONCLUSIONS: Serum levels of sICAM-1, sIL-2R, IL-6, and anti-p53 are not useful as prognostic factors for HCC in clinical practice. They do not improve the predictive ability of the CLIP score.

Aged↗