bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human subtelomeric duplicon structure and organization
Authors: Ambrosini Anthony , Paul Sheila , Hu Sufen , Riethman Harold 
Published: August 2007

Abstract
Background
Human subtelomeric segmental duplications ('subtelomeric repeats') comprise about 25% of the most distal 500 kb and 80% of the most distal 100 kb in human DNA. A systematic analysis of the duplication substructure of human subtelomeric regions was done in order to develop a detailed understanding of subtelomeric sequence organization and a nucleotide sequence-level characterization of subtelomeric duplicon families.

Results
The extent of nucleotide sequence divergence within subtelomeric duplicon families varies considerably, as does the organization of duplicon blocks at subtelomere alleles. Subtelomeric internal (TTAGGG)n-like tracts occur at duplicon boundaries, suggesting their involvement in the generation of the complex sequence organization. Most duplicons have copies at both subtelomere and non-subtelomere locations, but a class of duplicon blocks is identified that are subtelomere-specific. In addition, a group of six subterminal duplicon families are identified that, together with six single-copy telomere-adjacent segments, include all of the (TTAGGG)n-adjacent sequence identified so far in the human genome.

Conclusion
Identification of a class of duplicon blocks that is subtelomere-specific will facilitate high-resolution analysis of subtelomere repeat copy number variation as well as studies involving somatic subtelomere rearrangements. The significant levels of nucleotide sequence divergence within many duplicon families as well as the differential organization of duplicon blocks on subtelomere alleles may provide opportunities for allele-specific subtelomere marker development; this is especially true for subterminal regions, where divergence and organizational differences are the greatest. These subterminal sequence families comprise the immediate cis-elements for (TTAGGG)n tracts, and are prime candidates for subtelomeric sequences regulating telomere-specific (TTAGGG)n tract length in humans.
Using comparative genomics to reorder the human genome sequence into a virtual sheep genome
Authors: Dalrymple Brian P , Kirkness Ewen F , Nefedov Mikhail , McWilliam Sean , Ratnakumar Abhirami , Barris Wes , Zhao Shaying , Shetty Jyoti , Maddox Jillian F , O'Grady Margaret , Nicholas Frank , Crawford Allan M , Smith Tim , de Jong Pieter J , McEwan John , Oddy V Hutton , Cockett Noelle E ,   the International Sheep Genomics Consortium
Published: August 2007

Abstract
Background
Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes?

Results
A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser.

Conclusion
We demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited.
RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes
Authors: Sevin Emeric W , Barloy-Hubler Frédérique 
Published: August 2007

AbstractToxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not. The tool successfully confirmed all reported TA systems, and spotted new putative loci upon screening of sequenced genomes. RASTA-Bacteria is publicly available at http://genoweb.univ-rennes1.fr/duals/RASTA-Bacteria.
Exon expression profiling reveals stimulus-mediated exon use in neural cells
Authors: McKee Adrienne E , Neretti Nicola , Carvalho Luis E , Meyer Clifford A , Fox Edward A , Brodsky Alexander S , Silver Pamela A 
Published: August 2007

Abstract
Background:
Neuronal cells respond to changes in intracellular calcium ([Ca2+]i) by affecting both the abundance and architecture of specific mRNAs. Although calcium-induced transcription and transcript variation have both been recognized as important sources of gene regulation, the interplay between these two phenomena has not been evaluated on a genome-wide scale.

Results:
Here, we show that exon-centric microarrays can be used to resolve the [Ca2+]i-modulated gene expression response into transcript-level and exon-level regulation. Global assessments of affected transcripts reveal modulation within distinct functional gene categories. We find that transcripts containing calcium-modulated exons exhibit enrichment for calcium ion binding, calmodulin binding, plasma membrane associated, and metabolic proteins. Additionally, we uncover instances of regulated exon use in potassium channels, neuroendocrine secretory proteins and metabolic enzymes, and demonstrate that regulated changes in exon expression give rise to distinct transcript variants.

Conclusion:
Our findings connect extracellular stimuli to specific exon behavior, and suggest that changes in transcript and exon abundance are reflective of a coordinated gene expression response to elevated [Ca2+]i. The technology we describe here lends itself readily to the resolution of stimulus-induced gene expression at both the transcript and exon levels.
Quality of life and functional outcome after primary total hip replacement
Authors: Ng C. Y. , Ballantyne J. A. , Brenkel I. J. 
Published: August 2007

We have evaluated the quality of life and functional outcome after unilateral primary total hip replacement (THR). Between 5 January 1998 and 31 July 2000, we recruited a consecutive series of 627 patients undergoing this procedure and investigated them prospectively. Each was assessed before operation and reviewed after six months, 18 months, three years and five years. The Short Form-36 Health Survey (SF-36) and Harris Hip scores were evaluated at each appointment. All dimensions of the SF-36 except for mental health and general health perception, improved significantly after operation and this was maintained throughout the follow-up. The greatest improvement was seen at the six-month assessment. On average, women reported lower SF-36 scores pre-operatively, but the gender difference did not continue post-operatively. The Harris Hip scores improved significantly after operation, reaching a plateau after 18 months. The improved quality of life was sustained five years after THR.
Cement penetration and primary stability of the femoral component after impaction allografting
Authors: Albert C. , Patil S. , Frei H. , Masri B. , Duncan C. , Oxland T. , Fernlund G. 
Published: August 2007

This study explored the relationship between the initial stability of the femoral component and penetration of cement into the graft bed following impaction allografting.Impaction allografting was carried out in human cadaveric femurs. In one group the cement was pressurised conventionally but in the other it was not pressurised. Migration and micromotion of the implant were measured under simulated walking loads. The specimens were then cross-sectioned and penetration of the cement measured.Around the distal half of the implant we found approximately 70% and 40% of contact of the cement with the endosteum in the pressure and no-pressure groups, respectively. The distal migration/micromotion, and valgus/varus migration were significantly higher in the no-pressure group than in that subjected to pressure. These motion components correlated negatively with the mean area of cement and its contact with the endosteum.The presence of cement at the endosteum appears to play an important role in the initial stability of the implant following impaction allografting.
The influence of posterior condylar offset on knee flexion after total knee replacement using a cruciate-sacrificing mobile-bearing implant
Authors: Hanratty B. M. , Thompson N. W. , Wilson R. K. , Beverland D. E. 
Published: August 2007

We have studied the concept of posterior condylar offset and the importance of its restoration on the maximum range of knee flexion after posterior-cruciate-ligament-retaining total knee replacement (TKR). We measured the difference in the posterior condylar offset before and one year after operation in 69 patients who had undergone a primary cruciate-sacrificing mobile bearing TKR by one surgeon using the same implant and a standardised operating technique. In all the patients true pre- and post-operative lateral radiographs had been taken. The mean pre- and post-operative posterior condylar offset was 25.9 mm (21 to 35) and 26.9 mm (21 to 34), respectively. The mean difference in posterior condylar offset was + 1 mm (−6 to +5). The mean pre-operative knee flexion was 111° (62° to 146°) and at one year postoperatively, it was 107° (51° to 137°). There was no statistical correlation between the change in knee flexion and the difference in the posterior condylar offset after TKR (Pearson correlation coefficient r = −0.06, p = 0.69).
The role of polymethylmethacrylate bone cement in modern orthopaedic surgery
Authors: Webb J. C. J. , Spencer R. F. 
Published: August 2007

Polymethylmethacrylate remains one of the most enduring materials in orthopaedic surgery. It has a central role in the success of total joint replacement and is also used in newer techniques such as percutaneous vertebroplasty and kyphoplasty. This article describes the current uses and limitations of polymethylmethacrylate in orthopaedic surgery. It focuses on its mechanical and chemical properties and links these to its clinical performance. The behaviour of antibiotic-loaded bone cement are discussed, together with areas of research that are now shedding light upon the behaviour of this unique biomaterial.
Arthrodesis of the hindfoot for valgus deformity
Authors: Jackson W. F. M. , Tryfonidis M. , Cooke P. H. , Sharp R. J. 
Published: August 2007

Correction of valgus deformity of the hindfoot using a medial approach for a triple fusion has only recently been described for patients with tight lateral soft tissues which would be compromised using the traditional lateral approach. We present a series of eight patients with fixed valgus deformity of the hindfoot who had correction by hindfoot fusion using this approach. In addition, we further extended the indications to allow concomitant ankle fusion. The medial approach allowed us to excise medial ulcers caused by the prominent medial bony structures, giving simultaneous correction of the deformity and successful internal fixation. We had no problems with primary wound healing and experienced no subsequent infection or wound breakdown. From a mean fixed valgus deformity of 58.8° (45° to 66°) pre-operatively, we achieved a mean post-operative valgus angulation of 13.6° (7° to 23°). All the feet were subsequently accommodated in shoes. The mean time to arthrodesis was 5.25 months (3 to 9). We therefore recommend the medial approach for the correction of severe fixed valgus hindfoot deformities.
New Ceramifying Polymer Materials for Passive Fire Protection Applications
Authors: Thomson K. W. , Shanks R. A. , Genovese A. 
Published: August 2007

Abstract
A new class of polymer composites has been developed for flame retardancy and passive fire protection. The key feature is a controlled transition from a degrading polymer composite to a ceramic residue in a fire situation. The polymer can be thermoplastic, thermoset or elastomeric. The composites are processable using conventional equipment to form extruded profiles, sheet, moldings, each of which may be foamed. The composites can retain flexibility and durability within the required filler content range. Fire protection is afforded by formation of a ceramic by fusion and reaction of the fillers over a defined temperature range. Ceramic formation commences at relatively low temperature coincident with polymer pyrolysis to maintain structural integrity of the material and minimizes shrinkage. The ceramic is able to develop adequate strength to maintain a fire barrier. One form of the material has been implemented in fire resistant cable sheathing. The composites discussed were prepared from poly(siloxiane) elastomer to demonstrate the concept.
Introducing Standards and Sustainable Design
Authors: Kelly William E. 
Published: August 2007

Abstract
The ABET Engineering Criteria require a capstone design project where students use “appropriate engineering standards.” One of the ABET design constraints that students must consider is “sustainability.” The new United States Standards Strategy has as one of its goals to “establish standards education as a high priority within the United States private, public and academic sectors.” The first Fundamental Canon of the ASCE Code of Ethics states in part that civil engineers “shall strive to comply with the principles of sustainable development in the performance of their professional duties.” ASTM E 2432-05 Standard Guide for General Principles of Sustainability Relative to Buildings provides a framework for organizing student design projects to accomplish multiple objectives. However, IEEE’s experience in introducing standards in senior design courses indicates that the senior year may be too late and that the introduction to standards should occur in the first or second year. The purpose of this paper is to outline strategies for including standards and sustainability in courses throughout curricula to build the experience, knowledge, and interest necessary to fulfill the ABET capstone requirements in a meaningful way.
Retrospective Sampling Strategies Using Video Recordings to Estimate Fish Passage at Fishways
Authors: Davies Trevor D. , Kehler Daniel G. , Meade Ken R. 
Published: August 2007

Abstract
Reliable estimates of population size are critical for fisheries management and for testing ecological hypotheses but can be expensive and time consuming to obtain. Sampling methodologies have been developed to obviate complete enumeration, but their effectiveness can be limited by logistical constraints. A posteriori sampling from digital video recordings, however, permits the application of otherwise impractical sampling schemes. We evaluated the time savings of estimating total run size by a posteriori sampling of video recordings (assisted by motion detection software) in comparison with on-site counting methods. The evaluation was based on 9 years of complete counts enumerated either on site or by a posteriori counts from video recordings of alewives Alosa pseudoharengus migrating through a fishway in Nova Scotia. We compared results obtained using analytical estimation methods with results from simulation-based methods and found them to be the same for simple random sampling and daily stratified random sampling. We tested the application of using motion detection software to automatically omit sample units with zero counts from sampling strategies; large reductions in sampling requirements were obtained for data sets with large proportions of zero counts. We also evaluated the effect of sample unit size on sampling effort requirements; use of short but frequent sample units allowed for large reductions in sampling effort. Use of motion detection software in combination with shorter sample units achieved highly significant aggregate reductions in sampling effort. For example, at the shortest tested sample unit size of 1 min, it was possible to reduce sampling requirements to 4 min/d based on daily stratified random sampling to achieve an estimate of the true population within 20% and with 95% confidence. Finally, we evaluated linear interpolation to estimate fish passage for missed days; although average bias was small, bias was substantial when a peak run day was missed.
Genetic Identification of Hatchery Stocks of Brown Trout Using Mitochondrial DNA Polymorphism
Authors: Tiano Todd J. , Willis Catherine M. , Noble Amy A. , Luttenton Mark R. , Nikitin Alexey G. 
Published: August 2007

Abstract
Molecular genetics techniques provide an accurate and cost-effective way to identify hatchery strains and to measure genetic variation in fish populations. In this study, we sought to identify genetic differences at the mitochondrial DNA (mtDNA) level in two of the three hatchery strains of Michigan brown trout Salmo trutta by using restriction fragment length polymorphisms (RFLPs) of segments of mtDNA amplified by polymerase chain reaction. We show that the RFLP approach can provide valuable information about the genetic composition of Michigan brown trout strains and a method of population analysis that can be used to enhance short- and long-term fisheries management studies.
Evaluation of Video Technology for Monitoring of Multispecies Longline Catches
Authors: Ames Robert T. , Leaman Bruce M. , Ames Kelly L. 
Published: August 2007

Abstract
At-sea catch monitoring of the Alaskan longline fishery for Pacific halibut Hippoglossus stenolepis is insufficient. The International Pacific Halibut Commission (IPHC) conducted studies in 2002 and 2004 comparing catch composition data from electronic monitoring (EM) systems to those of at-sea observers. The EM systems use automated data loggers linked to digital video cameras, a transducer on shipboard hydraulic systems, and a global positioning system receiver. The goal of both studies was to determine whether EM technologies could provide precise and verifiable catch composition data on commercial longline vessels to supplement and complement the data collected by fisheries observers. The EM video analyst's catch data were similar to the observers' data in the 2002 study; however, the video analyst recorded fewer fish for 7 of the 17 species categories investigated. In 2004, the IPHC employed EM technology in another study incorporating recommendations from the 2002 study, including improved camera configurations. The video analyst's data showed increased agreement with the observer data. However, the observers recorded slightly fewer individuals of some species categories, opposite the findings of the 2002 study. This change suggests that incorporating the technology recommendations enhanced the video analyst's accuracy relative to the observer data. Our analysis also highlights the fact that data provided by human observers have their own suite of errors and that the comparisons between EM and observers have no absolute standard of reference. The findings indicate that EM technology can effectively address the lack of catch composition data in the Pacific halibut and other hook-and-line fisheries in Alaska.
A Method for Determining Stomach Fullness for Planktivorous Fishes
Authors: Phelps Quinton E. , Willis David W. , Powell Kipp A. , Chipps Steven R. 
Published: August 2007

Abstract
Mean stomach fullness provides a useful index for quantifying fish diets. However, estimating stomach fullness for planktivorous fishes can be time-consuming and prone to error because of small prey and unidentifiable remains. In this study we developed a predictive equation for estimating the stomach volume of yellow perch Perca flavescens as a function of total length (TL). We then used an optical plankton counter (OPC) to estimate the biovolume of invertebrate prey consumed. The OPC quickly estimated the digital size and abundance of zooplankton prey, which can then be converted to estimates of prey biovolume. Stomach volume (V (mm3)) for yellow perch (113–279 mm TL) was significantly related to body size (L (mm)) and was estimated as V = 3 × 10−7 · L2.96. Using the OPC, yellow perch stomach contents (99% Daphnia pulex) were converted to prey biovolume (mm3) and then divided by stomach volume (mm3) to estimate stomach fullness (%). This approach provided reasonable estimates of stomach fullness ranging from 3% to 85% (mean = 21%). Although the initial cost for the OPC equipment is relatively high, this method provided substantial time and labor savings compared with traditional approaches for quantifying zooplankton abundance and biomass (e.g., microscopic identification and enumeration and length–mass conversions). Similarly, the OPC can be used to estimate the abundance and biomass of freshwater zooplankton, thus reducing the time and costs associated with traditional plankton analyses. The approach is limited, however, in cases where very small prey (&lt;250 μm) are a dominant proportion of the sample because of the potential errors involved in detecting and estimating the biovolumes of small particles.
Development and Evaluation of Standard Weight Equations for Bridgelip Suckers and Largescale Suckers
Authors: Richter Tracy J. 
Published: August 2007

Abstract
Fisheries assessment tools originally created for use with game fish populations are now helping to assess individual nongame species and to evaluate fish communities. Length and weight measurements of individuals within a species can be summarized into condition indices that give insight into the health and condition of the individual and the aquatic community. Such data (weight (g) and total length (TL, mm)) were obtained for 105 populations of bridgelip suckers Catostomus columbianus and 135 populations of largescale suckers C. macrocheilus from three northwestern states. These data were used to develop standard weight (Ws) equations via the regression-line percentile (RLP) and empirical percentile (EmP) methods. Length constraints were 130–460 mm TL for bridgelip suckers and 170–640 mm TL for largescale suckers. The data set was limited by TL constraints and split into development and validation sets. The RLP method yielded the following Ws equations: log10Ws = −5.01699 + 3.02648·log10TL for bridgelip suckers and log10Ws = −4.94684 + 2.99720·log10TL for largescale suckers. Equations based on the EmP method were log10Ws = −5.09721 + 3.04947·log10TL for bridgelip suckers and log10Ws = −5.2586 + 3.12136·log10TL for largescale suckers. For both species, the relative weights produced from RLP and EmP equations differed by less than 10%. However, differences were inconsistent over the length range, indicating a length-related bias. Based on this assessment, use of EmP Ws equations for bridgelip suckers and largescale suckers is recommended. Further, the EmP method should be used to establish new Ws equations.