bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oscillating Relationship between the East Asian Winter Monsoon and ENSO
Authors: He Shengping , Wang Huijun 
Published: July 2013

AbstractThis work investigates the interdecadal variations of the relationship between the El Niño–Southern Oscillation (ENSO) and the East Asian winter monsoon (EAWM), further explores possible mechanisms, and finally considers a recent switch in the ENSO–EAWM relationship. The 23-yr sliding correlation between the Niño-3.4 index and the EAWM index reveals an obvious low-frequency oscillation with a period of about 50 yr in the ENSO–EAWM relationship. Warm ENSO events during high-correlation periods are associated with an unusually weak East Asian trough, a positive phase of the North Pacific Oscillation (NPO), significant southerly wind anomalies along coastal East Asia, and warmer East Asian continent and adjacent oceans. However, there are no robust and significant anomalies in the EAWM-related circulation during low-correlation periods. Because of the southeastward shift of the Walker circulation, the area of anomalously high pressure in the western Pacific retreats south of 25°N, confining it to the region of the Philippine Sea. In this sense, the Pacific–East Asian teleconnection is not well established. Consequently, ENSO’s impact on the EAWM is suppressed. Additionally, the low-frequency oscillation of the ENSO–EAWM relationship might be attributable to the combined effect of the Pacific decadal oscillation (PDO) and the Atlantic multidecadal oscillation owing to their modulation on the establishment of the NPO teleconnection. The observation of two full cycles of the ENSO–EAWM relationship, a transition to negative PDO in the early 2000s and an enhancement of the Walker circulation in the late 1990s, suggests a recovery of the ENSO–EAWM relationship.
Freshening of Subsurface Waters in the Northwest Pacific Subtropical Gyre: Observations and Dynamics
Authors: Yan Youfang , Chassignet Eric P. , Qi Yiquan , Dewar William K. 
Published: July 2013

Abstract
Subsurface salinity anomalies propagating between mid- and low latitudes along isopycnal surfaces have been shown to play an important role in modulating ocean and climate variability. In this study, a sustained freshening and southwestward propagation of subsurface salinity anomalies in the northwest Pacific subtropical gyre and its dynamical mechanism are investigated using observations, numerical outputs, and a predictive model. Analyses of the observations show a pronounced subsurface freshening with salinity decreasing about 0.25 PSU near the 24.5-σθ surface in the northwest Pacific subtropical gyre during 2003–11. This freshening is found to be related to the surface forcing of salinity anomalies in the outcrop zone (25°–35°N, 130°–160°E). A predictive model based on the assumption of salinity conservation along the outcrop isopycnals is derived and used to examine this surface-forcing mechanism. The resemblance between the spatial structures of the subsurface salinity derived from the predictive model and from observations and numerical outputs suggests that subsurface salinity anomalies are ventilated over the outcrop zone. A salinity anomaly with an amplitude of about 0.25 PSU generated by the surface forcing is subducted in the outcrop zone and then propagates southwestward, accompanied by potential vorticity anomalies, to the east of Luzon Strait (~15°N) in roughly one year. When the anomalies reach 15°N, they turn and move gradually eastward toward the central Pacific, associated with an eastward countercurrent on the southern subtropical gyre.
Spatial and Temporal Characteristics of Heavy Hourly Rainfall in the United States
Authors: Hitchens Nathan M. , Brooks Harold E. , Schumacher Russ S. 
Published: July 2013

Abstract
The climatology of heavy rain events from hourly precipitation observations by Brooks and Stensrud is revisited in this study using two high-resolution precipitation datasets that incorporate both gauge observations and radar estimates. Analyses show a seasonal cycle of heavy rain events originating along the Gulf Coast and expanding across the eastern two-thirds of the United States by the summer, comparing well to previous findings. The frequency of extreme events is estimated, and may provide improvements over prior results due to both the increased spatial resolution of these data and improved techniques used in the estimation. The diurnal cycle of heavy rainfall is also examined, showing distinct differences in the strength of the cycle between seasons.
Large-Scale Atmospheric and Oceanic Conditions during the 2011–12 DYNAMO Field Campaign
Authors: Gottschalck Jon , Roundy Paul E. , Schreck III Carl J. , Vintzileos Augustin , Zhang Chidong 
Published: July 2013

AbstractAn international field campaign, Dynamics of the Madden Julian Oscillation (DYNAMO), took place in the Indian Ocean during October 2011–March 2012 to collect observations for the Madden–Julian oscillation (MJO), especially its convective initiation processes. The large-scale atmospheric and oceanic conditions during the campaign are documented here. The ENSO and the Indian Ocean dipole (IOD) states, the monthly mean monsoon circulation and its associated precipitation, humidity, vertical and meridional/zonal overturning cells, and ocean surface currents are discussed. The evolution of MJO events is described using various fields and indices that have been used to subdivide the campaign into three periods. These periods were 1) 17 September–8 December 2011 (period 1), which featured two robust MJO events that circumnavigated the global tropics with a period of less than 45 days; 2) 9 December 2011–31 January 2012, which contained less coherent activity (period 2); and 3) 1 February–12 April 2012, a period that featured the strongest and most slowly propagating MJO event of the campaign (period 3). Activities of convectively coupled atmospheric Kelvin and equatorial Rossby (ER) waves and their interaction with the MJO are discussed. The overview of the atmospheric and oceanic variability during the field campaign raises several scientific issues pertaining to our understanding of the MJO, or lack thereof. Among others, roles of Kelvin and ER waves in MJO convective initiation, convection-circulation decoupling on the MJO scale, applications of MJO filtering methods and indices, and ocean–atmosphere coupling need further research attention.
Improving Intraseasonal Prediction with a New Ensemble Generation Strategy
Authors: Hudson Debra , Marshall Andrew G. , Yin Yonghong , Alves Oscar , Hendon Harry H. 
Published: July 2013

Abstract
The Australian Bureau of Meteorology has recently enhanced its capability to make coupled model forecasts of intraseasonal climate variations. The Predictive Ocean Atmosphere Model for Australia (POAMA, version 2) seasonal prediction forecast system in operations prior to March 2013, designated P2-S, was not designed for intraseasonal forecasting and has deficiencies in this regard. Most notably, the forecasts were only initialized on the 1st and 15th of each month, and the growth of the ensemble spread in the first 30 days of the forecasts was too slow to be useful on intraseasonal time scales. These deficiencies have been addressed in a system upgrade by initializing more often and through enhancements to the ensemble generation. The new ensemble generation scheme is based on a coupled-breeding approach and produces an ensemble of perturbed atmosphere and ocean states for initializing the forecasts. This scheme impacts favorably on the forecast skill of Australian rainfall and temperature compared to P2-S and its predecessor (version 1.5). In POAMA-1.5 the ensemble was produced using time-lagged atmospheric initial conditions but with unperturbed ocean initial conditions. P2-S used an ensemble of perturbed ocean initial conditions but only a single atmospheric initial condition. The improvement in forecast performance using the coupled-breeding approach is primarily reflected in improved reliability in the first month of the forecasts, but there is also higher skill in predicting important drivers of intraseasonal climate variability, namely the Madden–Julian oscillation and southern annular mode. The results illustrate the importance of having an optimal ensemble generation strategy.
Measurement of single low-density lipoprotein particles by atomic force microscopy
Authors: Sakurai Toshihiro , Takeda Seiji , Takahashi Jun-ya , Takahashi Yuji , Wada Norio , Trirongjitmoah Suchin , Namita Takeshi , Jin Shigeki , Ikuta Akiko , Furumaki Hiroaki , Hui Shu-Ping , Fuda Hirotoshi , Fujikawa Masato , Shimizu Koichi , Chiba Hitoshi 
Published: July 2013

Background The size of lipoprotein particles is relevant to the risk of coronary artery disease (CAD). Methods We investigated the feasibility of atomic force microscopy (AFM) for evaluating the size of large low-density lipoprotein (LDL) and small dense LDL (sd-LDL) separated by ultracentrifugation. The measurements by AFM in tapping mode were compared to those by electron microscopy (EM). Results There was a significant difference in particle sizes determined by AFM between large LDL (20.6 ± 1.9 nm, mean ± SD) and sd-LDL (16.2 ± 1.4 nm) obtained from six healthy volunteers ( P < 0.05). The particle sizes determined by EM for the same samples were 23.2 ± 1.4 nm for large LDL and 20.4 ± 1.4 nm for sd-LDL. The difference between large LDL and sd-LDL detected by EM was also statistically significant ( P < 0.05). In addition, the particle sizes of each lipoprotein fraction were significantly different between AFM and EM: P < 0.05 for large LDL and P < 0.05 for sd-LDL. Conclusions AFM can differentiate between sd-LDL and large LDL particles by their size, and might be useful for evaluating risk for CAD.
Investigation of soy protein hydrogels for biomedical applications: Materials characterization, drug release, and biocompatibility
Authors: Chien Karen B , Chung Eun J , Shah Ramille N 
Published: July 2013

Soy protein is emerging as a novel material for biomedical applications due to its abundance in nature, ease of isolation and processing, and inherent properties for mediating cell adhesion and growth. In this study, mechanically robust soy protein hydrogels were fabricated with varying weight percentages in water (15, 18, and 20 wt.%) without the use of chemical modifiers or crosslinkers. This fabrication method is beneficial because it allows for the direct injection of these soy hydrogels in vivo. The material properties, drug releasing capability, and biocompatibility in vitro and in vivo were assessed. The different concentrations of soy protein varied the rheological, swelling, and mechanical properties and affected the release of the model drug fluorescein from the hydrogels in vitro. Higher weight percent of soy increased the robustness of the hydrogels and released a lower amount of fluorescein over one week. Viability and growth of seeded L929 mouse fibroblasts demonstrated that the hydrogels were biocompatible in vitro for one week. Soy hydrogels were injectable in vivo into the subcutaneous pocket of mice, and histological staining showed minimal fibrous capsule formation for up to 20 days. The ease of fabrication and tailorable properties of soy hydrogels render it a promising biomaterial for tissue engineering and drug delivery applications, particularly for wound healing.
How valuable is P-wave dispersion in the determination of carboxyhemoglobin levels?
Authors: Sener MT , Anci Y , Kalkan K , Kir MZ , Emet M 
Published: July 2013

Objective: To determine whether or not wave/interval dispersions in electrocardiography (ECG) are increased, and to define whether wave and interval dispersions are correlated with carboxyhemoglobin (COHb) levels. Methods: ECG, complete blood count, and biochemical parameters were taken from 87 patients with carbon monoxide (CO) poisoning as well as 90 control patients with similar age, gender, and body mass index distribution. COHb levels were recorded in CO-poisoning patients. The COHb levels and the relationships with ECG parameters were studied. Results: Pmax, Pmin, Pd, PRmax, PRmin, PRd, QTmax, QTmin, QTd, cQTmax, cQTmin, cQTd, Tmax, Tmin, and Td in ECG were higher in intoxicated patients than the control group ( p < 0.05 for all). Pearson’s correlation analyses showed moderately significant positive correlations between COHb level and Pmax ( r = 0.224; p = 0.037) and Pd ( r = 0.222; p = 0.039). The receiver–operator characteristic (ROC) curve showed that a Pd value of 38 ms determined by ECG separates patients with a COHb ≥ 20% with area under the ROC curve of 0.78 (95%CI = 0.71–0.83), a sensitivity of 67.9% (95%CI = 59.4–75.6), a specificity of 95% (95%CI = 83.0–99.2], a positive predictive value of 97.9% (95%CI = 92.5–99.7), and a negative predictive value of 46.3% (95%CI = 35.3–57.7.) Conclusion: A significant increase in wave/interval dispersions in the ECG of CO-poisoning patients compared with controls may show that not only a part is affected but both atrium and the ventricles as a whole are affected by hypoxic ischemia. When COHb levels of the patients are unavailable, P dispersion on ECG may show CO poisoning level of the patient.
Segmental duplications in the silkworm genome
Authors: Zhao Qian , Zhu Zhenglin , Kasahara Masahiro , Morishita Shinichi , Zhang Ze 
Published: July 2013

Abstract

Background
Segmental duplications (SDs) or low-copy repeats play important roles in both gene and genome evolution. SDs have been extensively investigated in many organisms, however, there is no information about SDs in the silkworm, Bombyx mori.

Result
In this study, we identified and annotated the SDs in the silkworm genome. Our results suggested that SDs constitute ~1.4% of the silkworm genome sequence (≥1 kb in length and ≥90% in the identity of sequence); the number is similar to that in Drosophila melanogaster but smaller than mammalian organisms. Almost half (42%) of the SD sequences are not assigned to chromosomes, indicating that the SDs are challenges for the assembling of genome sequences. We also provided experimental validation of large duplications using qPCR. The analysis of SD content indicated that the genes related to immunity, detoxification, reproduction, and environmental signal recognition are significantly enriched in the silkworm SDs.

Conclusion
Our results suggested that segmental duplications have been problematic for sequencing and assembling of the silkworm genome. SDs may have important biological significances in immunity, detoxification, reproduction, and environmental signal recognition in the silkworm. This study provides insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research.
Disclosure of the differences of Mesorhizobium loti under the free-living and symbiotic conditions by comparative proteome analysis without bacteroid isolation
Authors: Tatsukami Yohei , Nambu Mami , Morisaka Hironobu , Kuroda Kouichi , Ueda Mitsuyoshi 
Published: July 2013

Abstract

Background
Rhizobia are symbiotic nitrogen-fixing soil bacteria that show a symbiotic relationship with their host legume. Rhizobia have 2 different physiological conditions: a free-living condition in soil, and a symbiotic nitrogen-fixing condition in the nodule. The lifestyle of rhizobia remains largely unknown, although genome and transcriptome analyses have been carried out. To clarify the lifestyle of bacteria, proteome analysis is necessary because the protein profile directly reflects in vivo reactions of the organisms. In proteome analysis, high separation performance is required to analyze complex biological samples. Therefore, we used a liquid chromatography-tandem mass spectrometry system, equipped with a long monolithic silica capillary column, which is superior to conventional columns. In this study, we compared the protein profile of Mesorhizobium loti MAFF303099 under free-living condition to that of symbiotic conditions by using small amounts of crude extracts.

Result
We identified 1,533 and 847 proteins for M. loti under free-living and symbiotic conditions, respectively. Pathway analysis by Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that many of the enzymes involved in the central carbon metabolic pathway were commonly detected under both conditions. The proteins encoded in the symbiosis island, the transmissible chromosomal region that includes the genes that are highly upregulated under the symbiotic condition, were uniquely detected under the symbiotic condition. The features of the symbiotic condition that have been reported by transcriptome analysis were confirmed at the protein level by proteome analysis. In addition, the genes of the proteins involved in cell surface structure were repressed under the symbiotic nitrogen-fixing condition. Furthermore, farnesyl pyrophosphate (FPP) was found to be biosynthesized only in rhizobia under the symbiotic condition.

Conclusion
The obtained protein profile appeared to reflect the difference in phenotypes under the free-living and symbiotic conditions. In addition, KEGG pathway analysis revealed that the cell surface structure of rhizobia was largely different under each condition, and surprisingly, rhizobia might provided FPP to the host as a source of secondary metabolism. M. loti changed its metabolism and cell surface structure in accordance with the surrounding conditions.
Ciprofloxacin prophylaxis in high risk neutropenic patients: effects on outcomes, antimicrobial therapy and resistance
Authors: Garnica Marcia , Nouér Simone A , Pellegrino Flávia LPC , Moreira Beatriz M , Maiolino Angelo , Nucci Marcio 
Published: July 2013

Abstract

Background
The use of quinolone prophylaxis in high-risk neutropenic patients is considered standard of care but the development of resistance is a concern. Previous studies have focused mainly on quinolone resistance among patients receiving prophylaxis, with very few data reporting its impact on the hospital microbial epidemiology.

Methods
We analyzed a cohort of 329 episodes of chemotherapy-induced neutropenia in adults, and compared two periods: 2005 (period 1, no prophylaxis, n=110) and 2006-2008 (period 2, ciprofloxacin prophylaxis, n=219). Outcomes analyzed were the frequency of febrile neutropenia, bacteremia, duration of antibiotic therapy and hospitalization, and antimicrobial resistance to ciprofloxacin and extended-spectrum beta-lactamase [ESBL] production. We analyzed resistance rates (by patients-day) in the cohort, as well as in other patients (neutropenic and non-neutropenic, 11,975 patients-day) admitted to the hematology unit in the same period, taking into consideration the general resistance patterns in the hospital.

Results
Quinolone prophylaxis (period 2) resulted in fewer episodes of febrile neutropenia (159/219 [73%] vs. 102/110 [93%], Chi-square 18.09, p = 0.00002), and bacteremia (49/219 [22] vs. 36/110 [33%], Chi-square 4.10, p = 0.04), shorter duration of antibiotic therapy (p = 0.0002) and hospitalization (p = 0.002), but more frequent use of carbapenems (79/219 [36%] vs. 15/110 [14%], Chi-square 18.06, p = 0.0002). In addition, period 2 was associated with higher rates of quinolone resistance (6.77 vs. 3.02 per 1,000 patients-day, p = 0.03). The rate of ESBL-producing enterobacteria in the two periods was slightly higher in patients receiving quinolone prophylaxis (1.27 vs. 0.38 per 1,000 patients-day, p = 0.26) as well as in the hematology unit overall (1.59 vs. 0.53 per 1,000 patients-day, p = 0.08), but remained stable in the whole hospital (0.53 vs. 0.56 per 1,000 patients-day, p = 0.74).

Conclusions
Ciprofloxacin prophylaxis was beneficial in high risk neutropenic patients, but important modifications in the prescription of carbapenems and on antimicrobial resistance patterns of isolates were observed. The importance of hospital or ward ecology must be taken into account when deciding for quinolone prophylaxis in high-risk neutropenic patients.
Inflammasome activation mediates inflammation and outcome in humans and mice with pneumococcal meningitis
Authors: Geldhoff Madelijn , Mook-Kanamori Barry B , Brouwer Matthijs C , Troost Dirk , Leemans Jaklien C , Flavell Richard A , Van der Ende Arie , Van der Poll Tom , Van de Beek Diederik 
Published: July 2013

Abstract

Background
Inflammasomes are multi-protein intracellular signaling complexes that have recently been hypothesized to play a role in the regulation of the inflammation response. We studied associations between inflammasome-associated cytokines IL-1β and IL-18 in cerebrospinal fluid (CSF) of patients with bacterial meningitis and clinical outcome, and pneumococcal serotype. In a murine model of pneumococcal meningitis we examined the pathophysiological roles of two inflammasome proteins, NLRP3 (Nod-like receptor protein-3) and adaptor protein ASC (apoptosis-associated speck-like protein).

Methods
In a nationwide prospective cohort study, CSF cytokine levels were measured and related to clinical outcome and pneumococcal serotype. In a murine model of pneumococcal meningitis using Streptococcus pneumoniae serotype 3, we examined bacterial titers, cytokine profiles and brain histology at 6 and 30 hours after inoculation in wild-type (WT), Asc and Nlrp3 deficient mice.

Results
In patients with bacterial meningitis, CSF levels of inflammasome associated cytokines IL-1β and IL-18 were related to complications, and unfavorable disease outcome. CSF levels of IL-1β were associated with pneumococcal serotype (p<0.001). In our animal model, Asc and Nlrp3 deficient mice had decreased systemic inflammatory responses and bacterial outgrowth as compared to WT mice. Differences between Asc
−/− and WT mice appeared sooner after bacterial inoculation and were more widespread (lower pro-inflammatory cytokine levels in both blood and brain homogenate) than in Nlrp3
-/-mice. Nlrp3 deficiency was associated with an increase of cerebral neutrophil infiltration and cerebral hemorrhages when compared to WT controls.

Conclusions
Our results implicate an important role for inflammasome proteins NLRP3 and ASC in the regulation of the systemic inflammatory response and the development of cerebral damage during pneumococcal meningitis, which may dependent on the pneumococcal serotype.