Publications by authors named "Pramod Shah"

33 Publications

Systematic Identification of Protein Targets of Sub5 Using Proteome Microarrays.

Int J Mol Sci 2021 Jan 13;22(2). Epub 2021 Jan 13.

Graduate Institute of Systems Biology and Bioinformatics, and Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Jhongli 32001, Taiwan.

Antimicrobial peptides (AMPs) are intensively studied in terms of alternative drugs. Sub5 is a synthetic 12-mer AMP with substitutions of five amino acids of bactenecin 2A (Bac2A), a linear-ized bactenecin variant of bovine. Sub5 is highly effective against fungi with an ability to trans-locate cell membrane, but its targets are unknown. Systematic analysis of Sub5 targets will facil-itate our understanding on its mechanism of action. In this study, we used high-throughput proteome microarrays to explore the potential protein targets of Sub5. The screening results showed 128 potential protein targets of Sub5. Bioinformatics analysis of protein targets of Sub5 revealed significant gene ontology (GO) enrichment in actin related pro-cess of "actin filament-based process", "actin filament organization", "actin cortical patch or-ganization", regulation of "actin filament bundle assembly". Moreover, the other enriched cat-egories in GO enrichment mostly contained actin associate proteins. In total, 11 actin-associated proteins were identified in the protein targets of Sub5. Protein family (PFAM) enrichment anal-ysis shows protein domain enriched in actin binding, i.e., "Cytoskeletal-regulatory complex EF hand (helix E-loop-helix F motif)". Being consistent with GO analysis, Search Tool for the Re-trieval of Interacting Genes/Proteins (STRING) analysis of the protein targets of Sub5 showed ac-tin network with involvement of 15 protein targets. Along with actin-network, STRING analysis showed protein-protein interaction network in ribonucleoprotein, transcription and translation, chromosome, histone, and ubiquitin related, DNA repair, and chaperone. Multiple Expression motifs for Motif Elicitation (MEME) suite provided a consensus binding motif of [ED][ED]EEE[ED][ED][ED][ED][ED], in total of 75 protein targets of Sub5. This motif was present in 9 out of 15 actin-related proteins identified among protein targets of Sub5.
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http://dx.doi.org/10.3390/ijms22020760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7828587PMC
January 2021

Systematic Analysis of Phosphatidylinositol-5-phosphate-Interacting Proteins Using Yeast Proteome Microarrays.

Anal Chem 2021 01 11;93(2):868-877. Epub 2020 Dec 11.

Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.

We used yeast proteome microarrays (∼5800 purified proteins) to conduct a high-throughput and systematic screening of PI5P-interacting proteins with PI5P-tagged fluorescent liposomal nanovesicles. Lissamine rhodamine B-dipalmitoyl phosphatidylethanol was incorporated into the liposome bilayer to provide the nanovesicles with fluorescence without any encapsulants, which not only made the liposome fabrication much easier without the need for purification but also improved the chip-probing quality. A special chip assay was washed very gently without the traditional spin-dry step. Forty-five PI5P-interacting proteins were identified in triplicate with this special chip assay. Subsequently, we used flow cytometry to validate these interactions, and a total of 41 PI5P-interacting proteins were confirmed. Enrichment analysis revealed that these proteins have significant functions associated with ribosome biogenesis, rRNA processing, ribosome binding, GTP binding, and hydrolase activity. Their component enrichment is located in the nucleolus. The InterPro domain analysis indicated that PI5P-interacting proteins are enriched in the P-loop containing nucleoside triphosphate hydrolases domain (P-loop). Additionally, using the MEME program, we identified a consensus motif (IVGPAGTGKSTLF) that contains the Walker A sequence, a well-known nucleotide-binding motif. Furthermore, using a quartz crystal microbalance, both the consensus motif and Walker A motif showed strong affinities to PI5P-containing liposomes but not to PI5P-deprived liposomes or PI-containing liposomes. Additionally, the glycine (G6) and lysine (K7) residues of the Walker A motif (-GPAGTGKS-) were found to be critical to the PI5P-binding ability. This study not only identified an additional set of PI5P-interacting proteins but also revealed the strong PI5P-binding affinity ( = 1.81 × 10 M) of the Walker A motif beyond the motif's nucleotide-binding characteristic.
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http://dx.doi.org/10.1021/acs.analchem.0c03463DOI Listing
January 2021

Calculated initial parenteral treatment of bacterial infections: Bacterial endocarditis.

GMS Infect Dis 2020 26;8:Doc08. Epub 2020 Mar 26.

Klinische Abteilung für Infektiologie und Tropenmedizin, Medizinische Universität Wien, Vienna, Austria.

This is the twelfth chapter of the guideline "Calculated initial parenteral treatment of bacterial infections in adults - update 2018" in the 2 updated version. The German guideline by the Paul-Ehrlich-Gesellschaft für Chemotherapie e.V. (PEG) has been translated to address an international audience. The bacterial endocarditis is characterised by a constant incidence but a shift in the patient population due to the use of prosthetic heart valves and foreign materials like pacemakers and the increasing application of invasive medical procedures. This is linked to a change in the predominant infecting organisms towards staphylococci. This chapter gives recommendations for the interdisciplinary management of infective endocarditis from the diagnostic workup over prevention to therapy with a focus on antibiotic therapy.
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http://dx.doi.org/10.3205/id000052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186797PMC
March 2020

Calculated parenteral initial therapy of bacterial infections: Bacterial meningitis.

GMS Infect Dis 2020 26;8:Doc07. Epub 2020 Mar 26.

Geriatrisches Zentrum, Evangelisches Krankenhaus Göttingen-Weende, Göttingen, Germany.

This is the thirteenth chapter of the guideline "Calculated initial parenteral treatment of bacterial infections in adults - update 2018" in the 2 updated version. The German guideline by the Paul-Ehrlich-Gesellschaft für Chemotherapie e.V. (PEG) has been translated to address an international audience. Bacterial meningitis is a life-threatening infectious disease with high mortality and disability rates requiring prompt initiation of antimicrobial treatment to lower these rates.
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http://dx.doi.org/10.3205/id000051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186794PMC
March 2020

Zum Beitrag „Ambulant erworbene Pneumonie“.

Authors:
Pramod M Shah

Dtsch Med Wochenschr 2020 04 1;145(7):489. Epub 2020 Apr 1.

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http://dx.doi.org/10.1055/a-1106-5053DOI Listing
April 2020

Systematical Analysis of the Protein Targets of Lactoferricin B and Histatin-5 Using Yeast Proteome Microarrays.

Int J Mol Sci 2019 Aug 28;20(17). Epub 2019 Aug 28.

Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan.

Antimicrobial peptides (AMPs) have potential antifungal activities; however, their intracellular protein targets are poorly reported. Proteome microarray is an effective tool with high-throughput and rapid platform that systematically identifies the protein targets. In this study, we have used yeast proteome microarrays for systematical identification of the yeast protein targets of Lactoferricin B (Lfcin B) and Histatin-5. A total of 140 and 137 protein targets were identified from the triplicate yeast proteome microarray assays for Lfcin B and Histatin-5, respectively. The Gene Ontology (GO) enrichment analysis showed that Lfcin B targeted more enrichment categories than Histatin-5 did in all GO biological processes, molecular functions, and cellular components. This might be one of the reasons that Lfcin B has a lower minimum inhibitory concentration (MIC) than Histatin-5. Moreover, pairwise essential proteins that have lethal effects on yeast were analyzed through synthetic lethality. A total of 11 synthetic lethal pairs were identified within the protein targets of Lfcin B. However, only three synthetic lethal pairs were identified within the protein targets of Histatin-5. The higher number of synthetic lethal pairs identified within the protein targets of Lfcin B might also be the reason for Lfcin B to have lower MIC than Histatin-5. Furthermore, two synthetic lethal pairs were identified between the unique protein targets of Lfcin B and Histatin-5. Both the identified synthetic lethal pairs proteins are part of the Spt-Ada-Gcn5 acetyltransferase (SAGA) protein complex that regulates gene expression via histone modification. Identification of synthetic lethal pairs between Lfcin B and Histatin-5 and their involvement in the same protein complex indicated synergistic combination between Lfcin B and Histatin-5. This hypothesis was experimentally confirmed by growth inhibition assay.
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http://dx.doi.org/10.3390/ijms20174218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747642PMC
August 2019

A replaceable liposomal aptamer for the ultrasensitive and rapid detection of biotin.

Sci Rep 2016 Feb 23;6:21369. Epub 2016 Feb 23.

Graduate Institute of Systems Biology and Bioinformatics, National Central University, Taoyuan City, 32001, Taiwan.

Biotin is an essential vitamin which plays an important role for maintaining normal physiological function. A rapid, sensitive, and simple method is necessary to monitor the biotin level. Here, we reported a replacement assay for the detection of biotin using a replaceable liposomal aptamer. Replacement assay is a competitive assay where a sample analyte replaces the labeled competitor of analyte out of its biorecognition element on a surface. It is user friendly and time-saving because of washing free. We used aptamer as a competitor, not a biorecognition element as tradition. To label aptamers, we used cholesterol-conjugated aptamers to tag signal-amplifying-liposomes. Without the need of conjugation procedure, aptamers can be easily incorporated into the surface of dye-encapsulating liposomes. Two aptamers as competitors of biotin, ST-21 and ST-21M with different affinities to streptavidin, were studied in parallel for the detection of biotin using replacement assays. ST-21 and ST-21M aptamers reached to limits of detection of 1.32 pg/80 μl and 0.47 pg/80 μl, respectively. The dynamic ranges of our assays using ST-21 and ST-21M aptamers were seven and four orders of magnitude, respectively. This assay can be completed in 20 minutes without washing steps. These results were overall better than previous reported assays.
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http://dx.doi.org/10.1038/srep21369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763257PMC
February 2016

Systematic Analysis of Intracellular-targeting Antimicrobial Peptides, Bactenecin 7, Hybrid of Pleurocidin and Dermaseptin, Proline-Arginine-rich Peptide, and Lactoferricin B, by Using Escherichia coli Proteome Microarrays.

Mol Cell Proteomics 2016 06 22;15(6):1837-47. Epub 2016 Feb 22.

From the ‡Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan; §Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan

Antimicrobial peptides (AMPs) act either through membrane lysis or by attacking intracellular targets. Intracellular targeting AMPs are a resource for antimicrobial agent development. Several AMPs have been identified as intracellular targeting peptides; however, the intracellular targets of many of these peptides remain unknown. In the present study, we used an Escherichia coli proteome microarray to systematically identify the protein targets of three intracellular targeting AMPs: bactenecin 7 (Bac7), a hybrid of pleurocidin and dermaseptin (P-Der), and proline-arginine-rich peptide (PR-39). In addition, we also included the data of lactoferricin B (LfcinB) from our previous study for a more comprehensive analysis. We analyzed the unique protein hits of each AMP in the Kyoto Encyclopedia of Genes and Genomes. The results indicated that Bac7 targets purine metabolism and histidine kinase, LfcinB attacks the transcription-related activities and several cellular carbohydrate biosynthetic processes, P-Der affects several catabolic processes of small molecules, and PR-39 preferentially recognizes proteins involved in RNA- and folate-metabolism-related cellular processes. Moreover, both Bac7 and LfcinB target purine metabolism, whereas LfcinB and PR-39 target lipopolysaccharide biosynthesis. This suggested that LfcinB and Bac7 as well as LfcinB and PR-39 have a synergistic effect on antimicrobial activity, which was validated through antimicrobial assays. Furthermore, common hits of all four AMPs indicated that all of them target arginine decarboxylase, which is a crucial enzyme for Escherichia coli survival in extremely acidic environments. Thus, these AMPs may display greater inhibition to bacterial growth in extremely acidic environments. We have also confirmed this finding in bacterial growth inhibition assays. In conclusion, this comprehensive identification and systematic analysis of intracellular targeting AMPs reveals crucial insights into the intracellular mechanisms of the action of AMPs.
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http://dx.doi.org/10.1074/mcp.M115.054999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5083092PMC
June 2016

The proteome targets of intracellular targeting antimicrobial peptides.

Proteomics 2016 Apr 22;16(8):1225-37. Epub 2016 Feb 22.

Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.

Antimicrobial peptides have been considered well-deserving candidates to fight the battle against microorganisms due to their broad-spectrum antimicrobial activities. Several studies have suggested that membrane disruption is the basic mechanism of AMPs that leads to killing or inhibiting microorganisms. Also, AMPs have been reported to interact with macromolecules inside the microbial cells such as nucleic acids (DNA/RNA), protein synthesis, essential enzymes, membrane septum formation and cell wall synthesis. Proteins are associated with many intracellular mechanisms of cells, thus protein targets may be specifically involved in mechanisms of action of AMPs. AMPs like pyrrhocoricin, drosocin, apidecin and Bac 7 are documented to have protein targets, DnaK and GroEL. Moreover, the intracellular targeting AMPs are reported to influence more than one protein targets inside the cell, suggesting for the multiple modes of actions. This complex mechanism of intracellular targeting AMPs makes them more difficult for the development of resistance. Herein, we have summarized the current status of AMPs in terms of their mode of actions, entry to cytoplasm and inhibition of macromolecules. To reveal the mechanism of action, we have focused on AMPs with intracellular protein targets. We have also included the use of high-throughput proteome microarray to determine the unidentified AMP protein targets in this review.
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http://dx.doi.org/10.1002/pmic.201500380DOI Listing
April 2016

Aerobic utilization of crude glycerol by recombinant Escherichia coli for simultaneous production of poly 3-hydroxybutyrate and bioethanol.

J Biosci Bioeng 2014 Mar 17;117(3):343-50. Epub 2013 Oct 17.

Graduate School of Biotechnology and Bioengineering, Yuan Ze University, 135 Yuan-Tung Road, Chung-Li, Taoyuan 320, Taiwan; Bio-refinery and Bioprocess Engineering Laboratory, Department of Chemical Engineering and Materials Science, Yuan Ze University, 135 Yuan-Tung Road, Chung-Li, Taoyuan 320, Taiwan. Electronic address:

Crude glycerol, an inevitable byproduct during biodiesel production, is emerging as a potential feedstock for fermentation, due to its availability and a reasonable price. Biological utilization of abundant crude glycerol to several value added products is contemporary research area with beneficial features. Solving the problem of proper disposal and raising economic viability of biodiesel industries. Several researches have been directed toward the production of numerous products by using Escherichia coli, an ideal organism for heterologous expression of various foreign proteins. In this fashion, recombinant E. coli strains were constructed for the simultaneous production of poly 3-hydroxybutyrate (P3HB) and bioethanol from crude glycerol. The incorporation of aldehyde reductase (Alrd) and aldehyde dehydrogenase (AldH) in recombinant strain showed 2-fold increment in crude glycerol utilization under aerobic condition. Moreover, these two enzymes introduced an alternative pathway leading toward the potential production of bioethanol which was more than redox-balancing steps. Acetate was accumulated as an intermediate product. Subsequently, acetate was utilized as substrate in the second pathway, which directly converted acetyl-CoA to P3HB. This strategy demonstrated a potential production manner of bioethanol as an extracellular product and P3HB as water insoluble inclusion bodies inside E. coli. The maximum production of bioethanol and P3HB in the recombinant strain was 0.8 g L(-1) (17.4 mmol L(-1)) and 30.2% (w/w dry cell weight), respectively, which were higher than the parental strain.
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http://dx.doi.org/10.1016/j.jbiosc.2013.08.018DOI Listing
March 2014

Human to human transmission is possible in orthopoxviruses.

Authors:
Pramod M Shah

Dtsch Arztebl Int 2009 Sep 18;106(38):623; author reply 623-4. Epub 2009 Sep 18.

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http://dx.doi.org/10.3238/arztebl.2009.0623bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770220PMC
September 2009

Higher dosage at later stages.

Authors:
Pramod M Shah

Dtsch Arztebl Int 2009 Jul 3;106(31-32):524-5; author reply 525. Epub 2009 Aug 3.

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http://dx.doi.org/10.3238/arztebl.2009.0524cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735838PMC
July 2009

Selection of Pneumococci.

Authors:
Pramod M Shah

Dtsch Arztebl Int 2009 Jan 23;106(4):57; author reply 57-8. Epub 2009 Jan 23.

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http://dx.doi.org/10.3238/arztebl.2009.0057cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695311PMC
January 2009

Concentrations of piperacillin-tazobactam in human jaw and hip bone.

J Craniomaxillofac Surg 2008 Dec 9;36(8):468-72. Epub 2008 Sep 9.

Oral and Maxillofacial Surgery (Head: Prof. Dr. Dr. W. Wagner), University Mainz, Germany.

Objectives: It is unclear to what extent pharmacokinetic data from bone outside the facial area can be transferred to the maxillofacial area. The aim of this study was to evaluate the penetration characteristics of piperacillin-tazobactam into human jaw and hip bone as a model for different bone characteristics.

Materials And Methods: The drug was administered at the start of surgery in a single 15-min intravenous infusion dose (4g piperacillin & 0.5g tazobactam i.v.). Plasma and bone samples of ten patients were analyzed.

Results: Mean concentration of piperacillin in plasma was 309microg/ml at 0.5h declining at 4h to 14microg/ml. The respective values for tazobactam were 34microg/ml declining to 2.8microg/ml. The piperacillin-tazobactam ratio dropped during the study interval from 0.5h: 9.2%+/-0.8 to 2h: 7.2%+/-1.1 and 4h: 4.9%+/-0.7. Mean bone concentrations of piperacillin and tazobactam were 9.0+/-11.6microg/g and 1.2+/-1.3microg/g, respectively. Mean penetration ratios for all bone samples were 15% (+/-17) for piperacillin and 13% (+/-14) for tazobactam without a difference between bone of different origin.

Discussion: Piperacillin-tazobactam levels in jaw bone tissue after a single dose are sufficient to assure antibacterial activity of the combination and are above the minimal inhibitory concentrations of the most relevant pathogens in head and neck surgery. Our data suggests the use of piperacillin-tazobactam as an alternative for the therapy of severe infections of the head and neck.
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http://dx.doi.org/10.1016/j.jcms.2008.06.003DOI Listing
December 2008

[No obvious difference in Streptococcus pneumoniae antibiotic resistance profiles--isolates from HIV-positive and HIV-negative patients].

Med Klin (Munich) 2008 Feb;103(2):69-74

Schwerpunkt Therapie der HIV-Infektion, Zentrum der Inneren Medizin, Klinik 2 (Hämatologie/Onkologie, Rheumatologie und Infektiologie), Klinikum der Johann Wolfgang Goethe-Universität Frankfurt/Main, Frankfurt/Main.

Background And Purpose: HIV patients are overexposed to hospital environment, immune suppression, and antibiotic prophylaxes. Therefore, with HIV positive patients an increased risk for resistant bacterial rods is to be expected. The purpose of this case-control study was to determine the susceptibility patterns of pneumococci from adult patients in relation to their HIV status and to compare both patient groups.

Patients And Methods: Between January 2001 and December 2005, samples from internal medicine patients of one university hospital laboratory were investigated on culture of Streptococcus pneumoniae and in case of a positive vial, a resistance test was done by agar diffusion method. All patients with culture-confirmed infection due to pneumococci underwent a standardized retrospective evaluation in regard to demographic and clinical characteristics including HIV status.

Results: A total amount of 135 Streptococcus pneumoniae cultures could be assigned to 64 HIV-positive (A) and 71 HIV-negative patients (B), with susceptibility results for 134 isolates. Full susceptibility was seen in 44 (69.8% [A]) versus 42 (59.2% [B]) samples, reduced susceptibility ("intermediate-susceptible") was found in eight (12.7% [A]) versus 17 (23.9% [B]). Eleven (17.5% [A]) and twelve (16.9% [B]), respectively, out of all pneumococci were tested resistant to at least one antibiotic. Among these, resistance to erythromycin was most relevant (11.1% [A] and 11.3% [B]). None of the tested rods was resistant to penicillin. All differences between groups for susceptibility testing were not found significant. HIV-negative patients were significantly older, needed more often hospitalization and intensive care, and cultures for pneumococci were more frequently positive in primary sterile materials, such as cerebrospinal fluid and blood. The difference concerning death within 28 days following positive sample was just not significant as well as in immune suppression status of patients. HIV patients experienced more frequently an infection relapse and were more frequently smokers.

Conclusion: No obvious difference in pneumococci resistance patterns was observed between HIV-positive and HIV-negative adult patients. The absence of resistance to penicillin underscores the importance of beta-lactams in case of typical community-acquired pneumonia; therefore, this class of antibiotics should be included in treatment guidelines as first-line drugs also for HIV patients. HIV-negative controls of this study were more aged and suffered from a higher morbidity, however, the fact that they were not significantly less immune suppressed may be special character of a university hospital control patient group. HIV patients presented in an earlier stage of their pneumococcal disease, probably due to a direct access to tertiary hospital medical supply. A higher relapse rate underscores the importance of pneumococcal vaccination for HIV patients.
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http://dx.doi.org/10.1007/s00063-008-1011-5DOI Listing
February 2008

Direct susceptibility testing of respiratory samples.

Authors:
Pramod M Shah

Clin Infect Dis 2007 Aug;45(3):401; author reply 401-3

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http://dx.doi.org/10.1086/519507DOI Listing
August 2007

Classification of community-acquired endocarditis due to coagulase-negative staphylococci.

Authors:
Pramod M Shah

Clin Infect Dis 2005 Jun;40(11):1704; author reply 1704-5

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http://dx.doi.org/10.1086/430174DOI Listing
June 2005

Malaria: blood slides under treatment.

Authors:
Pramod M Shah

Int J Infect Dis 2003 Sep;7(3):233; author reply 233

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http://dx.doi.org/10.1016/s1201-9712(03)90058-0DOI Listing
September 2003

Ertapenem, the first of a new group of carbapenems.

J Antimicrob Chemother 2003 Oct 1;52(4):538-42. Epub 2003 Sep 1.

JW Goethe-Universitaet, Frankfurt, Germany.

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http://dx.doi.org/10.1093/jac/dkg404DOI Listing
October 2003

Quinolones and arrhythmia.

Authors:
Pramod M Shah

Clin Infect Dis 2003 Sep;37(5):738

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http://dx.doi.org/10.1086/377171DOI Listing
September 2003

Pharmacokinetics and pharmacodynamics of fluoroquinolones.

Clin Microbiol Infect 1998 Apr;4 Suppl 2:S27-S41

Division of Clinical Pharmacology, Department of Medicine, Albany Medical College, Albany, New York, USA.

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April 1998

Procalcitonin, a new diagnostic and prognostic marker for severe infections.

Clin Microbiol Infect 1998 May;4(5):237-241

Klinikum der J. Gutenberg Universität, Klinik für Mund-, Kiefer- und Gesichtschirurgie, Mainz, and.

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http://dx.doi.org/10.1111/j.1469-0691.1998.tb00050.xDOI Listing
May 1998

Classification of oral cephalosporins.

Authors:
Pramod M Shah

Int J Antimicrob Agents 2002 Feb;19(2):163-4

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http://dx.doi.org/10.1016/s0924-8579(01)00478-2DOI Listing
February 2002