bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using differential introgression in hybrid zones to identify genomic regions involved in speciation
Authors: PAYSEUR BRET A. 
Published: June 2010

AbstractHybrids between species provide information about the evolutionary processes involved in divergence. In addition to creating hybrids in the laboratory, biologists can take advantage of natural hybrid zones to understand the factors that shape gene flow between divergent lineages. In the early stages of speciation, most regions of the genome continue to flow freely between populations. Alternatively, the subset of the genome that confers reproductive barriers between nascent species is expected to reject introgression. Now enabled by advances in genomics, this perspective is motivating detailed comparisons of gene flow across genomic regions in hybrid zones. Here, I review methods for measuring and interpreting introgression at multiple loci in hybrid zones, focusing on the problem of identifying loci that contribute to reproductive isolation. Emerging patterns from multi‐locus studies of hybrid zones are highlighted, including remarkable variance in introgression across the genome. Although existing methods have been useful, there is scope for development of new analytical approaches that better connect differential patterns of gene flow in hybrid zones with current knowledge of speciation mechanisms. I outline future prospects for differential introgression studies on a genomic scale.
Birdstrikes and barcoding: can DNA methods help make the airways safer?
Authors: WAUGH JOHN , EVANS MAX W. , MILLAR CRAIG D. , LAMBERT DAVID M. 
Published: June 2010

AbstractWhile flying remains one of the safest means of travel, reported birdstrikes on aircraft have risen. This is a result of increased aircraft flight movements, changes in agricultural methods and greater environmental awareness contributing to growing populations of hazardous bird species, as well as more diligent reporting of incidents. Measures to mitigate this hazard require accurate data about the species involved; however, the remains of birds from these incidents are often not easy to identify. Reported birdstrikes include a substantial number where the species cannot be determined from morphology alone. DNA barcoding offers a reliable method of identifying species from very small amounts of organic material such as blood, muscle and feathers. We compare species identification based on morphological criteria and identifications based on mitochondrial cytochromecoxidase subunit I DNA barcoding methods for New Zealand species. Our data suggest that DNA‐based identification can substantially add to the accuracy of species identifications, and these methods represent an important addition to existing procedures to improve air safety. In addition, we outline simple and effective protocols for the recovery and processing of samples for DNA barcoding.
Spatial correlations at different spatial scales are themselves highly correlated in isolation by distance processes
Authors: EPPERSON BRYAN K. 
Published: June 2010

AbstractAlthough many properties of spatial autocorrelation statistics are well characterized, virtually nothing is known about possible correlations among values at different spatial scales, which ultimately would influence how inferences about spatial genetics are made at multiple spatial scales. This article reports the results of stochastic space‐time simulations of isolation by distance processes, having a very wide range of amounts of dispersal for plants or animals, and analyses of the correlations among Moran’s I‐statistics for different mutually exclusive distance classes. In general, the stochastic correlations are extremely large (>0.90); however, the correlations bear a complex relationship with level of dispersal, spatial scale and spatial lag between distance classes. The correlations are so large that any existing or conceived statistical method that employs more than one distance class (or spatial scale) should not ignore them. This result also suggests that gains in statistical power via increasing sample size are limited, and that increasing numbers of assayed loci generally should be preferred. To the extent that sampling error for real data sets can be treated as white noise, it should be possible to account for stochastic correlations in formulating more precise statistical methods. Further, while the current results are for isolation by distance processes, they provide some guidance for some more complex stochastic space‐time processes of landscape genetics. Moreover, the results hold for several popular measures other than Moran’s I. In addition, in the results, the signal to noise ratios strongly decreased with distance, which also has several implications for optimal statistical methods using correlations at multiple spatial scales.
Detecting populations in the ‘ambiguous’ zone: kinship‐based estimation of population structure at low genetic divergence
Authors: PALSBØLL PER J. , ZACHARIAH PEERY M. , BÉRUBÉ MARTINE 
Published: June 2010

AbstractIdentifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Issues arise with most current population genetic inference methods when the genetic divergence is low among putative populations. Low levels of genetic divergence may be as a result of either high ongoing migration or historic high migration but no current, ongoing migration. We direct attention to recent developments in the use of the tempo‐spatial distribution of closely related individuals to detect population structure or estimate current migration rates. These ‘kinship‐based’ approaches complement more traditional population‐based genetic inference methods by providing a means to detect population structure and estimate current migration rates when genetic divergence is low. However, for kinship‐based methods to become widely adopted, formal estimation procedures applicable to a range of species life histories are needed.
Distribution of radiodense contrast medium after perineural injection of the palmar and palmar metacarpal nerves (low 4‐point nerve block): An in vivo and ex vivo study in horses
Authors: NAGY A. , BODÒ G. , DYSON S. J. , COMPOSTELLA F. , BARR A. R. S. 
Published: June 2010

SummaryReasons for performing study: Evidence‐based information is limited on distribution of local anaesthetic solution following perineural analgesia of the palmar (Pa) and palmar metacarpal (PaM) nerves in the distal aspect of the metacarpal (Mc) region (‘low 4‐point nerve block’).Objectives: To demonstrate the potential distribution of local anaesthetic solution after a low 4‐point nerve block using a radiographic contrast model.Methods: A radiodense contrast medium was injected subcutaneously over the medial or the lateral Pa nerve at the junction of the proximal three‐quarters and distal quarter of the Mc region (Pa injection) and over the ipsilateral PaM nerve immediately distal to the distal aspect of the second or fourth Mc bones (PaM injection) in both forelimbs of 10 mature horses free from lameness. Radiographs were obtained 0, 10 and 20 min after injection and analysed subjectively and objectively. Methylene blue and a radiodense contrast medium were injected in 20 cadaver limbs using the same techniques. Radiographs were obtained and the limbs dissected.Results: After 31/40 (77.5%) Pa injections, the pattern of the contrast medium suggested distribution in the neurovascular bundle. There was significant proximal diffusion with time, but the main contrast medium patch never progressed proximal to the mid‐Mc region. The radiological appearance of 2 limbs suggested that contrast medium was present in the digital flexor tendon sheath (DFTS). After PaM injections, the contrast medium was distributed diffusely around the injection site in the majority of the limbs. In cadaver limbs, after Pa injections, the contrast medium and the dye were distributed in the neurovascular bundle in 8/20 (40%) limbs and in the DFTS in 6/20 (30%) of limbs. After PaM injections, the contrast and dye were distributed diffusely around the injection site in 9/20 (45%) limbs and showed diffuse and tubular distribution in 11/20 (55%) limbs.Conclusions and potential relevance: Proximal diffusion of local anaesthetic solution after a low 4‐point nerve block is unlikely to be responsible for decreasing lameness caused by pain in the proximal Mc region. The DFTS may be penetrated inadvertently when performing a low 4‐point nerve block.
Use of blood culture medium enrichment for synovial fluid culture in horses: A comparison of different culture methods
Authors: DUMOULIN M. , PILLE F. , Van Den ABEELE A.‐M. , BOYEN F. , BOUSSAUW B. , OOSTERLINCK M. , PASMANS F. , GASTHUYS F. , MARTENS A. 
Published: June 2010

SummaryReasons for performing study: Standard methods for culturing equine synovial fluid (SF) are often unrewarding. Evidence‐based information on the relative efficiency of different systems used for optimisation of isolation of microorganisms from equine SF is lacking.Objectives: To compare the results of different culture systems performed in parallel on SF samples from horses clinically diagnosed with synovial sepsis.Methods: Synovial fluid specimens were collected between February 2007 and October 2008 from all horses admitted to a referral hospital that were clinically diagnosed with synovial sepsis and from control horses. Synovial fluid samples were cultured in parallel by: 1) direct agar culture (DA); agar culture after: 2) lysis‐centrifugation pretreatment (LC); 3) conventional enrichment (CE); 4) combined LC/CE; or 5) blood culture medium enrichment using an automated system (BACTEC 9050).Results: Ninety SF samples from 82 horses were included, together with 40 control samples. Seventy‐one of 90 samples (79%) were culture‐positive by using blood culture medium enrichment (BACTEC), which was significantly higher compared to all other methods. BACTEC enrichment was never negative while any of the other methods was positive. Although agar culture following LC and/or CE resulted in a slightly higher number of positive samples compared to DA, this difference was not significant. All control samples were culture negative by the 5 different techniques. Although the majority of samples containing isolates recovered without enrichment, culture results after BACTEC enrichment were available on the same day as for agar culture with or without LC (19/23 samples), while CE postponed recovery by at least one day in 20/23 samples.Conclusion: Blood culture medium enrichment is superior to other techniques for isolation of bacteria from SF of horses. The use of an automated system allows enrichment without substantially postponing recovery of microorganisms.Potential relevance: The efficient and fast isolation of microorganisms from infected SF by the BACTEC system allows for rapid susceptibility testing and a more appropriate antibiotic treatment.
The use of intra‐articular corticosteroids in the horse: What is known on a scientific basis?
Authors: McILWRAITH C. W. 
Published: June 2010

SummaryIntra‐articular use of corticosteroids has become a recent focus (or re‐focus) of attention in the Thoroughbred racing industry. This manuscript reviews the clinical use and scientific basis of intra‐articular corticosteroid administration including catastrophic injury, articular cartilage degradation and the development of osteoarthritis (OA), as well as the timing of injection relative to racing.
Retrospective evaluation of crib‐biting and windsucking behaviours and owner‐perceived behavioural traits as risk factors for colic in horses
Authors: MALAMED R. , BERGER J. , BAIN M. J. , KASS P. , SPIER S. J. 
Published: June 2010

SummaryReasons for performing study: Although crib‐biting (cribbing)/windsucking has previously been associated with 2 types of colic, additional research into the possible role of other behaviours on incidence of colic by type and severity has not been undertaken.Objectives: To investigate: a relationship between cribbing/windsucking and colic; a relationship between cribbing/windsucking and different types of colic, both medical and surgical; and whether horses displaying specific behaviour traits were more likely to have had colic.Methods: A matched case‐control retrospective study was conducted evaluating horses with various surgical and medical colic diagnoses, admitted to a referral hospital over a 3 year period. Computerised records and a validated internet questionnaire were used to obtain information on owner‐perceived behavioural traits and repetitive behaviours.Results: Cribbing/windsucking was significantly associated with colic but was unassociated with one category or severity of colic over another. No other repetitive behaviour was associated with colic. Age (≥20 years) was significantly associated with colic. An anxious temperament was not associated with risk of colic.Conclusion: Animals at higher risk for colic may be identified based on history of cribbing/windsucking behaviour, but this behaviour was unassociated with increased risk for a particular category or severity of colic. Horses characterised as being more anxious were not at increased risk for colic.Potential relevance: There is a need to elucidate a causal relationship between cribbing/windsucking and gastrointestinal function as development of more effective and humane strategies to treat cribbing/windsucking behaviour may help to improve equine welfare and reduce the risk of colic.
Considerations for pacing of thecricoarytenoid dorsalismuscle by neuroprosthesis in horses
Authors: DUCHARME N. G. , CHEETHAM J. , SANDERS I. , HERMANSON J. W. , HACKETT R. P. , SODERHOLM L. V. , MITCHELL L. M. 
Published: June 2010

SummaryReasons for performing study:The success rate of prosthetic laryngoplasty is limited and may be associated with significant sequelae. Nerve muscle pedicle transplantation has been attempted but requires a year before function is restored.Objective:To determine the optimal parameters for functional electrical stimulation of the recurrent laryngeal nerve in horses.Methods:An experimentalin vivostudy was performed on 7 mature horses (2–21 years). A nerve cuff was placed on the distal end of the common trunk of the recurrent laryngeal nerve (RLN). In 6 horses the ipsilateral adductor branch of RLN was also transected. The electrodes were connected to programmable internal stimulator. Stimulation was performed using cathodic phase and then biphasic pulses at 24 Hz with a 0.427 ms pulse duration. Stimulation‐response experiments were performed at monthly intervals, from one week following implantation. The study continued until unit failure or the end of project (12 months). Two of the horses were stimulated continuously for 60 min to assess onset of fatigue.Results:Excellent arytenoid cartilage abduction (mean arytenoid angle of 52.7°, range 48.5–56.2°) was obtained in 6 horses (laryngealgrades IorII(n = 3) andIII(n = 2). Poor abduction was obtained ingrade IVhorses (n = 2). Arytenoid abduction was maintained for up to a year in one horse. Technical implant failure resulted in loss of abduction in 6 horses at one week to 11 months post operatively. Mean tissue impedance was 1.06 kOhm (range 0.64–1.67 kOhm) at one week, twice this value at 2 months (mean 2.32, range 1.11–3.75 kOhm) and was stable thereafter. Maximal abduction was achieved at a stimulation range of 0.65–7.2 mA. No electrical leakage was observed. Constant stimulation of the recurrent laryngeal nerve for 60 min led to full abduction without evidence of muscle fatigue.Conclusions:Functional electrical stimulation of the recurrent laryngeal nerve leading to full arytenoid abduction can be achieved. The minimal stimulation amplitude for maximal abduction angle is slightly higher than those for man and dogs.Clinical relevance:This treatment modality could eventually be applicable to horses with recurrent laryngeal neuropathy.
Regional differences in biochemical, biomechanical and histomorphological characteristics of the equine suspensory ligament
Authors: SOUZA M. V. , Van WEEREN P. R. , Van SCHIE H. T. M. , Van De LEST C. H. A. 
Published: June 2010

SummaryReasons for performing study:Desmopathies of the suspensory ligament are relatively frequent and vary in prevalence over different anatomical regions. This variation may be because of regional differences in tissue characteristics.Objective:To characterise different regions of healthy forelimb suspensory ligaments (SLs) by means of biochemical, biomechanical and histomorphological techniques.Hypothesis:There is substantial topographical heterogeneity in the SL with respect to structural, compositional and functional characteristics.Methods:SLs were harvested from 38 limbs and used for biochemical (n = 20), biomechanical (n = 14) and histomorphological (n = 4) evaluation. Sulphated glycosaminoglycan (S‐GAG), DNA and collagen content, degree of lysyl hydroxylation and numbers of enzymatic and nonenzymatic cross‐links were determined in 7 regions of the SL: lateral and medial part of the origin (OM, OL), mid‐body (MB), axial and abaxial parts of the lateral and medial branches (ILAX, ILAB, IMAX and IMAB, respectively). Passive resistance to tensile loading was measured in 5 regions of the SL (all except OL and OM).Results:DNA content was lower in OL and OM than in all other parts. GAG content was also lower in OL and OM and highest in ILAB and IMAB. Collagen content was lower in OL/OM and highest in ILAX/IMAX. Pentosidine levels were highest in OL and significantly lower in the lateral insertion (ILAX/ILAB). There were no differences in hydroxylysylpyridinoline (HP) cross‐links or lysyl hydroxylation. Stiffness (P<0.01) and modulus of elasticity (P<0.01) were substantially higher in the MB region than in all other regions except for IMAB. Strain at failure was lower in the MB region (P<0.0001), resulting in a comparable force at rupture as in the other regions.Conclusions:Matrix composition differs to a relatively limited extent between different regions of the SL. The mid‐body of the ligament is stiffer than the branches, which have similar properties and relevance and mechanical differences between mid‐body and branches/origin may explain some use‐related differences in the prevalence of lesions.
SETS OF K-INDEPENDENT STRINGS
Authors: TI YEN-WU , CHANG CHING-LUEH , LYUU YUH-DAUH , SHEN ALEXANDER 
Published: June 2010

A bit string is random (in the sense of algorithmic information theory) if it is incompressible, i.e., its Kolmogorov complexity is close to its length. Two random strings are independent if knowing one of them does not simplify the description of the other, i.e., the conditional complexity of each string (using the other as a condition) is close to its length. We may define independence of a k-tuple of strings in the same way. In this paper we address the following question: what is that maximal cardinality of a set of n-bit strings if any k elements of this set are independent (up to a certain constant)? Lower and upper bounds that match each other (with logarithmic precision) are provided.
Business Intelligence Applications in Retail Business: OLAP, Data Mining & Reporting Services
Authors: Kocakoç Ipek Deveci , Erdem Sabri 
Published: June 2010

As a result of today's competitive business environment, companies have been trying to improve the utilization of funds effectively in their budgets for information technology investments. These companies retrieve more information with the same set of resources by means of business intelligence methods. According to Rubin (Chabrow, 2004) IT budgets are not simply declining or levelling off, rather, companies are shifting from a pure cost-cut mode to a model that emphasises agility and efficiency. Tremendous daily growth of the company data requires more funds and investment for establishing the technologies and infrastructure necessary for gathering fast and crucial information that supports the decision making process. This necessity gave birth to various business intelligence methods, which mainly aim to process mass amount of collected data from their existing application, and represent it in a way with which companies can apply to their daily competitive decisions. This application primarily concerns the implementation of business intelligence for a retail business company. The aim is to implement built-in business intelligence solutions of the Microsoft SQL Server that holds the commercial information of the company for the past three years. The customer company has already been using Microsoft products. The key items used for analyzing data are sales, momentary inventory and logistics information. The application can be grouped in five main areas: Building the data warehouse, constructing OLAP cubes, applying data mining algorithms on OLAP cubes, representing the results in reports with reporting services, and implementation.
Safe programmable speculative parallelism
Authors: Prabhu Prakash , Ramalingam Ganesan , Vaswani Kapil 
Published: June 2010

Execution order constraints imposed by dependences can serialize computation, preventing parallelization of code and algorithms. Speculating on the value(s) carried by dependences is one way to break such critical dependences. Value speculation has been used effectively at a low level, by compilers and hardware. In this paper, we focus on the use of speculation
by programmers
as an algorithmic paradigm to parallelize seemingly sequential code.

We propose two new language constructs,
speculative composition
and
speculative iteration
. These constructs enable programmers to declaratively express speculative parallelism in programs: to indicate when and how to speculate, increasing the parallelism in the program, without concerning themselves with mundane implementation details.

We present a core language with speculation constructs and mutable state and present a formal operational semantics for the language. We use the semantics to define the notion of a correct speculative execution as one that is equivalent to a non-speculative execution. In general, speculation requires a runtime mechanism to undo the effects of speculative computation in the case of mis predictions. We describe a set of conditions under which such rollback can be avoided. We present a static analysis that checks if a given program satisfies these conditions. This allows us to implement speculation efficiently, without the overhead required for rollbacks.
We have implemented the speculation constructs as a C# library, along with the static checker for safety. We present an empirical evaluation of the efficacy of this approach to parallelization.
Evaluating the accuracy of Java profilers
Authors: Mytkowicz Todd , Diwan Amer , Hauswirth Matthias , Sweeney Peter F. 
Published: June 2010

Performance analysts profile their programs to find methods that are worth optimizing: the "hot" methods. This paper shows that four commonly-used Java profilers (
xprof , hprof , jprofile, and yourkit
) often disagree on the identity of the hot methods. If two profilers disagree, at least one must be incorrect. Thus, there is a good chance that a profiler will mislead a performance analyst into wasting time optimizing a cold method with little or no performance improvement.

This paper uses causality analysis to evaluate profilers and to gain insight into the source of their incorrectness. It shows that these profilers all violate a fundamental requirement for sampling based profilers: to be correct, a sampling-based profilermust collect samples randomly.
We show that a proof-of-concept profiler, which collects samples randomly, does not suffer from the above problems. Specifically, we show, using a number of case studies, that our profiler correctly identifies methods that are important to optimize; in some cases other profilers report that these methods are cold and thus not worth optimizing.