bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site-Specific Recombination by SSV2 Integrase: Substrate Requirement and Domain Functions
Authors: Zhan Zhengyan , Zhou Ju , Huang Li 
Published: August 2015

ABSTRACT

SSV-type integrases, encoded by fuselloviruses which infect the hyperthermophilic archaea of the
Sulfolobales
, are archaeal members of the tyrosine recombinase family. These integrases catalyze viral integration into and excision from a specific site on the host genome. In the present study, we have established an
in vitro
integration/excision assay for SSV2 integrase (Int
SSV2
). Int
SSV2
alone was able to catalyze both integration and excision reactions
in vitro
. A 27-bp specific DNA sequence is minimally required for the activity of the enzyme, and its flanking sequences influence the efficiency of integration by the enzyme in a sequence-nonspecific manner. The enzyme forms a tetramer through interactions in the N-terminal part (residues 1 to 80), interacts nonspecifically with DNA and performs chemical catalysis in the C-terminal part (residues 165 to 328), and appears to recognize and bind the specific site of recombination in the middle portion (residues 81 to 164). It is worth noting that an N-terminally truncated mutant of Int
SSV2
(residues 81 to 328), which corresponded to the putative product of the 3′-end sequence of the Int
SSV2
gene of the integrated SSV2 genome, was unable to form tetramers but possessed all the catalytic properties of full-length Int
SSV2
except for the slightly reduced recombination activity. Our results suggest that, unlike λ integrase, SSV-type integrases alone are capable of catalyzing viral DNA recombination with the host genome in a simple and reversible fashion.

IMPORTANCE
Archaea are host to a variety of viruses. A number of archaeal viruses are able to integrate their genome into the host genome. Many known archaeal viral integrases belong to a unique type, or the SSV type, of tyrosine recombinases. SSV-type integrases catalyze viral integration into and excision from a specific site on the host genome. However, the molecular details of the recombination process have yet to be fully understood because of the lack of an established
in vitro
recombination assay system. Here we report an
in vitro
assay for integration and excision by SSV2 integrase, a member of the SSV-type integrases. We show that SSV2 integrase alone is able to catalyze both integration and excision and reveal how different parts of the target DNA and the enzyme serve their roles in these processes. Therefore, our results provide mechanistic insights into a simple recombination process catalyzed by an archaeal integrase.
Breast Milk of HIV-Positive Mothers Has Potent and Species-Specific
In Vivo
HIV-Inhibitory Activity
Authors: Wahl Angela , Baker Caroline , Spagnuolo Rae Ann , Stamper Lisa W. , Fouda Genevieve G. , Permar Sallie R. , Hinde Katie , Kuhn Louise , Bode Lars , Aldrovandi Grace M. , Garcia J. Victor 
Published: August 2015

ABSTRACT

Despite the nutritional and health benefits of breast milk, breast milk can serve as a vector for mother-to-child HIV transmission. Most HIV-infected infants acquire HIV through breastfeeding. Paradoxically, most infants breastfed by HIV-positive women do not become infected. This is potentially attributed to anti-HIV factors in breast milk. Breast milk of HIV-negative women can inhibit HIV infection. However, the HIV-inhibitory activity of breast milk from HIV-positive mothers has not been evaluated. In addition, while significant differences in breast milk composition between transmitting and nontransmitting HIV-positive mothers have been correlated with transmission risk, the HIV-inhibitory activity of their breast milk has not been compared. This knowledge may significantly impact the design of prevention approaches in resource-limited settings that do not deny infants of HIV-positive women the health benefits of breast milk. Here, we utilized bone marrow/liver/thymus humanized mice to evaluate the
in vivo
HIV-inhibitory activity of breast milk obtained from HIV-positive transmitting and nontransmitting mothers. We also assessed the species specificity and biochemical characteristics of milk's
in vivo
HIV-inhibitory activity and its ability to inhibit other modes of HIV infection. Our results demonstrate that breast milk of HIV-positive mothers has potent HIV-inhibitory activity and indicate that breast milk can prevent multiple routes of infection. Most importantly, this activity is unique to human milk. Our results also suggest multiple factors in breast milk may contribute to its HIV-inhibitory activity. Collectively, our results support current recommendations that HIV-positive mothers in resource-limited settings exclusively breastfeed in combination with antiretroviral therapy.

IMPORTANCE
Approximately 240,000 children become infected with HIV annually, the majority via breastfeeding. Despite daily exposure to virus in breast milk, most infants breastfed by HIV-positive women do not acquire HIV. The low risk of breastfeeding-associated HIV transmission is likely due to antiviral factors in breast milk. It is well documented that breast milk of HIV-negative women can inhibit HIV infection. Here, we demonstrate, for the first time, that breast milk of HIV-positive mothers (nontransmitters and transmitters) inhibits HIV transmission. We also demonstrate that breast milk can prevent multiple routes of HIV acquisition and that this activity is unique to human milk. Collectively, our results support current guidelines which recommend that HIV-positive women in resource-limited settings exclusively breastfeed in combination with infant or maternal antiretroviral therapy.
Functional Comparison of Mx1 from Two Different Mouse Species Reveals the Involvement of Loop L4 in the Antiviral Activity against Influenza A Viruses
Authors: Verhelst Judith , Spitaels Jan , Nürnberger Cindy , De Vlieger Dorien , Ysenbaert Tine , Staeheli Peter , Fiers Walter , Saelens Xavier 
Published: August 2015

ABSTRACTThe interferon-inducedMx1gene is an important part of the mammalian defense against influenza viruses.Mus musculusMx1 inhibits influenza A virus replication and transcription by suppressing the polymerase activity of viral ribonucleoproteins (vRNPs). Here, we compared the anti-influenza virus activity of Mx1 fromMus musculusA2G with that of its ortholog fromMus spretus. We found that the antiviral activity ofM. spretusMx1 was less potent than that ofM. musculusMx1. Comparison of theM. musculusMx1 sequence with theM. spretusMx1 sequence revealed 25 amino acid differences, over half of which were present in the GTPase domain and 2 of which were present in loop L4. However, thein vitroGTPase activity of Mx1 from the two mouse species was similar. Replacement of one of the residues in loop L4 inM. spretusMx1 by the corresponding residue of A2G Mx1 increased its antiviral activity. We also show that deletion of loop L4 prevented the binding of Mx1 to influenza A virus nucleoprotein and, hence, abolished the antiviral activity of mouse Mx1. These results indicate that loop L4 of mouse Mx1 is a determinant of antiviral activity. Our findings suggest that Mx proteins from different mammals use a common mechanism to inhibit influenza A viruses.IMPORTANCEMx proteins are evolutionarily conserved in vertebrates and inhibit a wide range of viruses. Still, the exact details of their antiviral mechanisms remain largely unknown. Functional comparison of theMxgenes from two species that diverged relatively recently in evolution can provide novel insights into these mechanisms. We show that bothMus musculusA2G Mx1 andMus spretusMx1 target the influenza virus nucleoprotein. We also found that loop L4 in mouse Mx1 is crucial for its antiviral activity, as was recently reported for primate MxA. This indicates that human and mouse Mx proteins, which have diverged by 75 million years of evolution, recognize and inhibit influenza A viruses by a common mechanism.
LONG RANGE DEPENDENCE AND THE DYNAMICS OF EXPLOITED FISH POPULATIONS
Authors: MENDES HUGO C. , MURTA ALBERTO , MENDES R. VILELA 
Published: August 2015

Long range dependence or long memory is a feature of many processes in the natural world, which provides important insights on the underlying mechanisms that generate the observed data. The usual tools available to characterize the phenomenon are mostly based on second-order correlations. However, the long memory effects may not be evident at the level of second-order correlations and may require a deeper analysis of the nature of the stochastic processes. After a short review of the notions and tools used to characterize long range dependence, we analyze data related to the abundance of exploited fish populations which provides an example of higher order long range dependence. In particular, we find that fish population time series were thought to have short term memory only because previous studies used averages over species instead of modeling each species individually.
Synthesis of Nanosized Titanium Oxide and Nitride Through Vacuum Arc Plasma Expansion Technique
Authors: Lepeshev A. A. , Karpov I. V. , Ushakov A. V. , Fedorov L. Yu. , Shaihadinov A. A. 
Published: August 2015

Physical vapor deposition techniques such vacuum arc plasma deposition — which are very commonly used in thin film technology — appear to hold much promise for the synthesis of nanocrystalline thin films as well as nanoparticles. Monodisperse and spherical titanium oxide (TiO2) and nitride nanoparticles were produced at room temperature as a cluster beam in the gas phase using a cluster-deposition source. Using the basic principles of the gas condensation method, this study has developed vacuum arc nanoparticle synthesis system. We demonstrate that major process deposition parameter is the pressure in the plasma chamber. This is the major advantage of these techniques over thermal evaporation. Our method affords TiN powders with high specific surface areas exceeding 200[Formula: see text]m2[Formula: see text]g[Formula: see text]. TEM micrograph of TiO2 nanoparticles prepared at an oxygen pressure of 60[Formula: see text]Pa show an average particle size of 6[Formula: see text]nm. TiO2 nanoparticles prepared at an oxygen pressure of 70[Formula: see text]Pa were observed to not have a reduced average particle size.
Crossing Modalities: A Cognitive Semantics Perspective on Quoting
Authors: Lampert Martina 
Published: August 2015

Elaborating on Talmy (2007a, forthcoming) and Lampert (2013, 2014), this follow- up study probes into quoting as an attention-and modality-sensitive phenomenon at the interface of speech and writing, taking inaugural addresses from Kennedy to Obama as cases in point.
Lexicalized to redirect some attention from a quotation’s referential content to concomitants closely associated with it, quotatives medium-specifically prime speech-internal properties of their targets, animating the ‘other voice’ through prosodic and gestural prompts in face-to-face interactions, while figural prompts demarcate verbatim citations in print.
Quotations from pre-scripted videotaped presidential inaugurals reveal a fundamental underlying cognitive principle: The orators refrain from ‘translating’ the figural delimiters into prosodic and gestural primes but rely on verbal primes to acknowledge another voice. Corroborating Talmy’s (2007b) analysis of the verbal mode’s evolutionary advantage over the analog devices available to the channels of oral performance, the quotative construction proves ultimately governed by a linguistic medium’s production and reception circumstances.
Distinguishing between Unorganized and Organized Convection When Examining Land–Atmosphere Relationships
Authors: Wang Jessica K. , Ford Trent W. , Quiring Steven M. 
Published: August 2015

AbstractIn this study, the robustness of a previously developed classification system that categorizes convective thunderstorm events initiated during various synoptic and dynamic conditions is analyzed. This classification system was used to distinguish between organized and unorganized convection and then used to determine whether unorganized convection occurs preferentially over wet or dry soils. The focus is on 12 events that occurred in synoptically benign (SB) environments where the Great Plains low-level jet was not present (noLLJ), and whether these events were accurately classified as unorganized convection is evaluated. Although there is a small sample size, the results show that the classification system fails to differentiate between local unorganized convection and large-scale organized convection under SB–noLLJ conditions. The authors conclude that past studies that have used this classification to study how soil moisture influences unorganized convection should be revisited. Additional variables and/or alternative precipitation datasets should be employed to enhance the robustness of the classification system.
The Role of Shallow Cloud Moistening in MJO and Non-MJO Convective Events over the ARM Manus Site
Authors: Zermeño-Díaz David M. , Zhang Chidong , Kollias Pavlos , Kalesse Heike 
Published: August 2015

Abstract
Observations from the Atmospheric Radiation Measurement Program (ARM) site at Manus Island in the western Pacific and (re)analysis products are used to investigate moistening by shallow cumulus clouds and by the circulation in large-scale convective events. Large-scale convective events are defined as rainfall anomalies larger than one standard deviation for a minimum of three consecutive days over a 10° × 10° domain centered at Manus. These events are categorized into two groups: Madden–Julian oscillation (MJO) events, with eastward propagation, and non-MJO events, without propagation. Shallow cumulus clouds are identified as continuous time–height echoes from 1-min cloud radar observations with their tops below the freezing level and their bases within the boundary layer. Daily moistening tendencies of shallow clouds, estimated from differences between their mean liquid water content and precipitation over their presumed life spans, and those of physical processes and advection from (re)analysis products are compared with local moistening tendencies from soundings. Increases in low-level moisture before rainfall peaks of MJO and non-MJO events are evident in both observations and reanalyses. Before and after the rainfall peaks of these events, precipitating and nonprecipitating shallow clouds exist all the time, but their occurrence fluctuates randomly. Their contributions to moisture tendencies through evaporation of condensed water are evident. These clouds provide perpetual background moistening to the lower troposphere but do not cause the observed increase in low-level moisture leading to rainfall peaks. Such moisture increase is mainly caused by anomalous nonlinear zonal advection.
Influence of Equatorial Waves on the Genesis of Super Typhoon Haiyan (2013)
Authors: Shu Shoujuan , Zhang Fuqing 
Published: August 2015

Abstract
The influence of equatorial wave disturbances on the genesis of Super Typhoon Haiyan (2013) is investigated through spectral, composite, and ensemble sensitivity analysis of various observational datasets in combination with predictions from an operational ensemble. Under the favorable large-scale environmental conditions of the Asian monsoon combined with the Madden–Julian oscillation (MJO), the incipient Haiyan develops from a cyclonic disturbance that originates from a train of westward-propagating mixed Rossby–gravity (MRG) waves. Haiyan eventually develops in the monsoon trough region at the leading edge of the moist MJO phase that has strong low-level convergence, high moisture content, and weak shear, along with high sea surface temperature. These favorable environmental conditions promote the intensification of deep moist convection that facilitates the development of the cyclonic disturbance from an MRG wave into a tropical depression, which later intensifies rapidly into Super Typhoon Haiyan, one of the world’s strongest and most destructive tropical storms ever recorded. Results from ensemble sensitivity analyses are consistent with this finding and further show that the uncertainties in tropical waves and their interactions can impact the large-scale environment surrounding Haiyan’s precursor and therefore limit the predictability of tropical cyclone formation and intensity. The better-performing members tend to have a stronger initial MRG wave disturbance, which provides a stronger initial seed for the later development of the storm, as well as a stronger moist MJO wave in the tropical region, which not only promotes deep convection near the precursor location, but also reduces the environmental vertical wind shear by strengthening the tropical westerlies.
A Multiregion Assessment of Observed Changes in the Areal Extent of Temperature and Precipitation Extremes
Authors: Dittus Andrea J. , Karoly David J. , Lewis Sophie C. , Alexander Lisa V. 
Published: August 2015

Abstract
This study examines trends in the area affected by temperature and precipitation extremes across five large-scale regions using the climate extremes index (CEI) framework. Analyzing changes in temperature and precipitation extremes in terms of areal fraction provides information from a different perspective and can be useful for climate monitoring. Trends in five temperature and precipitation components are analyzed, calculated using a new method based on standard extreme indices. These indices, derived from daily meteorological station data, are obtained from two global land-based gridded extreme indices datasets. The four continental-scale regions of Europe, North America, Asia, and Australia are analyzed over the period from 1951 to 2010, where sufficient data coverage is available. These components are also computed for the entire Northern Hemisphere, providing the first CEI results at the hemispheric scale. Results show statistically significant increases in the percentage area experiencing much-above-average warm days and nights and much-below-average cool days and nights for all regions, with the exception of North America for maximum temperature extremes. Increases in the area affected by precipitation extremes are also found for the Northern Hemisphere regions, particularly Europe and North America.
Need for Caution in Interpreting Extreme Weather Statistics
Authors: Sardeshmukh Prashant D. , Compo Gilbert P. , Penland Cécile 
Published: August 2015

AbstractGiven the reality of anthropogenic global warming, it is tempting to seek an anthropogenic component in any recent change in the statistics of extreme weather. This paper cautions that such efforts may, however, lead to wrong conclusions if the distinctively skewed and heavy-tailed aspects of the probability distributions of daily weather anomalies are ignored or misrepresented. Departures of several standard deviations from the mean, although rare, are far more common in such a distinctively non-Gaussian world than they are in a Gaussian world. This further complicates the problem of detecting changes in tail probabilities from historical records of limited length and accuracy.A possible solution is to exploit the fact that the salient non-Gaussian features of the observed distributions are captured by so-called stochastically generated skewed (SGS) distributions that include Gaussian distributions as special cases. SGS distributions are associated with damped linear Markov processes perturbed by asymmetric stochastic noise and as such represent the simplest physically based prototypes of the observed distributions. The tails of SGS distributions can also be directly linked to generalized extreme value (GEV) and generalized Pareto (GP) distributions. The Markov process model can be used to provide rigorous confidence intervals and to investigate temporal persistence statistics. The procedure is illustrated for assessing changes in the observed distributions of daily wintertime indices of large-scale atmospheric variability in the North Atlantic and North Pacific sectors over the period 1872–2011. No significant changes in these indices are found from the first to the second half of the period.
Evaluating the Hardness Characteristics of Hail through Compressive Strength Measurements
Authors: Giammanco Ian M. , Brown Tanya M. , Grant Rosemarie G. , Dewey Douglas L. , Hodel Jon D. , Stumpf Robert A. 
Published: August 2015

AbstractThroughout historical literature anecdotal or visual observations have been used to describe the hardness property of hailstones (e.g., hard, soft, slushy). A unique field measurement device was designed and built to apply a compressive force to the point of fracture on hailstones in the field. The device uses a pistol-grip clamp to apply a compressive load to a hailstone and integrates a fast-response load cell and associated data acquisition components to measure the applied force through the point of fracture. The strain rate applied to the stone is fast enough to produce a brittle failure, and the peak compressive force is appropriately scaled by the cross-sectional area to produce a compressive stress value. When compared to an Instron universal testing machine (UTM), the field measurement device exhibited a low bias induced by measurement hardware sampling limits. When a low-pass filter was applied to the Instron data to replicate the hardware properties of the field measurement device, good agreement was found for compressive force tests performed on laboratory ice spheres, and it was clear the device was capturing a relative measure of strength. The mean compressive stress for natural hail was similar to that of pure ice spheres, but individual thunderstorm events exhibited variability. Laboratory ice spheres also showed significant variability, which argues for large sample sizes when testing any material for impact resistance.
Microphysical Properties of Slow-Falling and Fast-Falling Ice Pellets Formed by Freezing Associated with Evaporative Cooling
Authors: Nagumo Nobuhiro , Fujiyoshi Yasushi 
Published: August 2015

Abstract
This paper describes a numerical and observational study focused on ice-pellet formation and microphysical properties near 0°C from an ice-pellet-dominated storm associated with an unusually warm and dry atmosphere on 10 April 2005, in Sapporo, Japan. A one-dimensional numerical model simulation indicated that precipitation particle temperatures were sensitive to environmental temperature and relative humidity and close to the wet-bulb temperature. The simulation demonstrated that completely melted snowflakes could refreeze by evaporative cooling. Moreover, initial freezing could be explained by contact ice nucleation at the height of the minimum wet-bulb temperature.
Observations using a 2D video distrometer (2DVD) indicated that ice pellets exhibited two modes of fall velocities at surface temperatures near 0°C during the same time period: slow falling and fast falling. The slow-falling ice pellets exhibited a velocity similar to the average terminal velocity of hail, whereas the velocities of the fast-falling ice pellets were closer to those of raindrops. Surface roundness and fracturing characteristics of ice pellets suggest that slow-falling ice pellets froze rapidly and uniformly in a relatively cold dry layer with a wet-bulb temperature near −4°C. In contrast, the fast-falling ice pellets exhibited the properties of ice particles with a wet smooth surface, suggesting that they froze slowly in a relatively warm layer by contacting ice crystals or splinters generated by preceding slow-falling ice pellets.