bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of shear heating, slip‐induced dilatancy and fluid flow on diversity of 1‐D dynamic earthquake slip
Authors: Suzuki Takehito , Yamashita Teruo 
Published: February 2014

AbstractWe theoretically study effects of thermal pressurization, slip‐induced dilatancy and fluid flow on slip evolution assuming 1‐D fault model. We generalize the analysis made in our former papers by introducing an upper limit for the inelastic porosity evolution. The expression for nondimensional parameter Ta, which is related to the upper limit, is derived in the present paper. We find that the parameter Ta together with two nondimensional parameters Su and derived in our former papers completely determine the qualitative nature of system behavior once the initial condition is given. For example, changes in Su and Ta generate two qualitatively different slip behaviors, both of which can be models for ordinary earthquake. The slip is accelerated with time after experiencing an initial deceleration in one of them, while the slip ceases after monotonic deceleration in the other. The initial slip deceleration observed in the former case may be interpreted as a dynamic event preceding the main shock in seismological observations. We mathematically derive the expression for the ranges of the nondimensional parameters in which the above two slip behaviors appear. Slow earthquakes are also modeled in the same framework, and nonzero values of the nondimensional parameter together with relatively large values of Su and Ta are found to contribute to the generation of such slow earthquakes. The mathematical framework constructed here can be applied to understanding of some other natural phenomena such as a kind of reaction‐diffusion system.
Interaction of gravity waves with the QBO: A satellite perspective
Authors: Ern M. , Ploeger F. , Preusse P. , Gille J. C. , Gray L. J. , Kalisch S. , Mlynczak M. G. , Russell J. M. , Riese M. 
Published: February 2014

AbstractOne of the most important dynamical processes in the tropical stratosphere is the quasi‐biennial oscillation (QBO) of the zonal wind. Still, the QBO is not well represented in weather and climate models. To improve the representation of the QBO in the models, a better understanding of the driving of the QBO by atmospheric waves is required. In particular, the contribution of gravity waves is highly uncertain because of the small horizontal scales involved, and there is still no direct estimation based on global observations. We derive gravity wave momentum fluxes from temperature observations of the satellite instruments HIRDLS and SABER. Momentum flux spectra observed show that particularly gravity waves with intrinsic phase speeds <30m/s (vertical wavelengths <10km) interact with the QBO. Gravity wave drag is estimated from vertical gradients of observed momentum fluxes and compared to the missing drag in the tropical momentum budget of ERA‐Interim. We find reasonably good agreement between their variations with time and in their approximate magnitudes. Absolute values of observed and ERA‐Interim missing drag are about equal during QBO eastward wind shear. During westward wind shear, however, observations are about 2 times lower than ERA‐Interim missing drag. This could hint at uncertainties in the advection terms in ERA‐Interim. The strong intermittency of gravity waves we find in the tropics might play an important role for the formation of the QBO and may have important implications for the parameterization of gravity waves in global models.
A generalized beta‐advection model to improve unusual typhoon track prediction by decomposing total flow into climatic and anomalous flows
Authors: Qian Weihong , Shan Xiaolong , Liang Haoyuan , Huang Jing , Leung Cheuk‐Hin 
Published: February 2014

AbstractUsing a novel approach of decomposing total flow into climatic and anomalous flows, we have developed a generalized beta‐advection model to improve unusual typhoon track prediction within 2–3 days. Typhoon Megi (2010) that experienced an unusual path is first used to introduce this model. Differing from the conventional beta‐advection model (BAM) in (i) decomposing the total flow into the climatic and anomalous flows and considering their interaction and (ii) taking the layer of minimum divergence anomaly and maximum vorticity anomaly instead of any average layers done by, for example, the shallow BAM, the medium BAM, and the deep BAM, this model is a combination of the climatic‐flow BAM and the anomalous‐flow BAM. In this paper, 19 cases of sudden right‐turning typhoon and 10 cases of straight‐moving typhoon in the South China Sea are studied to examine this model's capability. Results show that 15 right‐turning and 10 straight‐moving cases were successfully predicted by this combination model.
What controls the interannual variation of the wet season onsets over the Amazon?
Authors: Yin Lei , Fu Rong , Zhang Yong‐Fei , Arias Paola A. , Fernando D. Nelun , Li Wenhong , Fernandes Katia , Bowerman Adam R. 
Published: February 2014

AbstractPrevious studies have established that sea surface temperature anomalies (SSTAs) in the tropical Pacific and Atlantic are the main forcing of the interannual variation of the wet season onsets in the Amazon. However, this variation appears to be complex and not uniquely determined by SSTAs. What causes such a complexity and to what extent the interannual variation of the wet season onsets is predictable remain unclear. This study suggests that such a complex relationship is the result of several competing processes, which are nonlinearly related to the SSTAs. In particular, three dry season conditions are crucial for determining interannual variation of the wet season onset. (i) A poleward shift of the Southern Hemisphere subtropical jet (SHSJ) over the South American sector, initiated from a wave train‐like structure possibly forced by south central Pacific SST patterns, can prevent cold frontal systems from moving northward into the Amazon. This delays cold air incursion and results in late wet season onset over the southern Amazon. (ii) An anomalous anticyclonic center, which enhances westerly wind at 850 hPa over the southern Amazon and also the South American low‐level jets, leads to moisture export from the southern Amazon to La Plata basin and reduces convective systems that provide elevated diabatic heating. (iii) Smaller convective available potential energy (CAPE) limits local thermodynamically driven convection. Based on the stepwise and partial least squares regressions, these three selected preseasonal conditions (Niño 4, SHSJ, and CAPE) can explain 57% of the total variance of the wet season onset.
Organic and inorganic carbon dynamics in a karst aquifer: Santa Fe River Sink‐Rise system, north Florida, USA
Authors: Jin Jin , Zimmerman Andrew R. , Moore Paul J. , Martin Jonathan B. 
Published: February 2014

AbstractSpatiotemporal variations in dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), major ions concentrations and other geochemical parameters including stable carbon isotopes of DIC (δ13CDIC), were measured in surface water and deep and shallow well water samples of the Santa Fe River Sink‐Rise eogenetic karst system, north Florida, USA. Three end‐member water sources were identified: one DOC‐rich/DIC‐poor/δ13CDIC‐depleted, one DOC‐poor/DIC‐rich/δ13CDIC‐enriched, and one enriched in major ions. Given their spatiotemporal distributions, they were presumed to represent soil water, upper aquifer groundwater, and deep aquifer water sources, respectively. Using assumed ratios of Na+, Cl, and SO42− for each end‐member, a mixing model calculated the contribution of each water source to each sample. Then, chemical effects of biogeochemical reactions were calculated as the difference between those predicted by the mixing model and measured species concentrations. In general, carbonate mineral dissolution occurred throughout the Sink‐Rise system, surface waters were net autotrophic and the subsurface was in metabolic balance, i.e., no net DOC or DIC production or consumption. However, there was evidence for chemolithoautotrophy, perhaps by hydrogen oxidizing microbes, at some deep aquifer sites. Mineralization of this autochthonous natural dissolved organic matter (NDOM) led to localized carbonate dissolution as did surface water‐derived NDOM supplied to shallow well sites during the highest flow periods. This study demonstrates linkages between hydrology, abiotic and microbial processes and carbon dynamics and has important implications for groundwater quality, karst morphologic evolution, and hydrogeologic projects such as aquifer storage and recovery in karst systems.
A 170 year spring phenology index of plants in eastern China
Authors: Ge Quansheng , Wang Huanjiong , Zheng Jingyun , This Rutishauser , Dai Junhu 
Published: February 2014

AbstractExtending phenological records into the past is essential for the understanding of past ecological change and evaluating the effects of climate change on ecosystems. A growing body of historical phenological information is now available for Europe, North America, and Asia. In East Asia, long‐term phenological series are still relatively scarce. This study extracted plant phenological observations from old diaries in the period 1834–1962. A spring phenology index (SPI) for the modern period (1963–2009) was defined as the mean flowering time of three shrubs (first flowering of Amygdalus davidiana and Cercis chinensis, 50% of full flowering of Paeonia suffruticosa) according to the data availability. Applying calibrated transfer functions from the modern period to the historical data, we reconstructed a continuous SPI time series across eastern China from 1834 to 2009. In the recent 30 years, the SPI is 2.1–6.3 days earlier than during any other consecutive 30 year period before 1970. A moving linear trend analysis shows that the advancing trend of SPI over the past three decades reaches upward of 4.1 d/decade, which exceeds all previously observed trends in the past 30 year period. In addition, the SPI series correlates significantly with spring (February to April) temperatures in the study area, with an increase in spring temperature of 1°C inducing an earlier SPI by 3.1 days. These shifts of SPI provide important information regarding regional vegetation‐climate relationships, and they are helpful to assess long term of climate change impacts on biophysical systems and biodiversity.
CMIP5 multi‐model hindcasts for the mid‐1970s shift and early 2000s hiatus and predictions for 2016–2035
Authors: Meehl Gerald A. , Teng Haiyan 
Published: February 2014

AbstractCompared to uninitialized climate change projections, a multi‐model ensemble from the CMIP5 10 year decadal prediction experiments produces more warming during the mid‐1970s climate shift and less warming in the early 2000s hiatus in both the tropical Indo‐Pacific region and globally averaged surface air temperature (TAS) in closer agreement with observations. Assuming bias in TAS has stabilized in the 10 year predictions, after bias adjustment, TAS anomalies for the 2016–2035 period in the 30 year predictions initialized in 2006 are about 16% less than the uninitialized projections. One contributing factor for the improved climate simulation is the bias adjustment, which corrects the models' systematic errors and higher‐than‐observed decadal warming trend. Another important factor is the initialization with observations which constrains the ocean such that the starting points of the initialized simulations are close to the observed initial states.
Crustal structure beneath SE Tibet from joint analysis of receiver functions and Rayleigh wave dispersion
Authors: Sun Xiaoxiao , Bao Xuewei , Xu Mingjie , Eaton David W. , Song Xiaodong , Wang Liangshu , Ding Zhifeng , Mi Ning , Yu Dayong , Li Hua 
Published: February 2014

AbstractNew constraints on the pattern of crustal flow in SE Tibet are obtained from joint analysis of receiver functions and Rayleigh wave dispersion with a newly deployed seismic array. The crust in the Sichuan‐Yunnan Diamond Block has an average thickness of ~45 km and gradually thins toward the Indo‐China Block to the west and the Yangtze Block to the east. High VP/VS ratios are detected to the west of the Xiaojiang fault, but not in the Yangtze Block to the east. The S wave velocity profile reveals that intra‐crustal low‐velocity zones (IC‐LVZs) are strongly heterogeneous, with two LVZs in the middle and mid‐lower crust, respectively, in marked contrast to previous observations of a single LVZ. Combined with other observations, the two IC‐LVZs are interpreted as isolated channels of crustal flow at different depths beneath SE Tibet, resulting in the observed complex pattern of radial anisotropy and further elucidating patterns of flow and deformation.
Bacterial Endospores
Authors: Mury Sean P , Popham David L 
Published: February 2014

Abstract

The spores of bacteria formed mainly by members of the genera
Bacillus
and
Clostridium
are termed endospores because they develop singly within the mother or sporangial cells. Spore formation is a complex differentiation process involving two cells and a programme of gene expression requiring intracellular communication. Endospores exhibit complete metabolic dormancy and extreme resistance to multiple environmental insults, and can survive for centuries. The production of resistant spores by certain pathogenic bacterial species contributes to their transmission and difficulties in preventing their reoccurrence. Dormancy and resistance properties derive from alterations in the spore cell cytoplasmic contents, including dehydration, and from multiple integument layers. When presented with a nutrient‐rich environment, spores can rapidly germinate and re‐enter vegetative growth cycle.

Key Concepts:

Bacterial endospores can survive for decades and are highly resistant to numerous environmental insults.

The resistance properties of bacterial endospores contribute to their roles in food spoilage and in human and animal pathogenesis.

Bacterial endospores are cells with specialised modifications to their structure and contents.

Bacterial endospores are produced via a simple developmental process involving cooperative and regulated gene expression of two cells.

Heat resistance of bacterial endospores is determined by several factors, the most important being the relative dehydration of the spore core.

Bacterial endospores possess a unique mode of resistance to UV irradiation involving specialised DNA‐binding proteins.
Archaeal Cell Walls
Authors: Meyer Benjamin H , Albers Sonja‐Verena 
Published: February 2014

AbstractNext to the bacterial and eukaryal domains, Archaea form the third domain of life. One major difference to bacteria is the composition of the cell wall. The cell wall of most Archaea is formed by a proteinaceous surface (S‐) layer. S‐layer proteins have the intrinsic ability to form two‐dimensional crystals, which can have an oblique (p2), square (p4) or hexagonal (p3 or p6) symmetry. All currently studied archaeal S‐layer proteins were found to be modified by the attachment ofN‐linked and, in some cases, additionally byO‐linked glycans. Next to the S‐layer (glyco‐)proteins, sugar polymers like pseudomurein, methanochondroitin or heteropolysaccharides are also found in archaeal cell walls. These polymeric cell wall structures can either form the sole cell wall structure or be supported by an additional S‐layer cover. A few archaeal species even completely lack a cell wall.Key Concepts:Archaeal cell envelopes lack murein or a lipopolysaccharide (LPS)‐containing outer membrane.Most Archaea posses a glycosylated proteinaceous surface layer (S‐layer) as their sole cell wall structure.In some Archaea, the cell wall is composed of glycan polymers, like glutaminylglycan, heterosaccharide, methanochondroitin or pseudomurein.
Heterochromatin and Euchromatin
Authors: Eissenberg Joel C , Elgin Sarah CR 
Published: February 2014

Abstract

Eukaryotes are characterised by the extensive packaging of their genomes, initially in a nucleosomal array, and further into higher order domains. Differential packaging is used as a mechanism of gene regulation, with stable silencing of large domains achieved by packaging the
deoxyribonucleic acid (DNA)
into a heterochromatic structure. Chromosome rearrangements and transgene insertions that misplace euchromatic genes near or within the heterochromatin result in silencing of the euchromatic genes, testifying to a distinct heterochromatin assembly that can antagonise transcription. Most heterochromatic regions are rich in repetitious sequences, frequently derived from transposable elements, and such packaging helps to silence such elements. Domains of heterochromatin and euchromatin are defined by specific covalent modifications of histones and, in some cases, DNA, as well as by associations with a specific subset of nonhistone chromosomal proteins. Chromosomal domains may be targeted for heterochromatin formation by specific noncoding
ribonucleic acids (RNAs)
.

Key Concepts:

The chromatin of eukaryotes is differentially packaged into domains of euchromatin and heterochromatin.

Displacing a euchromatic gene to near or within the heterochromatin often results in silencing of the euchromatic gene in some of the cells in which it should be active, resulting in a variegating phenotype.

Euchromatin and heterochromatin are distinguishable biochemically by different covalent modifications of histones (and in some cases DNA) and by distinct nonhistone proteins.

Members of the HP1a chromo domain protein family bind methylated histone H3 and interact with the H3K9 histone methyltransferase to organise transcriptionally repressive heterochromatin.

The piRNA pathway is implicated in targeting transposon silencing through local heterochromatin formation.
Binary Fission in Bacteria
Authors: Margolin William 
Published: February 2014

Abstract

Given a suitable environment, most free‐living prokaryotic cells (including bacteria) will grow continually until, on reaching a critical size, they divide into two equal‐sized parts in a process called binary fission. To be successful, this process requires the accurate duplication and partition of the chromosomes, and subsequent splitting of the cytoplasm precisely at the cell midpoint. The latter process, known as cytokinesis, often uses a large transmembrane protein machine that includes homologues of actin and tubulin as well as enzymes that synthesise and degrade specific portions of the cell wall. The placement of this machine is often regulated by negatively acting morphogen gradients. Once assembled, numerous accessory proteins respond to various inputs to regulate how and when the machine constricts and cells physically separate.

Key Concepts:

The timing of chromosome duplication in bacteria responds to cell growth rate and initiates at a specific location only once per cell cycle.

Bacterial chromosomes are organised and condensed by DNA‐binding proteins, some of which are conserved from bacteria to humans.

Bacterial cells use homologues of eukaryotic cytoskeletal proteins actin and tubulin to organise their growth and division.

Morphogen gradients of negative spatial regulators help to position the cytokinetic ring in many bacteria.

Recent advances in synthetic biology of bacterial cytokinesis are increasing our understanding of key components.
Antibiotic Resistance Plasmids in Bacteria
Authors: Clewell Don B 
Published: February 2014

Abstract

Antibiotic resistance plasmids are bacterial extrachromosomal elements that carry genes conferring resistance to one or more antibiotics. They are notorious for their ability to transfer by conjugation between bacterial species and are significantly involved in the emergence and dissemination of multiple drug resistance associated with bacterial infections in humans. The information provided here includes some of the history and nature of antibiotic resistance as well as how plasmids have become significantly involved as intercellular carriers via the phenomenon of bacterial conjugation. The manner by which resistance determinants are able to move onto plasmids via their initial association with transposons and integrons is discussed. The existence of elements with both transpositional and conjugative properties, such as the conjugative transposons and integrative conjugative elements, is also noted.

Key Concepts:

Multiple antibiotic resistance represents a serious and growing clinical problem with regard to bacterial infections in humans.

Resistance genes are commonly found on plasmids, which are small extrachromosomal elements commonly found in bacteria.

Plasmids can vary widely with regard to their size and copy number in the cell.

Plasmids are commonly able to move from one bacterial cell to another by a mechanism known as conjugation, which involves cell‐to‐cell contact followed by transfer of a copy of plasmid DNA from a donor to a recipient.

Genes conferring antibiotic resistance are commonly found on elements known as integrons and transposons, which facilitate movement between different replicons such as between the bacterial chromosome and a plasmid.

Some transposable elements, known as conjugative transposons, also carry resistance traits; and, although unable to replicate autonomously, they can move from one bacterial cell to another by a plasmid‐like mechanism.

Excessive use of antibiotics in the treatment of human infections has, over time, contributed to the emergence and selection of resistant bacteria in the gut, a phenomenon that includes passage of resistance traits between nonpathogens and pathogens.
Bacterial Antibiotic Resistance
Authors: Martins Ana , Spengler Gabriella , Molnár József , Amaral Leonard 
Published: February 2014

Abstract

The mechanisms by which antibiotic resistance of bacteria takes place are discussed in detail. Among the mechanisms that have been recently elucidated are overexpressed efflux pumps that render the bacterium multidrug resistant; downregulation of porins; target modification; quorum sensing; biofilm production and secretion and plasmids that carry antibiotic resistance genes. The mechanisms discussed also include modulation by agents or genetic regulation that may provide improved antibiotic therapies.

Key Concepts:

Efflux pumps, porins and plasmid acquisition play an essential role in the development of multidrug resistance by bacteria.

Quorum sensing is essential in biofilm formation.

Efflux pumps must be essential for bacterial communication (quorum sensing).

Quorum sensing must play an important role in the development of resistance and bacterial survival.

Inhibition of EP and QS appear to be crucial to inhibit biofilm formation.