bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombination-filtered genomic datasets by information maximization
Authors: Woerner August E. , Cox Murray P. , Hammer Michael F. 
Published: May 2007

AbstractSummary: With the increasing amount of DNA sequence data available from natural populations, new computational methods are needed to efficiently process raw sequences into formats that are applicable to a variety of analytical methods. One highly successful approach to inferring aspects of demographic history is grounded in coalescent theory. Many of these methods restrict themselves to perfectly tree-like genealogies (i.e. regions with no observed recombination), because theoretical difficulties prevent ready statistical evaluation of recombining regions. However, determining which recombination-filtered dataset to analyze from a larger recombination-rich genomic region is a non-trivial problem. Current applications primarily aim to quantify recombination rates (rather than produce optimal recombination-filtered blocks), require significant manual intervention, and are impractical for multiple genomic datasets in high-throughput, automated research environments. Here, we present a fast, simple and automatable command-line program that extracts optimal recombination-filtered blocks (no four-gamete violations) from recombination-rich genomic re-sequence data.Availability: http://hammerlab.biosci.arizona.edu/software.htmlContact: mpcox@email.arizona.edu
Assortative mixing in Protein Contact Networks and protein folding kinetics
Authors: Bagler Ganesh , Sinha Somdatta 
Published: May 2007

AbstractMotivation: Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate 3D structures is one of the remarkable examples of biological self-organization. We investigated native state structures of 30 single-domain, two-state proteins, from complex networks perspective, to understand the role of topological parameters in proteins’ folding kinetics, at two length scales—as ‘Protein Contact Networks (PCNs)’ and their corresponding ‘Long-range Interaction Networks (LINs)’ constructed by ignoring the short-range interactions.Results: Our results show that, both PCNs and LINs exhibit the exceptional topological property of ‘assortative mixing’ that is absent in all other biological and technological networks studied so far. We show that the degree distribution of these contact networks is partly responsible for the observed assortativity. The coefficient of assortativity also shows a positive correlation with the rate of protein folding at both short- and long-contact scale, whereas, the clustering coefficients of only the LINs exhibit a negative correlation. The results indicate that the general topological parameters of these naturally evolved protein networks can effectively represent the structural and functional properties required for fast information transfer among the residues facilitating biochemical/kinetic functions, such as, allostery, stability and the rate of folding.Contact: sinha@ccmb.res.inSupplementary information: Supplementary data are available at Bioinformatics online.
The evolutionary forest algorithm
Authors: Leman Scotland C. , Uyenoyama Marcy K. , Lavine Michael , Chen Yuguo 
Published: May 2007

AbstractMotivation: Gene genealogies offer a powerful context for inferences about the evolutionary process based on presently segregating DNA variation. In many cases, it is the distribution of population parameters, marginalized over the effectively infinite-dimensional tree space, that is of interest. Our evolutionary forest (EF) algorithm uses Monte Carlo methods to generate posterior distributions of population parameters. A novel feature is the updating of parameter values based on a probability measure defined on an ensemble of histories (a forest of genealogies), rather than a single tree.Results: The EF algorithm generates samples from the correct marginal distribution of population parameters. Applied to actual data from closely related fruit fly species, it rapidly converged to posterior distributions that closely approximated the exact posteriors generated through massive computational effort. Applied to simulated data, it generated credible intervals that covered the actual parameter values in accordance with the nominal probabilities.Availability: A C++ implementation of this method is freely accessible at http://www.isds.duke.edu/~scl13Contact: scotland@stat.duke.edu
Virtual Laryngoscopy: a Noninvasive Tool for the Assessment of Laryngeal Tumor Extent
Authors: Yan Yuling , Luo Shouhua , McWhorter Andrew 
Published: May 2007

AbstractObjectives: Present a clinical application of virtual laryngoscopy (VL) in the assessment of laryngeal tumor and its extent.Study Design: CT data from two subjects are acquired for this preliminary study. One subject is a healthy volunteer and the other is a patient with laryngeal tumor. The laryngeal framework and upper airway are reconstructed using CT data, which allows for computer‐aided internal and external anatomical views and interactive fly‐through.Methods: These CT data are reconstructed into 0.5 mm slice images, resulting in a total of 200–300 image slices. An advanced commercial visualization software (AMIRA) is used for 3D image segmentation, reconstruction and surface rendering of laryngeal anatomical structures.Results: The 3D laryngeal framework and upper airway are reconstructed for both the tumor patient and the healthy subject. The conventional views of the reconstructed vocal folds are compared with those obtained from fiber‐optic laryngoscope. Additionally, unique views of the vocal folds obtained from retrograde visualization and fly‐through are presented, which are not possible to obtain using conventional endoscope imaging. The segmented anatomical model and the tumor from the patient's CT images were displayed individually to show the distribution of the tumor and its extent as well as spatial and contextual relationships to the larynx and airway anatomical structures.Conclusions: This study demonstrated the potential application of VL as a noninvasive clinical diagnostic tool for the assessment of laryngeal tumor and its extent. Our preliminary results demonstrated that the VL may provide valuable insights for the diagnosis and treatment planning for laryngeal and airway tumors. The noninvasive VL may complement the invasive laryngoscopic examinations for the staging of tumors and follow‐ups on surgical interventions.
Upper Lateral Cartilage‐Sparing Component Dorsal Hump Reduction in Primary Rhinoplasty
Authors: Arslan Emrah , Aksoy Alper 
Published: May 2007

AbstractBackground: Dorsal hump reduction is a critical step in rhinoplasty. Most of the reasons behind revisional procedures are related to incorrect hump reduction.Methods: The authors used a modified dorsal hump reduction method in their primary cases, the steps of which are as follows: 1) dissection of the nasal vault; 2) bilateral submucoperichondrial dissections to free the cartilaginous septum; 3) separation of the upper lateral cartilages from the cartilaginous septum; 4) partial dissection of the upper lateral cartilages from the inner surfaces of the nasal bones bilaterally; 5) separation of the bony septum from the nasal bones bilaterally; 6) reduction of the partially isolated nasal bones; 7) en bloc cartilaginous and bony septum removal. The authors have operated on 68 primary cases over a 2 year period (30 mo).Results: In the great majority of cases, the results were satisfactory. No revisions were performed in this patient group.Conclusions: This method is a good alternative to traditional techniques in noses with a high and narrow roof, thin skin, and weak middle nasal vault. Revision could be performed more easily when required. Initially, wide noses may not seem good candidates for this procedure; however, careful case‐based preoperative planning may overcome this difficulty.
Salvage Surgery with Free Flap Reconstruction: Factors Affecting Outcome After Treatment of Recurrent Head and Neck Squamous Carcinoma
Authors: Kim Alyn J. , Suh Jeffrey D. , Sercarz Joel A. , Abemayor Elliot , Head Christian , Funk Gerry , Blackwell Keith E. 
Published: May 2007

AbstractObjective: To determine factors predicting the outcome after salvage surgery with microvascular flap reconstruction for recurrent squamous cell cancer (SCC) of the head and neck.Study Design: This is a retrospective analysis of patients treated at an academic medical center.Methods. One hundred six patients underwent salvage surgery and microvascular flap reconstruction after prior unsuccessful cancer treatment using surgery, radiation, or chemotherapy. All patients had a follow‐up interval after salvage surgery of at least 24 months unless cancer rerecurrence occurred within 24 months after salvage surgery. Factors including age, sex, comorbidity level, tobacco use, alcohol use, disease‐free interval since prior therapy, prior radiation, prior chemotherapy, prior surgery, recurrent tumor T class, recurrent tumor N class, recurrent cancer stage, and tumor location were examined to determine their association with cancer rerecurrence after salvage surgery. Successful treatment was defined as patients who remained free from cancer rerecurrence for a minimum 2 year period after salvage surgery.Results: Advanced recurrent T class (P = .02) was significantly associated with cancer recurrence. Recurrent cancer stage and patient smoking status approached statistical significance (P = .06).Conclusion: Patients with recurrent T1 and T2 class are the best candidates for salvage surgery and microvascular flap reconstruction for treatment of recurrent SCC of the head and neck. Patients with T3 and T4 class recurrent cancers and patients who continue to smoke after initial diagnosis and treatment of head and neck SCC are poor candidates to undergo salvage surgery.
Influence of Age on the Surgical Outcome After Endoscopic Sinus Surgery for Chronic Rhinosinusitis With Nasal Polyposis
Authors: Lee Jae Yong , Lee Seung Won 
Published: May 2007

AbstractObjectives: To determine whether patient age is associated with the surgical outcome after endoscopic sinus surgery (ESS) with polypectomy.Study Design: A prospective, controlled case series.Materials and Methods: This study consisted of 60 patients who were diagnosed as having chronic rhinosinusitis (CRS) with nasal polyposis (NP) that was refractory to medical treatment. Three groups were classified according to patient age: pediatric (5–18 yr), adult (19–65 yr), and geriatric (over 65 yr). We collected 20 patients in each age group after applying the exclusion criteria. The extent of the polyps and the Lund‐Mackay score were calculated for each patient, and they underwent ESS with polypectomy. We compared the objective endoscopic findings and subjective improvements in symptoms among the groups 6 months after the procedure.Results: There were no statistical differences in polyp extent or Lund‐Mackay score between the three age groups. The objective surgical outcome based on the endoscopic findings was worst in the pediatric group (45%), whereas the geriatric group showed the best results (90%). The differences in objective outcome among the three groups were significant, and patient age was a predictive variable for surgical result based on multiple logistic regression analysis. No major complications occurred, and the overall improvement in subjective symptoms was statistically significant in all three age groups at 6 months postoperatively. The subjective surgical outcome did not differ statistically between the groups, with the exception of olfactory disturbance.Conclusions: The results of the present study suggest that patient age influences the objective postoperative outcome in the endoscopic treatment of CRS with NP, and that ESS is an effective and reliable method for improving the subjective symptoms in patients of all age groups despite the statistically different objective surgical outcomes between the groups.
Methane bubbling from northern lakes: present and future contributions to the global methane budget
Authors: Walter Katey M , Smith Laurence C , Stuart Chapin F 
Published: May 2007

Large uncertainties in the budget of atmospheric methane (CH
4
) limit the accuracy of climate change projections. Here we describe and quantify an important source of CH
4
—point-source ebullition (bubbling) from northern lakes—that has not been incorporated in previous regional or global methane budgets. Employing a method recently introduced to measure ebullition more accurately by taking into account its spatial patchiness in lakes, we estimate point-source ebullition for 16 lakes in Alaska and Siberia that represent several common northern lake types: glacial, alluvial floodplain, peatland and thermokarst (thaw) lakes. Extrapolation of measured fluxes from these 16 sites to all lakes north of 45° N using circumpolar databases of lake and permafrost distributions suggests that northern lakes are a globally significant source of atmospheric CH
4
, emitting approximately 24.2±10.5 Tg CH
4
yr
−1
. Thermokarst lakes have particularly high emissions because they release CH
4
produced from organic matter previously sequestered in permafrost. A carbon mass balance calculation of CH
4
release from thermokarst lakes on the Siberian yedoma ice complex suggests that these lakes alone would emit as much as approximately 49 000 Tg CH
4
if this ice complex was to thaw completely. Using a space-for-time substitution based on the current lake distributions in permafrost-dominated and permafrost-free terrains, we estimate that lake emissions would be reduced by approximately 12% in a more probable transitional permafrost scenario and by approximately 53% in a ‘permafrost-free’ Northern Hemisphere. Long-term decline in CH
4
ebullition from lakes due to lake area loss and permafrost thaw would occur only after the large release of CH
4
associated thermokarst lake development in the zone of continuous permafrost.
The stability of the stratospheric ozone layer during the end-Permian eruption of the Siberian Traps
Authors: Beerling David J , Harfoot Michael , Lomax Barry , Pyle John A 
Published: May 2007

The discovery of mutated palynomorphs in end-Permian rocks led to the hypothesis that the eruption of the Siberian Traps through older organic-rich sediments synthesized and released massive quantities of organohalogens, which caused widespread O
3
depletion and allowed increased terrestrial incidence of harmful ultraviolet-B radiation (UV-B, 280–315 nm; Visscher
et al
. 2004
Proc. Natl Acad. Sci. USA
101
, 12 952–12 956). Here, we use an extended version of the Cambridge two-dimensional chemistry–transport model to evaluate quantitatively this possibility along with two other potential causes of O
3
loss at this time: (i) direct effects of HCl release by the Siberian Traps and (ii) the indirect release of organohalogens from dispersed organic matter. According to our simulations, CH
3
Cl released from the heating of coals alone caused comparatively minor O
3
depletion (5–20% maximum) because this mechanism fails to deliver sufficiently large amounts of Cl into the stratosphere. The unusual explosive nature of the Siberian Traps, combined with the direct release of large quantities of HCl, depleted the model O
3
layer in the high northern latitudes by 33–55%, given a main eruptive phase of less than or equal to 200 kyr. Nevertheless, O
3
depletion was most extensive when HCl release from the Siberian Traps was combined with massive CH
3
Cl release synthesized from a large reservoir of dispersed organic matter in Siberian rocks. This suite of model experiments produced column O
3
depletion of 70–85% and 55–80% in the high northern and southern latitudes, respectively, given eruption durations of 100–200 kyr. On longer eruption time scales of 400–600 kyr, corresponding O
3
depletion was 30–40% and 20–30%, respectively. Calculated year-round increases in total near-surface biologically effective (BE) UV-B radiation following these reductions in O
3
layer range from 30–60 (kJ m
−2
d
−1
)
BE
up to 50–100 (kJ m
−2
d
−1
)
BE
. These ranges of daily UV-B doses appear sufficient to exert mutagenic effects on plants, especially if sustained over tens of thousands of years, unlike either rising temperatures or SO
2
concentrations.
Anaerobic methanotrophy and the rise of atmospheric oxygen
Authors: Catling D.C , Claire M.W , Zahnle K.J 
Published: May 2007

In modern marine sediments, the anoxic decomposition of organic matter generates a significant flux of methane that is oxidized microbially with sulphate under the seafloor and never reaches the atmosphere. In contrast, prior to
ca
2.4 Gyr ago, the ocean had little sulphate to support anaerobic oxidation of methane (AOM) and the ocean should have been an important methane source. As atmospheric O
2
and seawater sulphate levels rose on the early Earth, AOM would have increasingly throttled the release of methane. We use a biogeochemical model to simulate the response of early atmospheric O
2
and CH
4
to changes in marine AOM as sulphate levels increased. Semi-empirical relationships are used to parameterize global AOM rates and the evolution of sulphate levels. Despite broad uncertainties in these relationships, atmospheric O
2
concentrations generally rise more rapidly and to higher levels (of order approx. 10
−3
bar versus approx. 10
−4
bar) as a result of including AOM in the model. Methane levels collapse prior to any significant rise in O
2
, but counter-intuitively, methane re-rises after O
2
rises to higher levels when AOM is included. As O
2
concentrations increase, shielding of the troposphere by stratospheric ozone slows the effective reaction rate between oxygen and methane. This effect dominates over the decrease in the methane source associated with AOM. Thus, even with the inclusion of AOM, the simulated Late Palaeoproterozoic atmosphere has a climatologically significant level of methane of approximately 50 ppmv.
Alcohol dehydrogenase and aldehyde dehydrogenase polymorphisms and colorectal cancer: The Fukuoka Colorectal Cancer Study
Authors: Yin Guang , Kono Suminori , Toyomura Kengo , Moore Malcolm A. , Nagano June , Mizoue Tetsuya , Mibu Ryuichi , Tanaka Masao , Kakeji Yoshihiro , Maehara Yoshihiko , Okamura Takeshi , Ikejiri Koji , Futami Kitaroh , Yasunami Yohichi , Maekawa Takafumi , Takenaka Kenji , Ichimiya Hitoshi , Imaizumi Nobutoshi 
Published: May 2007

Alcohol dehydrogenase and aldehyde dehydrogenase are key enzymes in alcohol metabolism and therefore may be of importance to colorectal cancer development. The present case–control study was conducted to determine the influence of ADH2, ADH3 and ALDH2 polymorphisms in Fukuoka, Japan, with 685 incident cases of histologically confirmed colorectal adenocarcinomas and 778 community controls selected randomly from the study area. Alcohol use was ascertained by in‐person interview. Statistical adjustment was made for sex, age class, area, and alcohol use. Individuals with the allele 47Arg of the ADH2 polymorphism (slow metabolizers) had a statistically significant increase in risk, with an adjusted OR of 1.32 (95% CI = 1.07–1.63), compared with those having the ADH2*47His/His genotype. This association was not affected by the level of alcohol consumption. The ADH3 polymorphism showed no measurable association with the risk of colorectal cancer on either overall analysis or stratified analysis with alcohol use. The heterozygous ALDH2*487Glu/Lys genotype was not associated with an increase in the risk of colorectal cancer (adjusted OR 0.89, 95% CI = 0.71–1.13) compared with the ALDH2*487Glu/Glu genotype. Rather unexpectedly, the homozygous ALDH2*487Lys/Lys genotype was related to a statistically significantly decreased risk of colorectal cancer (adjusted OR 0.55, 95% CI = 0.33–0.93). It is unlikely that acetaldehyde metabolism determined by ALDH2 polymorphism contributes to the risk of colorectal cancer, whereas the role of ADH2 polymorphism deserves further investigation. (Cancer Sci 2007; 98: 1248–1253)
A vision of the next generation of behavioral therapies research in the addictions*
Authors: Carroll Kathleen M. , Rounsaville Bruce J. 
Published: May 2007

ABSTRACTWhither, or wither, empirically supported therapies? Increasingly rigorous research in behavioral therapies has yielded a large number of effective therapies, but comparatively little work, demonstrating that integrating empirically supported therapies (ESTs) into standard practice results in meaningful improvements in patient outcomes. Methodology and strategies for evaluating ESTs and their effectiveness in clinical practice is a fairly recent innovation, and a host of unanswered questions remain regarding issues such as selection among different ESTs and what type of ESTs should be emphasized in dissemination efforts, what type of clinicians should be trained in what type of ESTs, the most effective training strategies for various types of clinicians, the need for ongoing supervision to maintain minimum levels of treatment fidelity and skill. In this review, we call for broader use of new research strategies and methods relevant to dissemination of ESTs; these may include adaptive designs, identification of mechanisms of action to foster greater emphasis on effective change principles, training and adoption trials, as well as novel implementation strategies including computer‐assisted therapy and computer‐assisted training.
Factor and item‐response analysis DSM‐IV criteria for abuse of and dependence on cannabis, cocaine, hallucinogens, sedatives, stimulants and opioids
Authors: Gillespie Nathan A. , Neale Michael C. , Prescott Carol A. , Aggen Steven H. , Kendler Kenneth S. 
Published: May 2007

ABSTRACTAims  This paper explored, in a population‐based sample of males, the factorial structure of criteria for substance abuse and dependence, and compared qualitatively the performance of these criteria across drug categories using item–response theory (IRT).Design  Marginal maximum likelihood was used to explore the factor structure of criteria within drug classes, and a two‐parameter IRT model was used to determine how the difficulty and discrimination of individual criteria differ across drug classes.Participants  A total of 4234 males born from 1940 to 1974 from the population‐based Virginia Twin Registry were approached to participate.Measurements  DSM‐IV drug use, abuse and dependence criteria for cannabis, sedatives, stimulants, cocaine and opiates.Findings  For each drug class, the pattern of endorsement of individual criteria for abuse and dependence, conditioned on initiation and use, could be best explained by a single factor. There were large differences in individual item performance across substances in terms of item difficulty and discrimination. Cocaine users were more likely to have encountered legal, social, physical and psychological consequences.Conclusions  The DSM‐IV abuse and dependence criteria, within each drug class, are not distinct but best described in terms of a single underlying continuum of risk. Because individual criteria performed very differently across substances in IRT analyses, the assumption that these items are measuring equivalent levels of severity or liability with the same discrimination across different substances is unsustainable. Compared to other drugs, cocaine usage is associated with more detrimental effects and negative consequences, whereas the effects of cannabis and hallucinogens appear to be less harmful. Implications for other drug classes are discussed.