bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR‐Cas systems and RNA‐guided interference
Authors: Barrangou Rodolphe 
Published: March 2013

AbstractClustered regularly interspaced short palindromic repeats (CRISPR) together with associated sequences (cas) form the CRISPR‐Cas system, which provides adaptive immunity against viruses and plasmids in bacteria and archaea. Immunity is built through acquisition of short stretches of invasive nucleic acids into CRISPR loci as ‘spacers'. These immune markers are transcribed and processed into small noncoding interfering CRISPR RNAs (crRNAs) that guide Cas proteins toward target nucleic acids for specific cleavage of homologous sequences. Mechanistically, CRISPR‐Cas systems function in three distinct stages, namely: (1) adaptation, where new spacers are acquired from invasive elements for immunization; (2) crRNA biogenesis, where CRISPR loci are transcribed and processed into small interfering crRNAs; and (3) interference, where crRNAs guide the Cas machinery to specifically cleave homologous invasive nucleic acids. A number of studies have shown that CRISPR‐mediated immunity can readily increase the breadth and depth of virus resistance in bacteria and archaea. CRISPR interference can also target plasmid sequences and provide a barrier against the uptake of undesirable mobile genetic elements. These inheritable hypervariable loci provide phylogenetic information that can be insightful for typing purposes, epidemiological studies, and ecological surveys of natural habitats and environmental samples. More recently, the ability to reprogram CRISPR‐directed endonuclease activity using customizable small noncoding interfering RNAs has set the stage for novel genome editing and engineering avenues. This review highlights recent studies that revealed the molecular basis of CRISPR‐mediated immunity, and discusses applications of crRNA‐guided interference. WIREs RNA 2013, 4:267–278. doi: 10.1002/wrna.1159This article is categorized under:

RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms
Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs
Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action
Effects of management intensity and orchard features on bird communities in winter
Authors: Myczko Łukasz , Rosin Zuzanna M. , Skórka Piotr , Wylegała Przemysław , Tobolka Marcin , Fliszkiewicz Monika , Mizera Tadeusz , Tryjanowski Piotr 
Published: March 2013

AbstractThe knowledge and conservation of diminishing valuable habitats in agricultural landscapes are of key importance in saving declining farmland biodiversity. One of these habitats is the traditional orchard whose role in supporting birds is still poorly known, especially in winter. We counted birds in 106 orchards differing in management intensity (abandoned, traditional, and intensive) during December 2009 and January 2010 in Wielkopolska, western Poland and measured site characteristics and composition of surrounding landscapes for every orchard. Old abandoned and traditionally managed orchards had significantly higher bird species richness than intensive ones. Irrespective of orchard type, bird species richness as well as density were positively influenced by the cover of unmown herb layer in orchards and tree diversity. Tree and fruit densities positively affected bird species richness and density mainly in abandoned orchards while in other orchard types the effect of these variables was less pronounced. Land cover diversity in a landscape had a positive effect on species richness and density mostly in abandoned orchards and we believe that this effect reflects the elevated utilization of such orchards by birds from the surrounding landscape. Thus, abandoned, as well as traditionally managed orchards seems to be especially important habitats that offer food source and refuge for wintering birds and should be protected. We propose to diversify fruit production by planting various tree species, leaving part of the herb layer unmown and several trees unharvested in intensive orchards in order to improve suitability of modern orchards for birds.
Down‐Regulation of Hepatic Stearoyl‐CoA Desaturase‐1 Expression by Fucoxanthin via Leptin Signaling in Diabetic/Obese KK‐Ay Mice
Authors: Beppu Fumiaki , Hosokawa Masashi , Yim Mi‐Jin , Shinoda Taro , Miyashita Kazuo 
Published: March 2013

AbstractStearoyl‐coenzyme A desaturase‐1 (SCD1) is a rate‐limiting enzyme that catalyzes the biosynthesis of monounsaturated fatty acids from saturated fatty acids. Recently, SCD1 down‐regulation has been implicated in the prevention of obesity, and the improvement of insulin and leptin sensitivity. In this study, we examined the effect of fucoxanthin, a marine carotenoid, on hepatic SCD1 in obese mouse models of hyperleptinemia KK‐Ay and leptin‐deficiency ob/ob. In KK‐Ay mice, providing a diet containing 0.2 % fucoxanthin for 2 weeks markedly suppressed SCD1 mRNA and protein expressions in the liver. The fatty acid composition of liver lipids was also affected by an observed decrease in the ratio of oleic acid to stearic acid. Furthermore, serum leptin levels were significantly decreased in hyperleptinemia KK‐Ay mice after 2 weeks of fucoxanthin feeding. However, the suppressive effects of fucoxanthin on hepatic SCD1 and body weight gain were not observed in ob/ob mice. These results show that fucoxanthin down‐regulates SCD1 expression and alters fatty acid composition of the liver via regulation of leptin signaling in hyperleptinemia KK‐Ay mice but not in leptin‐deficient ob/ob mice.
Brugada syndrome and early repolarization syndrome: Cellular basis and clinical features
Authors: Nam Gi‐Byoung 
Published: March 2013

AbstractBrugada syndrome (BS) and early repolarization syndrome (ERS) are newly introduced electrical disorders responsible for ventricular fibrillation (VF) and sudden cardiac death in patients with structurally normal hearts. The electrocardiographic J wave, a hallmark of these two syndromes, plays a critical role in the pathophysiology of malignant ventricular tachyarrhythmias. BS and ERS share many clinical characteristics, including male preponderance, circadian distribution of VF episodes, prevalence of concomitant atrial tachyarrhythmias, dynamic behavior of J waves, and response to therapeutic managements. In this review, we compare the key clinical manifestations of BS and ERS with their underlying cellular electrophysiologic mechanisms.
Effect of small asymmetries on axisymmetric stenotic flow
Authors: Griffith Martin D. , Leweke Thomas , Thompson Mark C. , Hourigan Kerry 
Published: March 2013

AbstractFlow through axisymmetric and eccentric sinuous stenoses is investigated numerically, for Reynolds numbers up to 400. The eccentricity consists of an offset of the stenosis throat. A range of stenosis eccentricity is tested; the wake flow is found to be highly sensitive to small eccentricities in the stenosis geometry, even with stenosis offsets of the order of the machining precision of experimental test-sections. Comparisons are made between the numerically simulated flow through stenoses with small eccentricities and results from the literature of non-axisymmetric flows through nominally axisymmetric geometries. The effect of distortion to the inlet Poiseuille velocity profile is also investigated and found to have a significantly less severe effect on the downstream wake flow than geometric eccentricity.
HOSPITAL-BASED HEALTH TECHNOLOGY ASSESSMENT FOR INNOVATIVE MEDICAL DEVICES IN UNIVERSITY HOSPITALS AND THE ROLE OF HOSPITAL PHARMACISTS: LEARNING FROM INTERNATIONAL EXPERIENCE
Authors: Martelli Nicolas , Lelong Anne-Sophie , Prognon Patrice , Pineau Judith 
Published: March 2013

Objectives: Several models of hospital-based health technology assessment (HTA) have been developed worldwide, for the introduction of innovative medical devices and support evidence-based decision making in hospitals. Two such models, the HTA unit and mini-HTA models, are widespread in university hospitals and involve various stakeholders. The purpose of this work was to highlight the potential role of hospital pharmacists in hospital-based HTA activities.Methods: We searched for articles, reviews, and letters relating to hospital-based HTA, as defined by the Hospital-Based Health Technology Assessment Worldwide Surveypublished by the Health Technology Assessment International (HTAi) Society, in the Health Technology Assessment database, MEDLINE, EMBASE, and hospital pharmacyjournals.Results: The number of university hospitals performing hospital-based HTA has increased since the 2008 Hospital-Based Health Technology Assessment Worldwide Survey. Our own experience and international findings show that hospital pharmacists already contribute to hospital-based HTA activities and have developed study interpretation skills and a knowledge of medical devices.Conclusions: Promoting multidisciplinary approaches is one of the key success factors in hospital-based HTA. Hospital pharmacists occupy a position between hospital managers, clinicians, health economists, biomedical engineers, and patients and can provide a new perspective. In the future, hospital pharmacists are likely to become increasingly involved in hospital-based HTA activities.
CASE STUDIES THAT ILLUSTRATE DISINVESTMENT AND RESOURCE ALLOCATION DECISION-MAKING PROCESSES IN HEALTH CARE: A SYSTEMATIC REVIEW
Authors: Polisena Julie , Clifford Tammy , Elshaug Adam G. , Mitton Craig , Russell Erin , Skidmore Becky 
Published: March 2013

Objective:Technological change accounts for approximately 25 percent of health expenditure growth. To date, limited research has been published on case studies of disinvestment and resource allocation decision making in clinical practice. Our research objective is to systematically review and catalogue the application of frameworks and tools for disinvestment and resource allocation decision making in health care.Methods:An electronic literature search was executed for studies on disinvestment, obsolete and ineffective technologies, and priority healthcare setting, published from January 1990 until January 2012. Databases searched were MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, Embase, The Cochrane Library, PubMed, and HEED.Results:Fourteen case studies on the application of frameworks and tools for disinvestment and resource allocation decisions were included. Most studies described the application of program budgeting and marginal analysis (PBMA), and two reports used health technology assessment (HTA) methods for coverage decisions in a national fee-for-service structure. Numerous healthcare technologies and services were covered across the studies. We describe the multiple criteria considered for decision making, and the strengths and limitations of these frameworks and tools are highlighted.Conclusions:Disinvestment and resource allocation decisions require evidence to ensure their transparency and objectivity. PBMA was used to assess resource allocation of health services and technologies in a fixed budget jurisdiction, while HTA reviews focused on specific technologies, principally in fee-for-service structures. Future research can review the data requirements and explore opportunities to increase the quantity of available evidence for disinvestment and resource allocation decisions.
Populations of breeding birds in Byers Peninsula, Livingston Island, South Shetland Islands
Authors: Gil-Delgado J.A. , González-Solís J. , Barbosa A. 
Published: March 2013

AbstractData about breeding populations of birds in the Antarctica are rare and fragmented. Thus, information about the status of the breeding populations of Antarctic birds is crucial given the current scenario of climate change, which is particularly acute in Antarctica. This paper presents new information about the populations of the Antarctic tern Sterna vittata, the kelp gull Larus dominicanus, the southern giant petrel Macronectes giganteus, the Antarctic skua Catharacta antarctica lonnbergi, the chinstrap penguin Pygoscelis antarctica and the gentoo penguin Pygoscelis papua on Byers Peninsula (Livingston Island, South Shetland Islands). We used line transects counts to estimate both densities and numbers of nests of the different species. We estimate that there are 398.96 birds km-2 of southern giant petrels (2793 individuals), 62.4 birds km-2 of Antarctic tern (3746 individuals) and 269.1 birds km-2 of kelp gull (1884 individuals). Furthermore, we found 15 nests of Antarctic skua in 25 km2, from which we can estimate that 60–91 birds must breed on Byers Peninsula. We also censused two colonies of gentoo penguins (3000 and 1200 pairs) and 50 pairs of chinstrap. Compared to previous estimates, gentoo penguins seem to have increased whereas chinstrap penguin have decreased. Finally, the populations of Antarctic tern, southern giant petrel and kelp gull have stabilized or slightly increased.
Chronostratigraphy of the sedimentary record of Limnopolar Lake, Byers Peninsula, Livingston Island, Antarctica
Authors: Toro Manuel , Granados Ignacio , Pla Sergi , Giralt Santiago , Antoniades Dermot , Galán Luis , Cortizas Antonio Martínez , Lim Hyoun Soo , Appleby Peter G. 
Published: March 2013

AbstractThe chronostratigraphy of the sedimentary record of Limnopolar Lake, located on Byers Peninsula (Livingston Island, South Shetland Islands, Maritime Antarctica), is described based on radionuclides and radiocarbon age dating. The oldest moss macrofossil age was 6700±50 yrbp(7510±80 cal yrbp) from which the age/depth model estimates a basal age for the sedimentary record ofc.8300 cal yrbp, suggesting an earlier deglaciation of Byers Peninsula than reported in previous studies. Lithological units and other stratigraphic zones are described throughout the sediment core, showing different mineralogical composition and a fine alternation of clays and silty clays and moss layers ofDrepanocladus longifolius.Based on magnetic susceptibility analyses, a number of probable primary and reworked tephra layers were identified, seven of them confirmed by SEM observations, and most of them in agreement with the regional tephrachronology stratigraphy for the north-west Antarctic Peninsula. Sedimentation rates showed no significant changes during the last 5000 years with the exception of an abrupt event that took place around 5400 cal yrbp, which implied the sedimentation ofc.30 cm of clays in a very short time, probably related to a period of glacial re-advance that caused abrupt changes in geomorphological processes in the catchment.
Changes in radiobiological parameters in 131Cs permanent prostate implants
Authors: Kehwar Than S. , Jones Heather A. , Huq M. Saiful , Smith Ryan P. 
Published: March 2013

AbstractIn prostate permanent implants using 131Cs seeds, the prostatic edema developed during the implantation procedure, increases the separation between the seeds. This leads to a decrease in the prostate coverage and thus causes an edema induced dose reduction, which results in an increase in tumour cell surviving fraction (SF) with a corresponding decrease in tumour control probability (TCP). To investigate the impact of edema on the SF and the TCP, the expression of the SF of the linear quadratic (LQ) model was extended to account for the effects of edema using the exponential nature of edema resolution and the dose delivered to the edematous prostate. The SF and the TCP for edematous prostate implants were calculated for 31 patients who underwent real time 131Cs permanent seed implantation. The dose delivered to the edematous prostate was calculated to compute the SF and the TCP for these patients for edema half lives (EHL) ranging from 4 days to 34 days and for edemas of magnitudes (M0) varying from 5 to 60% of the actual prostate volume.A reduction in the dose delivered to the edematous prostate was found with the increase of EHL and edema magnitude which results in an increase of the SF, and corresponding decrease in the TCP. The dose reductions in 131Cs implants varied from 1.1% (for EHL = 4 days and M0 = 5%) to 32.3% (for EHL = 34 days and M0 = 60%). These are higher than the dose reduction in 125I implants, which vary from 0.3% (for EHL = 4 days and M0 = 5%) to 17.5% (for EHL = 34 days and M0 = 60%). As edema half life increased from 4 days to 34 days and edema magnitude increased from 5 to 60% the SF increased by 4.57 log, and the TCP decreased by 0.80. Compensation of edema induced increase in the SF and decrease in the TCP in 131Cs seed implants should be carefully done by redefining seed positions with the guidance of post-needle plans. The presented model in this study can be used to estimate the SF or the TCP for pre plan or real time permanent prostate implants using day 0 post-implant CT images.
A search for pulsars in the central parsecs of the Galactic center
Authors: Siemion Andrew , Bailes Matthew , Bower Geoff , Chennamangalam Jayanth , Cordes Jim , Demorest Paul , Deneva Julia , Desvignes Gregory , Ford John , Frail Dale , Jones Glenn , Kramer Michael , Lazio Joseph , Lorimer Duncan , McLaughlin Maura , Ransom Scott , Roshi Anish , Wagner Mark , Werthimer Dan , Wharton Robert 
Published: March 2013

AbstractThe discovery of a pulsar or pulsars orbiting near the Galactic Center (GC) could offer an unprecedented probe of strong-field gravity, the properties of our galaxy's supermassive black hole and insights into the paradoxical star formation history of the region. However, searching for pulsars near the GC is severely hampered by the large electron densities along our line of sight and the scattering-induced pulse broadening of the pulsar emission observed through it. As the broadened pulse length approaches the pulsar period, the periodicity in pulsar emission becomes nearly undetectable. Searches extended to higher frequencies, in an effort to reduce scattering, suffer from reduced intrinsic flux, higher system temperatures and increased atmospheric opacity. We are currently attempting to mitigate the challenges associated with searching for pulsars near the GC by employing new wide bandwidth receivers, upgraded IF distribution systems and novel digital spectrometers in a GC pulsar search campaign at the Green Bank Telescope in West Virginia, USA.Our search will cover two frequency bands, from 12-15 GHz (Ku Band) and 18-26 GHz (K Band), during a total of approximately 30 hours of observations, with expected characteristic 10-sigma sensitivities between 5-10 micro-Jy. Our first observations are scheduled for mid-March 2012. Here we will present the status of our observations and initial results.
Structure of Quark Stars
Authors: Weber Fridolin , Orsaria Milva , Rodrigues Hilario , Yang Shu-Hua 
Published: March 2013

AbstractThis paper gives an brief overview of the structure of hypothetical strange quarks stars (quark stars, for short), which are made of absolutely stable 3-flavor strange quark matter. Such objects can be either bare or enveloped in thin nuclear crusts, which consist of heavy ions immersed in an electron gas. In contrast to neutron stars, the structure of quark stars is determined by two (rather than one) parameters, the central star density and the density at the base of the crust. If bare, quark stars possess ultra-high electric fields on the order of 1018 to 1019 V/cm. These features render the properties of quark stars more multifaceted than those of neutron stars and may allow one to observationally distinguish quark stars from neutron stars.
Numerical modeling of core-collapse supernovae and compact objects
Authors: Sumiyoshi Kohsuke 
Published: March 2013

AbstractMassive stars (M ≥ 10M⊙) end their lives with spectacular explosions due to gravitational collapse. The collapse turns the stars into compact objects such as neutron stars and black holes with the ejection of cosmic rays and heavy elements. Despite the importance of these astrophysical events, the mechanism of supernova explosions has been an unsolved issue in astrophysics. This is because clarification of the supernova dynamics requires the full knowledge of nuclear and neutrino physics at extreme conditions, and large-scale numerical simulations of neutrino radiation hydrodynamics in multi-dimensions. This article is a brief overview of the understanding (with difficulty) of the supernova mechanism through the recent advance of numerical modeling at supercomputing facilities. Numerical studies with the progress of nuclear physics are applied to follow the evolution of compact objects with neutrino emissions in order to reveal the birth of pulsars/black holes from the massive stars.
How “free” are free neutrons in neutron-star crusts and what does it imply for pulsar glitches?
Authors: Chamel N. 
Published: March 2013

AbstractThe neutron superfluid permeating the inner crust of mature neutron stars is expected to play a key role in various astrophysical phenomena like pulsar glitches. Despite the absence of viscous drag, the neutron superfluid can still be coupled to the solid crust due to non-dissipative entrainment effects. Entrainment challenges the interpretation of pulsar glitches and suggests that a revision of the interpretation of other observed neutron-star phenomena might be necessary.
Rotating Radio Transients and their place among pulsars
Authors: Burke-Spolaor S. 
Published: March 2013

AbstractSix years ago, the discovery of Rotating Radio Transients (RRATs) marked what appeared to be a new type of sparsely-emitting pulsar. Since 2006, more than 70 of these objects have been discovered in single-pulse searches of archival and new surveys. With a continual inflow of new information about the RRAT population in the form of new discoveries, multi-frequency follow ups, coherent timing solutions, and pulse rate statistics, a view is beginning to form of the place in the pulsar population RRATs hold. Here we review the properties of neutron stars discovered through single pulse searches. We first seek to clarify the definition of the term RRAT, emphasising that “the RRAT population” encompasses several phenomenologies. A large subset of RRATs appears to represent the tail of an extended distribution of pulsar nulling fractions and activity cycles; these objects present several key open questions remaining in this field.
Discoveries of Rotating Radio Transients in the 350 MHz Green Bank Telescope Drift-scan Survey
Authors: Karako-Argaman Chen ,   the GBT Drift-scan Collaboration
Published: March 2013

AbstractRotating Radio Transients (RRATs) are a class of pulsars characterized by sporadic bursts of radio emission, which make them difficult to detect in typical periodicity-based pulsar searches. Using newly developed post-processing techniques for automatically identifying single bright astrophysical pulses, such as those emitted from RRATs, we have discovered approximately 30 new RRAT candidates in data from the Green Bank Telescope 350 MHz drift-scan survey. A total of 6 of these have already been confirmed and the remainder look extremely promising. Here we describe these techniques and present the most recent results on these new RRAT candidates.
Binary pulsar evolution: unveiled links and new species
Authors: Possenti Andrea 
Published: March 2013

AbstractIn the last years a series of blind and/or targeted pulsar searches led to almost triple the number of known binary pulsars in the galactic field with respect to a decade ago. The focus will be on few outliers, which are emerging from the average properties of the enlarged binary pulsar population. Some of them may represent the long sought missing links between two kinds of neutron star binaries, while others could represent the stereotype of new groups of binaries, resulting from an evolutionary path which is more exotic than those considered until recently. In particular, a new class of binaries, which can be dubbed Ultra Low Mass Binary Pulsars (ULMBPs), is emerging from recent data.