bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alignment-Free Population Genomics: An Efficient Estimator of Sequence Diversity
Authors: Haubold Bernhard , Pfaffelhuber Peter 
Published: August 2012

Abstract
Comparative sequencing contributes critically to the functional annotation of genomes. One prerequisite for successful analysis of the increasingly abundant comparative sequencing data is the availability of efficient computational tools. We present here a strategy for comparing unaligned genomes based on a coalescent approach combined with advanced algorithms for indexing sequences. These algorithms are particularly efficient when analyzing large genomes, as their run time ideally grows only linearly with sequence length. Using this approach, we have derived and implemented a maximum-likelihood estimator of the average number of mismatches per site between two closely related sequences, π. By allowing for fluctuating coalescent times, we are able to improve a previously published alignment-free estimator of π. We show through simulation that our new estimator is fast and accurate even with moderate recombination (ρ ≤ π). To demonstrate its applicability to real data, we compare the unaligned genomes of Drosophila persimilis and D. pseudoobscura. In agreement with previous studies, our sliding window analysis locates the global divergence minimum between these two genomes to the pericentromeric region of chromosome 3.
Proper Cyclin B3 Dosage Is Important for Precision of Metaphase-to-Anaphase Onset Timing inCaenorhabditis elegans
Authors: Tarailo-Graovac Maja , Chen Nansheng 
Published: August 2012

AbstractCyclin-dependent kinases (CDK) and their compulsory cofactors, the cyclins, are the two key classes of regulatory molecules that determine the eukaryotic cell's progress through the cell cycle by substrate phosphorylation. Cdk1 forms complexes with B-type cyclins and phosphorylates a number of substrates as cells prepare to enter mitosis. CYB-3 (Cyclin B3) is a B-type cyclin that has been recently shown to be required for the timely metaphase-to-anaphase transition, presumably by alleviating a spindle assembly checkpoint (SAC) block. Previously, we have shown that doubling the CYB-3 dosage suppresses sterility in the absence of the essential SAC component MDF-1/Mad1. Here we demonstrate the importance of the Mos1-mediated single-copy insertion method for understanding the effects of gene dosage by generating strains that have more (two or three) copies of the cyb-3 in wild-type and mdf-1(gk2) backgrounds to investigate dosage effect of CYB-3 on mitotic progression as well as development and fertility in the absence and the presence of the MDF-1 checkpoint component. We show that tripling the dosage of CYB-3 results in a significantly variable metaphase-to-anaphase transition, both in wild-type and mdf-1(gk2) mutant backgrounds. Although a majority of embryos initiate anaphase onset normally, a significant number of embryos initiate anaphase with a delay. We also show that tripling the dosage of CYB-3 has no effect on viability in the wild-type background; however, it does reduce the sterility caused by the absence of MDF-1. Together, these data reveal that proper dosage of CYB-3 is important for precision of timely execution of anaphase onset regardless of the presence of the MDF-1 checkpoint component.
Genetic Interactions Between ArabidopsisDET1andUVH6During Development and Abiotic Stress Response
Authors: Kim Esther , Ly Valentina , Hatherell Avril , Schroeder Dana F 
Published: August 2012

AbstractPlants must adapt to a variety of abiotic inputs, including visible light, ultraviolet (UV) light, and heat. In Arabidopsis thaliana, DE-ETIOLATED 1 (DET1) plays a role in visible light signaling, UV tolerance, and development. UV-HYPERSENSITIVE 6 (UVH6) mutants are UV and heat sensitive, as well as dwarf and pale, like det1. In this study, we examine the genetic interactions between these two genes. In dark-grown seedlings, uvh6 exhibits a weak de-etiolated phenotype but does not affect the stronger de-etiolated phenotype of det1. In the light, det1 is epistatic to uvh6 with regard to chlorophyll level, but their effect on all size parameters is additive and therefore independent. With regard to UV tolerance, det1 UV resistance is epistatic to uvh6 UV sensitivity. In heat stress experiments, det1 enhances heat-induced tissue damage in the uvh6 background but suppresses heat-induced growth inhibition. Thus, det1 acts epistatically to uvh6 with respect to de-etiolation, chlorophyll level, UV tolerance, and heat-induced growth inhibition, whereas det1 and uvh6 act additively to regulate plant size and heat-induced cell death. These data provide insight into interplay between light and heat signaling.
Loss of a 20S Proteasome Activator inSaccharomyces cerevisiaeDownregulates Genes Important for Genomic Integrity, Increases DNA Damage, and Selectively Sensitizes Cells to Agents With Diverse Mechanisms of Action
Authors: Doherty Kevin M , Pride Leah D , Lukose James , Snydsman Brian E , Charles Ronald , Pramanik Ajay , Muller Eric G , Botstein David , Moore Carol Wood 
Published: August 2012

AbstractCytoprotective functions of a 20S proteasome activator were investigated. Saccharomyces cerevisiae Blm10 and human 20S proteasome activator 200 (PA200) are homologs. Comparative genome-wide analyses of untreated diploid cells lacking Blm10 and growing at steady state at defined growth rates revealed downregulation of numerous genes required for accurate chromosome structure, assembly and repair, and upregulation of a specific subset of genes encoding protein-folding chaperones. Blm10 loss or truncation of the Ubp3/Blm3 deubiquitinating enzyme caused massive chromosomal damage and cell death in homozygous diploids after phleomycin treatments, indicating that Blm10 and Ubp3/Blm3 function to stabilize the genome and protect against cell death. Diploids lacking Blm10 also were sensitized to doxorubicin, hydroxyurea, 5-fluorouracil, rapamycin, hydrogen peroxide, methyl methanesulfonate, and calcofluor. Fluorescently tagged Blm10 localized in nuclei, with enhanced fluorescence after DNA replication. After DNA damage that caused a classic G2/M arrest, fluorescence remained diffuse, with evidence of nuclear fragmentation in some cells. Protective functions of Blm10 did not require the carboxyl-terminal region that makes close contact with 20S proteasomes, indicating that protection does not require this contact or the truncated Blm10 can interact with the proteasome apart from this region. Without its carboxyl-terminus, Blm10(−339aa) localized to nuclei in untreated, nonproliferating (G0) cells, but not during G1 S, G2, and M. The results indicate Blm10 functions in protective mechanisms that include the machinery that assures proper assembly of chromosomes. These essential guardian functions have implications for ubiquitin-independent targeting in anticancer therapy. Targeting Blm10/PA200 together with one or more of the upregulated chaperones or a conventional treatment could be efficacious.
Targeted Capture of Homoeologous Coding and Noncoding Sequence in Polyploid Cotton
Authors: Salmon Armel , Udall Joshua A , Jeddeloh Jeffrey A , Wendel Jonathan 
Published: August 2012

Abstract
Targeted sequence capture is a promising technology in many areas in biology. These methods enable efficient and relatively inexpensive sequencing of hundreds to thousands of genes or genomic regions from many more individuals than is practical using whole-genome sequencing approaches. Here, we demonstrate the feasibility of target enrichment using sequence capture in polyploid cotton. To capture and sequence both members of each gene pair (homeologs) of wild and domesticated Gossypium hirsutum, we created custom hybridization probes to target 1000 genes (500 pairs of homeologs) using information from the cotton transcriptome. Two widely divergent samples of G. hirsutum were hybridized to four custom NimbleGen capture arrays containing probes for targeted genes. We show that the two coresident homeologs in the allopolyploid nucleus were efficiently captured with high coverage. The capture efficiency was similar between the two accessions and independent of whether the samples were multiplexed. A significant amount of flanking, nontargeted sequence (untranslated regions and introns) was also captured and sequenced along with the targeted exons. Intraindividual heterozygosity is low in both wild and cultivated Upland cotton, as expected from the high level of inbreeding in natural G. hirsutum and bottlenecks accompanying domestication. In addition, levels of heterozygosity appeared asymmetrical with respect to genome (AT or DT) in cultivated cotton. The approach used here is general, scalable, and may be adapted for many different research inquiries involving polyploid plant genomes.
Patient–Clinician Information Engagement Improves Adherence to Colorectal Cancer Surveillance after Curative Treatment: Results from a Longitudinal Study
Authors: Tan Andy S.L. , Moldovan-Johnson Mihaela , Parvanta Sarah , Gray Stacy W. , Armstrong Katrina , Hornik Robert C. 
Published: August 2012

Abstract

Introduction.
Follow-up surveillance after curative treatment for colorectal cancer (CRC) patients is recommended to detect early cancer recurrences and improve survival outcomes. However, a substantial proportion of CRC patients do not undergo cancer surveillance. Several demographic and disease-related factors have been associated with cancer surveillance adherence. Thus far, patient-centered communication has not been studied as a determinant for undergoing cancer surveillance. The purpose of this study is to determine whether patient–clinician information engagement (PCIE) influences patients' self-reported adherence to recommended CRC surveillance procedures.

Methods.
The study was a longitudinal survey among Pennsylvanian patients diagnosed with CRC in 2005. CRC patients who were eligible for surveillance and participated in both the baseline and 1-year follow-up surveys were included in this analysis (n = 305). The main outcome measure was self-reported adherence to physical examination, carcinoembryonic antigen testing, and colonoscopy according to recommended guidelines.

Results.
Controlling for potential confounders, higher PCIE at baseline predicted a higher odds for CRC patients reporting adherence to recommended surveillance 1 year later by 2.8 times. Other significant predictors of adhering to recommended surveillance were a higher education level and having received systemic therapy.

Discussion.
In this longitudinal study among CRC patients who received curative treatment, greater patient engagement with clinicians about cancer-related information was found to improve patients' subsequent adherence to recommended surveillance. This finding provides support for encouraging greater patient–physician communication among CRC patients.
A long‐term database on raptor migration at Hawk Mountain Sanctuary, northeastern United States
Authors: Therrien J.-F , Goodrich L. J. , Barber D. R. , Bildstein K. L. 
Published: August 2012

In most northern temperate regions diurnal birds of prey, or raptors, migrate seasonally between their breeding and wintering grounds. Although their populations can be logistically difficult to survey and monitor because the birds are largely secretive and wide‐ranging, most raptors are obligate or facultative soaring migrants that congregate along major thermal and orographic updraft corridors during their seasonal movements. Hawk Mountain Sanctuary (41° N, 75° W), which straddles the Kittatinny Ridge, the southernmost ridge in the Appalachian Mountains in eastern Pennsylvania, witnesses large numbers of migrating raptors during autumn migration. The Sanctuary's long‐term migration‐count database is the oldest detailed archive on the timing and magnitude of migratory raptors in the world. Records comprise daily (1934–1965) or hourly (1966–present) counts of 18 North American species of raptors migrating past the Sanctuary, as well as detailed weather data recorded from the lookout during autumn migration (from 15 August to 15 December). The long‐term data set has been valuable in understanding raptor migration and population trends. Because top predators such as raptors are sensitive bio‐indicators of ecosystem changes, variations in the numbers of individual species also may reflect changes in the health of the environment. Thus, monitoring population trends of raptors can provide crucial information on environmental changes and threats facing wildlife species. Indeed, the Sanctuary's database has been key in identifying the now well‐known example of organochlorine contamination of top predators and has helped the conservation, management, and reintroduction of many species such as Osprey (Pandion haliaetus), Bald Eagle (Haliaeetus leucocephalus), and Peregrine Falcon (Falco peregrinus). This database is of prime significance to conservation ecology and long‐term fluctuations in numbers of migratory birds.The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at 〈http://esapubs.org/archive〉. (The accession number for each Data Paper is given directly beneath the title.)
Comparison of Radiographic and Surface Topography Measurements in Adolescents with Idiopathic Scoliosis
Authors: Frerich Jason M , Hertzler Kristen , Knott Patrick , Mardjetko Steven 
Published: August 2012

Purpose:In patients with adolescent idiopathic scoliosis (AIS), radiographic surveillance is the gold standard of assessing spinal deformity, but has negative long-term effects. The Formetric 4D surface topography system was compared to standard radiography as a safer option for evaluating patients with AIS.Methods:Fourteen volunteers with typical AIS patient stature had 30 repeated Formetric 4D measurements taken, and reproducibility was assessed. Sixty-four patients with AIS were then enrolled during routine clinic visits. Evaluation included standard radiographs and surface topography measurements. A comparison analysis was performed.Results:When assessing same-day repeated scans, a standard deviation of +/- 3.4 degrees for scoliosis curve measurements was determined, and the Reliability Coefficient (Cronbach) was very high (0.996). Cobb angles measured with the Formetric 4D differed from radiographic measurements by an average of 9.42 (lumbar) and 6.98 (thoracic) degrees, while the correlation between the two measurements was strong (95% confidence interval [CI]), 0.758 (lumbar) and 0.872 (thoracic) respectively.Conclusions:The Formetric 4D is comparable to radiography in terms of its test-retest reproducibility. Although this device does not predict curve magnitude exactly, the predictions correlate strongly with the Cobb angles determined from radiographs. It can be reliably used in the surveillance of patients with AIS.
Prediction of Functional Outcome at Six Months Following Total Hip Arthroplasty
Authors: Slaven Emily J. 
Published: August 2012

BackgroundRecovery of function such as the ability to walk without an assistive device after total hip arthroplasty (THA) is not always automatic.ObjectiveThis study investigated whether predetermined variables could be used to identify patients who might have functional limitations at 6 months following THA.DesignA prospective, observational cohort design was used.MethodDemographics and baseline measures, including age, sex, and preoperative Lower Extremity Functional Scale (LEFS) score, were collected 1 to 3 weeks prior to surgery from 40 participants who were scheduled to undergo THA. Six weeks after surgery, a second LEFS score was recorded along with each participant's body mass index and the THA procedure performed; walking speed and balance also were assessed at this time using the 10-Meter Walk Test, the Timed “Up & Go” Test, and the Functional Reach Test. At 6 months following surgery, each participant's functional outcome was determined from the final LEFS score and the need for an assistive device. Classification and regression tree (CART) analyses and logistic regression were used to establish which of the variables could predict outcome at 6 months.ResultsBody mass index, sex, and age were identified by CART analysis as predictors to classify participants who did not reach successful outcome status. Logistic regression revealed that sex (female) was the only individual variable that predicted outcome at 6 months. Walking speed was the only performance variable identified as a predictor for outcome using CART analysis.LimitationsOnly a limited number of variables were observed due to the small sample size.ConclusionIt is possible to identify those patients who are at risk for an unsuccessful outcome through the use of variables such as body mass index, age, and sex.
Intraventricular baclofen as an alternative to intrathecal baclofen for intractable spasticity or dystonia: outcomes and technical considerations
Authors: Turner Michael , Nguyen Ha Son , Cohen-Gadol Aaron A. 
Published: August 2012

Object
The aim of this study was to identify the benefits of intraventricular baclofen (IVB) therapy for the treatment of intractable spasticity or dystonia in a subset of patients who had experienced multiple revisions while receiving intrathecal baclofen (ITB) therapy.

Methods
The authors reviewed the charts of 22 consecutive patients with intractable spasticity or dystonia who initially underwent ITB therapy, subsequently suffered multiple revisions during ITB therapy, and ultimately received IVB therapy, all during a 12-year period from November 1998 to October 2010. The intraventricular catheters were positioned in the lateral ventricle, aided by stereonavigation.

Results
The surgical revision rate (the average number of surgical revisions per average number of follow-up years) during ITB therapy was 0.84, and was 0.50 during IVB therapy. The most frequent complication requiring surgical revision during ITB therapy was catheter occlusion, followed by pump malfunction/pump pocket issues, and infection. The most frequent complication requiring surgical revision during IVB therapy was infection, followed by catheter misplacement/migration. Four patients suffered infection that required removal of their intraventricular catheter, and currently have no baclofen system.

Conclusions
Some of these patients had a history of increasing revisions with increasing frequency during ITB therapy. Such a history puts them at risk for spinal arachnoiditis, a condition that complicates further ITB therapy. For such patients, the authors believe that IVB therapy may be a beneficial therapeutic option, given that the surgical revision rate was lower for IVB than for ITB. Intraventricular baclofen may be a cost-effective option for patients with mounting revisions during ITB therapy.
Spontaneous improvement of cervical alignment after correction of global sagittal balance following pedicle subtraction osteotomy
Authors: Smith Justin S. , Shaffrey Christopher I. , Lafage Virginie , Blondel Benjamin , Schwab Frank , Hostin Richard , Hart Robert , O'Shaughnessy Brian , Bess Shay , Hu Serena S. , Deviren Vedat , Ames Christopher P. , _ _ 
Published: August 2012

Object
Sagittal spinopelvic malalignment is a significant cause of pain and disability in patients with adult spinal deformity. Surgical correction of spinopelvic malalignment can result in compensatory changes in spinal alignment outside of the fused spinal segments. These compensatory changes, termed reciprocal changes, have been defined for thoracic and lumbar regions but not for the cervical spine. The object of this study was to evaluate postoperative reciprocal changes within the cervical spine following lumbar pedicle subtraction osteotomy (PSO).

Methods
This was a multicenter retrospective radiographic analysis of patients from International Spine Study Group centers. Inclusion criteria were as follows: adults (>18 years old) with spinal deformity treated using lumbar PSO, a preoperative C7–S1 plumb line greater than 5 cm, and availability of pre- and postoperative full-length standing radiographs.

Results
Seventy-five patients (60 women, mean age 59 years) were included. The lumbar PSO significantly improved sagittal alignment, including the C7–S1 plumb line, C7–T12 inclination, and pelvic tilt (p <0.001). After lumbar PSO, reciprocal changes were seen to occur in C2–7 cervical lordosis (from 30.8° to 21.6°, p <0.001), C2–7 plumb line (from 27.0 mm to 22.9 mm), and T-1 slope (from −38.9° to −30.4°, p <0.001). Ideal correction of sagittal malalignment (postoperative sagittal vertical alignment < 50 mm) was associated with the greatest relaxation of cervical hyperlordosis (−12.4° vs −5.7°, p = 0.037). A change in cervical lordosis correlated with changes in T-1 slope (r = −0.621, p <0.001), C7–T12 inclination (r = 0.418, p <0.001), T12–S1 angle (r = −0.339, p = 0.005), and C7–S1 plumb line (r = 0.289, p = 0.018). Radiographic parameters that correlated with changes in cervical lordosis on multivariate linear regression analysis included change in T-1 slope and change in C2–7 plumb line (r2 = 0.53, p <0.001).

Conclusions
Adults with positive sagittal spinopelvic malalignment compensate with abnormally increased cervical lordosis in an effort to maintain horizontal gaze. Surgical correction of sagittal malalignment results in improvement of the abnormal cervical hyperlordosis through reciprocal changes.
Pullout-proofing external ventricular drains
Authors: Whitney Nathaniel L. , Selden Nathan R. 
Published: August 2012

Object
The authors describe a method of securing an external ventricular drain (EVD) to prevent dislodgement and discourage CSF leakage and infection.

Methods
The EVD is secured using a single permanent suture, creating a box stitch around the exit site attached to a modified roman sandal. Multiple knots are tied after each loop to avoid “telescoping,” loosening, and pullout.

Results
In 12 years of high-volume pediatric practice by one of the authors, only one drain has broken, and none have pulled out.

Conclusions
The modified roman sandal technique tightly secures EVDs against pullout. Anecdotal evidence suggests that the strength of the suture construct securing the drain is greater than that of the drain tubing itself.
Molecular phylogenetics of Echinopsis (Cactaceae): Polyphyly at all levels and convergent evolution of pollination modes and growth forms
Authors: Schlumpberger Boris O. , Renner Susanne S. 
Published: August 2012

• Premise of the study: In its current circumscription, Echinopsis with 100–150 species is one of the largest and morphologically most diverse genera of Cactaceae. This diversity and an absence of correlated characters have resulted in numerous attempts to subdivide Echinopsis into more homogeneous subgroups. To infer natural species groups in this alliance, we here provide a plastid phylogeny and use it to infer changes in growth form, pollination mode, and ploidy level.• Methods: We sequenced 3800 nucleotides of chloroplast DNA from 162 plants representing 144 species and subspecies. The sample includes the type species of all genera close to, or included in, Echinopsis as well as a dense sample of other genera of the Trichocereeae and further outgroups. New and published chromosome counts were compiled and traced on the phylogeny, as were pollination modes and growth habits.• Key results: A maximum likelihood phylogeny confirms that Echinopsis s.l. is not monophyletic nor are any of the previously recognized genera that have more than one species. Pollination mode and, to a lesser extent, growth habit are evolutionarily labile, and diploidy is the rule in Echinopsis s.l., with the few polyploids clustered in just a few clades.• Conclusions : The use of evolutionary labile floral traits and growth habit has led to nonnatural classifications. Taxonomic realignments are required, but further study of less evolutionary labile traits suitable for circumscribing genera are needed. Surprisingly, polyploidy seems infrequent in the Echinopsis alliance and hybridization may thus be of minor relevance in the evolution of this clade.