bluuebunny/crossref_metadata_2025_split huggingface dataset:
Postprocessing Model-Predicted Rainfall Fields in the Spectral Domain Using Phase Information from Radar Observations
Authors: Radhakrishna Basivi , Zawadzki Isztar , Fabry Frédéric 
Published: December 2012

Abstract
In an attempt to combine the short-term skill of radar nowcasting and the long-term skill of numerical models, successive 15-min rainfall accumulations obtained from the U.S. national radar composites and predicted by the Weather Research and Forecasting (WRF) model are corrected by adjusting the phases of Fourier components in the spectral domain while keeping the amplitudes invariant. The phase information is first obtained by decomposing the radar and model fields into Fourier space. Then, to correct the model outputs, a new set of Fourier components is constructed using the phases from the radar image and amplitudes from the model image. The corrected model image can be obtained by inverse transformation of the new set of Fourier components. Scales of wavelengths starting from 50 to 500 km are playing a crucial role in correcting the positional and intensity errors of continental-scale precipitating systems predicted by the WRF model, while scales greater than 500 km are contributing very little, which is negligible. The model errors are characterized in terms of phase and power. Compared to power/amplitude correction, phase correction plays a major role in eliminating the positional and intensity errors. Scales that are responsible for the errors or not predicted by the model have a decorrelation time of about 2 h in both the zonal and meridional directions. The higher critical success index (CSI) and smaller RMS error values of the radar-extrapolated and phase-corrected fields compared with the WRF model–predicted fields indicate that the extrapolated phase information can be used to correct the model outputs up to a lead time of about 4 h.
On the Measurement of Heat Waves
Authors: Perkins S. E. , Alexander L. V. 
Published: December 2012

Abstract
Despite their adverse impacts, definitions and measurements of heat waves are ambiguous and inconsistent, generally being endemic to only the group affected, or the respective study reporting the analysis. The present study addresses this issue by employing a set of three heat wave definitions, derived from surveying heat-related indices in the climate science literature. The definitions include three or more consecutive days above one of the following: the 90th percentile for maximum temperature, the 90th percentile for minimum temperature, and positive extreme heat factor (EHF) conditions. Additionally, each index is studied using a multiaspect framework measuring heat wave number, duration, participating days, and the peak and mean magnitudes. Observed climatologies and trends computed by Sen's Kendall slope estimator are presented for the Australian continent for two time periods (1951–2008 and 1971–2008). Trends in all aspects and definitions are smaller in magnitude but more significant for 1951–2008 than for 1971–2008. Considerable similarities exist in trends of the yearly number of days participating in a heat wave and yearly heat wave frequency, suggesting that the number of available heat wave days drives the number of events. Larger trends in the hottest part of a heat wave suggest that heat wave intensity is increasing faster than the mean magnitude. Although the direct results of this study cannot be inferred for other regions, the methodology has been designed as such that it is widely applicable. Furthermore, it includes a range of definitions that may be useful for a wide range of systems impacted by heat waves.
Modification and Tests of Particle Probe Tips to Mitigate Effects of Ice Shattering
Authors: Korolev Alexei , Emery Edward , Creelman Kirk 
Published: December 2012

Abstract
Ice particle shattering may significantly contaminate measurements taken by airborne particle probes in ice clouds. Environment Canada and the NASA Glenn Research Center (GRC) undertook efforts to modify and test probe tips in order to mitigate the effect of shattering on measurements. This work presents an overview of the results obtained during the design work on the particle probe arm tips. Even though this work was focused on the modifications of three of the probes—Particle Measuring Systems Inc. (PMS) Forward Scattering Spectrometer Probe and optical array probe, and Droplet Measurement Technologies (DMT) Cloud Imaging Probe—the outcomes of this work bear a general character and are applicable to other similar instruments. The results of the airflow analysis around the probe’s housing and the simulations of particle bouncing from the probe tips are discussed here. The originally designed and modified tips were tested in a high-speed wind tunnel in ice and liquid sprays. The ice particle bouncing processes as well as patterns of water shedding over the surface of the probes arms were studied with the help of a high-speed video camera. It was found that at aircraft speed, after bouncing from a solid surface, ice particles may travel several centimeters across the airflow and bounce forward up to 1 cm. For the first time it has been directly documented with high-speed video recording that the sample volumes of particle probes with the originally designed tips are contaminated by shattered and bounced particles. A set of recommendations on the existing modification and the design of future particle probe housings is presented.
Sustaining Mobility
Authors: Bassett Thomas E. , Marpillero-Colomina Andrea 
Published: December 2012

Bogotá, Colombia, has been a pioneer in the development of efficient, low-cost urban transportation networks with its innovative bus rapid transit system. As the TransMilenio enters its second decade of operation, the long-term sustainability of the system has come into question. The current mayoral administration supports the construction of a subway network, which it claims will elevate Bogotá to the status of a “global city.” An examination of transportation development in Bogotá using interviews, field research, and primary source data in addition to extensive theoretical and comparative research reveals the ways in which politics and neoliberal policies have limited this development. La ciudad de Bogotá, Colombia, ha sido pionera en el desarrollo de transporte eficiente de bajo costo con su sistema innovador de transito rápido por autobús. Mientras el Transmilenio entra en su segunda década de operación, se cuestiona la sustentabilidad del sistema al largo plazo. La administración actual de la alcaldía apoya la construcción de una red subterránea, la cual se dice elevará a la ciudad de Bogotá al estatus de una “ciudad global.” Un examen del desarrollo del transporte en Bogotá por medio de entrevistas, trabajo de campo, y fuentes primarias de datos, aumentados con investigación teórica y comparativa, revela las formas en que la política y el neoliberalismo le han puesto limite a este desarrollo.
Platelet P2Y12 Blockers Confer Direct Postconditioning-Like Protection in Reperfused Rabbit Hearts
Authors: Yang Xi-Ming , Liu Yanping , Cui Lin , Yang Xiulan , Liu Yongge , Tandon Narendra , Kambayashi Junichi , Downey James M. , Cohen Michael V. 
Published: December 2012

Background: Blockade of platelet activation during primary percutaneous intervention for acute myocardial infarction is standard care to minimize stent thrombosis. To determine whether antiplatelet agents offer any direct cardioprotective effect, we tested whether they could modify infarction in a rabbit model of ischemia/reperfusion caused by reversible ligation of a coronary artery. Methods and Results: The P2Y12 (adenosine diphosphate) receptor blocker cangrelor administered shortly before reperfusion in rabbits undergoing 30-minute regional ischemia/3-hour reperfusion reduced infarction from 38% of ischemic zone in control hearts to only 19%. Protection was dose dependent and correlated with the degree of inhibition of platelet aggregation. Protection was comparable to that seen with ischemic postconditioning (IPOC). Cangrelor protection, but not its inhibition of platelet aggregation, was abolished by the same signaling inhibitors that block protection from IPOC suggesting protection resulted from protective signaling rather than anticoagulation. As with IPOC, protection was lost when cangrelor administration was delayed until 10 minutes after reperfusion and no added protection was seen when cangrelor and IPOC were combined. These findings suggest both IPOC and cangrelor may protect by the same mechanism. No protection was seen when cangrelor was used in crystalloid-perfused isolated hearts indicating some component in whole blood is required for protection. Clopidogrel had a very slow onset of action requiring 2 days of treatment before platelets were inhibited, and only then the hearts were protected. Signaling inhibitors given just prior to reperfusion blocked clopidogrel’s protection. Neither aspirin nor heparin was protective. Conclusions: Clopidogrel and cangrelor protected rabbit hearts against infarction. The mechanism appears to involve signal transduction during reperfusion rather than inhibition of intravascular coagulation. We hypothesize that both drugs protect by activating IPOC’s protective signaling to prevent reperfusion injury. If true, patients receiving P2Y12 inhibitors before percutaneous intervention may already be postconditioned thus explaining failure of recent clinical trials of postconditioning drugs.
The effect of plasma exchange on serum anti-JC virus antibodies
Authors: Subramanyam Meena , Plavina Tatiana , Khatri Bhupendra O , Fox Robert J , Goelz Susan E 
Published: December 2012

Objective: Natalizumab, a highly effective treatment for multiple sclerosis (MS) and Crohn’s disease, is associated with progressive multifocal leukoencephalopathy (PML). Upon suspicion or diagnosis of PML, plasma exchange (PLEX) is performed to remove natalizumab from the circulation, allowing immune reconstitution of the central nervous system. Since PLEX may also remove other circulating antibodies, we examined the effects of PLEX on serum immunoglobulin (IgG) and anti–JC virus (JCV) antibody levels in MS patients with and without PML. Methods: Serum samples from 12 natalizumab-treated patients without PML collected before, during and after PLEX were tested for IgG isotypes using a commercial assay, and for anti-JCV antibodies using a two-step enzyme-linked immunosorbent assay. Five natalizumab-treated PML patients who underwent PLEX were also tested for anti-JCV antibodies. Results: PLEX produced a two- to three-fold reduction in all IgG isotypes. Among patients without PML, 42% (five of 12 patients) had detectable anti-JCV antibodies before PLEX; in these patients, anti-JCV antibodies were reduced approximately two- to five-fold, with levels returning to 50–100 percent of baseline two weeks after the final PLEX. The five PML patients, all of whom had detectable anti-JCV antibodies before PLEX, experienced similar reductions in anti-JCV antibody levels following PLEX. Conclusions: Our results indicate that PLEX effectively removes circulating antibodies; however, levels of endogenous anti-JCV antibody, unlike exogenously administered natalizumab, were replenished relatively quickly following PLEX. While interpretation of anti-JCV antibody levels during or within two weeks after PLEX may be problematic, humoral JCV immunity is not abolished by PLEX and antibody levels are rapidly restored.
MRI characteristics of familial and sporadic multiple sclerosis patients
Authors: Tipirneni Anita , Weinstock-Guttman Bianca , Ramanathan Murali , Abdelrahman Nadir , Hussein Sara , Hagemeier Jesper , Durfee Jacqueline , Teter Barbara E , Hojnacki David , Dwyer Michael G , Zivadinov Robert 
Published: December 2012

Purpose: To investigate the MRI characteristics in a large cohort of multiple sclerosis (MS) patients with and without a family history of MS. Methods: Enrolled in this prospective study were 758 consecutive MS patients (mean age 46.2 ± 10.1 years, disease duration 13.6 ± 9.2 years and EDSS 3.4 ± 2.1), of whom 477 had relapsing–remitting, 222 secondary-progressive, and 30 primary-progressive disease courses and 29 had clinically isolated syndrome. One hundred and ninety-six patients (25.9%) had a positive family history of MS. Patients were assessed using measurements of lesions, brain atrophy, magnetization transfer ratio (MTR) and diffusion-weighted imaging. Results: The familial MS group had greater T1-lesion volume ( p=0.009) and a trend for lower MTR of T1-lesion volume ( p=0.047) than the sporadic MS group. No clinical differences were found between familial versus sporadic group, or by a degree of affected relative subgroups. Conclusions: While familial MS was associated with more severe T1-lesion volume and its MTR characteristics, there were no clinical status differences between familial and sporadic MS patients. Therefore, a better understanding of the genetic and/or epigenetic influences causing these differences can advance the understanding and management of MS.
Laquinimod prevents inflammation-induced synaptic alterations occurring in experimental autoimmune encephalomyelitis
Authors: Ruffini Francesca , Rossi Silvia , Bergamaschi Andrea , Brambilla Elena , Finardi Annamaria , Motta Caterina , Studer Valeria , Barbieri Francesca , De Chiara Valentina , Hayardeny Liat , Comi Giancarlo , Centonze Diego , Martino Gianvito 
Published: December 2012

Background There are two generally accepted strategies for treating multiple sclerosis (MS), preventing central nervous system (CNS) damage indirectly through immunomodulatory interventions and/or repairing CNS damage by promoting remyelination. Both approaches also provide neuroprotection since they can prevent, indirectly or directly, axonal damage. Objective Recent experimental and clinical evidence indicates that the novel immunomodulatory drug laquinimod can exert a neuroprotective role in MS. Whether laquinimod-mediated neuroprotection is exerted directly on neuronal cells or indirectly via peripheral immunomodulation is still unclear. Methods C57Bl/6 experimental autoimmune encephalomyelitis (EAE) mice, immunised with myelin oligodendrocyte glycoprotein (MOG)35-55 peptide, were treated for 26 days with subcutaneous daily injections of laquinimod (from 1 to 25 mg/kg). Patch clamp electrophysiology was performed on acute brain striatal slices from EAE mice treated with daily (25 mg/kg) laquinimod and on acute brain striatal slices from control mice bathed with laquinimod (1–30 µM). Results Both preventive and therapeutic laquinimod treatment fully prevented the alterations of GABAergic synapses induced by EAE, the first limiting also glutamatergic synaptic alterations. This dual effect might, in turn, have limited glutamatergic excitotoxicity, a phenomenon previously observed early during EAE and possibly correlated with later axonal damage. Furthermore, laquinimod treatment also preserved cannabinoid CB1 receptor sensitivity, normally lost during EAE. Finally, laquinimod per se was able to regulate synaptic transmission by increasing inhibitory post-synaptic currents and, at the same time, reducing excitatory post-synaptic currents. Conclusions Our data suggest a novel neuroprotective mechanism by which laquinimod might in vivo protect from neuronal damage occurring as a consequence of inflammatory immune-mediated demyelination.
High-dimensional immunomonitoring models of HIV-1–specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control
Authors: Ndhlovu Zaza M. , Chibnik Lori B. , Proudfoot Jacqueline , Vine Seanna , McMullen Ashley , Cesa Kevin , Porichis Filippos , Jones R. Brad , Alvino Donna Marie , Hart Meghan G. , Stampouloglou Eleni , Piechocka-Trocha Alicja , Kadie Carl , Pereyra Florencia , Heckerman David , De Jager Philip L. , Walker Bruce D. , Kaufmann Daniel E. 
Published: December 2012

Key PointsImmune monitoring models integrating multiple functions of HIV-1–specific CD8 T cells distinguish controllers from subjects with progressive HIV-1 infection. This strategy may have important applications in predictive model development and immune monitoring of HIV-1 vaccine trials.
Genome-wide study of methotrexate clearance replicates SLCO1B1
Authors: Ramsey Laura B. , Panetta John C. , Smith Colton , Yang Wenjian , Fan Yiping , Winick Naomi J. , Martin Paul L. , Cheng Cheng , Devidas Meenakshi , Pui Ching-Hon , Evans William E. , Hunger Stephen P. , Loh Mignon , Relling Mary V. 
Published: December 2012

Key Points
A genome-wide study of the association of over 5 million SNPs with methotrexate clearance in 1279 patients treated with HDMTX in multicenter COG trials 9904 and 9905. We replicated the finding that inherited variations in SLCO1B1 are the most important genetic variations influencing methotrexate clearance.
Enhanced normal short-term human myelopoiesis in mice engineered to express human-specific myeloid growth factors
Authors: Miller Paul H. , Cheung Alice M. S. , Beer Philip A. , Knapp David J. H. F. , Dhillon Kiran , Rabu Gabrielle , Rostamirad Shabnam , Humphries R. Keith , Eaves Connie J. 
Published: December 2012

Key Points
NSG-3GS mice support enhanced clonal outputs from human short-term repopulating cells (STRCs) without affecting their engrafting efficiency. Increased human STRC clone sizes enable their more precise and efficient measurement by peripheral blood monitoring.
De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
Authors: Hassan Musa A , Melo Mariane B , Haas Brian , Jensen Kirk D C , Saeij Jeroen P J 
Published: December 2012

AbstractBackgroundAccurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite,Toxoplasma gondii, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing inToxoplasma gondiiis unknown. In this study, we usedde novotranscript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing inToxoplasmaand to improve the currentToxoplasmagene annotations.ResultsWe used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novelToxoplasmagenes, and putative non-coding RNAs.ConclusionRNA-seq data andde novotranscript assembly provide a robust way to update incompletely annotated genomes, like theToxoplasmagenome. We have used RNA-seq to improve the annotation of severalToxoplasmagenes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.
CD11b+Ly6C++Ly6G- cells show distinct function in mice with chronic inflammation or tumor burden
Authors: Källberg Eva , Stenström Martin , Liberg David , Ivars Fredrik , Leanderson Tomas 
Published: December 2012

AbstractBackgroundS100A9 has been shown to be important for the function of so called Myeloid Derived Suppressor Cells (MDSC). Cells with a similar phenotype are also involved in pro-inflammatory processes, and we therefore wanted to investigate the gene expression and function of these cells in animals that were either subjected to chronic inflammation, or inoculated with tumors.MethodsCD11b+Ly6C++and Ly6G+cells were isolated from spleen, tumor tissue or inflammatory granulomas. S100A9, Arginase 1 and iNOS gene expression in the various CD11b+cell populations was analyzed using Q-PCR. The suppressive activity of the CD11b+cell populations from different donors was studied in co-culture experiments.ResultsS100A9 was shown to be expressed mainly in splenic CD11b+Ly6C+G+cells both at the RNA and protein level. Arginase I and iNOS expression could be detected in both CD11b+Ly6C+Ly6G+and CD11b+Ly6C+G-/C++G-derived from tumors or a site of chronic inflammation, but was very low in the same cell populations isolated from the spleen. CD11b+cells isolated from mice with peritoneal chronic inflammation were able to stimulate T lymphocytes, while CD11b+cells from mice with peritoneal tumors suppressed T cell growth.ConclusionAn identical CD11b+Ly6C++G-cell population appears to have the ability to adopt immune stimulatory or immune suppressive functions dependent on the presence of a local inflammatory or tumor microenvironment. Thus, there is a functional plasticity in the CD11b+Ly6C++G-cell population that cannot be distinguished with the current molecular markers.
Proline is required for male gametophyte development in Arabidopsis
Authors: Mattioli Roberto , Biancucci Marco , Lonoce Chiara , Costantino Paolo , Trovato Maurizio 
Published: December 2012

Abstract

Background
In crosses between the proline-deficient mutant homozygous for p5cs1 and heterozygous for p5cs2 (p5cs1 p5cs2/P5CS2), used as male, and different Arabidopsis mutants, used as females, the p5cs2 mutant allele was rarely transmitted to the outcrossed progeny, suggesting that the fertility of the male gametophyte carrying mutations in both P5CS1 and P5CS2 is severely compromised.

Results
To confirm the fertility defects of pollen from p5cs1 p5cs2/P5CS2 mutants, transmission of mutant alleles through pollen was tested in two ways. First, the number of progeny inheriting a dominant sulfadiazine resistance marker linked to p5cs2 was determined. Second, the number of p5cs2/p5cs2 embryos was determined. A ratio of resistant to susceptible plantlets close to 50%, and the absence of aborted embryos were consistent with the hypothesis that the male gametophyte carrying both p5cs1 and p5cs2 alleles is rarely transmitted to the offspring. In addition, in reciprocal crosses with wild type, about 50% of the p5cs2 mutant alleles were transmitted to the sporophytic generation when p5cs1 p5cs2/P5CS2 was used as a female, while less than 1% of the p5cs2 alleles could be transmitted to the outcrossed progeny when p5cs1 p5cs2/P5CS2 was used as a male. Morphological and functional analysis of mutant pollen revealed a population of small, degenerated, and unviable pollen grains, indicating that the mutant homozygous for p5cs1 and heterozygous for p5cs2 is impaired in pollen development, and suggesting a role for proline in male gametophyte development. Consistent with these findings, we found that pollen from p5cs1 homozygous mutants, display defects similar to, but less pronounced than pollen from p5cs1 p5cs2/P5CS2 mutants. Finally, we show that pollen from p5cs1 p5cs2/P5CS2 plants contains less proline than wild type and that exogenous proline supplied from the beginning of another development can partially complement both morphological and functional pollen defects.

Conclusions
Our data show that the development of the male gametophyte carrying mutations in both P5CS1 and P5CS2 is severely compromised, and indicate that proline is required for pollen development and transmission.