bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids
Authors: Humphrey Bruce , Thomson Nicholas R , Thomas Christopher M , Brooks Karen , Sanders Mandy , Delsol Anne A , Roe John M , Bennett Peter M , Enne Virve I 
Published: April 2012

Abstract

Background
Understanding the survival of resistance plasmids in the absence of selective pressure for the antibiotic resistance genes they carry is important for assessing the value of interventions to combat resistant bacteria. Here, several poorly explored questions regarding the fitness impact of IncP1 and IncN broad host range plasmids on their bacterial hosts are examined; namely, whether related plasmids have similar fitness impacts, whether this varies according to host genetic background, and what effect antimicrobial resistance gene silencing has on fitness.

Results
For the IncP1 group pairwise in vitro growth competition demonstrated that the fitness cost of plasmid RP1 depends on the host strain. For the IncN group, plasmids R46 and N3 whose sequence is presented for the first time conferred remarkably different fitness costs despite sharing closely related backbone structures, implicating the accessory genes in fitness. Silencing of antimicrobial resistance genes was found to be beneficial for host fitness with RP1 but not for IncN plasmid pVE46.

Conclusions
These findings suggest that the fitness impact of a given plasmid on its host cannot be inferred from results obtained with other host-plasmid combinations, even if these are closely related.
An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora
Authors: Mondego Jorge MC , Vidal Ramon O , Carazzolle Marcelo F , Tokuda Eric K , Parizzi Lucas P , Costa Gustavo GL , Pereira Luiz FP , Andrade Alan C , Colombo Carlos A , Vieira Luiz GE , Pereira Gonçalo AG ,   Brazilian Coffee Genome Project Consortium
Published: April 2012

AbstractBackgroundCoffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries.Coffea arabicaandC. canephoraare responsible for 70 and 30% of commercial production, respectively.C. arabicais an allotetraploid from a recent hybridization of the diploid species,C. canephoraandC. eugenioides.C. arabicahas lower genetic diversity and results in a higher quality beverage thanC. canephora. Research initiatives have been launched to produce genomic and transcriptomic data aboutCoffeaspp. as a strategy to improve breeding efficiency.ResultsAssembling the expressed sequence tags (ESTs) ofC. arabicaandC. canephoraproduced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters ofC. arabicaand 16,665 clusters ofC. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences betweenCoffeaspp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently groupC. arabicaandC. canephoraexpression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories.ConclusionWe present the first comprehensive genome-wide transcript profile study ofC. arabicaandC. canephora, which can be freely assessed by the scientific community athttp://www.lge.ibi.unicamp.br/coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles andCoffeaspp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.
Ethnomedicine of the Kagera Region, north western Tanzania. Part 3: plants used in traditional medicine in Kikuku village, Muleba District
Authors: Moshi Mainen J , Otieno Donald F , Weisheit Anke 
Published: April 2012

Abstract
Background
The Kagera region of north western Tanzania has a rich culture of traditional medicine use and practice. Traditional medicines are the mainstay of healthcare in this region and are known to support the management of many illnesses such as malaria, bacterial infections, epilepsy, gynecological problems and others. However, most of the plants being used have either not been documented or evaluated for safety and efficacy or both. This study, the sixth of an ongoing series, reports on the medicinal plants that are used at Kikuku village, Muleba District.

Methodology
A semi-structured questionnaire was used to collect information on the common/local names of the plants, parts of the plants used, diseases treated, methods of preparing the herbal remedies, dosage of the remedies administered, frequency and duration of treatment and toxicity of the medicines. A literature review was carried out for information on the ethnomedical uses of the reported plants.

Results
A total of 49 plant species belonging to 47 genera and 24 plant families were documented. The family Euphorbiaceae and Asteraceae had the highest representation. The plants are used for the treatment of skin conditions (10 plants; 20%), bacterial infections and wounds (14 plants; 28.6%), malaria (14 plants; 28.6%), gastrointestinal disorders (11 plants; 22.4%), gynecological problems including infertility (8 plants; 16.3%), hypertension (5 plants; 10.2%), viral infections (7 plants; 14.3%), chest problems (5 plants; 10.2%), diabetes (3 plants; 6.1%), cancer (2 plants; 4.1%), inflammatory conditions (arthritis, rheumatism), HIV and AIDS, and hernia each treated by 1 plant (3 plants in total; 6.1%). Information obtained from the literature indicate that 25 (51.0%) of the therapeutic claims are supported by laboratory results or have similar claims of ethnomedical use from other countries.

Conclusion
Herbal remedies comprise an important and effective component of the healthcare system in Kikuku village with plants in the families Euphorbiaceae and Asteraceae comprising an important part of plants used in the indigenous healthcare management in the village. Malaria and bacterial infections dominate the list of diseases that are managed using traditional medicines.
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
Authors: Caspeta Luis , Shoaie Saeed , Agren Rasmus , Nookaew Intawat , Nielsen Jens 
Published: April 2012

Abstract

Background

Pichia stipitis and Pichia pastoris have long been investigated due to their native abilities to metabolize every sugar from lignocellulose and to modulate methanol consumption, respectively. The latter has been driving the production of several recombinant proteins. As a result, significant advances in their biochemical knowledge, as well as in genetic engineering and fermentation methods have been generated. The release of their genome sequences has allowed systems level research.

Results
In this work, genome-scale metabolic models (GEMs) of P. stipitis (iSS884) and P. pastoris (iLC915) were reconstructed. iSS884 includes 1332 reactions, 922 metabolites, and 4 compartments. iLC915 contains 1423 reactions, 899 metabolites, and 7 compartments. Compared with the previous GEMs of P. pastoris, PpaMBEL1254 and iPP668, iLC915 contains more genes and metabolic functions, as well as improved predictive capabilities. Simulations of physiological responses for the growth of both yeasts on selected carbon sources using iSS884 and iLC915 closely reproduced the experimental data. Additionally, the iSS884 model was used to predict ethanol production from xylose at different oxygen uptake rates. Simulations with iLC915 closely reproduced the effect of oxygen uptake rate on physiological states of P. pastoris expressing a recombinant protein. The potential of P. stipitis for the conversion of xylose and glucose into ethanol using reactors in series, and of P. pastoris to produce recombinant proteins using mixtures of methanol and glycerol or sorbitol are also discussed.

Conclusions
In conclusion the first GEM of P. stipitis (iSS884) was reconstructed and validated. The expanded version of the P. pastoris GEM, iLC915, is more complete and has improved capabilities over the existing models. Both GEMs are useful frameworks to explore the versatility of these yeasts and to capitalize on their biotechnological potentials.
The MARVEL transmembrane motif of occludin mediates oligomerization and targeting to the basolateral surface in epithelia
Authors: Yaffe Yakey , Shepshelovitch Jeanne , Nevo-Yassaf Inbar , Yeheskel Adva , Shmerling Hedva , Kwiatek Joanna M. , Gaus Katharina , Pasmanik-Chor Metsada , Hirschberg Koret 
Published: April 2012

Summary
Occludin (Ocln), a MARVEL-motif-containing protein, is found in all tight junctions. MARVEL motifs are comprised of four transmembrane helices associated with the localization to or formation of diverse membrane subdomains by interacting with the proximal lipid environment. The functions of the Ocln MARVEL motif are unknown. Bioinformatics sequence- and structure-based analyses demonstrated that the MARVEL domain of Ocln family proteins has distinct evolutionarily conserved sequence features that are consistent with its basolateral membrane localization. Live-cell microscopy, fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC) were used to analyze the intracellular distribution and self-association of fluorescent-protein-tagged full-length human Ocln or the Ocln MARVEL motif excluding the cytosolic C- and N-termini (amino acids 60–269, FP-MARVEL-Ocln). FP-MARVEL-Ocln efficiently arrived at the plasma membrane (PM) and was sorted to the basolateral PM in filter-grown polarized MDCK cells. A series of conserved aromatic amino acids within the MARVEL domain were found to be associated with Ocln dimerization using BiFC. FP-MARVEL-Ocln inhibited membrane pore growth during Triton-X-100-induced solubilization and was shown to increase the membrane-ordered state using Laurdan, a lipid dye. These data demonstrate that the Ocln MARVEL domain mediates self-association and correct sorting to the basolateral membrane.
The impact of routine histopathological examination on cholecystectomy specimens from an Asian demographic
Authors: Chin KF , Mohammad AA , Khoo YY , Krishnasamy T 
Published: April 2012

INTRODUCTION Most gallbladder carcinoma cases are suspected pre-operatively or intra-operatively. In Malaysia histopathological examination of cholecystectomy specimens has become routine practice. The aim of this study was to assess the impact of routine histological examinations on cholecystectomy specimens from an Asian demographic, which may differ from a Caucasian demographic. METHODS A retrospective study was performed of all histopathoiogy reports for choiecystectomies (Iaparoscopic and open) undertaken over a period of 12 years (1997-2008) in a single teaching hospital. RESULTS A total of 1,375 gallbladder specimens were sent for histopathological analysis, with 7 (0.5%) being reported as malignant while only three (0.2%) were found to contain primary gallbladder carcinoma. Other premalignant findings included two specimens with dyspiastic changes of the mucosa and one tubuioviiious adenoma with a dyspiastic epithelium. From the ten malignant and premalignant specimens, seven were diagnosed pre-operatively, two were suspected intra-operatively and one was diagnosed with dyspiastic changes on the histopathoiogy report post-operatively. CONCLUSIONS This study supports earlier research carried out in the UK and the demographic difference does not affect the impact of the histology examination on cholecystectomy specimens in diagnosing this disease. A selective policy is recommended in Malaysia.
What is the role of minimally invasive surgery in a fast track hip and knee replacement pathway?
Authors: Lloyd JM , Wainwright T , Middleton RG 
Published: April 2012

Introduction Minimally invasive hip and knee replacement surgery (MIS) continues to receive coverage in both the popular press and scientific literature. The cited benefits include a smaller scar, less soft tissue trauma, faster recovery, reduced hospital stay, decreased blood loss and reduced post-operative pain. These outcomes are highly desirable and consistent with the aims of fast track hip and knee pathways. This paper evaluates the literature and discusses whether performing MIS over conventional surgical techniques offers advantages in a fast track hip and knee pathway. Methods An English language literature search was performed using the MEDLINE® and PubMed databases. Case series, randomised controlled trials and systematic reviews were included in the review. Results The reported improvements in recovery brought about by MIS must be considered multifactorial. In combination with improved clinical pathways, MIS can be associated with quicker recovery and shorter length of hospital stay. Conclusions There is insufficient evidence to indicate that surgical technique alone makes a significant difference to recovery or reduces soft tissue trauma. No consensus on whether to use MIS techniques in fast track hip and knee replacement pathways can therefore be drawn. This is especially important given that the complication rates of MIS in the low to medium volume surgeon appear unacceptably high compared with standard approaches. It is also too early to assess the long-term effects of MIS on implant survival.
Adjusting Eptifibatide Doses for Renal Impairment: A Model of Dosing Agreement Among Various Methods of Estimating Creatinine Clearance
Authors: Healy Martha F , Speroni Karen Gabel , Eugenio Kenneth R , Murphy Patricia M 
Published: April 2012

Background: Because of the renal elimination and increased risk for bleeding events at supratherapeutic doses of eptifibatide, the manufacturer recommends dosing adjustment in patients with renal dysfunction. Methods commonly used to estimate renal dysfunction in hospital settings may be inconsistent with those studied and recommended by the manufacturer Objective: To compare hypothetical renal dosing adjustments of eptifibatide using both the recommended method and several other commonly used formulas for estimating kidney function. Methods: Sex, age, weight, height, serum creatinine, and estimated glomerular filtration rate (eGFR) were obtained retrospectively from the records of patients who received eptifibatide during a 12-month period. Renal dosing decisions were determined for each patient based on creatinine clearance (CrCI) estimates via the Cockcroft-Gault formula (CG) with actual body weight (ABW), ideal body weight (IBW) or adjusted weight (ADJW), and eGFR from the Modification of Diet in Renal Disease formula. Percent agreement and Cohen κ were calculated comparing dosing decisions for each formula to the standard CG-ABW. Results: In this analysis of 179 patients, percent agreement as compared to CG-ABW varied (CG-IBW: 90.50%, CG-ADJW: 95.53%, and eGFR: 93.30%). All κ coefficients were categorized as good. In the 20% of patients receiving an adjusted dose by any of the methods, 68.6% could have received a dose different from that determined using the CG-ABW formula. Conclusions: In the patients with renal impairment (CrCI <50 mL/min) in this study, two thirds would have received an unnecessary 50% dose adjustment discordant from the manufacturer's recommendation. Because failure to adjust eptifibatide doses in patients with renal impairment has led to increased bleeding events, practitioners may be inclined to err on the side of caution. However, studies have shown that suboptimal doses of eptifibatide lead to suboptimal outcomes. Therefore, correct dosing of eptifibatide is important to both patient safety and efficacy.
Mineral Compositional Trends and Their Correlations with Petrophysical and Well-Logging Parameters Revealed by Quanta + Bestmin Analysis: Miocene of the Carpathian Foredeep, Poland
Authors: Środoń Jan , Kawiak Tadeusz 
Published: April 2012

AbstractThis study uses the data from Miocene rocks of the Carpathian Foredeep to test the performance of the computer programs QUANTA and BESTMIN in aiding the interpretation of geophysical log data. These programs were designed to help trace trends in the mineral composition of rocks, the chemical composition of minerals, and the effects of these data on petrophysical and geophysical logging parameters. Chemical and X-ray diffraction data for 65 samples of shales, sandstones, and carbonates taken from cored wells in the molasse basin of the Carpathian Foredeep were processed. Compositional differences were detected between rocks sourced from the platform and rocks sourced from the Carpathians. Quartz, K-feldspar, and zircon were more abundant in the coarse-grained rocks (sandstones), while calcite, ankerite, siderite, pyrite, barite, halite, celestite, apatite, anatase, chlorite, 2:1 minerals, and organic matter were more abundant in the fine-grained rocks (shales). Plagioclase reached its maximum in coarse shales. Ankerite, chlorite, and dioctahedral 2:1 minerals had more Fe in the coarse-grained rocks. The dioctahedral 2:1 minerals in fine-grained rocks had a greater concentration of smectitic layers. This information permitted the precise calculation of grain density, porosity, adsorbed water, and some geophysical logging parameters. It also permitted the calibration of well-log response, in particular, the macroscopic neutron absorption cross-section (Σa) combined with the photoelectric absorption factor (P{e}) or with Pe + Ca (calcium content, measurable in wells by spectroscopic techniques) with porosity and cation exchange capacity (CEC). The NaCl concentration in the pore waters was found to range from the values typical for seawater in shales to the freshwater level in clean sandstones.
The European Medicines Agency Review of Cabazitaxel (Jevtana®) for the Treatment of Hormone-Refractory Metastatic Prostate Cancer: Summary of the Scientific Assessment of the Committee for Medicinal Products for Human Use
Authors: Pean Elias , Demolis Pierre , Moreau Alexandre , Hemmings Robert James , O'Connor Daniel , Brown David , Shepard Terry , Abadie Eric , Pignatti Francesco 
Published: April 2012

Learning Objectives:
After completing this course, the reader will be able to: Summarize the efficacy outcomes of cabazitaxel pivotal trials in the treatment of hormone-refractory metastatic prostate cancer.Describe the safety profile and most common adverse effects of cabazitaxel in patients with hormone-refractory metastatic prostate cancer.
CME This article is available for continuing medical education credit at CME.TheOncologist.com
On March 17, 2011 the European Commission issued a marketing authorization valid throughout the European Union for Jevtana® (Sanofi-Aventis, Paris, France) for the treatment of patients with hormone-refractory metastatic prostate cancer previously treated with a docetaxel-containing regimen.
The active substance of Jevtana® is cabazitaxel acetone solvate, an antineoplastic agent that acts by disrupting the microtubular network in cells. The recommended dose of cabazitaxel is 25 mg/m2 administered as a 1-hour i.v. infusion every 3 weeks in combination with oral prednisone or prednisolone, 10 mg, administered daily throughout treatment.
In the main study submitted for this application, a 2.4-month longer median overall survival time and a 30% lower risk for death were observed for cabazitaxel, compared with mitoxantrone. The most common side effects with cabazitaxel were anemia, leukopenia, neutropenia, thrombocytopenia, and diarrhea.
This paper summarizes the scientific review of the application leading to approval in the European Union. The detailed scientific assessment report and product information, including the summary of product characteristics, are available on the European Medicines Agency Web site (http://www.ema.europa.eu).
Lapatinib for Advanced or Metastatic Breast Cancer
Authors: Opdam Frans L. , Guchelaar Henk-Jan , Beijnen Jos H. , Schellens Jan H.M. 
Published: April 2012

Abstract
Lapatinib is a potent reversible and selective inhibitor of the tyrosine kinase domains of epidermal growth factor receptor and human epidermal growth factor receptor (HER)-2 that exerts its action by competitive binding to the intracellular ATP-binding site of the receptor. It is registered for the treatment of advanced or metastatic HER-2+ breast cancer in combination with capecitabine and for hormone receptor–positive breast cancer in combination with an aromatase inhibitor. Lapatinib administered orally once daily is moderately to well tolerated, with rash and gastrointestinal adverse events as the main toxicities. In studies on the efficacy of lapatinib, direct comparisons between lapatinib and trastuzumab are lacking. Results of ongoing randomized phase III studies with lapatinib or trastuzumab in combination with taxanes as first-line agents for metastatic breast cancer as well as in the neoadjuvant and adjuvant settings are awaited.
Bevacizumab-Based Therapies in the First-Line Treatment of Metastatic Colorectal Cancer
Authors: Strickler John H. , Hurwitz Herbert I. 
Published: April 2012

Abstract
Since its approval for the first-line treatment of metastatic colorectal cancer (mCRC), bevacizumab has become a standard treatment option in combination with chemotherapy for patients with mCRC. Bevacizumab has demonstrated efficacy in combination with a number of different backbone chemotherapy regimens, and its widespread use has introduced several important questions regarding the selection and optimization of bevacizumab-based treatment regimens, its use in various patient populations, and the identification of associated adverse events. This review discusses the results of several phase II and phase III clinical trials, as well as large observational studies, to address the use of bevacizumab in the treatment of patients with mCRC in the first-line setting.