bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing Climate Models Using Thermal Infrared Spectra
Authors: Leroy Stephen , Anderson James , Dykema John , Goody Richard 
Published: April 2008

Abstract
An approach to test climate models with observations is presented. In this approach, it is possible to directly observe the longwave feedbacks of the climate system in time series of annual average outgoing longwave spectra. Tropospheric temperature, stratospheric temperature, water vapor, and carbon dioxide have clear and distinctive signatures in the infrared spectrum, and it is possible to detect trends of these signals unambiguously from trends in the outgoing longwave spectrum by optimal detection techniques. This approach is applied to clear-sky data in the tropics simulated from the output of an ensemble of climate models. Estimates of the water vapor–longwave feedback by this approach agree to within estimated errors with truth, and it is likely that an uncertainty of 50% can be obtained in 20 yr of a continuous time series. The correlation of tropospheric temperature and water vapor anomalies can provide a constraint on the water vapor–longwave feedback to 5% uncertainty in 20 yr, or 7% in 10 yr. Thus, it should be possible to place a strong constraint on climate models, which currently show a range of 30% in the water vapor–longwave feedback, in just 10 yr. These results may not hold in the presence of clouds, however, and so it may be necessary to supplement time series of outgoing longwave spectra with GPS radio occultation data, which are insensitive to clouds.
Potential Biases in Feedback Diagnosis from Observational Data: A Simple Model Demonstration
Authors: Spencer Roy W. , Braswell William D. 
Published: April 2008

Abstract
Feedbacks are widely considered to be the largest source of uncertainty in determining the sensitivity of the climate system to increasing anthropogenic greenhouse gas concentrations, yet the ability to diagnose them from observations has remained controversial. Here a simple model is used to demonstrate that any nonfeedback source of top-of-atmosphere radiative flux variations can cause temperature variability, which then results in a positive bias in diagnosed feedbacks. This effect is demonstrated with daily random flux variations, as might be caused by stochastic fluctuations in low cloud cover. The daily noise in radiative flux then causes interannual and decadal temperature variations in the model’s 50-m-deep swamp ocean. The amount of bias in the feedbacks diagnosed from time-averaged model output depends upon the size of the nonfeedback flux variability relative to the surface temperature variability, as well as the sign and magnitude of the specified (true) feedback. For model runs producing monthly shortwave flux anomaly and temperature anomaly statistics similar to those measured by satellites, the diagnosed feedbacks have positive biases generally in the range of −0.3 to −0.8 W m−2 K−1. These results suggest that current observational diagnoses of cloud feedback—and possibly other feedbacks—could be significantly biased in the positive direction.
Convective Boundary Layer Depth Estimation from Wind Profilers: Statistical Comparison between an Automated Algorithm and Expert Estimations
Authors: Bianco Laura , Wilczak James M. , White Allen B. 
Published: April 2008

Abstract
A previous study showed success in determining the convective boundary layer depth with radar wind-profiling radars using fuzzy logic methods, and improvements to the earlier work are discussed. The improved method uses the Vaisala multipeak picking (MPP) procedure to identify the atmospheric signal in radar spectra in place of a fuzzy logic peak picking procedure that was previously used. The method then applies fuzzy logic techniques to calculate the depth of the convective boundary layer. The planetary boundary layer depth algorithm is improved with respect to the one used in the previous study in that it adds information obtained from the small-scale turbulence (vertical profiles of the spectral width of the vertical velocity), while also still using vertical profiles of the radar-derived refractive index structure parameter C2n and the variance of vertical velocity. Modifications to the fuzzy logic rules (especially to those using vertical velocity data) that improve the algorithm’s accuracy in cloudy boundary layers are incorporated. In addition, a reliability threshold value to the fuzzy logic–derived score is applied to eliminate PBL depth data values with low score values. These low score values correspond to periods when the PBL structure does not match the conceptual model of the convective PBL built into the algorithm. Also, as a final step, an optional temporal continuity test on boundary layer depth has been developed that helps improve the algorithm’s skill. A comparison with independent boundary layer depth estimations made “by eye” by meteorologists at two radar wind-profiler sites, significantly different in their characteristics, shows that the new improved method gives significantly more accurate estimates of the boundary layer depth than does the previous method, and also much better estimates than the simpler “standard” method of selecting the peak of C2n. The new method produces an absolute error of the mixing-depth estimates comparable to the vertical range resolution of the profilers.
Revision Surgery for Failed Elbow Medial Collateral Ligament Reconstruction
Authors: Dines Joshua S. , Yocum Lewis A. , Frank Joshua B. , Attrache Neal S. El , Gambardella Ralph A. , Jobe Frank W. 
Published: April 2008

Background Although excellent results can be achieved in up to 90% of primary elbow medial ulnar collateral ligament reconstructions, retears of the ligament have been reported. As the number of primary reconstructions continues to increase, one could expect a commensurate increase in the number of revision medial collateral ligament reconstructions performed. Hypothesis Given the difficulty associated with revision procedures, the complication rate relative to primary reconstructions would increase while the percentage of athletes returning to their previous level of play would decrease. Study Design Case series; Level of evidence. 4. Methods This was a retrospective review of 15 patients who underwent revision surgery for retear of a reconstructed elbow medial collateral ligament. All patients had undergone previous elbow medial collateral ligament reconstruction and had new history and physical examination findings consistent with medial collateral ligament injury. Twelve subjects were professional baseball players and 3 were college-level players at the time of their revision procedure. Patients were evaluated at a minimum of 2 years after revision surgery. Outcomes were classified using the Conway scale. Results Average time to revision was 36 months. The technique used in the revision was the Jobe technique in 11 cases, DANE TJ in 3, and primary repair in 1. Thirty-three percent (5/15 excellent) returned to their previous level of play for at least 1 season. Additionally, there were 4 good, 2 fair, and 4 poor results. The ligament repair had a good outcome. Forty percent (6/15) of Patients had complications, 1 of whom required a subsequent surgery (lysis of adhesions). One subject experienced a retear of the medial collateral ligament. Conclusion The rate of return to play after revision medial collateral ligament surgery is much lower than after primary reconstruction. As was expected, the complication rate of revision surgery is higher as well. This study should help physicians when counseling baseball players who suffer retears of their medial collateral ligament.
Primary Repair of Ulnar Collateral Ligament Injuries of the Elbow in Young Athletes
Authors: Savoie Felix H. , Trenhaile Scott W. , Roberts John , Field Larry D. , Ramsey J. Randall 
Published: April 2008

Background Little data exist regarding the treatment of young high school and college athletes with medial ulnar collateral ligament insufficiency of the elbow. It would be logical to assume that younger patients would have less damage to the ligament, allowing the possibility of repair. Hypothesis Many young athletes with injuries to the medial ulnar collateral ligament have proximal or distal injuries that may be amenable to repair, indicating that graft reconstruction may not always be necessary to obtain satisfactory results. Study Design Case series; Level of evidence, 4. Methods Sixty patients who had direct repair of the medial ulnar collateral ligament were retrospectively evaluated using the Andrews and Carson elbow score. All patients had symptomatic instability that precluded them from participation in their desired sports, all failed a nonoperative treatment program, and all had comparative stress radiographs, magnetic resonance images, or computerized tomograms with contrast studies that had positive findings for insufficiency of the ligament. Results The mean age of the 47 male and 13 female patients was 17.2 years. The mean follow-up was 59.2 months. All patients underwent medial ulnar collateral ligament repair by one of the following procedures: suture plication with repair to bone drill holes (n = 9) or suture repair to bone using anchors (n = 51). The mean overall preoperative Andrews-Carson outcome score of 132 improved to 188 postoperatively ( P < .0001). Good-to-excellent overall results were obtained in 93% of patients. Fifty-eight of the 60 patients were able to return to sports within 6 months of the surgery at the same or higher level as before the injury. There were 4 failures, 2 early and 2 late (after return to play for 5 and 6 years of unrestricted play, respectively). Three patients sustained a complication of transient postoperative ulnar neuropathy symptoms that resolved spontaneously. Conclusion Primary repair of proximal and distal injuries of the medial ulnar collateral ligament is a viable alternative in the nonprofessional athlete. Graft reconstructions may not be necessary to obtain favorable outcomes and rapid return to sports in nonprofessional athletes who require surgical intervention for medial elbow instability.
Arthroscopic and Magnetic Resonance Image Appearance and Reconstruction of the Anterior Talofibular Ligament in Cases of Apparent Functional Ankle Instability
Authors: Takao Masato , Innami Ken , Matsushita Takashi , Uchio Yuji , Ochi Mitsuo 
Published: April 2008

Background Many patients report feeling functional ankle instability, despite having no clinically demonstrable lateral instability. Hypothesis Some patients who experience functional instability of the ankle have substantial abnormalities of the anterior talofibular ligament despite having apparently normal lateral laxity in clinical examination. Study Design Case series; Level of evidence, 4. Methods Fourteen patients who had functional ankle instability after sprain, despite having no clinically demonstrable lateral instability, were included in this study. All subjects underwent standard stress radiography, magnetic resonance imaging, and ankle arthroscopy. These patients were treated with anatomical reconstruction of the anterior talofibular ligament. Results Arthroscopic assessment revealed 3 cases with no ligamentous structure with scar tissue, 9 cases with partial ligament tears and scar tissue on the disrupted anterior talofibular ligament fiber, and 2 cases of abnormal course of the ligament at the fibular or talar attachment. Magnetic resonance imaging revealed the following: 5 cases of discontinuity of the anterior talofibular ligament, 2 cases of narrowing of the anterior talofibular ligament, 4 cases of high-intensity lesion in the anterior talofibular ligament, and 3 normal cases. The mean American Orthopaedic Foot and Ankle Society Ankle Hindfoot scale score was 66.2 ± 3.2 points at preoperation and 92.3 ± 4.4 points 2 years after surgery. Conclusion All patients in this study with functional ankle instability, despite their having no demonstrable abnormal lateral laxity, had morphologic ligamentous abnormality on arthroscopic assessment.
Meta-analysis of genome-wide linkage studies of asthma and related traits
Authors: Denham Samuel , Koppelman Gerard H , Blakey John , Wjst Matthias , Ferreira Manuel A , Hall Ian P , Sayers Ian 
Published: April 2008

Abstract

Background
Asthma and allergy are complex multifactorial disorders, with both genetic and environmental components determining disease expression. The use of molecular genetics holds great promise for the identification of novel drug targets for the treatment of asthma and allergy. Genome-wide linkage studies have identified a number of potential disease susceptibility loci but replication remains inconsistent. The aim of the current study was to complete a meta-analysis of data from genome-wide linkage studies of asthma and related phenotypes and provide inferences about the consistency of results and to identify novel regions for future gene discovery.

Methods
The rank based genome-scan meta-analysis (GSMA) method was used to combine linkage data for asthma and related traits; bronchial hyper-responsiveness (BHR), allergen positive skin prick test (SPT) and total serum Immunoglobulin E (IgE) from nine Caucasian asthma populations.

Results
Significant evidence for susceptibility loci was identified for quantitative traits including; BHR (989 pedigrees, n = 4,294) 2p12-q22.1, 6p22.3-p21.1 and 11q24.1-qter, allergen SPT (1,093 pedigrees, n = 4,746) 3p22.1-q22.1, 17p12-q24.3 and total IgE (729 pedigrees, n = 3,224) 5q11.2-q14.3 and 6pter-p22.3. Analysis of the asthma phenotype (1,267 pedigrees, n = 5,832) did not identify any region showing genome-wide significance.

Conclusion
This study represents the first linkage meta-analysis to determine the relative contribution of chromosomal regions to the risk of developing asthma and atopy. Several significant results were obtained for quantitative traits but not for asthma confirming the increased phenotype and genetic heterogeneity in asthma. These analyses support the contribution of regions that contain previously identified asthma susceptibility genes and provide the first evidence for susceptibility loci on 5q11.2-q14.3 and 11q24.1-qter.
Binning sequences using very sparse labels within a metagenome
Authors: Chan Chon-Kit Kenneth , Hsu Arthur L , Halgamuge Saman K , Tang Sen-Lin 
Published: April 2008

Abstract

Background
In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups. Most of the current methods of binning, such as BLAST, k-mer and PhyloPythia, involve assigning sequence fragments by comparing sequence similarity or sequence composition with already-sequenced genomes that are still far from comprehensive. We propose a semi-supervised seeding method for binning that does not depend on knowledge of completed genomes. Instead, it extracts the flanking sequences of highly conserved 16S rRNA from the metagenome and uses them as seeds (labels) to assign other reads based on their compositional similarity.

Results
The proposed seeding method is implemented on an unsupervised Growing Self-Organising Map (GSOM), and called Seeded GSOM (S-GSOM). We compared it with four well-known semi-supervised learning methods in a preliminary test, separating random-length prokaryotic sequence fragments sampled from the NCBI genome database. We identified the flanking sequences of the highly conserved 16S rRNA as suitable seeds that could be used to group the sequence fragments according to their species. S-GSOM showed superior performance compared to the semi-supervised methods tested. Additionally, S-GSOM may also be used to visually identify some species that do not have seeds.
The proposed method was then applied to simulated metagenomic datasets using two different confidence threshold settings and compared with PhyloPythia, k-mer and BLAST. At the reference taxonomic level Order, S-GSOM outperformed all k-mer and BLAST results and showed comparable results with PhyloPythia for each of the corresponding confidence settings, where S-GSOM performed better than PhyloPythia in the ≥ 10 reads datasets and comparable in the ≥ 8 kb benchmark tests.

Conclusion
In the task of binning using semi-supervised learning methods, results indicate S-GSOM to be the best of the methods tested. Most importantly, the proposed method does not require knowledge from known genomes and uses only very few labels (one per species is sufficient in most cases), which are extracted from the metagenome itself. These advantages make it a very attractive binning method. S-GSOM outperformed the binning methods that depend on already-sequenced genomes, and compares well to the current most advanced binning method, PhyloPythia.
Gene Ontology annotations: what they mean and where they come from
Authors: Hill David P , Smith Barry , McAndrews-Hill Monica S , Blake Judith A 
Published: April 2008

Abstract
To address the challenges of information integration and retrieval, the computational genomics community increasingly has come to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). Here we address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations, in the hope that this will lead both to better representations of biological reality through annotation and ontology development and to more informed use of GO resources by experimental scientists.
DNA from extinct giant lemurs links archaeolemurids to extant indriids
Authors: Orlando Ludovic , Calvignac Sébastien , Schnebelen Céline , Douady Christophe J , Godfrey Laurie R , Hänni Catherine 
Published: April 2008

Abstract

Background
Although today 15% of living primates are endemic to Madagascar, their diversity was even greater in the recent past since dozens of extinct species have been recovered from Holocene excavation sites. Among them were the so-called "giant lemurs" some of which weighed up to 160 kg. Although extensively studied, the phylogenetic relationships between extinct and extant lemurs are still difficult to decipher, mainly due to morphological specializations that reflect ecology more than phylogeny, resulting in rampant homoplasy.

Results
Ancient DNA recovered from subfossils recently supported a sister relationship between giant "sloth" lemurs and extant indriids and helped to revise the phylogenetic position of Megaladapis edwardsi among lemuriformes, but several taxa – such as the Archaeolemuridae – still await analysis. We therefore used ancient DNA technology to address the phylogenetic status of the two archaeolemurid genera (Archaeolemur and Hadropithecus). Despite poor DNA preservation conditions in subtropical environments, we managed to recover 94- to 539-bp sequences for two mitochondrial genes among 5 subfossil samples.

Conclusion
This new sequence information provides evidence for the proximity of Archaeolemur and Hadropithecus to extant indriids, in agreement with earlier assessments of their taxonomic status (Primates, Indrioidea) and in contrast to recent suggestions of a closer relationship to the Lemuridae made on the basis of analyses of dental developmental and postcranial characters. These data provide new insights into the evolution of the locomotor apparatus among lemurids and indriids.
Hidden layers of human small RNAs
Authors: Kawaji Hideya , Nakamura Mari , Takahashi Yukari , Sandelin Albin , Katayama Shintaro , Fukuda Shiro , Daub Carsten O , Kai Chikatoshi , Kawai Jun , Yasuda Jun , Carninci Piero , Hayashizaki Yoshihide 
Published: April 2008

Abstract

Background
Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undiscovered types of small RNAs in higher organisms, many studies to profile small RNA have focused on miRNA and/or siRNA rather than on the exploration of additional classes of RNAs.

Results
Here, we explored human small RNAs by unbiased sequencing of RNAs with sizes of 19–40 nt. We provide substantial evidences for the existence of independent classes of small RNAs. Our data shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA. In particular, tRNA cleavage is regulated depending on tRNA type and tissue expression. We also found small RNAs mapped to genomic regions that are transcribed in both directions by bidirectional promoters, indicating that the small RNAs are a product of dsRNA formation and their subsequent cleavage. Their partial similarity with ribosomal RNAs (rRNAs) suggests unrevealed functions of ribosomal DNA or interstitial rRNA. Further examination revealed six novel miRNAs.

Conclusion
Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs.
Multiple expressed MHC class II loci in salmonids; details of one non-classical region in Atlantic salmon (Salmo salar)
Authors: Harstad Håvard , Lukacs Morten F , Bakke Hege G , Grimholt Unni 
Published: April 2008

Abstract

Background
In teleosts, the Major Histocompatibility Complex (MHC) class I and class II molecules reside on different linkage groups as opposed to tetrapods and shark, where the class I and class II genes reside in one genomic region. Several teleost MHC class I regions have been sequenced and show varying number of class I genes. Salmonids have one major expressed MHC class I locus (UBA) in addition to varying numbers of non-classical genes. Two other more distant lineages are also identifyed denoted L and ZE. For class II, only one major expressed class II alpha (DAA) and beta (DAB) gene has been identified in salmonids so far.

Results
We sequenced a genomic region of 211 kb encompassing divergent MHC class II alpha (Sasa-DBA) and beta (Sasa-DBB) genes in addition to NRGN, TIPRL, TBCEL and TECTA. The region was not linked to the classical class II genes and had some synteny to genomic regions from other teleosts. Two additional divergent and expressed class II sequences denoted DCA and DDA were also identified in both salmon and trout. Expression patterns and lack of polymorphism make these genes non-classical class II analogues. Sasa-DBB, Sasa-DCA and Sasa-DDA had highest expression levels in liver, hindgut and spleen respectively, suggestive of distinctive functions in these tissues. Phylogenetic studies revealed more yet undescribed divergent expressed MHC class II molecules also in other teleosts.

Conclusion
We have characterised one genomic region containing expressed non-classical MHC class II genes in addition to four other genes not involved in immune function. Salmonids contain at least two expressed MHC class II beta genes and four expressed MHC class II alpha genes with properties suggestive of new functions for MHC class II in vertebrates. Collectively, our data suggest that the class II is worthy of more elaborate studies also in other teleost species.