Official Scoring Research Articles

BDM: An Assessment Metric for Protein Complex Structure Models Based on Distance Difference Matrix.

Protein complex structure prediction is an important problem in computational biology. While significant progress has been made for protein monomers, accurate evaluation of protein complexes remains challenging. Existing assessment methods in CASP, lack dedicated metrics for evaluating complexes. DockQ, a widely used metric, has some limitations. In this study, we propose a novel metric called BDM (Based on Distance difference Matrix) for assessing protein complex prediction structures. Our approach utilizes a distance difference matrix derived from comparing real and predicted protein structures, establishing a linear correlation with Root Mean Square Deviation (RMSD). BDM overcomes limitations associated with receptor-ligand differentiation and eliminates the requirement for structure alignment, making it a more effective and efficient metric. Evaluation of BDM using CASP14 and CASP15 test sets demonstrates superior performance compared to the official CASP scoring. BDM provides accurate and reasonable assessments of predicted protein complexes, wide adoption of BDM has the potential to advance protein complex structure prediction and facilitate related researches across scientific domains. Code is available at http://mialab.ruc.edu.cn/BDMServer/ .

Identifying outlier scores and outlier jurors to reduce manipulation in classical music competitions

AbstractManipulations in classical music competitions are a proven problem that has as yet not been eradicated from the competition practice. Several examples are provided. We aim to compare and analyze different methods of reducing manipulation in classical music competitions, focusing on outlier scores and on outlier jurors. First, we investigate the typical approach of correcting or discarding individual jurors' scores that significantly deviate from the mean or median of scores received by a given candidate. We then introduce a new method that involves the exclusion of outlier jurors (EOJ). This approach implies that all scores of jurors with ratings that substantially differ from those of other jurors are removed and not taken into account when determining the ranking of candidates. The properties of both approaches are discussed in hypothetical voting scenarios, where one or more jurors assign scores that deviate markedly from those awarded by other jurors. Finally, we present examples of applying various methods to real-world data from classical music competitions, demonstrating the potential effectiveness and implications of each approach in reducing manipulation within these events. Two examples are taken from the International Karol Szymanowski Music Competition, which took place in September 2023 in Katowice, Poland, where EOJ was adopted for the first time as the official scoring system in four competition categories: piano, violin, vocal, and string quartet.

Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy.

The refinement of predicted 3D models aims to bring them closer to the native structure by fixing errors including unusual bonds and torsion angles and irregular hydrogen bonding patterns. Refinement approaches based on molecular dynamics (MD) simulations using different types of restraints have performed well since CASP10. ReFOLD, developed by the McGuffin group, was one of the many MD-based refinement approaches, which were tested in CASP 12. When the performance of the ReFOLD method in CASP12 was evaluated, it was observed that ReFOLD suffered from the absence of a reliable guidance mechanism to reach consistent improvement for the quality of predicted 3D models, particularly in the case of template-based modelling (TBM) targets. Therefore, here we propose to utilize the local quality assessment score produced by ModFOLD6 to guide the MD-based refinement approach to further increase the accuracy of the predicted 3D models. The relative performance of the new local quality assessment guided MD-based refinement protocol and the original MD-based protocol ReFOLD are compared utilizing many different official scoring methods. By using the per-residue accuracy (or local quality) score to guide the refinement process, we are able to prevent the refined models from undesired structural deviations, thereby leading to more consistent improvements. This chapter will include a detailed analysis of the performance of the local quality assessment guided MD-based protocol versus that deployed in the original ReFOLD method.

Two-Step Imputation and AdaBoost-Based Classification for Early Prediction of Sepsis on Imbalanced Clinical Data.

Sepsis is a life-threatening response to infection that causes tissue damage, organ failure, and death. Effective early prediction of sepsis would improve patients' diagnosis and reduce the cost associated with late-stage sepsis infection by applying appropriate early intervention. However, effective early prediction is challenging because sepsis biomarkers are neither obvious nor definitive, and sepsis datasets are heavily imbalanced against positive diagnosis of sepsis while containing significant missing values. Early prediction of sepsis in ICUs using clinical data is the objective of the PhysioNet/Computing in Cardiology Challenge 2019. In this article, we proposed a machine learning algorithm to aid in the early detection of sepsis. We applied linear interpolation and implemented a sample weighted AdaBoost model to predict sepsis 6 hours before clinical diagnosis. Medical data contains more than 40,000 patients gathered from three geographically distinct U.S. hospital systems that consisted of a combination of hourly vital sign, lab values, and static patient descriptions. The challenge metric, however, did not directly reward models for their generalizability across institutions. The article is evaluated using a new metric called Utility Score that is defined as Official scoring criteria. Our approach was among the top 10% of entries to the Challenge on a hidden test set. Herein, we demonstrate that our proposed approach was the most effective of the Challenge entrants when such generalizability is explicitly accounted for in model evaluation.

Enhanced prognostic stratification of neoadjuvant treated lung squamous cell carcinoma by computationally-guided tumor regression scoring

IntroductionThe amount of residual tumor burden after neoadjuvant chemotherapy is an important prognosticator, but for non-small cell lung carcinoma (NSCLC), no official regression scoring system is yet established. Computationally derived histological regression scores could provide unbiased and quantitative readouts to complement the clinical assessment of treatment response. MethodsHistopathologic tumor regression was microscopically assessed on whole cases in a neoadjuvant chemotherapy-treated cohort (NAC, n = 55 patients) of lung squamous cell carcinomas (LSCC). For each patient, the slide showing the least pathologic regression was selected for subsequent computational analysis and histological features were quantified: percentage of vital tumor cells (cTu.Percentage), total surface covered by vital tumor cells (cTu.Area), area of the largest vital tumor fragment (cTu.Size.max), and total number of vital tumor fragments (cTu.Fragments). A chemo-naïve LSCC cohort (CN, n = 104) was used for reference. For 23 of the 55 patients [18F]-Fluorodeoxyglucose (FDG) PET/CT measurements of maximum standard uptake value (SUVmax), background subtracted lesion activity (BSL) and background subtracted volume (BSV) were correlated with pathologic regression. Survival analysis was carried out using Cox regression and receiver operating characteristic (ROC) curve analysis using a 3-years cutoff. ResultsAll computational regression parameters significantly correlated with relative changes of BSV FDG PET/CT values after neoadjuvant chemotherapy. ROC curve analysis of histological parameters of NAC patients showed that cTu.Percentage was the most accurate prognosticator of overall survival (ROC curve AUC = 0.77, p-value = 0.001, Cox regression HR = 3.6, p = 0.001, variable cutoff < = 30 %). ConclusionsThis study demonstrates the prognostic relevance of computer-derived histopathologic scores. Additionally, the analysis carried out on slides displaying the least pathologic regression correlated with overall pathologic response and PET/CT values. This might improve the objective histopathologic assessment of tumor response in neoadjuvant setting.

A Honeybug for Automated Cyber Reasoning Systems

Automated cyber reasoning systems are susceptible to deceit and manipulation. In the Cyber Grand Challenge, the Rubeus system patched binaries with a honeybug that enticed competitor systems to pursue the honeybug instead of exploiting actual vulnerabilities. Surmising how these automated systems operated, we were able to take advantage of differences from the official scoring system to detect and manipulate their behavior. Methods for detecting and countering automation in the real world may be used to thwart the ability of malicious actors to find vulnerabilities.

Evaluation of the Danish footpad lesion surveillance in conventional and organic broilers: Misclassification of scoring

Danish legislation prescribes surveillance of footpad dermatitis (FPD) at slaughter as an indicator of on-farm broiler welfare. The 3-point scale being used was originally developed in Sweden to score feet from conventional broilers, but the extent and causes of misclassifications have not been investigated, neither in conventional nor organic broilers. Hence, we investigated the performance of the official Danish FPD scoring system in conventional and organic broilers by assessing agreement between official scores from the slaughterhouse and consecutive scoring of the same feet by a reference method. We also investigated the impact of performing an incision of the footpad during scoring. In total, 902 conventional and 897 organic broiler feet (∼100 per flock from 18 flocks) were collected at a large Danish slaughterhouse for the official FPD surveillance system. Laboratory scoring, according to predefined criteria for visual and invasive investigations of the feet derived from the official system, was compared to the official scores assigned at slaughter. Footpad lesions were primarily chronic, representing a wide range of severity. Marked differences in color, shape, and degree of papillary hypertrophy and hyperkeratosis of organic and conventional feet were observed. Low agreement primarily regarding score 2 lesions was observed when comparing official and reference foot scores in conventional (0.31) and organic (0.05) broilers. Variation in agreement when comparing flock scores suggested a non-systematic bias, which might be attributed to differences among official raters. The very low agreement in feet from organic broilers shows that these were more difficult to score than conventional. This might be due to a mismatch between lesion characteristics and scoring criteria, or because the lesions were less severe. Strictly visual examination detected 3 out of 4 score 2 lesions identified by the reference method. This study indicated that a large proportion of severe FPD lesions go unnoticed in the official Danish scoring system. The results further suggested that the complexity and impracticality of the scoring criteria impede uniform scoring among raters and production systems.

Inter-rater agreement in visual assessment of footpad dermatitis in Danish broiler chickens

ABSTRACT1. The performance of the scoring in the Danish footpad dermatitis (FPD) surveillance system was evaluated by determining inter-rater agreement in visual inspection of FPD in broilers between two independent raters (R1 and R2) and the official scoring at a Danish slaughterhouse.2. FPD scores were evaluated in 1599 chicken feet. The two raters and the slaughterhouse scored equal proportions of score 0. So did R1 and R2 when assessing score 1 and the more severe lesion score 2, whereas the slaughterhouse scored a markedly higher proportion of score 1 and a lower proportion of score 2. Aggregated FPD flock scores ranged from 5 to 163 (R1 and R2) and from 8 to 107 (slaughterhouse).3. The level of agreement between the two raters was high for scores 0, 1 and 2 and for flock scores. Agreement between raters and the slaughterhouse was lower when R1 and R2 recorded score 2 than when they recorded scores 0 and 1.4. This study indicates that the occurrence and severity of lesions are underestimated in the official Danish FPD scoring system.

Functional Evaluation of Patients Undergoing Multiple Joint Replacements: A Retrospective Study of 50 Patients with a Minimum of Six Months of Follow-up.

Introduction: Polyarthritis is a challenging condition that an orthopedic surgeon faces in day-to-day practice. Some of the conditions where multiple joints are affected are rheumatoid arthritis, osteoarthritis, and ankylosing spondylitis. Multiple joint afflictions can cause severe impairment in the quality of life, which leads to a significant socioeconomic burden on the family and society. Joint replacement is considered as a treatment when severe joint pain or dysfunction is not alleviated by conservative management. Total joint arthroplasty remains one of the most commonly performed and universally accepted operative interventions for such patients.Materials and methods: Fifty patients were invited into the study. All patients included in the study were 18 years of age and older and had undergone two or more joint replacements with a minimum of six months duration from the last surgery. The data was collected during the preoperative and postoperative periods through patient records and questionnaires. The Short Form 36 Health Survey Questionnaire (SF-36) scores were generated from an online application that is readily available on the official website SF-36 scoring system. The results were compared, analyzed, and tested for significance using the Wilcoxon signed rank test.Results: The highest incidence of multiple joint replacements appears to be in the age-group of 51 - 70 years (52%), the mean age of patients being 51.7 +/- 14.4 years. The ratio of female to male patients was 1.6:1. On comparison of preoperative and postoperative (six months) physical component and mental component scores, the differences were found to be significant (p-value: < 0.01). This finding is irrespective of the diagnosis, gender, or age of the patient.Conclusion: In the study conducted on 50 patients, we found out that multiple joint arthroplasties are fruitful surgeries. The procedures are efficient in reducing the disabilities seen in patients with polyarthritis of various causes and improving the overall quality of life. We strongly recommend multiple joint arthroplasties to patients with severe disability. However, adequate medical management plays an equally important role to improve the overall results. Well-designed and larger studies are required to establish the treatment protocols and order of surgeries in patients with differing causes of polyarthritis.

The effect of imprisonment on recommitment: an analysis using exact, coarsened exact, and radius matching with the propensity score

This study examines the effect of prison versus community sanctions on recommitment to prison and compares two levels of community supervision, community control (house arrest) and probation, evaluating whether the findings are contingent on the type of matching methods used in the analysis. Logistic regression was conducted on unmatched and matched samples. Exact, coarsened exact, and radius-matching procedures were used to create a selection on observables design. Matching variables included current offense, demographics, criminal history, supervision violations, and a rich set of Florida Sentencing Guidelines information culled from an official scoring sheet. Florida judges use this instrument to sentence offenders within the framework of the state determinate sentencing system. The results show that with exact matching, there is no effect of imprisonment on recommitment, while the other procedures suggest a specific deterrent effect of imprisonment. All four analysis methods showed that offenders under community control are more likely to reoffend than those under normal probation. Analyses between the matched and unmatched prison observations demonstrate that the matched set of prisoners is composed of offenders who have less extensive criminal records and less serious conviction offenses than unmatched offenders regardless of the matching algorithm. Contrary to a prior analysis of these data, which found a criminogenic effect of prison, a null effect was found using exact matching. Comparing the matching procedures, the more precise the match the less likely there was an effect of prison. However, community control was criminogenic regardless of the matching procedure.

Development of an Automated Motion Evaluation System from Wearable Sensor Devices for Ski Jumping

We developed a system for the automatic evaluation of ski jumps on the base of machine learning algorithms. In several capture sessions during summer jump season, motions of four junior ski jumpers were captured by inertial sensors over the complete jump, from the start of the in-run to the end of the outrun phase. Additionally, style points were collected from an experienced judge to serve as ground truth and control data for the machine learning algorithms. All jumps were randomly separated into a training and a test database. Next, we determined kinematic factors such as body segment orientation and body joint position and segmented every jump into its main motion phases on the base of the raw sensor data. Specific motion characteristics that influence the performance and length of a jump were then used to create machine style knowledge from the training database in compliance to the official scoring guidelines. In a last step, we computed the similarity of every jump within the test database to the trained knowledge on a ski jump's style parameters and evaluated the presence or absence of jump errors. Results showed that the computed error annotations conform largely to the human-based judging scores. Adding automatic score measures to the algorithm in future, this method might be an important step towards better measurability and objectivity of performance-oriented sports in form of a mobile competition evaluation system.

Implementation and impact of pharmacist led medication reconciliation and patient education at discharge from an inpatient behavioral health unit

Transitions of care during a hospitalization, including admission, transfers between units, and discharge are critical processes for medication safety and areas where pharmacy can contribute. Medication discrepancies have a significant impact on patient outcomes and both The Joint Commission (TJC) and the American Society of Health-System Pharmacists (ASHP) have recognized the importance of medication reconciliation in preventing these discrepancies. In 2005, The Joint Commission made medication reconciliation a component of one of its Hospital National Patient Safety Goals (NPSG.08.01.01). Implementation challenges resulted in its suspension in 2009 and 2010 for revision. A modified goal was released in 2011 (NPSG.03.06.01) after a comprehensive review of published literature and available data. Official scoring of the goal started in July 2011.

Treatment of shoulder ulcers in sows – rubber mats and zinc ointment compared to chlortetracycline spray

BackgroundShoulder ulcers can have a significant impact on the welfare of sows. In Denmark, rubber mats are used for treatment of shoulder ulcers. The objective of the study was to compare a treatment consisting of a combination of rubber mats and zinc ointment with the effect of local antibiotic spray (chlortetracycline) on shoulder ulcers.MethodsA total of 304 sows with shoulder ulcers were observed shortly after farrowing (day 1) and on days 14 and 21 after the first observation. The sows were paired according to the grade of the shoulder ulcer using the official Danish scoring system. From each pair of sows, one sow was allocated to mat group (M) and the other to an antibiotic group (A) in a random way. In the M group, rubber mats were placed on the floor, and the ulcers were treated with zinc ointment once a day. In the A group, sows were treated with antibiotic spray daily. The size of the shoulder ulcer was measured manually on a continuous scale on days 1, 14 and 21. The data were analysed by use of two multivariable models where the response was the area of the shoulder ulcer on day 14 and day 21, respectively. Explanatory variables were treatment, herd, parity, body condition and size of ulcer on day 1. If a sow had an ulcer on both shoulders, the shoulder with the largest ulcer was selected.ResultsThe treatment consisting of mats and zinc ointment had a statistical significant effect on the size of the shoulder ulcer on day 14 and day 21 compared to daily treatment with antibiotic spray. For lean sows that were kept on rubber mats and zinc ointment, the average shoulder ulcer was significantly smaller on day 14 (3.8 cm2 versus 9.5 cm2 when antibiotic spray was used) and day 21 (3.4 cm2 versus 6.6 cm2) compared to lean sows that were only treated with antibiotic spray. For fat sows this was also the case when using the lesion on day 21 as the response (2.0 cm2 versus 5.7 cm2) but not on day 14. Moreover, the size of the lesion on day 1 was statistically associated with the size of the lesion on day 14 and on day 21. The treatment was equally effective in the three herds.ConclusionsRubber mats and daily smearing with zinc ointment slow progression and contribute to the healing of shoulder ulcers compared with housing on slats and daily spraying with antibiotics. It is recommended to place a rubber mat in the farrowing crate at the first sign of shoulder ulcers.

Official Body and Texture Criticisms of Dairy Products Judged in the National Contest

Summary A study of the official body and texture criticisms of butter, cheese, and ice cream samples used in the Students’ National Contest in the Judging of Dairy Products during the fourteen-year period from 1926 to 1939, inclusive, showed: 1, that certain body and texture defects are more current than others; 2, that while butter is comparatively free of body and texture defects some occur infrequently; 3, that body and texture defects are very frequently encountered in the greater majority of samples of cheese and ice cream; and 4, that some association of defects exists in those products. Predominating body and texture criticism of butter was “leaky”; those of cheese were “open,” “weak,” “pasty” and “mealy,” and of ice cream “coarse” and “weak” for the frozen ice cream and “curdy” for the melting appearance. One criticism seemed adequate to describe any body and texture defect of butter, but an approximate average of two was necessary to describe properly the body and texture defects of cheese and ice cream. As in the previous report (1) the result of this study and analysis of trends in official body and texture judgments is in no way intended as a guide to future scoring, but merely to classify and make available the body and texture criticisms for those who may not have access to the official scoring records as well as calling attention to this phase of dairy products judging. Inasmuch as the samples used may have been selected in many cases for a specific defect, the percentages distribution reported herein may not necessarily apply to commercial products as a whole. However, the body and texture criticisms encountered in these studies appear to be representative of those encountered in the commercial products throughout the country.

Official Flavor Criticisms of Dairy Products Judged in the National Contest

Summary A study of the official flavor criticisms of butter, cheese, milk, and ice cream samples used in the Students' National Contest in the Judging of Dairy Products during the period 1927 to 1938, inclusive, shows that relatively few flavor criticisms are used by the official judges, despite the relatively high percentage of samples criticized in that respect. Predominating flavor criticisms of butter were old cream, neutralizer, unclean, coarse, burnt and acidy; of cheese , unclean, bitter and acidy; of milk , feed, cooked and unclean; and of ice cream , old ingredient, unnatural and lacks fine flavor. With the possible exception of milk, two or more criticisms were used to describe the flavor of the lower scoring samples. The result of this study and analysis of trends in official flavor judgments is in no way intended as a guide to future scoring, but merely to classify and make available the flavor criticisms for those who may not have access to the official scoring records. Inasmuch as the samples used were selected in many cases for a specific flavor, the percentages distribution reported herein may not necessarily apply to commercial products as a whole. However, the flavor criticisms encountered in these studies appear to be representative of those encountered in the commercial products throughout the country.