bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of atypical lateral fire spread to wind and slope
Authors: Simpson Colin. C. , Sharples Jason J. , Evans Jason P. 
Published: February 2016

AbstractThis study presents new knowledge of the environmental sensitivity of a dynamic mode of atypical wildland fire spread on steep lee‐facing slopes. This is achieved through a series of idealized numerical simulations performed with the Weather Research and Forecasting (WRF) and WRF‐Fire coupled atmosphere‐fire models. The sensitivity of the atypical lateral fire spread across lee slopes is tested for a varying background wind speed, wind direction relative to the terrain aspect, and lee slope steepness. The results indicate that the lateral spread characteristics are highly sensitive to each of these environmental conditions, and there is a broad agreement with the empirical thresholds calculated for lateral spread events observed in the 2003 Canberra bushfires. A theory to explain these environmental thresholds and their apparent interdependency is presented. The results are expected to have important implications for the management of wildland fires in rugged terrain.
Hurricane‐induced ocean waves and stokes drift and their impacts on surface transport and dispersion in the Gulf of Mexico
Authors: Curcic Milan , Chen Shuyi S. , Özgökmen Tamay M. 
Published: February 2016

AbstractHurricane Isaac induced large surface waves and a significant change in upper ocean circulation in the Gulf of Mexico before making landfall at the Louisiana coast on 29 August 2012. Isaac was observed by 194 surface drifters during the Grand Lagrangian Deployment (GLAD). A coupled atmosphere‐wave‐ocean model was used to forecast hurricane impacts during GLAD. The coupled model and drifter observations provide an unprecedented opportunity to study the impacts of hurricane‐induced Stokes drift on ocean surface currents. The Stokes drift induced a cyclonic (anticyclonic) rotational flow on the left (right) side of the hurricane and accounted for up to 20% of the average Lagrangian velocity. In a significant deviation from drifter measurements prior to Isaac, the scale‐dependent relative diffusivity is estimated to be 6 times larger during the hurricane, which represents a deviation from Okubo's (1971) canonical results for lateral dispersion in nonhurricane conditions at the ocean surface.
Evaluating the impact of U.S. Historical Climatology Network homogenization using the U.S. Climate Reference Network
Authors: Hausfather Zeke , Cowtan Kevin , Menne Matthew J. , Williams Claude N. 
Published: February 2016

AbstractNumerous inhomogeneities including station moves, instrument changes, and time of observation changes in the U.S. Historical Climatological Network (USHCN) complicate the assessment of long‐term temperature trends. Detection and correction of inhomogeneities in raw temperature records have been undertaken by NOAA and other groups using automated pairwise neighbor comparison approaches, but these have proven controversial due to the large trend impact of homogenization in the United States. The new U.S. Climate Reference Network (USCRN) provides a homogenous set of surface temperature observations that can serve as an effective empirical test of adjustments to raw USHCN stations. By comparing nearby pairs of USHCN and USCRN stations, we find that adjustments make both trends and monthly anomalies from USHCN stations much more similar to those of neighboring USCRN stations for the period from 2004 to 2015 when the networks overlap. These results improve our confidence in the reliability of homogenized surface temperature records.
Propagation of biases in climate models from the synoptic to the regional scale: Implications for bias adjustment
Authors: Addor Nans , Rohrer Marco , Furrer Reinhard , Seibert Jan 
Published: February 2016

AbstractBias adjustment methods usually do not account for the origins of biases in climate models and instead perform empirical adjustments. Biases in the synoptic circulation are for instance often overlooked when postprocessing regional climate model (RCM) simulations driven by general circulation models (GCMs). Yet considering atmospheric circulation helps to establish links between the synoptic and the regional scale, and thereby provides insights into the physical processes leading to RCM biases. Here we investigate how synoptic circulation biases impact regional climate simulations and influence our ability to mitigate biases in precipitation and temperature using quantile mapping. We considered 20 GCM‐RCM combinations from the ENSEMBLES project and characterized the dominant atmospheric flow over the Alpine domain using circulation types. We report in particular a systematic overestimation of the frequency of westerly flow in winter. We show that it contributes to the generalized overestimation of winter precipitation over Switzerland, and this wet regional bias can be reduced by improving the simulation of synoptic circulation. We also demonstrate that statistical bias adjustment relying on quantile mapping is sensitive to circulation biases, which leads to residual errors in the postprocessed time series. Overall, decomposing GCM‐RCM time series using circulation types reveals connections missed by analyses relying on monthly or seasonal values. Our results underscore the necessity to better diagnose process misrepresentation in climate models to progress with bias adjustment and impact modeling.
The sensitivity of simulated competition between different plant functional types to subgrid‐scale representation of vegetation in a land surface model
Authors: Shrestha R. K. , Arora V. K. , Melton J. R. 
Published: February 2016

AbstractThe Canadian Land Surface Scheme coupled to the Canadian Terrestrial Ecosystem Model is used to simulate competition between the model's seven non‐crop plant functional types (PFTs) for available space. Our objective is to assess if the model is successfully able to reproduce the observed mix of PFTs and their fractional coverages and to what extent the simulated competition is affected by the manner in which the subgrid‐scale variability of vegetation is represented. The model can be run either in a composite (single tile) configuration, where structural vegetation attributes of PFTs are aggregated for use in grid‐averaged energy and water balance calculations, or a mosaic (multiple tiles) configuration, where separate energy and water balance calculations are performed for each PFT. The model realistically simulates the fractional coverages of trees, grasses, and bare ground, as well as that of individual tree and grass PFTs and their succession patterns. Our results show that the model is not overly sensitive to the manner in which subgrid‐scale variability of vegetation is represented. Of the seven sites chosen across the globe to illustrate the difference between the two configurations, the simulated fractional coverage of PFTs are generally very similar (root‐mean‐square difference, RMSD, < 5%) between the composite and mosaic configurations at locations characterized by low heterogeneity (e.g., Amazonia, Vancouver Island, and the Tibetan Plateau), whereas at locations characterized by high heterogeneity (e.g., India, South Sudan and California), the two configurations yield somewhat different results (RMSD > 5%).
The Neotethyan Sanandaj‐Sirjan zone of Iran as an archetype for passive margin‐arc transitions
Authors: Hassanzadeh Jamshid , Wernicke Brian P. 
Published: February 2016

AbstractThe Sanandaj‐Sirjan zone of Iran is a northwest trending orogenic belt immediately north of the Zagros suture, which represents the former position of the Neotethys Ocean. The zone contains the most extensive, best preserved record of key events in the formation and evolution of the Neotethys, from its birth in Late Paleozoic time through its demise during the mid‐Tertiary collision of Arabia with Eurasia. The record includes rifting of continental fragments off of the northern margin of Gondwanaland, formation of facing passive continental margins, initiation of subduction along the northern margin, and progressive development of a continental magmatic arc. The latter two of these events are critical phases of the Wilson Cycle that, elsewhere in the world, are poorly preserved in the geologic record because of superimposed events. Our new synthesis reaffirms the similarity between this zone and various terranes to the north in Central Iran. Late Paleozoic rifting, preserved as A‐type granites and accelerated subsidence, was followed by a phase of pronounced subsidence and shallow marine sedimentation in Permian through Triassic time, marking the formation and evolution of passive margins on both sides of the suture. Subduction and arc magmatism began in latest Triassic/Early Jurassic time, culminating at ~170 Ma. The extinction of arc magmatism in this zone, and its shift northeastward to form the subparallel Urumieh‐Dokhtar arc, occurred diachronously along strike, in Late Cretaceous or Paleogene time. Post‐Cretaceous uplift transformed the zone from a primarily marine borderland into a marine archipelago that persisted until mid‐Tertiary time.
A large increase in U.S. methane emissions over the past decade inferred from satellite data and surface observations
Authors: Turner A. J. , Jacob D. J. , Benmergui J. , Wofsy S. C. , Maasakkers J. D. , Butz A. , Hasekamp O. , Biraud S. C. 
Published: February 2016

AbstractThe global burden of atmospheric methane has been increasing over the past decade, but the causes are not well understood. National inventory estimates from the U.S. Environmental Protection Agency indicate no significant trend in U.S. anthropogenic methane emissions from 2002 to present. Here we use satellite retrievals and surface observations of atmospheric methane to suggest that U.S. methane emissions have increased by more than 30% over the 2002–2014 period. The trend is largest in the central part of the country, but we cannot readily attribute it to any specific source type. This large increase in U.S. methane emissions could account for 30–60% of the global growth of atmospheric methane seen in the past decade.
Differentiation of Mouse Embryonic Stem Cells into Ventral Foregut Precursors
Authors: Rothová Michaela , Hölzenspies Jurriaan J. , Livigni Alessandra , Villegas Santiago Nahuel , Brickman Joshua M. 
Published: February 2016

AbstractAnterior definitive endoderm (ADE), the ventral foregut precursor, is both an important embryonic signaling center and a unique multipotent precursor of liver, pancreas, and other organs. Here, a method is described for the differentiation of mouse embryonic stem cells (mESCs) to definitive endoderm with pronounced anterior character. ADE‐containing cultures can be produced in vitro by suspension (embryoid body) culture or in a serum‐free adherent monolayer culture. ESC‐derived ADE cells are committed to endodermal fates and can undergo further differentiation in vitro towards ventral foregut derivatives. © 2016 by John Wiley & Sons, Inc.
Genetic Manipulation ofNocardiaSpecies
Authors: Dhakal Dipesh , Kumar Jha Amit , Pokhrel Anaya , Shrestha Anil , Sohng Jae Kyung 
Published: February 2016

AbstractNocardiaspp. are aerobic, Gram‐positive, catalase positive, and non‐motile actinomycetes. They are associated with human infections. However, some species produce important natural products, degrade toxic chemicals, and are involved in biotransformation of valuable products. The lack of robust genetic tools has hindered detailed studies and advanced research. This unit describes the major genetic engineering approaches usingNocardiasp. CS682 as a prototype. These methods will certainly help in understanding the basis of their pathogenicity as well as biosynthetic and biotransforming abilities. It can be expected that knowledge of the biochemistry behind their pathogenicity will be crucial in developing effective treatment strategies. These genetic tools can be utilized to develop rational metabolic engineering approaches for crafting host strains with higher production or biotransformation ability. © 2016 by John Wiley & Sons, Inc.
Facile synthesis of biocompatible polyglycerol hydrogel based on epichlorohydrin
Authors: Yang Q. Z. , Fan C. J. , Yang X. G. , Liao L. Q. , Liu L. J. 
Published: February 2016

ABSTRACTA series of hydrophilic polyglycerol (PG) hydrogel was designed and synthesized via one pot with epichlorohydrin (ECH), H2O, and NaOH as the starting materials. The equilibrium swelling ratios of PG hydrogels could be tuned by simply changing the feed amount of NaOH. The gels were characterized by carbon nuclear magnetic resonance (13C NMR) spectroscopy, X‐ray photoelectron spectroscopy, and Fourier transform infrared spectroscopy. The As‐synthesized PG hydrogels showed temperature‐sensitive swelling behaviors. The results of MTT assay suggested that the PG hydrogels prepared by this novel synthesis method showed comparable cytocompatibility with the recognized poly(ethylene glycol) hydrogel. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43451.
Synthesis of composite latexes of polyhedral oligomeric silsesquioxane and fluorine containing poly(styrene‐acrylate) by emulsion copolymerization
Authors: Liao Wenbo , Huang Xiangxuan , Ye Lingyun , Lan Shanhong , Fan Hongbo 
Published: February 2016

ABSTRACTA novel octavinyl polyhedral oligomeric silsesquioxane/fluorine containing poly (styrene‐acrylate) (OvPOSS/FPSA) composite latexes with star‐type structure was synthesized by emulsion copolymerization. The structures of OvPOSS/FPSA composite materials were characterized by Fourier Transform Infrared, which indicated that OvPOSS could be grafted onto FPSA latexes by emulsion copolymerization. Transmission electron microscopy images disclosed that FPSA latexes possessed obvious core–shell structure and OvPOSS/FPSA composite latexes probably present star‐shape structure. Dynamic light scattering data indicated that the average diameter of OvPOSS/FPSA was slightly larger than that of FPSA, which was probably attributed to the encapsulation of POSS cages. Atomic force microscopy photos illustrated that the grafting reaction had increased the roughness of the composite surface. The water contact angle of composite films was found increasing as the percentage of OvPOSS increasing. Thermogravimetric analysis curves demonstrated that the OvPOSS/FPSA composite films displayed much better thermal stability than that of FPSA. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43455.
Effect of alanine, leucine, and arginine substitution on antimicrobial activity against candida albicans and action mechanism of a cationic octadecapeptide derived from α‐amylase of rice
Authors: Taniguchi Masayuki , Ochiai Akihito , Takahashi Kiyoshi , Nakamichi Shun‐ichi , Nomoto Takafumi , Saitoh Eiichi , Kato Tetsuo , Tanaka Takaaki 
Published: February 2016

ABSTRACTAmyI‐1‐18, an antimicrobial peptide, is a cationic α‐helical octadecapeptide derived from α‐amylase of rice (Oryza sativa L. japonica) that contains four cationic amino acid residues (two arginines and two lysines). To enhance the antifungal activity of AmyI‐1‐18 against Candida albicans, 11 analogs bearing substitutions with alanine, leucine, and/or arginine, which were designed on the basis of the helical wheel projection of AmyI‐1‐18, were synthesized, and their antifungal activity was investigated. The antifungal activities of four analogs obtained by replacing arginine or lysine with alanine were significantly reduced. The results suggested that the cationic arginine and lysine residues in AmyI‐1‐18 are important for its antifungal activity. The antifungal activities of two single leucine‐substituted analogs were not improved, but among three single arginine‐substituted analogs, AmyI‐1‐18(D15R) had approximately a twofold higher antifungal activity [50% growth‐inhibitory concentration (IC50): 31 μM] than AmyI‐1‐18 (IC50: 64 μM) and exhibited low hemolytic activity (4% at 100 μM). Flow cytometric analysis using propidium iodide revealed that the antifungal activity of AmyI‐1‐18(D15R) was dependent on its membrane‐disrupting activity in a manner different from that of AmyI‐1‐18. Further enhancement of the cationicity and hydrophobicity of AmyI‐1‐18(D15R) resulted in no improvement in antifungal activity and a significant increase in hemolytic activity. In this study, the results demonstrated that the antifungal activity of AmyI‐1‐18 against C. albicans was enhanced through increasing its membrane‐disrupting activity by replacing aspartic acid at position 15 with arginine without a significant increase in hemolytic activity. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 219–229, 2016.
Salt‐resistant short antimicrobial peptides
Authors: Mohanram Harini , Bhattacharjya Surajit 
Published: February 2016

ABSTRACTAntimicrobial peptides (AMPs) are promising leads for the development of antibiotics against drug resistant bacterial pathogens. However, in vivo applications of AMPs remain obscure due to salt and serum mediated inactivation. The high cost of chemical synthesis of AMPs also impedes potential clinical application. Consequently, short AMPs resistant toward salt and serum inactivation are desirable for the development of peptide antibiotics. In this work, we designed a 12‐residue amphipathic helical peptide RR12 (R‐R‐L‐I‐R‐L‐I‐L‐R‐L‐L‐R‐amide) and two Trp containing analogs of RR12 namely RR12Wpolar (R‐R‐L‐I‐W‐L‐I‐L‐R‐L‐L‐R‐amide), and RR12Whydro (R‐R‐L‐I‐R‐L‐W‐L‐R‐L‐L‐R‐amide). Designed peptides demonstrated potent antibacterial activity; MIC ranging from 2 to 8 μM, in the presence of sodium chloride (150 mM and 300 mM). Antibacterial activity of these peptides was also detected in the presence of human serum. Designed peptides, in particular RR12 and RR12Whydro, were only poorly hemolytic. As a mode of action; these peptides demonstrated efficient permeabilization of bacterial cell membrane and lysis of cell structure. We further investigated interactions of the designed peptides with lipopolysaccharide (LPS), the major component of the outer membrane permeability barrier of Gram‐negative bacteria. Designed peptides adopted helical conformations in complex with LPS. Binding of peptides with LPS has yielded dissociation the aggregated structures of LPS. Collectively, these designed peptides hold ability to be developed for salt‐resistant antimicrobial compounds. Most importantly, current work provides insights for designing salt‐resistant antimicrobial peptides. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 345–356, 2016.
Aryl–aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization
Authors: Anderson Jordan M. , Kier Brandon L. , Jurban Brice , Byrne Aimee , Shu Irene , Eidenschink Lisa A. , Shcherbakov Alexander A. , Hudson Mike , Fesinmeyer R. M. , Andersen Niels H. 
Published: February 2016

ABSTRACTWe have extended our studies of Trp/Trp to other Aryl/Aryl through‐space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T‐shape orientation. Designated as an edge‐to‐face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W ≫ Y ≥ F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225–232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y, and F/Y clusters, is a negative feature at 197–200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp‐cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross‐strand aryl/aryl clusters for the design of stable β‐sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 337–356, 2016.
St Gallen molecular subtypes in screening-detected and symptomatic breast cancer in a prospective cohort with long-term follow-up
Authors: Falck A K , Röme A , Fernö M , Olsson H , Chebil G , Bendahl P O , Rydén L 
Published: February 2016

Abstract

Background
Diagnosis by screening mammography is considered an independent positive prognostic factor, although the data are not fully in agreement. The aim of the study was to explore whether the mode of detection (screening-detected versus symptomatic) adds prognostic information to the St Gallen molecular subtypes of primary breast cancer, in terms of 10-year cumulative breast cancer mortality (BCM).

Methods
A prospective cohort of patients with primary breast cancer, who had regularly been invited to screening mammography, were included. Tissue microarrays were constructed from primary tumours and lymph node metastases, and evaluated by two independent pathologists. Primary tumours and lymph node metastases were classified into St Gallen molecular subtypes. Cause of death was retrieved from the Central Statistics Office.

Results
A total of 434 patients with primary breast cancer were included in the study. Some 370 primary tumours and 111 lymph node metastases were classified into St Gallen molecular subtypes. The luminal A-like subtype was more common among the screening-detected primary tumours (P = 0·035) and corresponding lymph node metastases (P = 0·114) than among symptomatic cancers. Patients with screening-detected tumours had a lower BCM (P = 0·017), and for those diagnosed with luminal A-like tumours the 10-year cumulative BCM was 3 per cent. For patients with luminal A-like lymph node metastases, there was no BCM. In a stepwise multivariable analysis, the prognostic information yielded by screening detection was hampered by stage and tumour biology.

Conclusion
The prognosis was excellent for patients within the screening programme who were diagnosed with a luminal A-like primary tumour and/or lymph node metastases. Stage, molecular pathology and mode of detection help to define patients at low risk of death from breast cancer.