Modeling above‐ground litterfall in eastern Mediterranean conifer forests using fractional tree cover,and remotely sensed and ground data

Question: How can we model above‐ground litterfall in Mediterranean conifer forests using remotely sensed and ground data, and geographic information systems (GIS)? Location: Eastern Mediterranean conifer forest of Turkey. Methods: Above‐ground litterfall from Mediterranean forest stands of Pinus nigra, Cedrus libani, Pinus brutia and Juniperus excelsa and mixed Abies cilicica, C. libani and P. nigra was modeled as a function of fractional tree cover using a regression tree algorithm, based on IKONOS and Landsat TM/ETM+data. Landsat TM/ETM+images for the study area were used to map actual stand patterns, based on a land‐cover map of species stands using a supervised classification. Results: Total amount of annual above‐ground litterfall for the entire study area (12 260 km²) was estimated at 417.2 Mg ha^?1 for P. brutia, 291.1 Mg ha^?1 for the mixed stand, 115.5 Mg ha^?1 for P. nigra, 54.6 Mg ha^?1 for J. excelsa and 45.9 Mg ha^?1 for C. libani. The maps generated indicate the distribution of the seasonal amount of total above‐ground litterfall for different species and the distribution of species stands in the study area. There was an increase in the amount of above‐ground litterfall for P. brutia stand in summer, for J. excelsa in autumn and for C. libani, P. nigra and the mixed stand of A. cilicica, P. nigra and C. libani in winter. Conclusion: Application of this model helps to improve the accuracy of estimated litterfall input to soil organic carbon pools in the Mediterranean conifer forests.     

NMR and amber analysis of the neamine pharmacophore for the design of novel aminoglycoside antibiotics

The dependence of the solution structure of neamine on pH was determined by NMR and AMBER molecular dynamics methods at pD 3.3, pD 6.5, and pD 7.4 in D₂O at 25 °C. Unlike neamine structures at pD 3.3 and 6.5, which essentially showed only one conformer, slowly exchanging primary, P-state, and secondary, S-state, neamine conformers populated on the NMR time scale at ∼80% and ∼20%, respectively, were detected at pD 7.4 with kinetic constants k_on(P→S) = 1.9771 s⁻¹ and k_off(S→P) = 1.1319 s⁻¹. A tertiary, T-state, neamine species populated at ∼3% was also detected by NMR at pD 7.4. The pKa values determined by NMR titration experiments are pKa1 6.44 ± 0.13 for N3 of ring-II, pKa2 7.23 ± 0.09 for N2′ of ring-I, pKa3 7.77 ± 0.19 for N1 of ring-II, and pKa4 8.08 ± 0.15 for N6′ of ring-I. Ring-I and ring-II of the P-state neamine and ring-I of the S and T-states of neamine possess the ⁴C₁ chair conformation between pD 3.3 and pD = 7.4. In contrast, ring-II of the S and T-states of neamine most likely adopt the ⁶rH₁ half-chair conformation. The P and S-states of neamine exhibit a negative syn-ψ glycosidic geometry. The exocyclic aminomethyl group of ring-I adopts the gt exocyclic rotamer conformation around physiological pHs while the gg exocyclic rotamer conformation predominates in acidic solutions near and below pH 4.5. Neamine exists in the P-state as a mixture of tetra-/tri-/di-protonated species between pD 4.5 and pD 7.4, while the S-state neamine exist only in a di-protonated species around physiological pDs. The existence of the S-state neamine may facilitate binding of neamine-like aminoglycosides by favorable entropy of binding to the A-site of 16S ribosomal RNA, suggesting that novel aminoglycoside compounds carrying a S-state neamine pharmacophore can be developed.     

Remarkable similarity in genome nucleotide sequences between the Schwarz FF-8 and AIK-C measles virus vaccine strains and apparent nucleotide differences in the phosphoprotein gene

The Schwarz FF-8 (FF-8) and AIK-C measles virus vaccine strains are currently used for vaccination in Japan. Here, the complete genome nucleotide sequence of the FF-8 strain has been determined and its genome sequence found to be remarkably similar to that of the AIK-C strain. These two strains are differentiated only by two nucleotide differences in the phosphoprotein gene. Since the FF-8 strain does not possess the amino acid substitutions in the phospho- and fusion proteins which are responsible for the temperature-sensitivity and small syncytium formation phenotypes of the AIK-C strain, respectively, other unidentified common mechanisms likely attenuate both the FF-8 and AIK-C strains.     

Multivariate statistical monitoring as applied to clean‐in‐place (CIP) and steam‐in‐place (SIP) operations in biopharmaceutical manufacturing

Multivariate statistical process monitoring (MSPM) is becoming increasingly utilized to further enhance process monitoring in the biopharmaceutical industry. MSPM can play a critical role when there are many measurements and these measurements are highly correlated, as is typical for many biopharmaceutical operations. Specifically, for processes such as cleaning‐in‐place (CIP) and steaming‐in‐place (SIP, also known as sterilization‐in‐place), control systems typically oversee the execution of the cycles, and verification of the outcome is based on offline assays. These offline assays add to delays and corrective actions may require additional setup times. Moreover, this conventional approach does not take interactive effects of process variables into account and cycle optimization opportunities as well as salient trends in the process may be missed. Therefore, more proactive and holistic online continued verification approaches are desirable. This article demonstrates the application of real‐time MSPM to processes such as CIP and SIP with industrial examples. The proposed approach has significant potential for facilitating enhanced continuous verification, improved process understanding, abnormal situation detection, and predictive monitoring, as applied to CIP and SIP operations. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:505–515, 2014     

Spatial relationships between shearing stresses and pressure on the plantar skin surface during gait

Based on the hypothesis that diabetic foot lesions have a mechanical etiology, extensive efforts have sought to establish a relationship between ulcer occurrence and plantar pressure distribution. However, these factors are still not fully understood. The purpose of this study was to simultaneously record shear and pressure distributions in the heel and forefoot and to answer whether: (i) peak pressure and peak shear for anterior-posterior (AP) and medio-lateral (ML) occur at different locations, and if (ii) peak pressure is always centrally located between sites of maximum AP and ML shear stresses. A custom built system was used to collect shear and pressure data simultaneously on 11 subjects using the 2-step method. The peak pressure was found to be 362 kPa ± 106 in the heel and 527 kPa ± 123 in the forefoot. In addition, the average peak shear values were higher in the forefoot than in the heel. The greatest shear on the plantar surface of the forefoot occurred in the anterior direction (mean and std. dev.: 37.7 ± 7.6 kPa), whereas for the heel, peak shear the foot was in the posterior direction (21.2 ± 5 kPa). The results of this study suggest that the interactions of the shear forces caused greater "spreading" in the forefoot and greater tissue "dragging" in the heel. The results also showed that peak shear stresses do not occur at the same site or time as peak pressure. This may be an important factor in locating where skin breakdown occurs in patients at high-risk for ulceration.     

Towards Active Tracking of Beating Heart Motion in the Presence of Arrhythmia for Robotic Assisted Beating Heart Surgery

In robotic assisted beating heart surgery, the control architecture for heart motion tracking has stringent requirements in terms of bandwidth of the motion that needs to be tracked. In order to achieve sufficient tracking accuracy, feed-forward control algorithms, which rely on estimations of upcoming heart motion, have been proposed in the literature. However, performance of these feed-forward motion control algorithms under heart rhythm variations is an important concern. In their past work, the authors have demonstrated the effectiveness of a receding horizon model predictive control-based algorithm, which used generalized adaptive predictors, under constant and slowly varying heart rate conditions. This paper extends these studies to the case when the heart motion statistics change abruptly and significantly, such as during arrhythmias. A feasibility study is carried out to assess the motion tracking capabilities of the adaptive algorithms in the occurrence of arrhythmia during beating heart surgery. Specifically, the tracking performance of the algorithms is evaluated on prerecorded motion data, which is collected in vivo and includes heart rhythm irregularities. The algorithms are tested using both simulations and bench experiments on a three degree-of-freedom robotic test bed. They are also compared with a position-plus-derivative controller as well as a receding horizon model predictive controller that employs an extended Kalman filter algorithm for predicting future heart motion.     

smyRNA: A Novel Ab Initio ncRNA Gene Finder

Background

Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs.

Methodology/Principal Findings

We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences.

Conclusions/Significance

Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown) ncRNA families. Availability: http://compbio.cs.sfu.ca/taverna/smyrna     

DFT and TDDFT investigation of the Schiff base formed by tacrine and saccharin

Schiff bases have many chemical and biological applications in medicine and pharmaceuticals due to the presence of an imine group (?C=N?). These bases are used in many different fields of technology, and in photochemistry because of their photochromic properties. Here, the structural and electronic properties of the Schiff base formed by tacrine and saccharin (TacSac) were explored using density functional theory with the B3LYP, M06-2X, M06L, and ωB97XD functionals in combination with the 6-311++G(d,p) basis set. The time-dependent formalism was used at the B3LYP/6-311++G(d,p) level to obtain electronic transitions. The calculations were repeated in an implicit solvent model mimicking water, using the polarizable continuum model in conjunction with a solvation model based on a density approach. The results indicate that TacSac cannot form spontaneously, but can be obtained in mild reactions. However, the resulting Schiff base displays different characteristics to its monomers. It also has the potential for use in photochemical intramolecular charge-transfer systems.

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Graphical Abstract Intramolecular charge transfer between HOMO and LUMO of TacSac