bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of New Precipitation and Reconstructed Streamflow Products to Streamflow Trend Attribution in Northern Eurasia
Authors: Adam Jennifer C. , Lettenmaier Dennis P. 
Published: April 2008

Abstract
River runoff to the Arctic Ocean has increased over the last century, primarily during the winter and spring and primarily from the major Eurasian rivers. Some recent studies have suggested that the additional runoff is due to increased northward transport of atmospheric moisture (and associated increased precipitation), but other studies show inconsistencies in long-term runoff and precipitation trends, perhaps partly due to biases in the observational datasets. Through trend analysis of precipitation, temperature, and streamflow data, the authors investigate the extent to which Eurasian Arctic river discharge changes are attributable to precipitation and temperature changes as well as to reservoir construction and operation between the years of 1936 and 2000. Two new datasets are applied: a gridded precipitation product, in which the low-frequency variability is constrained to match that of long-term bias-corrected precipitation station data, and a reconstructed streamflow product, in which the effects of reservoirs have been minimized using a physically based reservoir model. It is found that reservoir operations have primarily affected streamflow seasonality, increasing winter discharge and decreasing summer discharge. To understand the influences of climate on streamflow changes, the authors hypothesize three cases that would cause precipitation trends to be inconsistent with streamflow trends: first, for the coldest basins in northeastern Siberia, streamflow should be sensitive to warming primarily as a result of the melting of excess ground ice, and for these basins positive streamflow trends may exceed precipitation trends in magnitude; second, evapotranspiration (ET) in the warmer regions of western Siberia and European Russia is sensitive to warming and increased precipitation, therefore observed precipitation trends may exceed streamflow trends; and third, streamflow from the central Siberian basins should respond to both effects. It is found that, in general, these hypotheses hold true. In the coldest basins, streamflow trends diverged from precipitation trends starting in the 1950s to 1960s, and this divergence accelerated thereafter. In the warmest basins, precipitation trends consistently exceeded streamflow trends, suggesting that increased precipitation contributed to increases in both ET and streamflow. In the central basins, permafrost degradation and ET effects appear to be contributing to long-term streamflow trends in varying degrees for each basin. The results herein suggest that the extent and state of the permafrost underlying a basin is a complicating factor in understanding long-term changes in Eurasian Arctic river discharge.
Estimating Annual Global Upper-Ocean Heat Content Anomalies despite Irregular In Situ Ocean Sampling*
Authors: Lyman John M. , Johnson Gregory C. 
Published: April 2008

Abstract
The effects of irregular in situ ocean sampling on estimates of annual globally integrated upper ocean heat content anomalies (OHCA) are investigated for sampling patterns from 1955 to 2006. An analytical method is presented for computing the effective area covered by an objective map for any given in situ sampling distribution. To evaluate the method, appropriately scaled sea surface height (SSH) anomaly maps from Archiving, Validation, and Interpretation of Satellite Oceanographic data (AVISO) are used as a proxy for OHCA from 1993 to 2006. Use of these proxy data demonstrates that the simple area integral (SI) of such an objective map for sparse datasets does not agree as well with the actual integral as the weighted integral (WI), defined as the simple integral weighted by the ratio of the total area over the “observed” area. From 1955 to 1966, in situ ocean sampling is inadequate to estimate accurately annual global integrals of the proxy upper OHCA. During this period, the SI for the sampling pattern of any given year underestimates the 13-yr trend in proxy OHCA from 1993 to 2006 by around 70%, and confidence limits for the WI are often very large. From 1967 to 2003 there appear to be sufficient data to estimate annual global integrals. Limited by the constraints of this analysis, the SI for any given year’s sampling pattern still underestimates the 1993–2006 13-yr trend in the proxy by around 30%, but the WI matches the trend well with small confidence limits. For 2004 through 2006 in situ sampling, with near-global in situ Argo data coverage, the 1993–2006 13-yr trend in the proxy is equally well represented by the SI or WI.
The Role of Ekman Ocean Heat Transport in the Northern Hemisphere Response to ENSO
Authors: Alexander Michael A. , Scott James D. 
Published: April 2008

Abstract
The influence of oceanic Ekman heat transport (Qek) on air–sea variability associated with ENSO teleconnections is examined via a pair of atmospheric general circulation model (AGCM) experiments. In the mixed layer model (MLM) experiment, observed sea surface temperatures (SSTs) for the years 1950–99 are specified over the tropical Pacific, while a grid of mixed layer models is coupled to the AGCM elsewhere over the global oceans. The same experimental design was used in the Ekman transport/mixed layer model (EKM) experiment with the addition of Qek in the mixed layer ocean temperature equation. The ENSO signal was evaluated using differences between composites of El Niño and La Niña events averaged over the 16 ensemble members in each experiment.
In both experiments the Aleutian low deepened and the resulting surface heat fluxes cooled the central North Pacific and warmed the northeast Pacific during boreal winter in El Niño relative to La Niña events. Including Qek amplified the ENSO-related SSTs by ∼⅓ in the central and northeast North Pacific, producing anomalies comparable to those in nature. Differences between the ENSO-induced atmospheric circulation anomalies in the EKM and MLM experiments were not significant over the North Pacific. The sea level pressure (SLP) and SST response to ENSO over the Atlantic strongly projects on the North Atlantic Oscillation (NAO) and the SST tripole pattern in observations and both model experiments. The La Niña anomalies, which are stronger than during El Niño, include high pressure and positive SSTs in the central North Atlantic. Including Ekman transport enhanced the Atlantic SST anomalies, which in contrast to the Pacific, appeared to strengthen the overlying atmospheric circulation.
High-Resolution, Mobile Doppler Radar Observations of Cyclic Mesocyclogenesis in a Supercell
Authors: French Michael M. , Bluestein Howard B. , Dowell David C. , Wicker Louis J. , Kramar Matthew R. , Pazmany Andrew L. 
Published: April 2008

Abstract
On 15 May 2003, two ground-based, mobile, Doppler radars scanned a supercell that moved through the Texas Panhandle and cyclically produced mesocyclones. The two radars collected data from the storm during a rapid cyclic mesocyclogenesis stage and a more slowly evolving tornadic period. A 3-cm-wavelength radar scanned the supercell continuously for a short time after it was cyclic but close to the time of tornadogenesis. A 5-cm-wavelength radar scanned the supercell the entire time it exhibited cyclic behavior and for an additional 30 min after that. The volumetric data obtained with the 5-cm-wavelength radar allowed for the individual circulations to be analyzed at multiple levels in the supercell. Most of the circulations that eventually dissipated moved rearward with respect to storm motion and were located at distances progressively farther away from the region of rear-flank outflow. The circulations associated with a tornado did not move nearly as far rearward relative to the storm. The mean circulation diameters were approximately 1–4 km and had lifetimes of 10–30 min. Circulation dissipation often, but not always, occurred following decreases in circulation diameter, while changes in maximum radial wind shear were not reliable indicators of circulation dissipation. In one instance, a pair of circulations rotated cyclonically around, and moved toward, each other; the two circulations then combined to form one circulation. Single-Doppler radial velocities from both radars were used to assess the differences between the pretornadic circulations and the tornadic circulations. Storm outflow in the rear flank of the storm increased notably during the time cyclic mesocyclogenesis slowed and tornado formation commenced. Large storm-relative inflow likely advected the pretornadic circulations rearward in the absence of organized outflow. The development of strong outflow in the rear flank probably balanced the strong inflow, allowing the tornadic circulations to stay in areas rich in vertical vorticity generation.
Extraction of semantic biomedical relations from text using conditional random fields
Authors: Bundschus Markus , Dejori Mathaeus , Stetter Martin , Tresp Volker , Kriegel Hans-Peter 
Published: April 2008

Abstract

Background
The increasing amount of published literature in biomedicine represents an immense source of knowledge, which can only efficiently be accessed by a new generation of automated information extraction tools. Named entity recognition of well-defined objects, such as genes or proteins, has achieved a sufficient level of maturity such that it can form the basis for the next step: the extraction of relations that exist between the recognized entities. Whereas most early work focused on the mere detection of relations, the classification of the type of relation is also of great importance and this is the focus of this work. In this paper we describe an approach that extracts both the existence of a relation and its type. Our work is based on Conditional Random Fields, which have been applied with much success to the task of named entity recognition.

Results
We benchmark our approach on two different tasks. The first task is the identification of semantic relations between diseases and treatments. The available data set consists of manually annotated PubMed abstracts. The second task is the identification of relations between genes and diseases from a set of concise phrases, so-called GeneRIF (Gene Reference Into Function) phrases. In our experimental setting, we do not assume that the entities are given, as is often the case in previous relation extraction work. Rather the extraction of the entities is solved as a subproblem. Compared with other state-of-the-art approaches, we achieve very competitive results on both data sets. To demonstrate the scalability of our solution, we apply our approach to the complete human GeneRIF database. The resulting gene-disease network contains 34758 semantic associations between 4939 genes and 1745 diseases. The gene-disease network is publicly available as a machine-readable RDF graph.

Conclusion
We extend the framework of Conditional Random Fields towards the annotation of semantic relations from text and apply it to the biomedical domain. Our approach is based on a rich set of textual features and achieves a performance that is competitive to leading approaches. The model is quite general and can be extended to handle arbitrary biological entities and relation types. The resulting gene-disease network shows that the GeneRIF database provides a rich knowledge source for text mining. Current work is focused on improving the accuracy of detection of entities as well as entity boundaries, which will also greatly improve the relation extraction performance.
Conserved co-expression for candidate disease gene prioritization
Authors: Oti Martin , van Reeuwijk Jeroen , Huynen Martijn A , Brunner Han G 
Published: April 2008

Abstract

Background
Genes that are co-expressed tend to be involved in the same biological process. However, co-expression is not a very reliable predictor of functional links between genes. The evolutionary conservation of co-expression between species can be used to predict protein function more reliably than co-expression in a single species. Here we examine whether co-expression across multiple species is also a better prioritizer of disease genes than is co-expression between human genes alone.

Results
We use co-expression data from yeast (S. cerevisiae), nematode worm (C. elegans), fruit fly (D. melanogaster), mouse and human and find that the use of evolutionary conservation can indeed improve the predictive value of co-expression. The effect that genes causing the same disease have higher co-expression than do other genes from their associated disease loci, is significantly enhanced when co-expression data are combined across evolutionarily distant species. We also find that performance can vary significantly depending on the co-expression datasets used, and just using more data does not necessarily lead to better prioritization. Instead, we find that dataset quality is more important than quantity, and using a consistent microarray platform per species leads to better performance than using more inclusive datasets pooled from various platforms.

Conclusion
We find that evolutionarily conserved gene co-expression prioritizes disease candidate genes better than human gene co-expression alone, and provide the integrated data as a new resource for disease gene prioritization tools.
A novel function for the presenilin family member spe-4: inhibition of spermatid activation in Caenorhabditis elegans.
Authors: Gosney Ryoko , Liau Wei-Siang , LaMunyon Craig W 
Published: April 2008

Abstract

Background
Sperm cells must regulate the timing and location of activation to maximize the likelihood of fertilization. Sperm from most species, including the nematode Caenorhabditis elegans, activate upon encountering an external signal. Activation for C. elegans sperm occurs as spermatids undergo spermiogenesis, a profound cellular reorganization that produces a pseudopod. Spermiogenesis is initiated by an activation signal that is transduced through a series of gene products. It is now clear that an inhibitory pathway also operates in spermatids, preventing their premature progression to spermatozoa and resulting in fine-scale control over the timing of activation. Here, we describe the involvement of a newly assigned member of the inhibitory pathway: spe-4, a homolog of the human presenilin gene PS1. The spe-4(hc196) allele investigated here was isolated as a suppressor of sterility of mutations in the spermiogenesis signal transduction gene spe-27.

Results
Through mapping, complementation tests, DNA sequencing, and transformation rescue, we determined that allele hc196 is a mutation in the spe-4 gene. Our data show that spe-4(hc196) is a bypass suppressor that eliminates the need for the spermiogenesis signal transduction. On its own, spe-4(hc196) has a recessive, temperature sensitive spermatogenesis-defective phenotype, with mutants exhibiting (i) defective spermatocytes, (ii) defective spermatids, (iii) premature spermatid activation, and (iv) spermatozoa defective in fertilization, in addition to a small number of functional sperm which appear normal microscopically.

Conclusion
A fraction of the sperm from spe-4(hc196) mutant males progress directly to functional spermatozoa without the need for an activation signal, suggesting that spe-4 plays a role in preventing spermatid activation. Another fraction of spermatozoa from spe-4(hc196) mutants are defective in fertilization. Therefore, prematurely activated spermatozoa may have several defects: we show that they may be defective in fertilization, and earlier work showed that they obstruct sperm transfer from males at mating. hc196 is a hypomorphic allele of spe-4, and its newly-discovered role inhibiting spermiogenesis may involve known proteolytic and/or calcium regulatory aspects of presenilin function, or it may involve yet-to-be discovered functions.
Evidence of a chimeric genome in the cyanobacterial ancestor of plastids
Authors: Gross Jeferson , Meurer Jörg , Bhattacharya Debashish 
Published: April 2008

Abstract

Background
Horizontal gene transfer (HGT) is a vexing fact of life for microbial phylogeneticists. Given the substantial rates of HGT observed in modern-day bacterial chromosomes, it is envisaged that ancient prokaryotic genomes must have been similarly chimeric. But where can one find an ancient prokaryotic genome that has maintained its ancestral condition to address this issue? An excellent candidate is the cyanobacterial endosymbiont that was harnessed over a billion years ago by a heterotrophic protist, giving rise to the plastid. Genetic remnants of the endosymbiont are still preserved in plastids as a highly reduced chromosome encoding 54 – 264 genes. These data provide an ideal target to assess genome chimericism in an ancient cyanobacterial lineage.

Results
Here we demonstrate that the origin of the plastid-encoded gene cluster for menaquinone/phylloquinone biosynthesis in the extremophilic red algae Cyanidiales contradicts a cyanobacterial genealogy. These genes are relics of an ancestral cluster related to homologs in Chlorobi/Gammaproteobacteria that we hypothesize was established by HGT in the progenitor of plastids, thus providing a 'footprint' of genome chimericism in ancient cyanobacteria. In addition to menB, four components of the original gene cluster (menF, menD, menC, and menH) are now encoded in the nuclear genome of the majority of non-Cyanidiales algae and plants as the unique tetra-gene fusion named PHYLLO. These genes are monophyletic in Plantae and chromalveolates, indicating that loci introduced by HGT into the ancestral cyanobacterium were moved over time into the host nucleus.

Conclusion
Our study provides unambiguous evidence for the existence of genome chimericism in ancient cyanobacteria. In addition we show genes that originated via HGT in the cyanobacterial ancestor of the plastid made their way to the host nucleus via endosymbiotic gene transfer (EGT).
MDM2 gene SNP309 T/G and p53gene SNP72 G/C do not influence diffuse large B-cell non-Hodgkin lymphoma onset or survival in central European Caucasians
Authors: Bittenbring Joerg , Parisot Frédérique , Wabo Alain , Mueller Monika , Kerschenmeyer Lynn , Kreuz Markus , Truemper Lorenz , Landt Olfert , Menzel Alain , Pfreundschuh Michael , Roemer Klaus 
Published: April 2008

Abstract

Background
SNP309 T/G (rs2279744) causes higher levels of MDM2, the most important negative regulator of the p53 tumor suppressor. SNP72 G/C (rs1042522) gives rise to a p53 protein with a greatly reduced capacity to induce apoptosis. Both polymorphisms have been implicated in cancer. The SNP309 G-allele has recently been reported to accelerate diffuse large B-cell lymphoma (DLBCL) formation in pre-menopausal women and suggested to constitute a genetic basis for estrogen affecting human tumorigenesis. Here we asked whether SNP309 and SNP72 are associated with DLBCL in women and are correlated with age of onset, diagnosis, or patient's survival.

Methods
SNP309 and SNP72 were PCR-genotyped in a case-control study that included 512 controls and 311 patients diagnosed with aggressive NHL. Of these, 205 were diagnosed with DLBCL.

Results
The age of onset was similar in men and women. The control and patients group showed similar SNP309 and SNP72 genotype frequencies. Importantly and in contrast to the previous findings, similar genotype frequencies were observed in female patients diagnosed by 51 years of age and those diagnosed later. Specifically, 3/20 female DLBCL patients diagnosed by 51 years of age were homozygous for SNP309 G and 2/20 DLBCL females in that age group were homozygous for SNP72 C. Neither SNP309 nor SNP72 had a significant influence on event-free and overall survival in multivariate analyses.

Conclusion
In contrast to the previous study on Ashkenazi Jewish Caucasians, DLBCL in pre-menopausal women of central European Caucasian ethnicity was not associated with SNP309 G. Neither SNP309 nor SNP72 seem to be correlated with age of onset, diagnosis, or survival of patients.
Extensor-tendons reconstruction using autogenous palmaris longus tendon grafting for rheumatoid arthritis patients
Authors: Chu Po-Jung , Lee Hung-Maan , Hou Yao-Tung , Hung Sheng-Tsai , Chen Jung-Kuei , Shih Jui-Tien 
Published: April 2008

Abstract

Background
The purpose of the study is to retrospectively review the clinical outcome of our study population of middle-aged RA patients who had suffered extensor-tendon rupture. We reported the outcome of autogenous palmaris tendon grafting of multiple extensor tendons at wrist level in 14 middle-aged rheumatoid patients.

Methods
Between Feb. 2000 to Feb. 2004, thirty-six ruptured wrist level extensor tendons were reconstructed in fourteen rheumatoid patients (11 women and three men) using autogenous palmaris longus tendon as a free interposition graft. In each case, the evaluation was based on both subjective and objective criteria, including the range of MCP joint flexion after surgery, the extension lag at the metacarpophalangeal joint before and after surgery, and the ability of the patient to work.

Results and Discussion
The average of follow-up was 54.1 months (range, 40 to 72 months). The average range of MCP joint flexion after reconstruction was 66°. The extension lag at the metacarpophalangeal joint significantly improved from a preoperative mean of 38° (range, 25°–60°) to a postoperative mean of 16° (range, 0°–30°). Subjectively all patients were satisfied with the clinical results, and achieved a return to their level of ability before tendon rupture. We found good functional results in our series of interposition grafting using palmaris longus to reconstruct extensor tendon defects in the rheumatoid patients.

Conclusion
Reconstruction for multiple tendon ruptures is a salvage procedure that is often associated with extensor lag and impairment of overall function. Early aggressive treatment of extensor tendon reconstruction using autogenous palmaris longus tendon as a free interposition graft in the rheumatoid wrist is another viable option to achieve good clinical functional result.
Does preservation of the sub-valvular apparatus during mitral valve replacement affect long-term survival and quality of life? A Microsimulation Study
Authors: Rao Christopher , Hart Jonathan , Chow Andre , Siannis Fotios , Tsalafouta Polyxeni , Murtuza Bari , Darzi Ara , Wells Frank C , Athanasiou Thanos 
Published: April 2008

AbstractBackgroundTechniques to preserve the sub-valvular apparatus in order to reduce morbidity and mortality following mitral valve replacement have been frequently reported. However, it is uncertain what impact sub-valvular apparatus preservation techniques have on long-term outcomes following mitral valve replacement. This study investigated the effect of sub-valvular apparatus preservation on long-term survival and quality of life following mitral valve replacement.MethodsA microsimulation model was used to compare long-term survival and quality-adjusted life years following mitral valve replacement after conventional valve replacement and sub-valvular apparatus preservation. Probabilistic sensitivity analysis and alternative analysis were performed to investigate uncertainty associated with the results.ResultsOur Analysis suggests that patients survive longer if the sub-valvular apparatus are preserved (65.7% SD 1.5%, compared with 58.1% SD 1.6% at 10 years). The quality adjusted life years gained over a 10 year period where also greater after sub-valvular apparatus preservation. (6.54 QALY SD 0.07 QALY, compared with 5.61 QALY, SD 0.07 QALY). The superiority of preservation techniques was insensitive to patient age, parameter or model uncertainty.ConclusionThis study suggests that long-term outcomes may be improved when the sub-valvular apparatus are preserved. Given the lack of empirical data further research is needed to investigate health-related quality of life after mitral valve replacement, and to establish whether outcomes differ between preservation techniques.