List Of Matches Research Articles

Modular reifiable matching: a list-of-functors approach to two-level types

This paper presents Modular Reifiable Matching (MRM): a new approach to two level types using a fixpoint of list-of-functors representation. MRM allows the modular definition of datatypes and functions by pattern matching, using a style similar to the widely popular Datatypes a la Carte (DTC) approach. However, unlike DTC, MRM uses a fixpoint of list-of-functors approach to two-level types. This approach has advantages that help with various aspects of extensibility, modularity and reuse. Firstly, modular pattern matching definitions are collected using a list of matches that is fully reifiable. This allows for extensible pattern matching definitions to be easily reused/inherited, and particular matches to be overridden. Such flexibility is used, among other things, to implement extensible generic traversals . Secondly, the subtyping relation between lists of functors is quite simple, does not require backtracking, and is easy to model in languages like Haskell. MRM is implemented as a Haskell library, and its use and applicability are illustrated through various examples in the paper.

Computerized Dental Comparison: A Critical Review of Dental Coding and Ranking Algorithms Used in Victim Identification.

Comparison of antemortem and postmortem dental records is a leading method of victim identification, especially for incidents involving a large number of decedents. This process may be expedited with computer software that provides a ranked list of best possible matches. This study provides a comparison of the most commonly used conventional coding and sorting algorithms used in the United States (WinID3) with a simplified coding format that utilizes an optimized sorting algorithm. The simplified system consists of seven basic codes and utilizes an optimized algorithm based largely on the percentage of matches. To perform this research, a large reference database of approximately 50,000 antemortem and postmortem records was created. For most disaster scenarios, the proposed simplified codes, paired with the optimized algorithm, performed better than WinID3 which uses more complex codes. The detailed coding system does show better performance with extremely large numbers of records and/or significant body fragmentation.

ProSight Lite: graphical software to analyze top-down mass spectrometry data.

Many top-down proteomics experiments focus on identifying and localizing PTMs and other potential sources of “mass shift” on a known protein sequence. A simple application to match ion masses and facilitate the iterative hypothesis testing of PTM presence and location would assist with the data analysis in these experiments. ProSight Lite is a free software tool for matching a single candidate sequence against a set of mass spectrometric observations. Fixed or variable modifications, including both PTMs and a select number of glycosylations, can be applied to the amino acid sequence. The application reports multiple scores and a matching fragment list. Fragmentation maps can be exported for publication in either portable network graphic (PNG) or scalable vector graphic (SVG) format. ProSight Lite can be freely downloaded from http://prosightlite.northwestern.edu, installs and updates from the web, and requires Windows 7 or a higher version.

Phonetic-based Sindhi spellchecker system using a hybrid model

This article presents a novel architecture using a hybrid model for developing a Sindhi spellchecker system which has yet not been developed prior to this work. The compound textual forms and glyphs of Sindhi language presents a substantial challenge for developing a Sindhi spellchecker system and generating a similar suggestion list for misspelled words. In order to implement such a system, phonetic-based Sindhi language rules and patterns must be taken into account for increasing the accuracy and efficiency. In this research work, a simple and efficient combinational hybrid system is proposed, using three different algorithms, the Edit Distance algorithm to find the measure of similarity between two Sindhi strings. The phonetic-based SoundEx and ShapeEx algorithms are developed for pattern or glyph matching, generating accurate and an efficient suggestion list for incorrect or misspelled Sindhi words. The proposed system is established with a blend between Phonetic-based SoundEx algorithm and ShapeEx algorithm for pattern or glyph matching, generating accurate and efficient suggestion list for incorrect or misspelled Sindhi words. In this article, a table of phonetically similar-sounding Sindhi characters is presented which are grouped together along with another table containing similar glyph or shape-based character groups. The system has been successfully integrated into a pre-developed Sindhi word processer application. The Sindhi word segmentation methodology and algorithms required for the spellchecker has already been published and so are not discussed in detail in this article.

Does the amount of time medical students spend in the operating room during the general surgery core clerkship affect their career decision?

BackgroundThe amount of time medical students (MS) spend in the operating room (OR) during their general surgery core clerkship has not been previously studied as a predictor for choosing a career in surgery. We hypothesize that MS choosing a career in surgery spend more time in the OR. MethodsOperative records for surgery cases at our institution from 2009 to 2013 were linked to the schedules of MS from classes of 2010 to 2014. Total number of minutes, cases, and average number of minutes in the OR were calculated and compared with the match lists. Univariate analysis was conducted to assess for associations (P < .05). ResultsA total of 117 students and 1,524 procedures were included. Twenty-two MS chose a surgical career (19%). An average of 2,018.5 minutes per rotation was spent in the OR (81.2 min/d), but neither the amount of time nor the number of cases was associated with choosing a career in surgery. ConclusionsQuality of the educational experience trumps quantity regarding what most influences MS career decision.

ProSight Lite: Graphical software to analyze top-down mass spectrometry data

Many top-down proteomics experiments focus on identifying and localizing PTMs and other potential sources of “mass shift” on a known protein sequence. A simple application to match ion masses and facilitate the iterative hypothesis testing of PTM presence and location would assist with the data analysis in these experiments. ProSight Lite is a free software tool for matching a single candidate sequence against a set of mass spectrometric observations. Fixed or variable modifications, including both PTMs and a select number of glycosylations, can be applied to the amino acid sequence. The application reports multiple scores and a matching fragment list. Fragmentation maps can be exported for publication in either portable network graphic (PNG) or scalable vector graphic (SVG) format. ProSight Lite can be freely downloaded from http://prosightlite.northwestern.edu, installs and updates from the web, and requires Windows 7 or a higher version.

Assessment of moral reasoning skills in the orthopaedic surgery resident applicant.

Assessing orthopaedic surgery residency applicants is a complex process. One important applicant characteristic not commonly measured during the interview process is moral behavior, a key component of the guidelines of the Accreditation Council for Graduate Medical Education for professionalism competency. We sought to determine whether a relationship exists between the results of residency selection interviews, as measured by match rank order, and moral reasoning skills, as measured by the revised version of the Defining Issues Test (DIT-2). The DIT-2, a psychological tool that has been validated in assessing moral reasoning in >30,000 subjects, was administered to orthopaedic surgery residency candidates on a voluntary basis during their interview day. Data were collected annually from four applicant classes (2009 to 2012) at one institution. Each candidate was interviewed by an orthopaedic faculty team and was ranked comparatively with the other interviewing applicants. The five-part aggregate interview method for ranking applicants for the match list included a focused interview station presenting ethical dilemmas as one part of determining rank order. One hundred and twenty-four fourth-year medical students interviewing for orthopaedic surgery residency were assessed with the DIT-2. The results from the DIT-2 produced a postconventional score, which correlates with various levels of moral development. Each applicant's postconventional score was then compared with the patient's overall rank order. Applicants had highly variable moral reasoning skills, with no relationship to the final rank list. Despite a wide range of DIT-2 scores, the interview process did not differentiate applicants based on moral reasoning skills. It remains unclear whether the DIT-2 could (or should) be used as an additional data point to help stratify orthopaedic residency applicants and to predict their performance.

From the Desk of the Program Director: Show Me the Rankings!

From the Desk of the Program Director: Show Me the Rankings!

Does an English appeal court ruling increase the risks of miscarriages of justice when complex DNA profiles are searched against the national DNA database?

Likelihood ratio (LR) methods to interpret multi-contributor, low template, complex DNA mixtures are becoming standard practice. The next major development will be to introduce search engines based on the new methods to interrogate very large national DNA databases, such as those held by China, the USA and the UK. Here we describe a rapid method that was used to assign a LR to each individual member of database of 5 million genotypes which can be ranked in order. Previous authors have only considered database trawls in the context of binary match or non-match criteria. However, the concept of match/non-match no longer applies within the new paradigm introduced, since the distribution of resultant LRs is continuous for practical purposes. An English appeal court decision allows scientists to routinely report complex DNA profiles using nothing more than their subjective personal 'experience of casework' and 'observations' in order to apply an expression of the rarity of an evidential sample. This ruling must be considered in context of a recent high profile English case, where an individual was extracted from a database and wrongly accused of a serious crime. In this case the DNA evidence was used to negate the overwhelming exculpatory (non-DNA) evidence. Demonstrable confirmation bias, also known as the 'CSI-effect, seriously affected the investigation. The case demonstrated that in practice, databases could be used to select and prosecute an individual, simply because he ranked high in the list of possible matches. We have identified this phenomenon as a cognitive error which we term: 'the naïve investigator effect'. We take the opportunity to test the performance of database extraction strategies either by using a simple matching allele count (MAC) method or LR. The example heard by the appeal court is used as the exemplar case. It is demonstrated that the LR search-method offers substantial benefits compared to searches based on simple matching allele count (MAC) methods.

An Enhanced Graph Representation and Heuristic Tabu Search Approach for Flexible and Efficient 3D Shape Matching

3D shape matching is widely used in engineering design for model retrieval, shape similarity assessment or collaborative development. In this paper, an enhanced graph representation and heuristic tabu search based approach is presented to enable flexible and efficient 3D shape matching. The core idea includes (1) generic shape features are recognized from boundary representation (B-rep) of 3D shape as many as possible to incorporate domain design knowledge, (2) an enhanced graph representation of 3D shape is constructed by mixing faces of B-rep and recognized features, to achieve meaningful matching results at low-level of faces or high-level of features satisfying various design intents, and (3) a tabu list of possible improper matches is built to reduce the search space so that the optimal result can be efficiently obtained. Finally, Two examples are demonstrated to show that both two levels of 3D shape matching results can be efficiently obtained for various design intents in the engineering applications, only not more than 18% computation time is required when compared with a typical shape matching method, and it takes only 20 s when the number of matching nodes is more than 460.

Council of Emergency Medicine Residency Directors' standardized letter of recommendation: the program director's perspective.

The standardized letter of evaluation (SLOE) was created in 1997 to provide residency program directors (PDs) with a summative evaluation that incorporates normative grading (i.e., comparisons to peers applying to emergency medicine [EM] training). Although the standard letter of recommendation (SLOR) has become increasingly popular and important in decision-making, it has not been studied in the past 12 years. To assess the SLOR's effectiveness and limitations, the perspective of EM PDs was surveyed in this study. After validation of the questionnaire by 10 retired PDs, the survey was sent to the PD of each of the 159 EM residencies that existed at that time. The survey was circulated via the Council of Emergency Medicine Residency Directors' (CORD) listserv from January 24, 2013, to February 13, 2013. Weekly e-mail reminders to all PDs served to increase participation. A total of 150 of 159 PDs (94.3%) completed the questionnaire. Nearly all respondents (149 of 150; 99.3%) agreed that the SLOR is an important evaluative tool and should continue to be used. In the application process, 91 of 150 (60.7%) programs require one or more SLORs, and an additional 55 (36.7%) recommend but do not require a SLOR to be considered for interview. When asked to identify the top three factors in deciding who should be interviewed, the SLOR was ranked first (139 of 150; 92.7%), with EM rotation grades ranked second (73 of 150; 48.7%). The factors that were most often identified as the top three that diminish the value of the SLOR in order were 1) "inflated evaluations" (121 of 146; 82.9%), 2) "inconsistency between comments and grades" (106 of 146; 72.6%), and 3) "inadequate perspective on candidate attributes in the written comments" and "inexperienced authors" (60 of 146; 41.1% each). The SLOR appears to be the most important tool in the EM PD's armamentarium for determining which candidates should be interviewed for residency training. Although valuable, the SLOR's potential utility is hampered by a number of factors, the most important of which is inflated evaluations. Focused changes in the SLOR template should be mindful that it appears, in general, to be successful in its intended purpose.

PEP Search in MyCompoundID: Detection and Identification of Dipeptides and Tripeptides Using Dimethyl Labeling and Hydrophilic Interaction Liquid Chromatography Tandem Mass Spectrometry

Small peptides, such as dipeptides and tripeptides, are naturally present in many biological samples (e.g., human biofluids and cell extracts). They have attracted great attention in many research fields because of their important biological functions as well as potential roles as disease biomarkers. Tandem mass spectrometry (MS/MS) can be used to profile these small peptides. However, the type and number of fragment ions generated in MS/MS are often limited for unambiguous identification. Herein we report a novel database-search strategy based on the use of MS/MS spectra of both unlabeled and dimethyl labeled peptides to identify and confirm amino acid sequences of di/tripeptides that are separated using hydrophilic interaction (HILIC) liquid chromatography (LC). To facilitate the di/tripeptide identification, a database consisting of all the predicted MS/MS spectra from 400 dipeptides and 8000 tripeptides was created, and a search tool, PEP Search, was developed and housed at the MyCompoundID website ( www.mycompoundid.org/PEP). To evaluate the identification specificity of this method, we used acid hydrolysis to degrade a standard protein, cytochrome c, to produce many di/tripeptides with known sequences for LC/MS/MS. The resultant MS/MS spectra were searched against the database to generate a list of matches which were compared to the known sequences. We correctly identified the di/tripeptides in the protein hydrolysate. We then applied this method to detect and identify di/tripeptides naturally present in human urine samples with high confidence. We envisage the use of this method as a complementary tool to various LC/MS techniques currently available for small molecule or metabolome profiling with an added benefit of covering all di/tripeptide chemical space.

Mapping the Extracellular and Membrane Proteome Associated with the Vasculature and the Stroma in the Embryo

In order to map the extracellular or membrane proteome associated with the vasculature and the stroma in an embryonic organism in vivo, we developed a biotinylation technique for chicken embryo and combined it with mass spectrometry and bioinformatic analysis. We also applied this procedure to implanted tumors growing on the chorioallantoic membrane or after the induction of granulation tissue. Membrane and extracellular matrix proteins were the most abundant components identified. Relative quantitative analysis revealed differential protein expression patterns in several tissues. Through a bioinformatic approach, we determined endothelial cell protein expression signatures, which allowed us to identify several proteins not yet reported to be associated with endothelial cells or the vasculature. This is the first study reported so far that applies in vivo biotinylation, in combination with robust label-free quantitative proteomics approaches and bioinformatic analysis, to an embryonic organism. It also provides the first description of the vascular and matrix proteome of the embryo that might constitute the starting point for further developments.

Rural Track Training Based at a Small Regional Campus

Ten years of data for the rural-based Trover Campus (ULTC) were compared with data for the main campus of the University of Louisville School of Medicine to determine whether educational outcomes were equivalent and whether this method of optimizing the affinity model was effective in placing graduates in rural practice. Demographic data and academic measures were compared for 1,391 graduates (60 from ULTC) for 2001-2010. A noninferiority model was developed to compare clinical experiences for each campus cohort. Residency match lists were examined for specialty choice. Graduates from 2001 to 2006 were matched to the American Medical Association Masterfile to determine practice site. ULTC students scored lower on United States Medical Licensing Examination (USMLE) Step 1 and Step 2 Clinical Skills (CK) but tended to close this gap after clinical training when compared with Louisville graduates. The noninferiority model indicates that ULTC students' scores were noninferior to Louisville students' on adjusted shelf exams for obstetrics-gynecology, pediatrics, and surgery, and Step 2 CK (P<.001). ULTC graduates were 4.5 times more likely to choose family medicine (P<.001) and over 6 times more likely to choose a nonmetropolitan area as a practice site (P=.001). These data support the value of a small regional rural clinical campus in optimizing the affinity model to place rural students into rural practice. The ULTC students showed equivalent adjusted test scores and slightly narrowed the gap in unadjusted USMLE scores compared with the main campus students.

Reading the Senses: Writing about Food and Wine

Reading the Senses: Writing about Food and Wine

A survey of the beliefs regarding international emergency medicine among fourth-year medical students planning on matching in emergency medicine

BackgroundWith the recent growth of fellowships in international emergency medicine, the authors sought to evaluate medical students’ attitudes toward international emergency medicine and to determine the effects these attitudes have on their residency selection.MethodsStudy design: Cross-sectional survey. Data collection: An anonymous, eight-question online survey was distributed to all members of the American Academy of Emergency Medicine Resident and Student section. This survey was also distributed to fourth-year medical students rotating through the Emergency Department at Los Angeles County and the University of Southern California.ResultsNinety-eight surveys were collected, 61 from rotating students and 37 from the AAEM mailing. There were no statistically significant differences in responses between the two groups. Of the respondents, 49.4% of have been exposed to IEM, and 46.9% have participated in international health projects. Ninety-four percent agree that IEM is an exciting career option. Seventy-nine percent said programs with IEM opportunities are more appealing than those without, and 45% said the presence of IEM opportunities would be an important factor in rank list; 53% believe that IEM requires formal public health training, and 63% believe it requires tropical medicine training; 68.3%of respondents speak a language in addition to English. This subset was more likely to have participated in IEM projects previously (p = 0.026) but not more likely to make match choices based on IEM.ConclusionsHalf of medical students surveyed had prior experience in international health, and most agree that international emergency medicine is an exciting career option. Over two thirds believe that the presence of IEM opportunities will be a factor in their match list decision.

FOXP2 Targets Show Evidence of Positive Selection in European Populations

Forkhead box P2 (FOXP2) is a highly conserved transcription factor that has been implicated in human speech and language disorders and plays important roles in the plasticity of the developing brain. The pattern of nucleotide polymorphisms in FOXP2 in modern populations suggests that it has been the target of positive (Darwinian) selection during recent human evolution. In our study, we searched for evidence of selection that might have followed FOXP2 adaptations in modern humans. We examined whether or not putative FOXP2 targets identified by chromatin-immunoprecipitation genomic screening show evidence of positive selection. We developed an algorithm that, for any given gene list, systematically generates matched lists of control genes from the Ensembl database, collates summary statistics for three frequency-spectrum-based neutrality tests from the low-coverage resequencing data of the 1000 Genomes Project, and determines whether these statistics are significantly different between the given gene targets and the set of controls. Overall, there was strong evidence of selection of FOXP2 targets in Europeans, but not in the Han Chinese, Japanese, or Yoruba populations. Significant outliers included several genes linked to cellular movement, reproduction, development, and immune cell trafficking, and 13 of these constituted a significant network associated with cardiac arteriopathy. Strong signals of selection were observed for CNTNAP2 and RBFOX1, key neurally expressed genes that have been consistently identified as direct FOXP2 targets in multiple studies and that have themselves been associated with neurodevelopmental disorders involving language dysfunction.

Graduate Medical Education in Sleep Medicine: Did the Canary Just Die?

it is for this reason that the admission ticket for recognition as a new medical specialty by the Accreditation Council for Graduate Medical Education and the American Board of Medical Specialties includes a suffi cient number of active training programs and trainees in the prospective specialty. Because without practitio-ners, there is no specialty. In the most recent Sleep Medicine fellowship match, 64 programs offered 129 positions to start in July 2013. Thus, it is alarming that 31 positions or ~25% went unfi lled. It is possible that in some cases programs deliberately did not rank any candidates leading to seemingly unfi lled positions on the match list. Conversely, candidates may have per-ceived that some programs were of insuffi cient qual-ity. However, given the openings in some prestigious programs, it is likely that there is a paucity of demand. This begs several questions. Is this the beginning of a trend, i.e., the proverbial “Canary in the coal mine”? And if so, why?Unfortunately, it is impossible to know if this past year’s match is a blip in the radar or a harbinger of future results. However, if these results portend the outcome of future matches, several explanations are possible. First, potential trainees have become aware that there is decline in polysomnography use and re-imbursement, thus making specialization in Sleep Medicine less fi nancially attractive. Second, many trainees enter the fi eld after having already completed 4 to 6 years of post graduate medical training. Thus, some may view the extra year of training required for Sleep Medicine as neither intellectually nor fi nancial-ly worthwhile. Third, and perhaps the most potential-ly worriesome, Sleep Medicine may not be perceived as intellectually stimulating with most patients being evaluated and treated for sleep disordered breathing problems.What can be done? Obviously, there must be in-creased efforts to develop new practice paradigms to make Sleep Medicine fi nancially viable and not com-pletely dependent on performing laboratory polysom-nography. More importantly, we as Sleep Medicine practitioners need to promote our fi eld to potential trainees. Large numbers of the general populace suffer from sleep disorders and thus the potential to improve the quality of life for many is great. Furthermore, there is diversity to the fi eld. It is not just about treat-ing sleep disordered breathing although some believe this to be the case. Moreover, there are few disciplines where medical devices, pharmaceuticals and behav-ioral modalities are all used as primary treatments for patients. We should be communicating to potential trainees that Sleep Medicine is a diverse and complex specialty with the potential to help many patients. If we can do this, our fi eld will have a promising future. If not, there will be uncertainty.

A Web Site for Detecting Protein Structural Domain Neighbours

A query protein structure is compared with the VAST program to a database of target structures from the PDB (PDB40, list of protein structures having less than 40% of identical residues: 19 500 structures version 2011). The threshold of the VAST program is lowered in order to find the largest possible number of structures having a local similarity with the query protein. The purpose of the web site is to define structural domains in the query protein using the recurrence of these locally similar substructures. (http://genome.jouy.inra.fr/domire/). The list of matches is subsequently sorted according to two criteria: the number of aligned residues by VAST is at least 40% of the number of residues of the target, and 80% of the target length is aligned including gaps of non aligned residues if less than 40. Besides this list, a residue-residue alignment of the structural neighbour on the amino acid sequence of the query protein is provided together with a 3D view of their superposition. The object of this sorting is to help in detecting remote homologues and isolated protein structures matching the domain structures of a protein.

Complex matching of RDF datatype properties

Property mapping is a fundamental component of ontology matching, and yet there is little support that goes beyond the identification of single property matches. Real data often requires some degree of composition, trivially exemplified by the mapping of "first name" and "last name" to "full name" on one end, to complex matchings, such as parsing and pairing symbol/digit strings to SSN numbers, at the other end of the spectrum. In this paper, we propose a two-phase instance-based technique for complex datatype property matching. Phase 1 computes the Estimate Mutual Information matrix of the property values to 1 find simple, 1:1 matches, and 2 compute a list of possible complex matches. Phase 2 applies Genetic Programming to the much reduced search space of candidate matches to find complex matches. We conclude with experimental results that illustrate how the technique works. Furthermore, we show that the proposed technique greatly improves results over those obtained if the Estimate Mutual Information matrix or the Genetic Programming techniques were to be used independently.