Reconstructing the free-energy landscape of Met-enkephalin using dihedral Principal Component Analysis and Well-tempered Metadynamics

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers however from the same limitation, i.e. the non trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachadran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates. We illustrate the robustness of this method in the case of the small and very diffusive Metenkephalin pentapeptide, and highlight a criterion to limit the number of CVs necessary to biased the metadynamics simulation. The free-energy landscape (FEL) of Met-enkephalin built on CVs generated from dPCA is found rugged compared with the FEL built on CVs extracted from PCA of the Cartesian coordinates of the atoms.Comment: 17 pages, 9 figures (4 in color

Faktor-faktor yang Mempengaruhi Jumlah Pengangguran di Provinsi Bali

After the Bali bombing which resulted in the Termination of Employment ( FLE) experienced by the majority of people who work in the tourism sector . This is also indicated by the presence of unemployment in Bali which is dominated by young people . This condition can worsen the social and economic problems. This study aimed to examine the effect of the level of investment , economic growth , inflation and population growth simultaneously and partially on the number of unemployed in the province of Bali in 1986-2012 . The data is secondary data obtained from BPS and BKPMD Bali Province . Data analysis techniques in this study using the technique of multiple linear regression analysis . The analysis showed that the variables of economic growth and inflation is negative and significant effect on the number of unemployed in the province of Bali . Variable population growth and a significant positive impact on the number of pengangangguran in Bali Province . While the investment rate does not affect significantly the number of unemployed in the province of Bali

Local softness, softness dipole and polarizabilities of functional groups: application to the side chains of the twenty amino acids

The values of molecular polarizabilities and softnesses of the twenty amino acids were computed ab initio (MP2). By using the iterative Hirshfeld scheme to partition the molecular electronic properties, we demonstrate that the values of the softness of the side chain of the twenty amino acid are clustered in groups reflecting their biochemical classification, namely: aliphatic, basic, acidic, sulfur containing, and aromatic amino acids . The present findings are in agreement with previous results using different approximations and partitioning schemes [P. Senet and F. Aparicio, J. Chem. Phys. 126,145105 (2007)]. In addition, we show that the polarizability of the side chain of an amino acid depends mainly on its number of electrons (reflecting its size) and consequently cannot be used to cluster the amino acids in different biochemical groups, in contrast to the local softness. Our results also demonstrate that the global softness is not simply proportional to the global polarizability in disagreement with the intuition that "a softer moiety is also more polarizable". Amino acids with the same softness may have a polarizability differing by a factor as large as 1.7. This discrepancy can be understood from first principles as we show that the molecular polarizability depends on a "softness dipole vector" and not simply on the global softness

Standardization of Marine Meteorological Data from FINO Offshore Platforms

KlimawandelDer Ausbau der Offshore-Windenergie gehört zu den erklärten Zielen der Bundesregierung. Um bessere Ken ntnisse der Bedingungen auf See zu erlangen, wurden drei Forschungsplattformen in der Nordsee (FINO 1 und 3) und Ostsee (FINO 2) errichtet. An diesen werden meteorologische und ozeanographische Größen in unterschiedlichen Höhen gemessen, um unter anderem Aussagen zu Vertikalprofilen der Windgeschwindigkeit treffen zu können. Da sich die Plattformen und Masten im Design unterscheiden und sich insbesondere bei den Windmessungen deutlich ein richtungsabhängiger Einfluss auf die Messungen zeigt, ist für die Vergleichbarkeit der Standorte eine standardisierte Auswertung der Messergebnisse erforderlich. Ziel des Projektes FINO-Wind ist es, die Vergleichbarkeit der Daten der drei Standorte zu verbessern und den Datennutzern nach standardisierten Methoden qualitätsgeprüfte Daten zur Verfügung zu stellen. Es sollen deshalb Standardisierungsverfahren zur Auswertung der Winddaten entwickelt werden. Insbesondere die verschiedenen Masteffekte werden eingehend untersucht und durch Windkanalmessungen, Vergleich mit LiDAR-Daten, CFD (Computational Fluid Dynamics)-Modellierungen und Anwendung der UAM (Uniform ambient flow mast correction)-Methode abgeschätzt. Daraus werden Korrekturfaktoren für Windmessungen abgeleitet, die später angewendet werden sollen. Die Messdaten, die als 10-Minuten-Werte vorliegen, werden des Weiteren einer umfassenden und automatisierten Qualitätsprüfung unterzogen. Dabei durchlaufen die Daten in aufeinanderfolgenden Schritten formale, klimatologische, zeitliche, Wiederholungs- und Konsistenzprüfungen und werden nach erfolgreichem Abschluss jeder Sequenz mit spezifischen Qualitätsflags gekennzeichnet. Aus der Analyse und dem Vergleich der Instrumentierung in unterschiedlichen Höhen, der Installation und Ausrichtung sowie die Mastkonstruktionen sollen Empfehlungen herausgearbeitet werden, wie zukünftige Anwendungen im Bereich der Offshore-Windmessungen verbessert werden können

PENENTUAN KANDUNGAN TOTAL FLAVONOID DAN TOTAL FENOL DARI AKAR KERSEN (Mutingia calabura) SERTA AKTIVITASNYA SEBAGAI ANTIOKSIDAN

Penelitian ini bertujuan untuk mengetahui kadar fenol dan flavonoid total dari ekstrak akar kersen serta aktivitas antioksidannya. Hasil ekstraksi 1 kg akar kersen menghasilkan ekstrak etanol (30,56 g), kloroform (6,52 g), etilasetat (6,1 g), n-butanol (3,21 g) dan air (4,65 g). Penapisan fitokimia menunjukkan ekstrak yang positif flavonoid adalah ekstrak air, kloroform, etanol dan etil asetatsedangkankelimaekstrak tersebut positif mengandung polifenol.  Ekstrak etanol, n-butanol, kloroform, etil asetat, dan air memiliki kandungan total fenol berturut-turut yaitu 12,62%, 3,81%, 6,12%, 8,75%, dan 11,93%. Kandungan flavonoid pada ekstrak etanol, kloroform, etil asetat, dan air berturut-turut yaitu 0,22%, 0,05%, 0,12%, dan 0,03%. Aktivitas antioksidan pada ekstrak etanol diukur dengan metode DPPH dan dinyatakan dengan nilai IC50 sebesar 36,44 pp

Enzymatic Mechanisms Involved in Evasion of Fungi to the Oxidative Stress: Focus on Scedosporium apiospermum

The airways of patients with cystic fibrosis (CF) are frequently colonized by various filamentous fungi, mainly Aspergillus fumigatus and Scedosporium species. To establish within the respiratory tract and cause an infection, these opportunistic fungi express pathogenic factors allowing adherence to the host tissues, uptake of extracellular iron, or evasion to the host immune response. During the colonization process, inhaled conidia and the subsequent hyphae are exposed to reactive oxygen species (ROS) and reactive nitrogen species (RNS) released by phagocytic cells, which cause in the fungal cells an oxidative stress and a nitrosative stress, respectively. To cope with these constraints, fungal pathogens have developed various mechanisms that protect the fungus against ROS and RNS, including enzymatic antioxidant systems. In this review, we summarize the different works performed on ROS- and RNS-detoxifying enzymes in fungi commonly encountered in the airways of CF patients and highlight their role in pathogenesis of the airway colonization or respiratory infections. The potential of these enzymes as serodiagnostic tools is also emphasized. In addition, taking advantage of the recent availability of the whole genome sequence of S. apiospermum, we identified the various genes encoding ROS- and RNS-detoxifying enzymes, which pave the way for future investigations on the role of these enzymes in pathogenesis of these emerging species since they may constitute new therapeutics targets

Improving nutritional care quality in the orthopedic ward of a Septic Surgery Center by implementing a preventive nutritional policy using the Nutritional Risk Score: a pilot study.

Septic Surgery Center (SSC) patients are at a particularly high risk of protein-energy malnutrition (PEM), with a prevalence of 35-85% found in various studies. Previous collaboration between our hospital's SSC and its Clinical Nutrition Team (CNT) only focussed on patients with severe PEM. This study aimed to determine whether it was possible to improve the quality of nutritional care in septic surgery patients with help of a nutritional policy using the Nutritional Risk Score (NRS). Nutritional practices in the SSC were observed over three separate periods: in the 3 months leading up to the implementation baseline, 6 months after implementation of preventive nutritional practices, and at 3 years. The nutritional care quality indicator was the percentage of patients whose nutritional care, as prescribed by the SSC, was adapted to their specific requirements. We determined the septic surgery team's NRS completion rate and calculated the nutritional policy's impact on SSC length of stay. Data before (T <sub>0</sub> ) and after (T <sub>1</sub> + T <sub>2</sub> ) implementation of the nutritional policy were compared. Ninety-eight patients were included. The nutritional care-quality indicator improved from 26 to 81% between T <sub>0</sub> and T <sub>2</sub> . During the T <sub>1</sub> and T <sub>2</sub> audits, septic surgery nurses calculated NRS for 100% and 97% of patients, respectively. Excluding patients with severe PEM, SSC length of stay was significantly reduced by 23 days (p = 0.005). These findings showed that implementing a nutritional policy in an SSC is possible with the help of an algorithm including an easy-to-use tool like the NRS

Lucas Kraglievich (1886-1932)

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