bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring the depth of the zonal jets on Jupiter and Saturn from odd gravity harmonics
Authors: Kaspi Yohai 
Published: December 2012

ABSTRACTThe low‐order even gravity harmonics J2, J4, and J6 are well constrained for Jupiter and Saturn from spacecraft encounters over the past few decades. These gravity harmonics are dominated by the oblate shape and radial density distribution of these gaseous planets. In the lack of any north–south asymmetry, odd gravity harmonics will be zero. However, the winds on these planets are not hemispherically symmetric, and therefore can contribute to the odd gravity harmonics through dynamical variations to the density field. Here it is shown that even relatively shallow winds (reaching ~ 40 bars) can cause considerable odd gravity harmonics that can be detectable by NASA's Juno and Cassini missions to Jupiter and Saturn. Moreover, these measurements will have better sensitivity to the odd harmonics than to the high‐order even harmonics, which have been previously proposed as a proxy for deep winds. Determining the odd gravity harmonics will therefore help constrain the depth of the jets on these planets, and may provide valuable information about the planet's core and structure.
Biogenic silica standing stock and export in the Santa Barbara Channel ecosystem
Authors: Krause Jeffrey W. , Brzezinski Mark A. , Siegel David A. , Thunell Robert C. 
Published: December 2012

AbstractTime‐series datasets of surface‐water biogenic silica (bSiO2) and deep‐water bSiO2 export in the Santa Barbara Channel (SBC) allow for elucidation of the important scales of spatial and temporal variability and an evaluation of potential controlling mechanisms. Changes in local upwelling strength is the most important factor controlling seasonal variations for the surface bSiO2 dataset and accounts for ~65% of the variance. bSiO2 export is also highly seasonal; however, the maximum export is generally offset from the bSiO2 standing stock maximum by 0.5–2 months, and export is enhanced for a longer period than is surface biomass. Strong cross‐channel gradients in surface [bSiO2] occur during periods of elevated bSiO2 and account for ~13% of the variability in standing stocks; these gradients appear to be sustained by a combination of both local (cyclonic flow in the western SBC) and nonlocal (advection of water into the SBC) processes. Since 2000, a significant linear decline in water‐column‐integrated bSiO2 has occurred concurrent with a significant increase in bSiO2 export. During this same period, phytoplankton biomass and net primary production increased in the general California Current. Coupling our results with previous studies supports the idea that a significant amount of the exported bSiO2 caught in 540 m sediment traps originates outside the SBC, and variability is driven by both local and the broader California Current Ecosystem effects. However, we cannot rule out a significant role for local episodic events in stimulating production of rapidly settling particles.
Surface reflectance of Mars observed by CRISM/MRO: 1. Multi‐angle Approach for Retrieval of Surface Reflectance from CRISM observations (MARS‐ReCO)
Authors: Ceamanos X. , Douté S. , Fernando J. , Schmidt F. , Pinet P. , Lyapustin A. 
Published: December 2012

AbstractThis article addresses the correction for aerosol effects in near‐simultaneous multi‐angle observations acquired by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) aboard the Mars Reconnaissance Orbiter. In the targeted mode, CRISM senses the surface of Mars using 11 viewing angles, which allow it to provide unique information on the scattering properties of surface materials. In order to retrieve these data, however, appropriate strategies must be used to compensate the signal sensed by CRISM for aerosol contribution. This correction is particularly challenging as the photometric curve of these suspended particles is often correlated with the also anisotropic photometric curve of materials at the surface. This article puts forward an innovative radiative transfer‐based method named Multi‐angle Approach for Retrieval of Surface Reflectance from CRISM Observations (MARS‐ReCO). The proposed method retrieves photometric curves of surface materials in reflectance units after removing aerosol contribution. MARS‐ReCO represents a substantial improvement regarding previous techniques as it takes into consideration the anisotropy of the surface, thus providing more realistic surface products. Furthermore, MARS‐ReCO is fast and provides error bars on the retrieved surface reflectance. The validity and accuracy of MARS‐ReCO is explored in a sensitivity analysis based on realistic synthetic data. According to experiments, MARS‐ReCO provides accurate results (up to 10% reflectance error) under favorable acquisition conditions. In the companion article, photometric properties of Martian materials are retrieved using MARS‐ReCO and validated using in situ measurements acquired during the Mars Exploration Rovers mission.
Evolution of intracellular compartmentalization
Authors: Diekmann Yoan , Pereira-Leal José B. 
Published: December 2012

Cells compartmentalize their biochemical functions in a variety of ways, notably by creating physical barriers that separate a compartment via membranes or proteins. Eukaryotes have a wide diversity of membrane-based compartments, many that are lineage- or tissue-specific. In recent years, it has become increasingly evident that membrane-based compartmentalization of the cytosolic space is observed in multiple prokaryotic lineages, giving rise to several types of distinct prokaryotic organelles. Endosymbionts, previously believed to be a hallmark of eukaryotes, have been described in several bacteria. Protein-based compartments, frequent in bacteria, are also found in eukaryotes. In the present review, we focus on selected intracellular compartments from each of these three categories, membrane-based, endosymbiotic and protein-based, in both prokaryotes and eukaryotes. We review their diversity and the current theories and controversies regarding the evolutionary origins. Furthermore, we discuss the evolutionary processes acting on the genetic basis of intracellular compartments and how those differ across the domains of life. We conclude that the distinction between eukaryotes and prokaryotes no longer lies in the existence of a compartmentalized cell plan, but rather in its complexity.
Issues Regarding the Use of Sedatives in Fisheries and the Need for Immediate‐Release Options
Authors: Trushenski J. T. , Bowker J. D. , Cooke S. J. , Erdahl D. , Bell T. , MacMillan J. R. , Yanong R. P. , Hill J. E. , Fabrizio M. C. , Garvey J. E. , Sharon S. 
Published: December 2012

AbstractThe lack of an immediate‐release sedative (i.e., one for which no postsedation holding or withdrawal period is required) jeopardizes fish and fisheries research and poses considerable risk to those involved in aquatic resource management and the operation of public hatcheries and commercial fish farms. Carbon dioxide may be used as an immediate‐release sedative, but it is slow‐acting and difficult to apply uniformly and effectively. Tricaine methanesulfonate (MS‐222) is easier to apply but requires a 21‐d withdrawal period. The lack of an immediate‐release sedative approved by the U.S. Food and Drug Administration (FDA) is a consequence of numerous factors, including the complexities of the approval process, the substantial human and monetary resources involved, and the specialized nature of the work. Efforts are currently underway to demonstrate the safety and effectiveness of benzocaine‐ and eugenol‐based products as immediate‐release sedatives. However, pursuing approvals within the current framework will consume an exorbitant amount of public and private resources and will take years to complete, even though both compounds are “generally recognized as safe” for certain applications by the FDA. We recommend using risk management–based approaches to increase the efficiency of the drug approval process and the availability of safe and effective drugs, including immediate‐release sedatives, for use in the fisheries and aquaculture disciplines.
Patient- and Device-Specific Risk Factors for Peripherally Inserted Central Venous Catheter—Related Bloodstream Infections
Authors: Pongruangporn Makhawadee , Ajenjo M. Cristina , Russo Anthony J. , McMullen Kathleen M. , Robinson Catherine , Williams Robert C. , Warren David K. 
Published: December 2012

Objective.To determine the patient- and device-specific risk factors for hospital-acquired peripherally inserted central venous catheter–related bloodstream infections (PICC BSIs) in adult patients.Design.Nested case-control study.Setting.Barnes-Jewish Hospital, a 1,252-bed tertiary care teaching hospital.Patients.Adult patients with PICCs placed from January 1, 2006, through July 31, 2008.Methods.PICC BSI cases were identified using the National Healthcare Safety Network definition. Uninfected control patients with PICCs in place were randomly selected at a 3: 1 ratio. Patient- and device-related variables were examined using multivariate analysis.Results.The overall PICC BSI rate was 3.13 per 1,000 catheter-days. Independent risk factors for PICC BSIs included congestive heart failure (odds ratio [OR], 2.0 [95% confidence interval (CI), 1.26–3.17];P= .003), intra-abdominal perforation (OR, 5.66 [95% CI, 1.76–18.19];P= .004),Clostidium difficileinfection (OR, 2.25 [95% CI, 1.17–4.33];P= .02), recent chemotherapy (OR, 3.36 [95% CI, 1.15–9.78];P= .03), presence of tracheostomy (OR, 5.88 [95% CI, 2.99–11.55];P< .001), and type of catheter (OR for double lumen, 1.89 [95% CI, 1.15–3.10];P= .01; OR for triple lumen, 2.87 [95% CI, 1.39–5.92];P= .004). Underlying chronic obstructive pulmonary disease (OR, 0.48 [95% CI, 0.29–0.78];P= .03) and admission to surgical (OR, 0.43 [95% CI, 0.24–0.79];P= .006) or oncology and orthopedic (OR, 0.35 [95% CI, 0.13–0.99];P= .05) services were less likely to be associated with having a PICC BSI.Conclusions.We identified several novel factors related to PICC BSIs. These factors may inform preventive measures.
Characterization of disordered proteins with ENSEMBLE
Authors: Krzeminski Mickaël , Marsh Joseph A. , Neale Chris , Choy Wing-Yiu , Forman-Kay Julie D. 
Published: December 2012

Abstract
Summary: ENSEMBLE is a computational approach for determining a set of conformations that represents the structural ensemble of a disordered protein based on input experimental data. The disordered protein can be an unfolded or intrinsically disordered state. Here, we introduce the latest version of the program, which has been enhanced to facilitate its general release and includes an intuitive user interface, as well as new approaches to treat data and analyse results.
Availability and implementation: ENSEMBLE is a program implemented in C and embedded in a Perl wrapper. It is supported on main Linux distributions. Source codes and installation files, including a detailed example, can be freely downloaded at http://abragam.med.utoronto.ca/∼JFKlab.
Contact: forman@sickkids.ca
Supplementary information: Supplementary Material are available at Bioinformatics online.
Detection of the Rossiter–McLaughlin effect in the 2012 June 6 Venus transit
Authors: Molaro P. , Monaco L. , Barbieri M. , Zaggia S. 
Published: December 2012

Abstract
Eclipsing bodies on stars produce radial velocity variations on the photospheric stellar lines known as the Rossiter–McLaughlin (RM) effect. The body occults a small area of the stellar disc and, due to the rotation of the star, the stellar line profiles are distorted according to the projected location of the body on to the stellar disc. The effect originally observed in eclipsing binaries was also shown to be produced by extrasolar planets transits. Here we report the detection of the RM effect in the Sun due to the Venus transit of 2012 June 6. We used the integrated sunlight as reflected by the Moon at night time to record part of the transit by means of the high-precision HARPS spectrograph at the 3.6-m La Silla European Southern Observatory (ESO) telescope. The observations show that the partial Venus eclipse of the solar disc in correspondence of the passage in front of the receding hemisphere produced a modulation in the radial velocity with a negative amplitude of ≈−1 m s−1, in agreement with the theoretical model. The radial velocity change is comparable to the solar jitter and more than a factor of 2 smaller than previously detected in extrasolar hot Neptunes. This detection, facilitated by an amplification factor of 3.5 of the Venus radius due to proximity, anticipates the study of transits of Earth-size bodies in solar-type stars by means of a high-resolution spectrograph attached to a 40-m class telescope.
First Report of Downy Mildew Caused by Peronospora sordida on Butterflybush (Buddleja stachyoides) in Brazil
Authors: Albuquerque S. T. , Rocha F. B. , Barreto R. W. 
Published: December 2012

Butterflybush (common name in Brazil, verbasco), Buddleja stachyoides Cham. & Schltdl. (Buddlejaceae), is an erect herb or small shrub, native to Brazil, that is listed both as a folk medicinal plant and as a pasture weed (4). In March 2012, a group of B. stachyoides plants growing in a pasture in Viçosa (state of Minas Gerais, Brazil), were found bearing typical downy mildew symptoms. The only pathogen reported associated with this plant species is Podosphaera xanthii (1) and because there is no record of downy mildew on members of Buddleja in Brazil, an investigation was carried out to clarify the pathogen identity. Diseased plants had lesions on living leaves that were vein-delimited, chlorotic, coalescing, and becoming necrotic adaxially and bearing downy mildew-like colonies over diseased tissues abaxially. The samples were dried in a plant press and a representative specimen was deposited in the local herbarium at the Universidade Federal de Viçosa (Accession No. VIC 31836). Reproductive structures were scraped from leaves with a scalpel and mounted in lactophenol. Preliminary observations indicated the pathogen as belonging to Peronospora (Peronosporaceae). The pathogen had the following morphology: Sporangiophores are 288 to 641 μm long, dichotomously branching up to seven times, hyaline, smooth, 5 to 16 μm wide at the trunk, branches 63 to 202 μm long; tips subacute, in pairs or rarely single, 5 to 19 μm long; sporangia subglobose to ellipsoidal, 12 to 22 × 11 to 17 μm, pale yellowish brown, non-papillate. Only one species of Peronospora is known to infect members of Buddleja, namely Peronospora hariotii Gäum. (1). Nevertheless, the pathogen on B. stachyoides has smaller sporangia as compared to those of P. hariotii (20 to 26 × 16 to 21 μm) (2) and it was closer to P. sordida (3). DNA of the pathogen from B. stachyoides was extracted and the cytochrome c oxidase subunit II (COX2) and internal transcribed spacer (ITS) regions were sequenced. Sequences were deposited in GenBank (COX2 as JX982637; ITS as JX982638). A BLAST search yielded 99% and 100% of maximum identity with P. sordida for COX2 and ITS, respectively. A more detailed phylogenetic study is necessary to clarify the relationship between P. sordida, P. hariotii, and related species causing downy mildew on closely related hosts. To our knowledge, this is the first report of P. sordida occurring on a member of the genus Buddleja. This is also the first time that P. sordida is reported from South America. References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , 19 October 2012. (2) S. M. Francis. C.M.I. Descr. Pathog. Fungi Bact. 767:1, 1983. (3) G. Hall. I.M.I. Descr. Fungi Bact. 1062:1, 1991. (4) K. G. Kissmann and D. Groth. Plantas Infestantes e Nocivas. São Paulo, BASF, 1997.
Intraoperative Infusion of 0.6–0.9 µg · kg−1 · min−1 Remifentanil Induces Acute Tolerance in Young Children after Laparoscopic Ureteroneocystostomy
Authors: Kim Sung-Hoon , Lee Min H. , Seo Hyungseok , Lee In-Gyu , Hong Jeong-Yeon , Hwang Jai-Hyun 
Published: December 2012

Abstract

Background:
Intraoperative infusion of opioids has been associated with increased postoperative pain and analgesic requirements, but the development of tolerance in young children is less clear. This prospective, randomized, double-blinded study was designed to test the hypothesis that the intraoperative administration of remifentanil results in postoperative opioid tolerance in a dose-related manner in young children.

Methods:
We enrolled 60 children (aged 1–5 yr) who were undergoing elective laparoscopic ureteroneocystostomy. Patients were randomized and received an intraoperative infusion of 0, 0.3, 0.6, or 0.9 µg·kg−1·min−1 remifentanil. Postoperative pain was managed by a parent/nurse-controlled analgesia pump using fentanyl. The primary outcome included the total fentanyl consumptions at 24 and 48 h postsurgery. Secondary outcomes were the postoperative pain scores and adverse effects.

Results:
The children who received 0.6 and 0.9 µg·kg−1·min−1 remifentanil required more postoperative fentanyl than the children who received saline or 0.3 µg·kg−1·min−1 remifentanil (all P < 0.001) for 24 h after surgery. The children who received 0.3–0.9 µg·kg−1·min−1 intraoperative remifentanil reported higher pain scores at 1 h after surgery than the children who received saline (P = 0.002, P = 0.023, and P = 0.006, respectively). No significant intergroup differences in recovery variables were observed, but vomiting was more frequent in the 0.9 µg·kg−1·min−1 remifentanil group than in the other groups (P = 0.027).

Conclusions:
The intraoperative use of 0.3 µg·kg−1·min−1 remifentanil for approximately 3 h (range: 140–265 min) did not induce acute tolerance, but the administration of 0.6 and 0.9 µg·kg−1·min−1 remifentanil to young children resulted in acute tolerance for 24 h after surgery in an apparently dose-related manner.
A Cyclic Nucleotide-Gated Channel (CNGC16) in Pollen Is Critical for Stress Tolerance in Pollen Reproductive Development
Authors: Tunc-Ozdemir Meral , Tang Chong , Ishka Maryam Rahmati , Brown Elizabeth , Groves Norman R. , Myers Candace T. , Rato Claudia , Poulsen Lisbeth R. , McDowell Stephen , Miller Gad , Mittler Ron , Harper Jeffrey F. 
Published: December 2012

Abstract
Cyclic nucleotide-gated channels (CNGCs) have been implicated in diverse aspects of plant growth and development, including responses to biotic and abiotic stress, as well as pollen tube growth and fertility. Here, genetic evidence identifies CNGC16 in Arabidopsis (Arabidopsis thaliana) as critical for pollen fertility under conditions of heat stress and drought. Two independent transfer DNA disruptions of cngc16 resulted in a greater than 10-fold stress-dependent reduction in pollen fitness and seed set. This phenotype was fully rescued through pollen expression of a CNGC16 transgene, indicating that cngc16-1 and 16-2 were both loss-of-function null alleles. The most stress-sensitive period for cngc16 pollen was during germination and the initiation of pollen tube tip growth. Pollen viability assays indicate that mutant pollen are also hypersensitive to external calcium chloride, a phenomenon analogous to calcium chloride hypersensitivities observed in other cngc mutants. A heat stress was found to increase concentrations of 3′,5′-cyclic guanyl monophosphate in both pollen and leaves, as detected using an antibody-binding assay. A quantitative PCR analysis indicates that cngc16 mutant pollen have attenuated expression of several heat-stress response genes, including two heat shock transcription factor genes, HsfA2 and HsfB1. Together, these results provide evidence for a heat stress response pathway in pollen that connects a cyclic nucleotide signal, a Ca2+-permeable ion channel, and a signaling network that activates a downstream transcriptional heat shock response.
UBIQUITIN-SPECIFIC PROTEASE16 Modulates Salt Tolerance in Arabidopsis by Regulating Na+/H+ Antiport Activity and Serine Hydroxymethyltransferase Stability
Authors: Zhou Huapeng , Zhao Jinfeng , Yang Yongqing , Chen Changxi , Liu Yanfen , Jin Xuehua , Chen Limei , Li Xueyong , Deng Xing Wang , Schumaker Karen S. , Guo Yan 
Published: December 2012

Abstract
Protein ubiquitination is a reversible process catalyzed by ubiquitin ligases and ubiquitin-specific proteases (UBPs). We report the identification and characterization of UBP16 in Arabidopsis thaliana. UBP16 is a functional ubiquitin-specific protease and its enzyme activity is required for salt tolerance. Plants lacking UBP16 were hypersensitive to salt stress and accumulated more sodium and less potassium. UBP16 positively regulated plasma membrane Na+/H+ antiport activity. Through yeast two-hybrid screening, we identified a putative target of UBP16, SERINE HYDROXYMETHYLTRANSFERASE1 (SHM1), which has previously been reported to be involved in photorespiration and salt tolerance in Arabidopsis. We found that SHM1 is degraded in a 26S proteasome–dependent process, and UBP16 stabilizes SHM1 by removing the conjugated ubiquitin. Ser hydroxymethyltransferase activity is lower in the ubp16 mutant than in the wild type but higher than in the shm1 mutant. During salt stress, UBP16 and SHM1 function in preventing cell death and reducing reactive oxygen species accumulation, activities that are correlated with increasing Na+/H+ antiport activity. Overexpression of SHM1 in the ubp16 mutant partially rescues its salt-sensitive phenotype. Taken together, our results suggest that UBP16 is involved in salt tolerance in Arabidopsis by modulating sodium transport activity and repressing cell death at least partially through modulating SMH1stability and activity.
Erythrocyte membrane transporters during human ageing: Modulatory role of tea catechins
Authors: Pandey Kanti Bhooshan , Jha Rashmi , Rizvi Syed Ibrahim 
Published: December 2012

Summary

Ageing is associated with many physiological and cellular changes, many of which are due to alterations in the plasma membrane. The functions of membrane transporter proteins are crucial for the maintenance of ionic homeostasis between the extra‐ and intracellular environments.

The aim of the present study was to determine the status of erythrocyte membrane transporters, specifically Ca2+‐ATPases, Na+/K+‐ATPases and the Na+/H+ exchanger (NHE), during ageing in humans. Furthermore, because tea catechins have been reported to possess strong anti‐oxidant potential, the study was extended to evaluate the effect of (–)‐epicatechin (EC), (–)‐epicatechin‐3‐gallate (ECG), (–)‐epigallocatechin (EGC) and (–)‐epigallocatechin‐3‐gallate (EGCG) on these transporters as a function of human age.

The study was performed on 97 normal healthy subjects (62 men, 35 women; 16–80 years old). To investigate the effects of tea catechins, subjects were divided into three groups: young (<40 years old; n = 34); middle‐aged (40–60 years old; n = 32); and old (>60 years old; n = 31). Erythrocyte ghosts/cell suspension from each group were incubated with ECG, EGCG, EGC and EC (10 μmol/L) for 30 min at 37°C prior to assay.

Ageing significantly increased NHE activity and decreased Ca2+‐ATPase activity. There were no significant changes in Na+/K+‐ATPase activity during the ageing process.

(–)‐Epigallocatechin‐3‐gallate, EGC, ECG and EC effectively mitigated the changes in membrane transporter activity in erythrocytes from all age groups; however, the effect was more pronounced in the old age group.

We hypothesize that impairment in ‐bound transporters may be one of the possible mechanisms underlying the pathological events during ageing. A higher intake of catechin‐rich food may provide some protection against age‐dependent diseases.