bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Chronology of El Niño Events from Primary Documentary Sources in Northern Peru*
Authors: Garcia-Herrera R. , Barriopedro D. , Hernández E. , Diaz H. F. , Garcia R. R. , Prieto M. R. , Moyano R. 
Published: April 2008

AbstractThe authors present a chronology of El Niño (EN) events based on documentary records from northern Peru. The chronology, which covers the period 1550–1900, is constructed mainly from primary sources from the city of Trujillo (Peru), the Archivo General de Indias in Seville (Spain), and the Archivo General de la Nación in Lima (Peru), supplemented by a reassessment of documentary evidence included in previously published literature. The archive in Trujillo has never been systematically evaluated for information related to the occurrence of El Niño–Southern Oscillation (ENSO). Abundant rainfall and river discharge correlate well with EN events in the area around Trujillo, which is very dry during most other years. Thus, rain and flooding descriptors, together with reports of failure of the local fishery, are the main indicators of EN occurrence that the authors have searched for in the documents. A total of 59 EN years are identified in this work. This chronology is compared with the two main previous documentary EN chronologies and with ENSO indicators derived from proxy data other than documentary sources. Overall, the seventeenth century appears to be the least active EN period, while the 1620s, 1720s, 1810s, and 1870s are the most active decades. The results herein reveal long-term fluctuations in warm ENSO activity that compare reasonably well with low-frequency variability deduced from other proxy data.
Decadal Sea Level Changes in the 50-Year GECCO Ocean Synthesis
Authors: Köhl Armin , Stammer Detlef 
Published: April 2008

AbstractAn estimate of the time-varying ocean circulation, obtained over the period 1952–2001, is analyzed here with respect to its decadal and longer-term changes in sea level. The estimate results from a synthesis of most of the ocean datasets available during this 50-yr period with the Estimating the Circulation and Climate of the Ocean/Massachusetts Institute of Technology (ECCO/MIT) ocean circulation model. Over the period 1992 through 2001, the increase in thermosteric sea level rise on average amounts to 1.2 mm yr−1 over the top 750 m and 1.8 mm yr−1 over the total water column. This corresponds to an increase in upper-ocean heat content of 1.5 × 1022 J yr−1 and is in agreement with the estimates of Willis et al. However, over the period 1962 through 2001 the global net thermosteric sea level rise is estimated as 0.66 mm yr−1 over the top 750 m, which is twice the recent estimate from Antonov et al. (0.33 mm yr−1). The corresponding trend over the total water column of 0.92 mm yr−1 is also about twice their value for the layer of 0–3000 m (0.40 mm yr−1). For the last decade, the global heat flux into the ocean of 1.5 W m−2 is twice as large as the recent estimate by Willis et al. due to the heat content change in deeper layers. Regional changes in sea level are predominantly associated with an intensification of the subtropical gyre circulation and a corresponding redistribution of heat. The horizontal advection of heat due to an increase in wind stress curl is found to explain a major fraction of the estimated regional sea level trends over the last 40 years. However, the mechanisms appear different during the last decade when in some regions changes in surface heat flux may explain as much as 50% of the sea level changes.
Changes in Tropical Cyclone Activity due to Global Warming: Results from a High-Resolution Coupled General Circulation Model
Authors: Gualdi S. , Scoccimarro E. , Navarra A. 
Published: April 2008

AbstractThis study investigates the possible changes that greenhouse global warming might generate in the characteristics of tropical cyclones (TCs). The analysis has been performed using scenario climate simulations carried out with a fully coupled high-resolution global general circulation model. The capability of the model to reproduce a reasonably realistic TC climatology has been assessed by comparing the model results from a simulation of the twentieth century with observations. The model appears to be able to simulate tropical cyclone–like vortices with many features similar to the observed TCs. The simulated TC activity exhibits realistic geographical distribution, seasonal modulation, and interannual variability, suggesting that the model is able to reproduce the major basic mechanisms that link TC occurrence with large-scale circulation. The results from the climate scenarios reveal a substantial general reduction of TC frequency when the atmospheric CO2 concentration is doubled and quadrupled. The reduction appears particularly evident for the tropical western North Pacific (WNP) and North Atlantic (ATL). In the NWP the weaker TC activity seems to be associated with reduced convective instabilities. In the ATL region the weaker TC activity seems to be due to both the increased stability of the atmosphere and a stronger vertical wind shear. Despite the generally reduced TC activity, there is evidence of increased rainfall associated with the simulated cyclones. Finally, the action of the TCs remains well confined to the tropical region and the peak of TC number remains equatorward of 20° latitude in both hemispheres, notwithstanding the overall warming of the tropical upper ocean and the expansion poleward of warm SSTs.
The Stabilized Radiometer Platform (STRAP)—An Actively Stabilized Horizontally Level Platform for Improved Aircraft Irradiance Measurements
Authors: Bucholtz Anthony , Bluth Robert T. , Kelly Ben , Taylor Scott , Batson Keir , Sarto Anthony W. , Tooman Tim P. , McCoy Robert F. 
Published: April 2008

Abstract
Measurements of solar and infrared irradiance by instruments rigidly mounted to an aircraft have historically been plagued by the introduction of offsets and fluctuations into the data that are solely due to the pitch and roll movements of the aircraft. The Stabilized Radiometer Platform (STRAP) was developed to address this problem. Mounted on top of an aircraft and utilizing a self-contained, coupled Inertial Navigation System–GPS, STRAP actively keeps a set of uplooking radiometers horizontally level to within ±0.02° for aircraft pitch and roll angles of up to approximately ±10°. The system update rate of 100 Hz compensates for most pitch and roll changes experienced in normal flight and in turbulence. STRAP was mounted on a Twin Otter aircraft and its performance evaluated during normal flight and during a series of flight maneuvers designed to test the accuracy, range, and robustness of the platform. The measurements from an identical pair of solar pyranometers—one mounted on STRAP and the other rigidly mounted nearby directly to the aircraft—are compared to illustrate the accuracy and capability of the new platform. Results show that STRAP can keep radiometers level within the specified pitch and roll range, that it is able to recover from flight maneuvers outside of this range, and that it greatly increases the quantity of useful radiometer data from any given flight. Of particular note, STRAP now allows accurate measurements of the downwelling solar irradiance during spiral ascents or descents of the aircraft, greatly expanding the utility of aircraft radiometer measurements.
Pressure Perturbations and Upslope Flow over a Heated, Isolated Mountain
Authors: Geerts Bart , Miao Qun , Demko J. Cory 
Published: April 2008

AbstractSurface and upper-air data, collected as part of the Cumulus Photogrammetric, In Situ, and Doppler Observations (CuPIDO) experiment during the 2006 monsoon season around the Santa Catalina Mountains in southeast Arizona, are used to study the diurnal variation of the mountain-scale surface convergence and its thermal forcing. The thermal forcing is examined in terms of a horizontal pressure gradient force, which is derived assuming hydrostatic balance. The mountain is ∼30 km in diameter, ∼2 km high, and relatively isolated. The environment is characterized by weak winds, a deep convective boundary layer in the afternoon, and sufficient low-level moisture for orographic cumulus convection on most days.The katabatic, divergent surface flow at night and anabatic, convergent flow during the day are in phase with the diurnal variation of the horizontal pressure gradient force, which points toward the mountain during the day and away from the mountain at night. The daytime pressure deficit over the mountain of 0.5–1.0 mb is hydrostatically consistent with the observed 1–2-K virtual potential temperature excess over the mountain. The interplay between surface convergence and orographic thunderstorms is examined, and the consequence of deep convection (outflow spreading) is more apparent than its possible trigger (enhanced convergence).
The Association of a Varus Hindfoot and Fracture of the Fifth Metatarsal Metaphyseal-Diaphyseal Junction
Authors: Raikin Steven M. , Slenker Nicholas , Ratigan Brian 
Published: April 2008

BackgroundFractures to the fifth metatarsal metaphyseal-diaphyseal junction (Jones fracture) have high nonunion rates. Surgical intramedullary screw fixations have excellent results but a high refracture rate. This has been associated with inadequate screw size and too early return to activity.HypothesisVarus hindfoot alignment overloads the lateral column of the foot and acts as a predisposing factor to the development of and failure of treatment of Jones fractures.Study DesignCase series; Level of evidence, 4.MethodsTwenty-one primary Jones fractures (20 patients) treated surgically with a 4.5-mm cannulated screw were retrospectively reviewed. Detailed clinical and radiographic data and outcomes were recorded, including measurements of hindfoot alignment.ResultsA 100% union rate with return to prior activity level and no refractures were found at a mean follow-up of 49 months. Clinical varus was present in 16 feet, whereas radiographic measurements revealed 18 of 21 hindfeet to be in varus. The mean calcaneal pitch angle was 28.5°, and the mean Meary angle was 13° convex upward. Patients with varus alignment were fitted postoperatively with lateral hindfoot and forefoot posted orthotic inserts to correct alignment.ConclusionThe majority of patients sustaining Jones fractures have evidence of varus hindfoot alignment. This may be a predisposing factor to developing the fracture or refracture after fixation. Postoperative varus unloading (lateral hindfoot and forefoot posting) orthotic insert appears to be helpful in preventing reinjury or refracture of Jones fractures.
Mapping proteins to disease terminologies: from UniProt to MeSH
Authors: Mottaz Anaïs , Yip Yum L , Ruch Patrick , Veuthey Anne-Lise 
Published: April 2008

Abstract

Background
Although the UniProt KnowledgeBase is not a medical-oriented database, it contains information on more than 2,000 human proteins involved in pathologies. However, these annotations are not standardized, which impairs the interoperability between biological and clinical resources. In order to make these data easily accessible to clinical researchers, we have developed a procedure to link diseases described in the UniProtKB/Swiss-Prot entries to the MeSH disease terminology.

Results
We mapped disease names extracted either from the UniProtKB/Swiss-Prot entry comment lines or from the corresponding OMIM entry to the MeSH. Different methods were assessed on a benchmark set of 200 disease names manually mapped to MeSH terms. The performance of the retained procedure in term of precision and recall was 86% and 64% respectively. Using the same procedure, more than 3,000 disease names in Swiss-Prot were mapped to MeSH with comparable efficiency.

Conclusions
This study is a first attempt to link proteins in UniProtKB to the medical resources. The indexing we provided will help clinicians and researchers navigate from diseases to genes and from genes to diseases in an efficient way. The mapping is available at: http://research.isb-sib.ch/unimed.
Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots
Authors: Mangelsen Elke , Kilian Joachim , Berendzen Kenneth W , Kolukisaoglu Üner H , Harter Klaus , Jansson Christer , Wanke Dierk 
Published: April 2008

Abstract

Background
WRKY proteins belong to the WRKY-GCM1 superfamily of zinc finger transcription factors that have been subject to a large plant-specific diversification. For the cereal crop barley (Hordeum vulgare), three different WRKY proteins have been characterized so far as regulators in sucrose signaling, pathogen defense, and in response to cold and drought. However, their phylogenetic relationship remained unresolved.

Results
In this study, we used available sequence information to identify a minimum number of 45 barley WRKY transcription factor (HvWRKY) genes. According to their structural features, the HvWRKY factors were classified into the previously defined polyphyletic WRKY subgroups 1 to 3. Furthermore, we could assign putative orthologs of the HvWRKY proteins in Arabidopsis and rice. While in most cases clades of orthologous proteins were formed within each group or subgroup, other clades were composed of paralogous proteins for the grasses and Arabidopsis only, which is indicative of specific gene radiation events. To gain insight into their putative functions, we examined expression profiles of WRKY genes from publicly available microarray data resources and found group specific expression patterns. While putative orthologs of the HvWRKY transcription factors have been inferred from phylogenetic sequence analysis, we performed a comparative expression analysis of WRKY genes in Arabidopsis and barley. Indeed, highly correlative expression profiles were found between some of the putative orthologs.

Conclusion

HvWRKY genes have not only undergone radiation in monocot or dicot species, but exhibit evolutionary traits specific to grasses. HvWRKY proteins exhibited not only sequence similarities between orthologs with Arabidopsis, but also relatedness in their expression patterns. This correlative expression is indicative for a putative conserved function of related WRKY proteins in monocot and dicot species.
Array-CGH in patients with Kabuki-like phenotype: Identification of two patients with complex rearrangements including 2q37 deletions and no other recurrent aberration
Authors: Cuscó Ivon , del Campo Miguel , Vilardell Mireia , González Eva , Gener Blanca , Galán Enrique , Toledo Laura , Pérez-Jurado Luis A 
Published: April 2008

Abstract

Background
Kabuki syndrome (KS) is a multiple congenital anomaly syndrome characterized by specific facial features, mild to moderate mental retardation, postnatal growth delay, skeletal abnormalities, and unusual dermatoglyphic patterns with prominent fingertip pads. A 3.5 Mb duplication at 8p23.1-p22 was once reported as a specific alteration in KS but has not been confirmed in other patients. The molecular basis of KS remains unknown.

Methods
We have studied 16 Spanish patients with a clinical diagnosis of KS or KS-like to search for genomic imbalances using genome-wide array technologies. All putative rearrangements were confirmed by FISH, microsatellite markers and/or MLPA assays, which also determined whether the imbalance was de novo or inherited.

Results
No duplication at 8p23.1-p22 was observed in our patients. We detected complex rearrangements involving 2q in two patients with Kabuki-like features: 1) a de novo inverted duplication of 11 Mb with a 4.5 Mb terminal deletion, and 2) a de novo 7.2 Mb-terminal deletion in a patient with an additional de novo 0.5 Mb interstitial deletion in 16p. Additional copy number variations (CNV), either inherited or reported in normal controls, were identified and interpreted as polymorphic variants. No specific CNV was significantly increased in the KS group.

Conclusion
Our results further confirmed that genomic duplications of 8p23 region are not a common cause of KS and failed to detect other recurrent rearrangement causing this disorder. The detection of two patients with 2q37 deletions suggests that there is a phenotypic overlap between the two conditions, and screening this region in the Kabuki-like patients should be considered.
Association between promoter -1607 polymorphism of MMP1 and Lumbar Disc Disease in Southern Chinese
Authors: Song You-Qiang , Ho Daniel WH , Karppinen Jaro , Kao Patrick YP , Fan Bao-Jian , Luk Keith DK , Yip Shea-Ping , Leong John CY , Cheah Kathryn SE , Sham Pak , Chan Danny , Cheung Kenneth MC 
Published: April 2008

Abstract

Background
Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD.

Methods
Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom® platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test.

Results
Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04–1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01–2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033–2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029–2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele.

Conclusion
We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism.
Evaluation of patients on sertindole treatment after failure of other antipsychotics: A retrospective analysis
Authors: Azorin Jean-Michel , Murteira Susana , Hansen Karina , Toumi Mondher 
Published: April 2008

Abstract

Background
Use of the atypical antipsychotic sertindole was suspended for four years due to safety concerns. During the suspension, the regulatory authorities required further studies, including this one, to be conducted. The purpose of this study was to determine if a subset of patients with psychotic illness exists which particularly benefits from sertindole treatment after failure of other antipsychotic drugs, including atypical antipsychotics.

Methods
This was a retrospective single-arm observational crossover study of 344 patients, who served as their own controls. Patients mainly from the Sertindole Safety Study who had shown good response to sertindole, and who had followed up to four alternating six month periods of treatment with sertindole and other antipsychotics, were included. (In Period 1 patients took non-sertindole treatment, in Period 2, sertindole was taken, in Period 3, patients reverted to non-sertindole treatment, and in Period 4, sertindole was taken again.) Patient records for each period of treatment were assessed for objective data: number and duration of hospitalizations due to worsening of psychotic symptoms; the amount of self-harming behaviour; indicators of social status. Retrospective evaluation of changes in clinical symptoms from the patients' records was also conducted. Dates and reasons for stopping and/or switching medication were also recorded.

Results
There was improvement in all objective measured parameters during the periods of sertindole treatment. In particular, the average number of hospitalizations per year due to worsening of psychotic symptoms was reduced in the following way in the group studied over four treatment periods: Period 1 (non-sertindole treatment) 3.4; Period 2 (sertindole treatment) 1.0; Period 3 (non-sertindole treatment) 2.0; Period 4 (sertindole treatment) 1.8. The duration of hospitalizations also decreased significantly during the periods of sertindole treatment. Results showed that patients improved in objective social parameters when switched to sertindole treatment; assessment of the patients' affective lives showed a significant increase in the number of patients having a stable relationship during sertindole treatment; and assessment of the number of patients employed showed an increase after the first and second switch to sertindole treatment (from Period 1 to Period 2 and from Period 3 to Period 4, respectively).
Adverse events and lack of efficacy were the main reasons for switching to sertindole.

Conclusion
A group of patients benefited from sertindole after other antipsychotic treatments, including that with atypical antipsychotics, had failed. Further studies are needed to investigate if there is a specific patient profile that corresponds to these responders.
Multiple origins of resistance-conferring mutations in Plasmodium vivax dihydrofolate reductase
Authors: Hawkins Vivian N , Auliff Alyson , Prajapati Surendra Kumar , Rungsihirunrat Kanchana , Hapuarachchi Hapuarachchige C , Maestre Amanda , O'Neil Michael T , Cheng Qin , Joshi Hema , Na-Bangchang Kesara , Sibley Carol Hopkins 
Published: April 2008

Abstract

Background
In order to maximize the useful therapeutic life of antimalarial drugs, it is crucial to understand the mechanisms by which parasites resistant to antimalarial drugs are selected and spread in natural populations. Recent work has demonstrated that pyrimethamine-resistance conferring mutations in Plasmodium falciparum dihydrofolate reductase (dhfr) have arisen rarely de novo, but spread widely in Asia and Africa. The origin and spread of mutations in Plasmodium vivax dhfr were assessed by constructing haplotypes based on sequencing dhfr and its flanking regions.

Methods
The P. vivax dhfr coding region, 792 bp upstream and 683 bp downstream were amplified and sequenced from 137 contemporary patient isolates from Colombia, India, Indonesia, Papua New Guinea, Sri Lanka, Thailand, and Vanuatu. A repeat motif located 2.6 kb upstream of dhfr was also sequenced from 75 of 137 patient isolates, and mutational relationships among the haplotypes were visualized using the programme Network.

Results
Synonymous and non-synonymous single nucleotide polymorphisms (SNPs) within the dhfr coding region were identified, as was the well-documented in-frame insertion/deletion (indel). SNPs were also identified upstream and downstream of dhfr, with an indel and a highly polymorphic repeat region identified upstream of dhfr. The regions flanking dhfr were highly variable. The double mutant (58R/117N) dhfr allele has evolved from several origins, because the 58R is encoded by at least 3 different codons. The triple (58R/61M/117T) and quadruple (57L/61M/117T/173F, 57I/58R/61M/117T and 57L/58R/61M/117T) mutant alleles had at least three independent origins in Thailand, Indonesia, and Papua New Guinea/Vanuatu.

Conclusion
It was found that the P. vivax dhfr coding region and its flanking intergenic regions are highly polymorphic and that mutations in P. vivax dhfr that confer antifolate resistance have arisen several times in the Asian region. This contrasts sharply with the selective sweep of rare antifolate resistant alleles observed in the P. falciparum populations in Asia and Africa. The finding of multiple origins of resistance-conferring mutations has important implications for drug policy.