Miracle-dz/UniFAR-FTUs huggingface dataset:
Conceptual space based gross outlier removal for geometric model fitting

In this paper, we propose an efficient and robust gross outlier removal method, called the Conceptual Space based Gross Outlier Removal (CSGOR) method, to remove gross outliers for geometric model fitting. In the proposed method, each data point is mapped to a conceptual space by computing the preference of "good" model hypotheses. In the conceptual space, the distributions of inliers and gross outliers are significantly different. Specifically, inliers of each model instance are distributed in a subspace and they are far away from the origin of the conceptual space, while gross outliers are distributed near the origin. In this manner, the problem of densely gross outlier removal is formulated as a binary classification problem. The main advantage of the proposed method is that it can handle data with a large proportion of outliers and effectively remove gross outliers in data. Experimental results on both synthetic and real data have demonstrated the efficiency and effectiveness of the proposed method.
CoABind: a novel algorithm for Coenzyme A (CoA)‐ and CoA derivatives‐binding residues prediction

Motivation: Coenzyme A (CoA)‐protein binding plays an important role in various cellular functions and metabolic pathways. However, no computational methods can be employed for CoA‐binding residues prediction. Results: We developed three methods for the prediction of CoA‐ and CoA derivatives‐binding residues, including an ab initio method SVMpred, a template‐based method TemPred and a consensus‐based method CoABind. In SVMpred, a comprehensive set of features are designed from two complementary sequence profiles and the predicted secondary structure and solvent accessibility. The engine for classification in SVMpred is selected as the support vector machine. For TemPred, the prediction is transferred from homologous templates in the training set, which are detected by the program HHsearch. The assessment on an independent test set consisting of 73 proteins shows that SVMpred and TemPred achieve Matthews correlation coefficient (MCC) of 0.438 and 0.481, respectively. Analysis on the predictions by SVMpred and TemPred shows that these two methods are complementary to each other. Therefore, we combined them together, forming the third method CoABind, which further improves the MCC to 0.489 on the same set. Experiments demonstrate that the proposed methods significantly outperform the state‐of‐the‐art general‐purpose ligand‐binding residues prediction algorithm COACH. As the first‐of‐its‐kind method, we anticipate CoABind to be helpful for studying CoA‐protein interaction. Availability and implementation: http://yanglab.nankai. edu.cn/CoABind Supplementary information: Supplementary data are available at Bioinformatics online.
FAQIH : Framework for Agent-based Query-enabled Integrated Information for Health and Nutrition

As the processes of urbanization and globalization continue to gain momentum, issues relating to interdependencies among water, food, nutrition and public health policy have increased in complexity and scope. Thus, it is no longer sufficient for subject-matter experts to develop models for each of their underlying domains of expertise (e.g., nutrition, healthcare, and land and water management) independently. Both expert stakeholders and ordinary citizens would benefit from reliable and continually up-to-date models on which to base their decisions. In this preliminary overview paper, the authors propose to develop a Framework for Agentbased Query-Enabled Integrated Information for Health and Nutrition (FAQIH) to support healthcare professionals, policy makers, and citizens to obtain the knowledge they seek.
Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm

The transition to selfing in Capsella rubella accompanies its recent divergence from the ancestral outcrossing C. grandiflora species about 100,000 years ago. Whether the change in mating system was accompanied by the evolution of additional reproductive barriers that enforced species divergence remained unknown. Here, we show that C. rubella and C. grandiflora are reproductively separated by an endosperm-based, non-reciprocal postzygotic hybridization barrier. While hybridizations of C. rubella maternal plants with C. grandiflora pollen donors resulted in complete seed abortion caused by endosperm cellularization failure, the reciprocal hybridization resulted in the formation of small seeds with precociously cellularized endosperm. Strikingly, the transcriptomic response of both hybridizations mimicked respectively the response of paternal and maternal excess hybridizations in Arabidopsis thaliana, suggesting unbalanced genome strength causes hybridization failure in both species. These results provide strong support for the theory that crosses between plants of different mating systems will be unbalanced, with the outcrosser behaving like a plant of increased ploidy, evoking a response that resembles an interploidy-type seed failure. Seed incompatilibity of C. rubella pollinated by C. grandiflora followed the Bateson-Dobzhansky-Muller model, involving negative genetic interaction of multiple paternal C. grandiflora loci with at least one maternal C. rubella locus. Given that both species only recently diverged, our data suggest that a fast evolving mechanism underlies the post-zygotic hybridization barrier(s) separating both species.
Scheduling Harvard SEAS Courses with Simulated Annealing Daniel Nachajon and Ely Spears

The timetabling problem, or the task of generating a working schedule, is a multidimensional combinatorial optimization problem and is therefore very difficult to solve via heuristics or IP for large problems of interest, such as scheduling the courses at a university. In this work, our primary objective is to create a feasible schedule for a full semester of course at the School of Engineering and Applied Sciences (SEAS) at Harvard University. Though this is a medium-to-small sized problem within the larger task of scheduling an entire semester of courses for the whole university, it is a good training and reconnaissance for what a really large problem will require. Using real data of courses to be scheduled, professors attributed to those courses, rooms available, time slots, and room capacities as fixed hard facts, we solved the problem using a simulated annealing (SA) approach under various parameter conditions. Namely, we were interested in comparing various cooling schemes and compare with results obtained in [1].
Maintenance of physical activity following an individualized motivationally tailored intervention

This study examined predictors of exercise maintenance following completion of a physical activity intervention. Sedentary adults recruited through newspaper advertisements were randomly assigned to receive either (a) a motivation-matched intervention with feedback reports that were individually tailored (IT) to psychological variables from social cognitive theory and the Transtheoretical Model via computer expert system, or (b) a standard, print-based intervention (ST). The intervention phase of the study included mailed assessments and intervention materials at baseline, 1, 3, and 6 months. An assessment-only follow-up was conducted 6 months after the end of the intervention (Month 12). Participants were assessed for current physical activity participation, motivational readiness for physical activity, a number of psychological constructs posited to influence participation in physical activity (e.g., self-efficacy), and current affect. Significantly more participants in the IT condition met or exceeded exercise participation goals at the end of the intervention period and maintained, this level of physical activity through the Month 12 follow-up compared to ST participants. Prospective analyses revealed significant differences in several psychological constructs both at program entry (baseline) and the end of the intervention period between individuals who maintained their physical activity participation through Month 12 and those who did not. Results suggest that the maintenance of physical activity following the end of an active intervention program, may be influenced by attitudes and behaviors acquired along with increased participation in physical activity, as well as by preexisting characteristics that individuals bring into treatment.
Risk Factors for Suicidal Thoughts and Behaviors: A Meta-Analysis of 50 Years of Research

Suicidal thoughts and behaviors (STBs) are major public health problems that have not declined appreciably in several decades. One of the first steps to improving the prevention and treatment of STBs is to establish risk factors (i.e., longitudinal predictors). To provide a summary of current knowledge about risk factors, we conducted a meta-analysis of studies that have attempted to longitudinally predict a specific STB-related outcome. This included 365 studies (3,428 total risk factor effect sizes) from the past 50 years. The present random-effects meta-analysis produced several unexpected findings: across odds ratio, hazard ratio, and diagnostic accuracy analyses, prediction was only slightly better than chance for all outcomes; no broad category or subcategory accurately predicted far above chance levels; predictive ability has not improved across 50 years of research; studies rarely examined the combined effect of multiple risk factors; risk factors have been homogenous over time, with 5 broad categories accounting for nearly 80% of all risk factor tests; and the average study was nearly 10 years long, but longer studies did not produce better prediction. The homogeneity of existing research means that the present meta-analysis could only speak to STB risk factor associations within very narrow methodological limits—limits that have not allowed for tests that approximate most STB theories. The present meta-analysis accordingly highlights several fundamental changes needed in future studies. In particular, these findings suggest the need for a shift in focus from risk factors to machine learning-based risk algorithms.
Quantifying Electromigration Processes in Sn-0.7Cu Solder with Lab-Scale X-Ray Computed Micro-Tomography

electromigration phenomena in conductors experiencing high current densities. The influence of interconnect microstructure on device failures related to electromigration in BGA and flip chip solder interconnects has become a significant interest with reduced individual solder interconnect volumes. A survey indicates that x-ray computed micro-tomography (μXCT) is an emerging, novel means for characterizing the microstructures' role in governing electromigration failures. This work details the design and construction of a lab-scale μXCT system to characterize electromigration in the Sn-0.7Cu lead-free solder system by leveraging in situ 3D imaging.
The potential impact of sleep-related movement disorders on stroke risk: a population-based longitudinal study

Abstract Background Sleep-related movement disorders (SRMD) have been shown to increase the risk of cardiovascular diseases. However, the relationship between SRMD and stroke remains unclear. Aim To explore the relationship between SRMD and stroke in the general population. Design Two cohorts of patients with SRMD and without SRMD were followed up for the occurrence of hemorrhagic and ischemic stroke. Methods The study cohort enrolled 604 patients who were initially diagnosed as SRMD between 2000 and 2005. 2,416 age- and sex-matched patients without prior stroke were selected as the comparison cohort. A Cox-proportional hazard regression analysis was performed for multivariate adjustment. Results Patients with SRMD had a higher risk for developing all-cause stroke [adjusted hazard ratio (HR) = 2.29, 95% confidence interval (CI) = 1.42–3.80]. Patients of below 45 years old had the greatest stroke risk (HR = 4.03, 95% CI = 3.11–5.62), followed by patients aged ≥65 years (HR = 2.64, 95% CI = 1.12–3.44) and 45–64 years (HR = 1.07, 95% CI = 1.02–1.71). The age-stratified analysis suggested that the increased risk of hemorrhagic stroke was more significant than ischemic stroke among all age groups. Furthermore, males with SRMD were at greater risk to develop all-cause stroke (HR = 2.98, 95% CI = 1.74–4.50) than that of females (HR = 1.94, 95% CI = 1.01–3.77). Conclusions Patients with SRMD were found to have an increased risk of all-cause stroke along with a higher possibility of hemorrhagic stroke over ischemic stroke.
Selection for Intramuscular Fat in Duroc Swine – An Update

Long-term progress or improvement in many economically important traits is ultimately the responsibility of the seedstock supplier. If selection progress is to be made in traits of economic importance, the trait must: 1) be accurately measurable, 2) show sufficient heritability, and 3) display an adequate level of variation. For such reasons, tremendous progress has been made in the swine industry toward increasing lean meat percentage over the past quarter century. However, in more recent years, meat quality traits have received more attention and have become more important in breeding programs as producers and processors try to meet consumer demands for high quality, nutritious products.
Stress Dynamics of Information Systems Managers: A Contingency Model

A field study of 109 information systems (is) managers explores the relationship among organizational characteristics, job satisfaction, and work stress. The results indicate that work overload is the major source of perceived is work stress, followed by role conflict, job-induced anxiety, and then role ambiguity. Four organizational contextual factors—Is climate, clarity and sharing of organizational mission, quality of work life, and flexibility of organizational processes—were found to influence signiftcantly work stress and job satisfaction as perceived by is managers. As expected, job satisfaction was signiftcantly related to is work stress while is technological sophistication was not related to is stress or job satisfaction factors. Contrary to predictions, neither the clarity and awareness of organizational policies nor the quality of is resources were found to have impact on any is stressor.
Historical comparisons of morbidity and mortality for vaccine-preventable diseases in the United States.

CONTEXT National vaccine recommendations in the United States target an increasing number of vaccine-preventable diseases for reduction, elimination, or eradication. OBJECTIVE To compare morbidity and mortality before and after widespread implementation of national vaccine recommendations for 13 vaccine-preventable diseases for which recommendations were in place prior to 2005. DESIGN, SETTING, AND PARTICIPANTS For the United States, prevaccine baselines were assessed based on representative historical data from primary sources and were compared to the most recent morbidity (2006) and mortality (2004) data for diphtheria, pertussis, tetanus, poliomyelitis, measles, mumps, rubella (including congenital rubella syndrome), invasive Haemophilus influenzae type b (Hib), acute hepatitis B, hepatitis A, varicella, Streptococcus pneumoniae, and smallpox. MAIN OUTCOME MEASURES Number of cases, deaths, and hospitalizations for 13 vaccine-preventable diseases. Estimates of the percent reductions from baseline to recent were made without adjustment for factors that could affect vaccine-preventable disease morbidity, mortality, or reporting. RESULTS A greater than 92% decline in cases and a 99% or greater decline in deaths due to diseases prevented by vaccines recommended before 1980 were shown for diphtheria, mumps, pertussis, and tetanus. Endemic transmission of poliovirus and measles and rubella viruses has been eliminated in the United States; smallpox has been eradicated worldwide. Declines were 80% or greater for cases and deaths of most vaccine-preventable diseases targeted since 1980 including hepatitis A, acute hepatitis B, Hib, and varicella. Declines in cases and deaths of invasive S pneumoniae were 34% and 25%, respectively. CONCLUSIONS The number of cases of most vaccine-preventable diseases is at an all-time low; hospitalizations and deaths have also shown striking decreases.
The Identification and Characterization of Novel N-glycan-based Biomarkers in Gastric Cancer

Background and Aims To identify and validate N-glycan biomarkers in gastric cancer (GC) and to elucidate their underlying molecular mechanism of action. Methods In total, 347 individuals, including patients with GC (gastric cancer) or atrophic gastritis and healthy controls, were randomly divided into a training group (n=287) and a retrospective validation group (n=60). Serum N-glycan profiling was achieved with DNA sequencer-assisted/fluorophore-assisted carbohydrate electrophoresis (DSA-FACE). Two diagnostic models were constructed based on the N-glycan profiles using logistic stepwise regression. The diagnostic performance of each model was assessed in retrospective, prospective (n=60), and follow-up (n=40) cohorts. Lectin blotting was performed to determine total core-fucosylation, and the expression of genes involved in core-fucosylation in GC was analyzed by reverse transcriptase-polymerase chain reaction. Results We identified at least 9 N-glycan structures (peaks) and the levels of core fucose residues and fucosyltransferase were significantly decreased in GC. Two diagnostic models, designated GCglycoA and GCglycoB, were constructed to differentiate GC from control and atrophic gastritis. The areas under the receiver operating characteristic (ROC) curves (AUC) for both GCglycoA and GCglycoB were higher than those for CEA, CA19-9, CA125 and CA72-4. Compared with CEA, CA19-9, CA125 and CA72-4, the sensitivity of GCglycoA increased 29.66%, 37.28%, 56.78% and 61.86%, respectively, and the accuracy increased 10.62%, 16.82%, 25.67% and 28.76%, respectively. For GCglycoB, the sensitivity increased 27.97%, 35.59%, 55.09% and 60.17% and the accuracy increased 21.26%, 24.64%, 31.40% and 34.30% compared with CEA, CA19-9, CA125 and CA72-4, respectively. After curative surgery, the core fucosylated peak (peak 3) and the total core fucosylated N-glycans (sumfuc) were reversed. Conclusions The results indicated that the diagnostic models based on N-glycan markers are valuable and noninvasive alternatives for identifying GC. We concluded that decreased core-fucosylation in both tissue and serum from GC patients may result from the decreased expression of fucosyltransferase.
Foam-Reinforced Elderly Human Tibia Approximates Young Human Tibia Better than Porcine Tibia

Background Because there is an insufficient supply of young human knees, an alternative is needed for evaluating anterior cruciate ligament reconstructions. The authors determined whether an elderly human tibia reinforced with foam is a better substitute for a young human tibia than a porcine tibia in this study of the tibial fixation of a soft tissue anterior cruciate ligament graft using 3 devices. Hypothesis A foam-reinforced elderly human tibia more closely approximates the performance of a young human tibia than a porcine tibia. Study Design Biomechanical study. Methods Failure mode, stiffness, yield, and slippage were determined for a double-looped tendon graft fixed with either an interference screw, WasherLoc, or tandem washers in young human tibiae, foam-reinforced tibiae from elderly humans, and porcine tibiae. Results The stiffness and yield of interference screw and WasherLoc fixation in foam-reinforced tibiae more closely approximate those in young human tibiae than in porcine tibiae. Slippage of all combinations of tibiae and fixation devices was similar. Conclusions A foam-reinforced human tibia more closely approximates the performance of a young human tibia than that of a porcine tibia in this study. Clinical Relevance Fixation devices should be tested in foam-reinforced tibiae from elderly humans rather than tibiae from large farm animals when the supply of young human knees is insufficient.
Autism spectrum disorders—A genetics review

Abstract: Autism is an etiologically and clinically heterogeneous group of disorders, diagnosed solely by the complex behavioral phenotype. On the basis of the high-heritability index, geneticists are confident that autism will be the first behavioral disorder for which the genetic basis can be well established. Although it was initially assumed that major genome-wide and candidate gene association studies would lead most directly to common autism genes, progress has been slow. Rather, most discoveries have come from studies of known genetic disorders associated with the behavioral phenotype. New technology, especially array chromosomal genomic hybridization, has both increased the identification of putative autism genes and raised to approximately 25%, the percentage of children for whom an autism-related genetic change can be identified. Incorporating clinical geneticists into the diagnostic and autism research arenas is vital to the field. Interpreting this new technology and deciphering autism's genetic montage require the skill set of the clinical geneticist including knowing how to acquire and interpret family pedigrees, how to analyze complex morphologic, neurologic, and medical phenotypes, sorting out heterogeneity, developing rational genetic models, and designing studies. The current emphasis on deciphering autism spectrum disorders has accelerated the field of neuroscience and demonstrated the necessity of multidisciplinary research that must include clinical geneticists both in the clinics and in the design and implementation of basic, clinical, and translational research.
Synthesis of N-(6-Arylbenzo[d]thiazole-2-acetamide Derivatives and Their Biological Activities: An Experimental and Computational Approach

A new series of N-(6-arylbenzo[d]thiazol-2-yl)acetamides were synthesized by C-C coupling methodology in the presence of Pd(0) using various aryl boronic pinacol ester/acids. The newly synthesized compounds were evaluated for various biological activities like antioxidant, haemolytic, antibacterial and urease inhibition. In bioassays these compounds were found to have moderate to good activities. Among the tested biological activities screened these compounds displayed the most significant activity for urease inhibition. In urease inhibition, all compounds were found more active than the standard used. The compound N-(6-(p-tolyl)benzo[d]thiazol-2-yl)acetamide was found to be the most active. To understand this urease inhibition, molecular docking studies were performed. The in silico studies showed that these acetamide derivatives bind to the non-metallic active site of the urease enzyme. Structure-activity studies revealed that H-bonding of compounds with the enzyme is important for its inhibition.