bluuebunny/crossref_metadata_2025 huggingface dataset:
Errors in Transfusion Medicine: Have We Learned Our Lesson?
Authors: Fastman Barbara Rabin , Kaplan Harold S.
Published: November 2011

The phrase “patient safety” represents freedom from accidental or preventable harm due to events occurring in the healthcare setting. Practitioners aim to reduce, if not prevent, medical errors and adverse outcomes. Yet studies performed from many perspectives show that medical error constitutes a serious worldwide problem. Transfusion medicine, with its interdisciplinary intricacies and the danger of fatal outcomes, serves as an exemplar of lessons learned. Opportunity for error in complex systems is vast, and although errors are traditionally blamed on humans, they are often set up by preexisting factors. Transfusion has inherent hazards such as clinical vulnerabilities (eg, contracting an infectious agent or experiencing a transfusion reaction), but there also exists the possibility of hazards associated with process errors. Sample collection errors, or preanalytic errors, may occur when samples are drawn from donors during blood donation, as well as when drawn from patients prior to transfusion‐related testing, and account for approximately one‐third of events in transfusion. Errors in the analytic phase of the transfusion chain, slips and errors in the laboratory, comprise close to one‐third of patient safety–related transfusion events. As many as 40% of mistransfusions are due to errors in the postanalytic phase: often failures in the final check of the right blood and the right patient at the bedside. Bar‐code labels, radiofrequency identification tags, and even palm vein–scanning technology are increasingly being utilized in patient identification. The last phase of transfusion, careful monitoring of the recipient for adverse signs or symptoms, when performed diligently can help prevent or manage a potentially fatal reaction caused by an earlier process error or an unavoidable physiologic condition. Ways in which we can and do deal with potential hazards of transfusion are discussed, including a method of hazard reduction termed inherently safer design. This approach aims to lessen risk, with elimination of a hazard or the reduction of its occurrence as primary. In blood transfusion, elimination and marked reduction of some hazards has been employed to good effect. However, there is still a heavy reliance on procedural methods in the essentially manual steps constituting the phases of the transfusion chain. Some hospitals have created a new role of transfusion safety officer to assist in the effort of monitoring, identifying, and resolving conditions that may lessen safety. Mt Sinai J Med 78:854–864, 2011. © 2011 Mount Sinai School of Medicine
Improving Quality in Healthcare: Start With the Patient
Authors: DuPree Erin , Anderson Rebecca , Nash Ira S.
Published: November 2011

In the decade since the Institute of Medicine released To Err Is Human, patient harm from medical errors is still widespread. Healthcare has not undergone the transformative change that is needed to reduce medical errors and improve quality. This article discusses patient‐centeredness as an organizing principle for transforming healthcare. We also describe important efforts that depict the shift from a provider‐focused system to one that is more patient‐centered. Finally, the article discusses challenges for the future and the importance of involving patients in the quest to deliver safe, quality care. Mt Sinai J Med 78:813–819, 2011. © 2011 Mount Sinai School of Medicine
Patient Safety Training Simulations Based on Competency Criteria of the Accreditation Council for Graduate Medical Education
Authors: Issenberg S. Barry , Chung Hyun Soo , Devine Luke Adam
Published: November 2011

This report reviews and critically evaluates the development of 3 movements in healthcare that have had a profound impact on changes occurring at all levels of medical education: patient safety, healthcare simulation, and competency‐based education (exemplified by the Accreditation Council for Graduate Medical Education). The authors performed a critical and selective review of the literature from 1999 to 2011 to identify uses of simulation to address patient‐safety issues aligned according to the Accreditation Council for Graduate Medical Education 6 core competencies: (1) patient care; (2) medical knowledge; (3) interpersonal and communication skills; (4) professionalism; (5) practice‐based learning; and (6) systems‐based practice. The research synthesis is reported to inform and provide evidence about how simulation is used to train and evaluate learners on a range of patient‐safety issues for each of the core competencies: There is emerging evidence that simulation can be used in training efforts to reduce medical errors related to medical knowledge and patient care (particular invasive procedures as well as improved communication and teamwork skills). There remains limited evidence on its impact to improve patient safety related to more complex competencies of practice‐based learning and systems‐based practice. Simulation‐based learning can lead to positive patient outcomes and reduction of medical errors particularly when used for individual skills. However, particular attention needs to be placed on the organizational context in which it is implemented if improvements in practice‐based learning and systems‐based practice are to be realized. Mt Sinai J Med 78:842–853, 2011. © 2011 Mount Sinai School of Medicine
Reforming Way Medical Students and Physicians Are Taught About Quality and Safety
Authors: DesHarnais Susan I. , Nash David B.
Published: November 2011

The purpose of this article is to briefly review the history of how quality and safety have been addressed in the United States by those who have been teaching medical students and residents, and then discuss why and how this training must change in the future to more effectively address the problems of improving healthcare quality and safety. Although it has become clear that the curriculum in medical schools should encompass quality and safety training, medical schools have been very slow to implement the reforms that are necessary to accomplish such a goal. These changes, although desirable from a rational perspective, involve basic changes in the culture of medical schools and teaching hospitals. Moreover, the cost of implementing these changes would be very large, and, if imposed by outside agencies, would likely constitute an unfunded mandate. It should also be noted that at the present time there are very few people who are well trained to develop and teach these classes. In order to accomplish the goal of improving patient safety, it is essential that we provide much more training and knowledge regarding patient safety to medical students, including knowledge of interventions known to be effective in preventing errors; education in technical performance; information about organizational and team issues; and training in disclosing errors to patients. This training should occur early in the training of professionals, preferably while they are still in school, if such training is to change the culture of medicine. Some suggestions and plans for implementation are discussed, using some innovative programs as examples. Mt Sinai J Med 78:834–841, 2011. © 2011 Mount Sinai School of Medicine
Mitochondrial Pathology in Parkinson's Disease
Authors: Schapira Anthony H. V.
Published: November 2011

The last 25 years have witnessed remarkable advances in our understanding of the etiology and pathogenesis of Parkinson's disease. The ability to undertake detailed biochemical analyses of the Parkinson's disease postmortem brain enabled the identification of defects of mitochondrial and free‐radical metabolism. The discovery of the first gene mutation for Parkinson's disease, in alpha‐synuclein, ushered in the genetic era for the disease and the subsequent finding of several gene mutations causing parkinsonism, 15 at the time of writing. Technological advances both in sequencing technology and software analysis have allowed association studies of sufficiently large size accurately to describe genes conferring an increased risk for Parkinson's disease. What has been so surprising is the convergence of these 2 separate disciplines (biochemistry and genetics) in terms of reinforcing the importance of the same pathways (ie, mitochondrial dysfunction and free‐radical metabolism). Other pathways are also important in pathogenesis, including protein turnover, inflammation, and post‐translational modification, particularly protein phosphorylation and ubiquitination. However, even these additional pathways overlap with each other and with those of mitochondrial dysfunction and oxidative stress. This review explores these concepts with particular relevance to mitochondrial involvement. Mt Sinai J Med 78:872–881, 2011. © 2011 Mount Sinai School of Medicine
Few sex differences in the use of drugs for secondary prevention after stroke: a nationwide observational study
Authors: Sjölander Maria , Eriksson Marie , Glader Eva‐Lotta
Published: November 2011

Purpose

This observational study describes the sex differences in the use of secondary preventive drugs after ischemic stroke in terms of prescribing and persistence. Also, sex differences in patient‐ and treatment‐related factors associated with drug use were investigated.

Methods

In this nationwide register‐based study, the Swedish Stroke Register was linked to the Swedish Prescribed Drug Register for information on drugs prescribed for, and bought by, stroke patients. Background factors were included from the Swedish Stroke Register.

Results

Included in the database were 9331 men and 9018 women. Men were more often prescribed statins, 48.8% versus 38.1% [age‐adjusted prevalence ratio (PR) = 0.86, 95%CI = 0.82–0.91], and warfarin, 38.4% versus 26.4% after stroke (age‐adjusted PR = 0.88, 95%CI = 0.79–0.97). There were no differences in prescribing of antihypertensive or antiplatelet drugs. No sex differences were seen regarding not continuing drug treatment after discharge (primary non‐adherence). Women had slightly higher persistence to antihypertensive treatment 2 years after discharge, 76.3% versus 71.9% for men (age‐adjusted PR = 1.05, 95%CI = 1.00–1.09), but there were no differences in persistence to antiplatelet, warfarin or statin treatments. Similar factors were related to statin and warfarin prescribing for both men and women. Only antihypertensive treatment before stroke was associated to persistence to antihypertensive treatment, and this increased persistence for both men and women.

Conclusions

This study showed few differences between men and women after stroke. Patients' use of secondary preventive drugs needs to be improved, and from a public health perspective, poor persistence is probably a greater problem than differences between the sexes. Copyright © 2011 John Wiley & Sons, Ltd.
Investigation of the Sub‐Bandgap Photoresponse in CuGaS2 : Fe for Intermediate Band Solar Cells
Authors: Marsen Björn , Klemz Sascha , Unold Thomas , Schock Hans‐Werner
Published: November 2011

Transition‐metal doped chalcopyrite thin films have been proposed as a suitable absorber material for intermediate band solar cells. In this work, CuGa1−xFexS2 thin films were grown by vacuum co‐evaporation at a substrate temperature of 400 °C with various amounts of incorporated Fe. The optical response of thin films grown on soda‐lime glass was evaluated by transmittance/reflectance measurements. Photovoltaic devices were fabricated from CuGa1−xFexS2 thin films concurrently deposited on Mo‐coated glass substrates using the standard chalcopyrite glass/Mo/absorber/CdS/ZnO device structure. The device characteristics of these solar cells were evaluated by current–voltage and quantum efficiency measurements. For Fe‐containing CuGaS2 films, distinct sub‐gap absorption bands at 1·2 eV and 1·9 eV are detected, which increase in prominence with increasing Fe content. On the other hand, the solar cell parameters were found to deteriorate with increasing iron content, indicating an increase in non‐radiative recombination when high levels of iron are incorporated. However, for the lowest iron content (x = 0·003), an increase in the sub‐gap photoresponse at about 1·9 eV is observed, which is attributed to a combination of sufficient intermediate band absorption and carrier collection at this dilution level. Copyright © 2011 John Wiley & Sons, Ltd.
Short chain amphiphilic diblock co‐oligomers via RAFT polymerization
Authors: Siauw Meiliana , Hawkett Brian S. , Perrier Sébastien
Published: November 2011

We demonstrate the ability of the reversible addition‐fragmentation chain transfer (RAFT) process to produce well‐defined block co‐oligomers for which each block has a narrow molecular weight distribution and degrees of polymerization ranging from 2 to 33. We exploit RAFT versatility to control the structure of the co‐oligomers and produce amphiphilic block co‐oligomers of styrene, acrylic acid and ethylene glycol. A detailed study shows that the amphiphilic diblock co‐oligomers self‐assemble in solution and form micelles or particles, depending on the hydrophobicity of the diblock. These oligomers present an excellent alternative to traditional amphiphilic molecules, by combining the properties of polymers with those of single molecule surfactants. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Polymer‐based fluoride‐selective chemosensor: Synthesis, sensing property, and its use for the design of molecular‐scale logic devices
Authors: Lu Wei , Chen Dan , Jiang Han , Jiang Liming , Shen Zhiquan
Published: November 2011

A new styryl‐type monomer, 2‐(4‐vinylbenzyloxy)‐1‐naphthaldehyde thiosemicarbazone (VNT), was synthesized and then copolymerized with methyl methacrylate (MMA) by reversible addition fragmentation chain transfer polymerization affording a series of poly(MMA‐co‐VNT)s with different functional unit content, predetermined molecular weight, and narrow molecular‐weight distribution. The desired copolymers were structurally confirmed by various spectroscopic characterizations. Colorimetric and fluorescent titration spectra revealed that the copolymers are highly selective toward fluoride anions over other competitive species including Cl−, Br−, I−, H2PO4−, AcO−, and HSO4−. On addition of F−, a remarkable colorless‐to‐yellow color change is easily observed by naked eyes. The influence of the copolymer composition and molecular weight on its sensing capacity was then carefully investigated. The results showed that higher VNT‐incorporation amount within the copolymer chains leads to higher sensitivity toward F− ions. Interestingly, the chromogenic process of the polymeric sensor can be switched back and forth by successively adding F− and HSO4− anions into the dimethyl sulfoxide solution of the polymer, which may be represented by a complementary “IMPLICATION/INHIBIT” logic gate at molecular level using both the ions as the chemical inputs. Based on such a reversible and reproducible sensing system, we designed a molecular‐scale sequential information processing circuit displaying “writing–reading–erasing–reading” behavior and “multiwrite” function in the form of binary logic. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Development of an ELISA to detect the secreted prostate cancer biomarker AGR2 in voided urine
Authors: Wayner Elizabeth A. , Quek Sue‐Ing , Ahmad Rumana , Ho Melissa E. , Loprieno Michelle A. , Zhou Yong , Ellis William J. , True Lawrence D. , Liu Alvin Y.
Published: November 2011

BACKGROUND

Comparative transcriptomics between sorted cells identified AGR2 as one of the highest up‐regulated genes in cancer. Overexpression in primary tumors was verified by tissue microarray analysis. AGR2 encodes a 19‐kDa secreted protein that might be found in urine.

METHODS

Monoclonal antibodies were generated against AGR2. One antibody pair, P1G4 (IgG1) to capture and P3A5 (IgG2a) to detect, showed good performance characteristics in a sandwich ELISA. This assay could detect AGR2 at sub ng/ml quantities.

RESULTS

AGR2 was detected in tissue digestion media of tumor specimens and culture media of AGR2‐secreting prostate cancer cell lines. Additional testings involved frozen section immunohistochemistry, immunoprecipitation, and Western blot analysis. Voided urine samples were collected from pre‐operative cancer patients, and urinary protein was desalted and concentrated by filtration. The amount of AGR2 detected was scored as pg/100 µg total protein, and then converted to pg/ml urine. The developed ELISA detected AGR2 protein, ranging from 3.6 to 181 pg/ml, in an initial cohort of samples. AGR2 was not detected in the urine of non‐cancer and a bladder cancer patient.

CONCLUSIONS

For prostate cancer, an AGR2 urine test could be used for diagnosis. The data, although derived from a small number of samples assayed, showed that developing such a test for clinical application is viable because AGR2 is specific to cancer cells, and apparently secreted into urine. Prostate 72:1023–1034, 2012. © 2011 Wiley Periodicals, Inc.
Contrasting DNA damage checkpoint responses in epithelium of the human seminal vesicle and prostate
Authors: Jäämaa Sari , Sankila Anna , Rantanen Ville , Peltonen Karita , Järvinen Päivi M. , af Hällström Taija M. , Ruutu Mirja , Taari Kimmo , Andersson Leif C. , Laiho Marikki
Published: November 2011

BACKGROUND

Prostate and seminal vesicle are two similar hormone responsive human organs that differ dramatically in their cancer incidence. DNA damage response (DDR) is required for maintenance of genomic integrity.

METHODS

In this study we investigated the DDR and cell cycle checkpoint activation of these organs using orthotopic cultures of human surgery‐derived tissues and primary cultures of isolated prostate and seminal vesicle cells.

RESULTS

We find that the activation of ATM signaling pathway by ionizing radiation (IR) was comparable in both tissues. Previously, we have shown that the prostate secretory cells express low levels of histone variant H2AX and phosphorylated H2AX (γH2AX) after IR. Here we demonstrate that H2AX levels are low also in the secretory seminal vesicle cells suggesting that this is a common phenotype of postmitotic cells. We consequently established primary epithelial cell cultures from both organs to compare their DDR. Interestingly, contrary to human prostate epithelial cells (HPEC), primary seminal vesicle epithelial cells (HSVEC) displayed effective cell cycle checkpoints after IR and expressed higher levels of Wee1A checkpoint kinase. Furthermore, HSVEC but not HPEC cells were able to activate p53 and to induce p21 cell cycle inhibitor.

DISCUSSION

Our results show that during replication, the checkpoint enforcement is more proficient in the seminal vesicle than in the prostate epithelium cells. This indicates a more stringent enforcement of DDR in replicating seminal vesicle epithelial cells, and suggests that epithelial regeneration combined with sub‐optimal checkpoint responses may contribute to high frequency of genetic lesions in the prostate epithelium. Prostate 72:1060–1070, 2012. © 2011 Wiley Periodicals, Inc.
Hexim‐1 modulates androgen receptor and the TGF‐β signaling during the progression of prostate cancer
Authors: Mascareno Eduardo J. , Belashov Ivan , Siddiqui M. A. Q. , Liu Fang , Dhar‐Mascareno Manya
Published: November 2011

BACKGROUND

Androgen and TGF‐β signaling are important components during the progression of prostate cancer. However, whether common molecular events participate in the activation of these signaling pathways are less understood.

METHOD

Hexim 1 expression was detected by immunohistochemistry of human tissue microarrays and TRAMP mouse models. The in vivo significance of Hexim‐1 was established by crossing the TRAMP mouse model of prostate cancer with Hexim‐1 heterozygous mice. TRAMP C2 cell line was also modified to delete one copy of Hexim‐1 gene to generate TRAMP‐C2‐Hexim‐1+/− cell lines.

RESULTS

In this report, we observed that Hexim‐1 protein expression is absent in normal prostate but highly expressed in adenocarcinoma of the prostate and a characteristic sub‐cellular distribution among normal, benign hyperplasia, and adenocarcinoma of the prostate. Heterozygosity of the Hexim‐1 gene in the prostate cancer mice model and the TRAMP‐C2 cell line, leads to increased Cdk9‐dependent serine phosphorylation on protein targets such as the androgen receptor (AR) and the TGF‐β‐dependent downstream transcription factors, such as the SMAD proteins.

CONCLUSION

Our results suggest that changes in the Hexim‐1 protein expression and cellular distribution significantly influences the AR activation and the TGF‐β signaling. Thus, Hexim‐1 is likely to play a significant role in prostate cancer progression. Prostate 72:1035–1044, 2012. © 2011 Wiley Periodicals, Inc.
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
Authors: Beuming Thijs , Che Ye , Abel Robert , Kim Byungchan , Shanmugasundaram Veerabahu , Sherman Woody
Published: November 2011

Water plays an essential role in determining the structure and function of all biological systems. Recent methodological advances allow for an accurate and efficient estimation of the thermodynamic properties of water molecules at the surface of proteins. In this work, we characterize these thermodynamic properties and relate them to various structural and functional characteristics of the protein. We find that high‐energy hydration sites often exist near protein motifs typically characterized as hydrophilic, such as backbone amide groups. We also find that waters around alpha helices and beta sheets tend to be less stable than waters around loops. Furthermore, we find no significant correlation between the hydration site‐free energy and the solvent accessible surface area of the site. In addition, we find that the distribution of high‐energy hydration sites on the protein surface can be used to identify the location of binding sites and that binding sites of druggable targets tend to have a greater density of thermodynamically unstable hydration sites. Using this information, we characterize the FKBP12 protein and show good agreement between fragment screening hit rates from NMR spectroscopy and hydration site energetics. Finally, we show that water molecules observed in crystal structures are less stable on average than bulk water as a consequence of the high degree of spatial localization, thereby resulting in a significant loss in entropy. These findings should help to better understand the characteristics of waters at the surface of proteins and are expected to lead to insights that can guide structure‐based drug design efforts. Proteins 2011. © 2012 Wiley Periodicals, Inc.
On the T2 trap in zinc oxide thin films
Authors: Schmidt Matthias , Ellguth Martin , Karsthof Robert , v. Wenckstern Holger , Pickenhain Rainer , Grundmann Marius , Brauer Gerhard , Ling Francis C. C.
Published: November 2011

We investigated the electronic properties of the T2 deep‐level in zinc oxide thin films. It was found that T2 preferentially forms under zinc‐rich conditions and can be generated by either annealing the samples at reduced oxygen partial pressures ($p_{{\rm O}_{2} } < 1\;{\rm bar}$) or implanting zinc or copper ions, respectively. A strong dependence of its activation energy and high temperature limit of its cross‐section for electron capture on the T2 concentration in the sample is reported. Double DLTS measurements showed that the T2 activation energy decreases with increasing electric field due to phonon assisted tunnelling. Furthermore T2 can be photo‐ionised with a threshold photon energy of about 700 meV. Depth‐resolved concentration profiles of the T2 level in the samples were measured by optical capacitance–voltage spectroscopy.
Analyses on multiple resonance behaviors and microwave reflection loss in magnetic Co microflowers
Authors: Ma Zhi , Liu Qingfang , Yuan Jing , Wang Zhenkun , Cao Chentao , Wang Jianbo
Published: November 2011

Triple dielectric and magnetic resonance behaviors have been observed and studied in Co microflowers within a frequency range of 0.1–18.0 GHz. To characterize such triple‐resonance behaviors, the dielectric resonance was resolved by fitting the Lorentzian dispersion law, magnetic resonance spectra was fitted by the Landau–Lifshitz–Gilbert equation. It is demonstrated that our fitted and calculated resonance frequencies agree well with the experimental data. Dielectric resonance in permittivity was due to the dipole polarization. Magnetic resonance in permeability was due to the natural/exchange resonance. Both the permittivity and permeability determined and contributed to the microwave reflection loss.
Double‐shell metamaterial coatings for plasmonic cloaking
Authors: Filonov Dmitry S. , Slobozhanyuk Alexey P. , Belov Pavel A. , Kivshar Yuri S.
Published: November 2011

We study a double‐shell cloak for hiding objects with the dimensions comparable with the radiation wavelength. We demonstrate that the structure consisting of a dielectric layer and a layer of an epsilon‐near‐zero material can suppress sub‐ stantially the scattering from a sphere and at the same time shield its interiors. The double‐layer coating allows to cloak different objects with various material and geometrical parameters. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Precision profiling and identification of human serum peptides using Fourier transform ion cyclotron resonance mass spectrometry
Authors: Nicolardi Simone , Palmblad Magnus , Hensbergen Paul J. , Tollenaar Rob A. E. M. , Deelder André M. , van der Burgt Yuri E. M.
Published: November 2011

Many biomarker discovery studies are based on matrix‐assisted laser desorption/ionisation (MALDI) peptide profiles. In this study, 96 human serum samples were analysed on a Bruker solariXTM MALDI Fourier transform ion cyclotron resonance (FTICR) system equipped with a 15 tesla magnet. Isotopically resolved peptides were observed in ultrahigh resolution FTICR profiles up to m/z 6500 with mass measurement errors (MMEs) of previously identified peptides at a sub‐ppm level. For comparison with our previous platform for peptide profile mass analysis (i.e. Ultraflex II) the corresponding time‐of‐flight (TOF) spectra were obtained with isotopically resolved peptides up to m/z 3500. The FTICR and TOF systems performed rather similar with respect to the repeatability of the signal intensities. However, the mass measurement precision improved at least 10‐fold in ultrahigh resolution data and thus simplified spectral alignment necessary for robust and quantitatively precise comparisons of profiles in large‐scale clinical studies. From each single MALDI‐FTICR spectrum an m/z‐list was obtained with sub‐ppm precision for all different species, which is beneficial for identification purposes and interlaboratory comparisons. Furthermore, the FTICR system allowed new peptide identifications from collision‐induced dissociation (CID) spectra using direct infusion of reversed‐phase (RP) C18‐fractionated serum samples on an electrospray ionisation (ESI) source. Copyright © 2011 John Wiley & Sons, Ltd.
Thermodynamic study of gaseous vanadium phosphates by high‐temperature mass spectrometry
Authors: Shugurov S. M. , Lopatin S. I.
Published: November 2011

Knowledge of the structures of gaseous oxyacid salts of the MmXOn type is of interest for understanding the nature of chemical bonds. Gaseous VPO2 and VPO3 have been identified by Knudsen effusion mass spectrometry during the vaporization of mixtures of V2O3 and alkali earth phosphates from molybdenum and tungsten effusion cells. The structures and molecular parameters of the gaseous vanadium phosphates under study were determined using quantum chemical calculations. On the basis of equilibrium constants measured for gas‐phase reactions, the standard formation enthalpies were determined to be −273 ± 17 and −615 ± 16 kJ⋅mol–1 for VPO2 and VPO3, respectively. Copyright © 2011 John Wiley & Sons, Ltd.
Removal of 3'‐phosphate group by bacterial alkaline phosphatase improves oligonucleotide sequence coverage of RNase digestion products analyzed by collision‐induced dissociation mass spectrometry
Authors: Krivos Kady L. , Addepalli Balasubrahmanyam , Limbach Patrick A.
Published: November 2011

RNase mapping by nucleobase‐specific endonucleases combined with liquid chromatography/tandem mass spectrometry (LC/MS/MS) is a powerful analytical method for characterizing ribonucleic acids (RNAs). Endonuclease digestion of RNA yields products that contain a 3'‐terminal phosphate group. MS/MS via collision‐induced dissociation (CID) of these digestion products on a linear ion trap generates fragmentation pathways that include the loss of phosphoric acid (‐H3PO4; –98 u), which does not provide information about the sequence of the digestion products and can reduce ion abundance from other pathways that provide sequence information. Here we investigate the use of bacterial alkaline phosphatase (BAP) after RNase digestion to remove the 3'‐terminal phosphate from all RNase digestion products prior to LC/MS/MS analysis. RNase digestion products lacking the 3'‐phosphate were found to produce CID spectra with more consistent, high‐abundance c‐ and y‐type fragment ions as well as significantly more a‐Base and w‐type ions than digestion products retaining the 3'‐phosphate. In this manner, RNase mapping with LC/MS/MS can provide more complete RNA sequence information from fragment ions of higher abundance that are easier to interpret and identify. Copyright © 2011 John Wiley & Sons, Ltd.
Continuous‐flow step gradient mass spectrometry based method for the determination of kinetic parameters of immobilized mushroom tyrosinase in equilibrating conditions: comparison with free enzyme
Authors: Salwiński Aleksander , Delépée Raphaël , Maunit Benoît
Published: November 2011

A mass spectrometry (MS)‐based methodology for enzymatic assay in equilibrium conditions was designed and evaluated. This on‐line assay involves the introduction of a continuous‐flow step gradient (CFSG) of a substrate solution in the column containing immobilized enzyme and the simultaneous tracking of the product formation. We showed that the constant concentration of substrate in the entire bioreactor for an appropriate duration ensures the equilibration of the studied enzyme (mushroom tyrosinase). Under these conditions, it was demonstrated also that the kinetic and enzymatic parameters (Michaelis‐Menten constant, KM, the maximal specific activity, SAmax) are independent of the flow rate of the mobile phase. The feasibility of the mentioned approach for inhibitory tests was also investigated. The coupling of the mass spectrometer to the bio‐reactor allows the selective monitoring of the enzymatic reaction products and increases their detection level. Very high sensitivity, 500 pmol/min/column, and selective monitoring of the products of the enzymatic reaction are allowed by MS detection. The methodology developed here constitutes a sensitive analytical tool to study enzymes requiring long equilibration times. Copyright © 2011 John Wiley & Sons, Ltd.
Characterization of diazeniumdiolate nitric oxide donors (NONOates) by electrospray ionization mass spectrometry
Authors: Rivera‐Tirado Edgardo , López‐Casillas Marcos , Wesdemiotis Chrys
Published: November 2011

Diazeniumdiolates (also called NONOates) have been analyzed by electrospray ionization mass spectrometry (ESI‐MS). The samples used are commercially available and included Diethylamine NONOate, DETA NONOate, Spermine NONOate, MAHMA NONOate, PROLI NONOate, Dipropylenetriamine NONOate, PAPA NONOate, and Sulpho NONOate. These compounds have been found to ionize upon ESI by protonation, deprotonation and sodiation. The MSn experiments provided strong evidence that such ions release NO, HNO, N2O, NO2, N2O2, N3O3, N4O3 and N4O4 when collisionally activated. Thus, the facile donation of NO units is a property of such compounds. Negative‐mode mass spectrometry has been particularly useful for the analysis of most of the NONOates studied here. The experiments have demonstrated the capabilities of mass spectrometry, along with CAD (MS/MS), to detect and characterize such compounds. Copyright © 2011 John Wiley & Sons, Ltd.
Fabrication, morphology and mechanical properties of Al2O3–Al graded coatings on China low activation martensitic steel substrates
Authors: Song Binbin , Wu Ping , Chen Sen , Zhang Shiping , Yan Dan , Xue Lian
Published: November 2011

Al2O3, Al2O3/Al and Al2O3–Al graded coatings were fabricated on China low activation martensitic steel and silicon substrates by RF magnetron sputtering. The coating composition and cross‐section morphologies were investigated using X‐ray photoelectron spectroscopy, Auger electron spectroscopy and field‐emission scanning electron microscopy. The mechanical properties of the coatings were studied using nanoindentation, wafer‐curvature measurements and microscratch tests. The results show that usable Al2O3–Al graded coatings could be fabricated. With a more continuous compositional gradient, the interface zone was more compact. The hardness and elastic modulus of Al2O3–Al graded coatings were less than those of Al2O3 coatings, but greater than those of Al2O3/Al coatings. After annealing at 773 K for 3 h, the hardness of Al2O3–Al graded coating showed a small increase. The residual stresses in Al2O3–Al graded coatings declined to about 0.3 GPa, compared with the 6.6 GPa for Al2O3 coating. The adhesion of Al2O3 was improved by deposition of Al or Al compositional gradient oxide layers. Copyright © 2011 John Wiley & Sons, Ltd.
Epitaxy‐like orientation of nanoscale Ag islands grown on air‐oxidized Si(110)‐(5 × 1) surfaces
Authors: Roy Anupam , Dash J. K. , Rath A. , Dev B. N.
Published: November 2011

Growth of Ag islands under ultra‐high vacuum condition on air‐oxidized Si(110)‐(5 × 1) surfaces has been investigated by in situ reflection high energy electron diffraction and ex situ scanning electron microscopy and cross‐sectional transmission electron microscopy. A thin oxide is formed on Si via exposure of the clean Si(110)‐(5 × 1) surface to air. The oxide layer has a short range order. Deposition of Ag at different thicknesses and at different substrate temperatures reveal that the crystalline qualities of the Ag film are almost independent of the thickness of the Ag layer and depend only on the substrate temperature. Ag deposition at room temperature leads to the growth of randomly oriented Ag islands while preferred orientation evolves when Ag is deposited at higher temperatures. For deposition at 550 °C sharp spots in the reflection high energy electron diffraction pattern corresponding to an epitaxial orientation with the underlying Si substrate are observed. The presence of a short range order on the oxidized surface apparently influences the crystallographic orientation of the Ag islands. Copyright © 2011 John Wiley & Sons, Ltd.
Posttranscriptional Upregulation by MicroRNAs
Authors: Vasudevan Shobha
Published: November 2011

MicroRNAs are small non‐coding RNA guide molecules that regulate gene expression via association with effector complexes and sequence‐specific recognition of target sites on other RNAs; misregulated microRNA expression and functions are linked to a variety of tumors, developmental disorders, and immune disease. MicroRNAs have primarily been demonstrated to mediate posttranscriptional downregulation of expression; translational repression, and deadenylation‐dependent decay of messages through partially complementary microRNA target sites in mRNA untranslated regions (UTRs). However, an emerging assortment of studies, discussed in this review, reveal that microRNAs and their associated protein complexes (microribonucleoproteins or microRNPs) can additionally function to posttranscriptionally stimulate gene expression by direct and indirect mechanisms. These reports indicate that microRNA‐mediated effects can be selective, regulated by the RNA sequence context, and associated with RNP factors and cellular conditions. Like repression, translation upregulation by microRNAs has been observed to range from fine‐tuning effects to significant alterations in expression. These studies uncover remarkable, new abilities of microRNAs and associated microRNPs in gene expression control and underscore the importance of regulation, in cis and trans, in directing appropriate microRNP responses. WIREs RNA 2012, 3:311–330. doi: 10.1002/wrna.121

This article is categorized under:

Translation > Translation Mechanisms

Translation > Translation Regulation

Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action
Ghrelin Agonist TZP‐101/Ulimorelin Accelerates Gastrointestinal Recovery Independently of Opioid Use and Surgery Type: Covariate Analysis of Phase 2 Data
Authors: Bochicchio Grant , Charlton Philippa , Pezzullo John C. , Kosutic Gordana , Senagore Anthony
Published: November 2011

Background

Delayed recovery of gastrointestinal (GI) motility is a common complication following surgery. TZP‐101/ulimorelin is a macrocyclic peptidomimetic ghrelin receptor agonist with GI promotility effects that significantly accelerates time to recovery of GI motility compared to placebo following partial colectomy. It is also well tolerated. The objectives of this analysis were to identify predictors of GI motility recovery in patients undergoing partial colectomy and to evaluate whether these factors affect ulimorelin acceleration of GI recovery.

Methods

Covariate analysis assessed the effect of eight variables—age, sex, body mass index, type of surgery (right colectomy, left colectomy, other), duration of surgery, blood loss, total opioid consumption, country—on recovery of GI motility in 236 patients randomized to ulimorelin (n = 168) or placebo (n = 68). The primary endpoint was the recovery of GI function (time from the end of surgery to first bowel movement). Stepwise regression identified a parsimonious model of the smallest subset of variables best predicting GI recovery.

Results

Recovery was shorter for segmental/subtotal colectomies vs. right colectomies (P = 0.016) and longer with increased total opioid use (P = 0.037). The remaining variables had no statistically significant effect on GI recovery. Effects of ulimorelin 480 μg/kg (the most effective dose) on time to GI tract recovery remained statistically and clinically significant (hazard ratio = 1.81, P = 0.014) when adjusted for surgery type and/or total opioid use.

Conclusions

Two factors, type of surgery and total opioid use, independently modified times to recovery of GI motility following partial large bowel resection surgery. Acceleration of recovery of GI motility by ulimorelin was independent of these factors.
Production of multiple extracellular enzyme activities by novel submerged culture of Aspergillus kawachii for ethanol production from raw cassava flour
Authors: Sugimoto Toshikazu , Makita Tomohiro , Watanabe Koutaro , Shoji Hiroshi
Published: November 2011

Cassava is a starch-containing root crop that is widely used as a raw material in a variety of industrial applications, most recently in the production of fuel ethanol. In the present study, ethanol production from raw (uncooked) cassava flour by simultaneous saccharification and fermentation (SSF) using a preparation consisting of multiple enzyme activities from Aspergillus kawachii FS005 was investigated. The multi-activity preparation was obtained from a novel submerged fermentation broth of A. kawachii FS005 grown on unmilled crude barley as a carbon source. The preparation was found to consist of glucoamylase, acid-stable α-amylase, acid carboxypeptidase, acid protease, cellulase and xylanase activities, and exhibited glucose and free amino nitrogen (FAN) production rates of 37.7 and 118.7 mg/l/h, respectively, during A. kawachii FS005-mediated saccharification of uncooked raw cassava flour. Ethanol production from 18.2% (w/v) dry uncooked solids of raw cassava flour by SSF with the multi-activity enzyme preparation yielded 9.0% (v/v) of ethanol and 92.3% fermentation efficiency. A feasibility study for ethanol production by SSF with a two-step mash using raw cassava flour and the multi-activity enzyme preparation manufactured on-site was verified on a pilot plant scale. The enzyme preparation obtained from the A. kawachii FS005 culture broth exhibited glucose and FAN production rates of 41.1 and 135.5 mg/l/h, respectively. SSF performed in a mash volume of about 1,612 l containing 20.6% (w/v) dry raw cassava solids and 106 l of on-site manufactured A. kawachii FS005 culture broth yielded 10.3% (v/v) ethanol and a fermentation efficiency of 92.7%.
Characterization of alginate lyase gene using a metagenomic library constructed from the gut microflora of abalone
Authors: Sim Su-Jung , Baik Keun Sik , Park Seong Chan , Choe Han Na , Seong Chi Nam , Shin Tai-Sun , Woo Hee Chul , Cho Jeong-Yong , Kim Duwoon
Published: November 2011

A metagenomic fosmid library was constructed using a genomic DNA mixture extracted from the gut microflora of abalone. The library gave an alginate lyase positive clone (AlyDW) harboring a 31.7-kbp insert. The AlyDW insert consisted of 22 open reading frames (ORFs). The deduced amino acid sequences of ORFs 11–13 were similar to those of known alginate lyase genes, which are found adjacent in the genome of Klebsiella pneumoniae subsp. aerogenes, Vibrio splendidus, and Vibrio sp. belonging to the phylum Gammaproteobacteria. Among the three recombinant proteins expressed from the three ORFs, alginate lyase activity was only observed in the recombinant protein (AlyDW11) coded by ORF 11. The expressed protein (AlyDW11) had the highest alginate lyase activity at pH 7.0 and 45°C in the presence of 1 mM AgNO3. The alginate lyase activity of ORF 11 was confirmed to be endolytic by thin-layer chromatography. AlyDW11 preferred poly(β-d-mannuronate) as a substrate over poly(α-l-guluronate). AlyDW11 contained three highly conserved regions, RSEL, QIH, and YFKAGVYNQ, which may act to stabilize the three-dimensional conformation and function of the alginate lyase.
Alginate production and alg8 gene expression by Azotobacter vinelandii in continuous cultures
Authors: Díaz-Barrera Alvaro , Soto Erik , Altamirano Claudia
Published: November 2011

Alginates are polysaccharides that are used as thickening agents, stabilizers, and emulsifiers in various industries. These biopolymers are produced by fermentation with a limited understanding of the processes occurring at the cellular level. The objective of this study was to evaluate the effects of agitation rate and inlet sucrose concentrations (ISC) on alginate production and the expression of the genes encoding for alginate-lyases (algL) and the catalytic subunit of the alginate polymerase complex (alg8) in chemostat cultures of Azotobacter vinelandii ATCC 9046. Increased alginate production (2.4 g l−1) and a higher specific alginate production rate (0.1 g g−1 h−1) were obtained at an ISC of 15 g l−1. Carbon recovery of about 100% was obtained at an ISC of 10 g l−1, whereas it was close to 50% at higher ISCs, suggesting that cells growing at lower sucrose feed rates utilize the carbon source more efficiently. In each of the steady states evaluated, an increase in algL gene expression was not related to a decrease in alginate molecular weight, whereas an increase in the molecular weight of alginate was linked to higher alg8 gene expression, demonstrating a relationship between the alg8 gene and alginate polymerization in A. vinelandii for the first time. The results obtained provide a possible explanation for changes observed in the molecular weight of alginate synthesized and this knowledge can be used to build a recombinant strain able to overexpress alg8 in order to produce alginates with higher molecular weights.
A new approach for reconstructing glacier variability based on lake sediments recording input from more than one glacier
Authors: Vasskog Kristian , Paasche Øyvind , Nesje Atle , Boyle John F. , Birks H.J.B.
Published: November 2011

We explore the possibility of building a continuous glacier reconstruction by analyzing the integrated sedimentary response of a large (440 km2) glacierized catchment in western Norway, as recorded in the downstream lake Nerfloen (N61°56’, E6°52’). A multi-proxy numerical analysis demonstrates that it is possible to distinguish a glacier component in the ~ 8000-yr-long record, based on distinct changes in grain size, geochemistry, and magnetic composition. Principal Component Analysis (PCA) reveals a strong common signal in the 15 investigated sedimentary parameters, with the first principal component explaining 77% of the total variability. This signal is interpreted to reflect glacier activity in the upstream catchment, an interpretation that is independently tested through a mineral magnetic provenance analysis of catchment samples. Minimum glacier input is indicated between 6700–5700 cal yr BP, probably reflecting a situation when most glaciers in the catchment had melted away, whereas the highest glacier activity is observed around 600 and 200 cal yr BP. During the local Neoglacial interval (~ 4200 cal yr BP until present), five individual periods of significantly reduced glacier extent are identified at ~ 3400, 3000–2700, 2100–2000, 1700–1500, and ~ 900 cal yr BP.
Cholesterol-lowering efficacy of a microencapsulated bile salt hydrolase-activeLactobacillus reuteriNCIMB 30242 yoghurt formulation in hypercholesterolaemic adults
Authors: Jones Mitchell L. , Martoni Christopher J. , Parent Mathieu , Prakash Satya
Published: November 2011

Several studies have reported limited or no reduction in serum cholesterol in response to probiotic formulations. Recently, probiotics have shown promise in treating metabolic disease due to improved strain selection and delivery technologies. The aim of the present study was to evaluate the cholesterol-lowering efficacy of a yoghurt formulation containing microencapsulated bile salt hydrolase (BSH)-activeLactobacillus reuteriNCIMB 30242, taken twice per d over 6 weeks, in hypercholesterolaemic adults. A total of 114 subjects completed this double-blind, placebo-controlled, randomised, parallel-arm, multi-centre study. This interventional study included a 2-week washout, 2-week run-in and 6-week treatment period. Subjects were randomised to consume either yoghurts containing microencapsulatedL. reuteriNCIMB 30242 or placebo yoghurts. Over the intervention period, subjects consuming yoghurts containing microencapsulatedL. reuteriNCIMB 30242 attained significant reductions in LDL-cholesterol (LDL-C) of 8·92 % (P = 0·016), total cholesterol (TC) of 4·81 % (P = 0·031) and non-HDL-cholesterol (HDL-C) of 6·01 % (P = 0·029) over placebo, and a significant absolute change in apoB-100 of − 0·19 mmol/l (P = 0·049). Serum concentrations of TAG and HDL-C were unchanged over the course of the study. Present results show that consumption of microencapsulated BSH-activeL. reuteriNCIMB 30242 yoghurt is efficacious and safe for lowering LDL-C, TC, apoB-100 and non-HDL-C in hypercholesterolaemic subjects. The efficacy of microencapsulated BSH-activeL. reuteriNCIMB 30242 yoghurts appears to be superior to traditional probiotic therapy and akin to that of other cholesterol-lowering ingredients.