Miracle-dz/UniFAR-FTUs huggingface dataset:
A survey of genetic improvement search spaces

Genetic Improvement (GI) uses automated search to improve existing software. Most GI work has focused on empirical studies that successfully apply GI to improve software's running time, fix bugs, add new features, etc. There has been little research into why GI has been so successful. For example, genetic programming has been the most commonly applied search algorithm in GI. Is genetic programming the best choice for GI? Initial attempts to answer this question have explored GI's mutation search space. This paper summarises the work published on this question to date.
Deriving knowledge from local optima networks for evolutionary optimization in inventory routing problem

This paper proposes an evolutionary approach to solve the Inventory Routing Problem (IRP) using knowledge extracted from Local Optima Networks (LONs). Solving the IRP involves a simultaneous optimization of the transportation routes and the inventory levels. One of important steps in solving IRP is determining the optimal route of each supplying vehicle for each date of the planning horizon. As the transportation cost is based only on the distance matrix, constant in time and independent of the supplying vehicle, this step consists of solving a TSP problem on a certain subset of facilities. This paper aims at improving solving IRP by deriving some knowledge on the full TSP problem and reusing it in solving TSP sub-problems. Experiments carried out on popular benchmark IRP instances prove that using the knowledge derived from LONs increases the efficiency of the evolutionary algorithm and the proposed approach outperforms simple evolutionary algorithms in solving IRP.
A Water-saving Irrigation Decision-making Model for Greenhouse Tomatoes based on Genetic Optimization T-S Fuzzy Neural Network

In order to improve the utilization of irrigation water resources of greenhouse tomatoes, a water-saving irrigation decision-making model based on genetic optimization T-S fuzzy neural network is proposed in this paper. The main work are as follows: Firstly, the traditional genetic algorithm is optimized by introducing the constraint operator and update operator of the Krill herd (KH) algorithm. Secondly, the weights and thresholds of T-S fuzzy neural network are optimized by using the improved genetic algorithm. Finally, on the basis of the real data set, the genetic optimization T-S fuzzy neural network is used to simulate and predict the irrigation volume for greenhouse tomatoes. The performance of the genetic algorithm improved T-S fuzzy neural network (GA-TSFNN), the traditional T-S fuzzy neural network algorithm (TSFNN), BP neural network algorithm(BPNN) and the genetic algorithm improved BP neural network algorithm (GA-BPNN) is compared by simulation. The simulation experiment results show that compared with the TSFNN, BPNN and the GA-BPNN, the error of the GA-TSFNN between the predicted value and the actual value of
Evolving recurrent neural networks for emergent communication

Recent research showed that deep neural networks can be trained to create shared languages to communicate and cooperate with each other. These approaches used fixed, handcrafted network architectures which were trained with reinforcement learning. We extend this approach by using neuroevolution to automate network design and find network weights of communicating agents. We show that neuroevolution is a viable approach for training agents to develop novel languages so as to communicate amongst themselves.
A tabu search-based memetic algorithm for the multi-objective flexible job shop scheduling problem

In this paper we propose a tabu search-based memetic algorithm (TSM) for the multi-objective flexible job shop scheduling problem (FJSSP), with the objectives to minimize the makespan, the total workload and the critical workload. The problem is addressed in a Pareto manner, which targets a set of Pareto optimal solutions. The novelty of our method lies in the use of tabu search (TS) as the local search method as well as a mutation operator and the use of the hypervolume indicator to avoid stagnation by increasing the flow of individuals in the local search. To the best of our knowledge, the use of TS in the context of multi-objective FJSSP has not been reported so far. We apply our algorithm on well known test instances and compare our results to state-of-the art algorithms. The results show that our approach yields competitive solutions in 6 of the 10 instances against two of their algorithms proving that the use of TS as a local search method can provide competitive results.
Method Variance and Marker Variables: A Review and Comprehensive CFA Marker Technique

Lindell and Whitney introduced a partial correlation technique, now referred to as the correlational marker technique, for controlling method variance using a marker variable that is theoretically unrelated to substantive variables in a study. This article (a) first reviews their specific analysis plan, and then (b) reviews empirical studies that have followed all or part of this plan. The authors also (c) describe a structural equation method that has been applied to the analysis of marker variables and (d) review empirical studies using this analytical approach. Next, the authors (e) develop a comprehensive confirmatory factor analysis (CFA) marker technique analysis plan, and (f) demonstrate this plan with an empirical example. Finally, the authors (g) describe how marker variables can be examined along with other method variance processes, (h) discuss the important role of theory in the critical step of selecting marker variables, and (i) discuss assumptions and limitations of the Comprehensive CFA Marker Technique.
PbI2-MoS2 Heterojunction: Van der Waals Epitaxial Growth and Energy Band Alignment.

Van der Waals (vdW) epitaxy offers a promising strategy without lattice and processing constrains to prepare atomically clean and electronically sharp interfaces for fundamental studies and electronic device demonstrations. Herein, PbI2 was thermally deposited at high vacuum conditions onto CVD-grown monolayer MoS2 flakes in a vdW epitaxial manner to form 3D-2D heterojunctions, which is promising for vdW epitaxial growth of perovskite films. XRD, XPS, Raman, and AFM measurements reveal the structural properties of the high-quality heterojunctions. Photoluminescence (PL) measurements reveal that the PL emissions from the bottom MoS2 flakes are greatly quenched compared to their as-grown counterparts, which can be ascribed to the band alignment-induced distinct interfacial charge transfer behaviors. Strong interlayer excitons can be detected at PbI2/MoS2 interface, indicating an effective type-II band alignment, which can be further confirmed by UPS measurements. The results provide a new material platform for the application of the vdW heterojunctions in electronic and optoelectronic devices.
Ease of Use and Usefulness of Medication Reminder Apps among Rural Aging Adults

ABSTRACT Older adults manage multiple medications for chronic disease and those living in rural areas are impacted by health care disparities due to health provider shortages and fewer pharmacies. The use of downloadable medication reminder apps on smartphones may serve as a strategy for medication self-management of chronic diseases. In this feasibility study, thirteen rural older adult participants downloaded Medisafe® and used the app to manage their daily medications. The community-dwelling aging adults in this pilot perceived the Medisafe® as not difficult to use, useful for medication tracking and providing reminders for the self-management of multiple medications.
Comparison of the impact factors of subscription access and open access orthopedics and sports medicine journals in the SCImago database.

OBJECTIVES This study aims to compare the annual impact factors (IFs) for the period 1999-2017 and the tri-annual IFs in 2011, 2014 and 2017 of the subscription access (SA) and open access (OA) journals published in the field of orthopedics, traumatology and sports medicine according to the SCImago Journal Rank (SJR). MATERIAL AND METHODS All data for this study were obtained from the SCImago Journal & Country Rank database. We compared the change in the mean annual IFs of 197 SA journals with 52 OA journals in the field of orthopedics and sports medicine for the period between 1999 and 2017. In addition, we determined and compared the changes in the mean tri-annual IFs of these journals in 2011, 2014 and 2017. The mean publication fee values of the OA journals as well as the correlation between the three-year IFs of the year 2017 and the publication fee values were evaluated. RESULTS From 1999 to 2017, the mean IF of SA journals increased 0.47-fold to 0.69, while the mean IF of the OA journals increased 0.85-fold to 0.63. Significant positive correlation was observed between the tri-annual IF and publication fee of OA journals in 2017 (r=0.458, p=0.001). CONCLUSION We can predict that the mean IFs of OA journals in the field of orthopedics and sports medicine will reach the mean IFs of SA journals after several years. Choosing OA journals becomes advantageous when the desire for a higher number of citations is the most important factor.
Computer-based cognitive training for older adults: Determinants of adherence

The possibilities of computer-based cognitive training (CCT) in postponing the onset of dementia are currently unclear, but promising. Our aim is to investigate older adults´ adherence to a long-term CCT program, and which participant characteristics are associated with adherence to the CCT. This study was part of the Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER). Participants were 60-77-year-old individuals with increased dementia risk, recruited from previous population-based studies. The participants included in this study (n = 631) had been randomized to receive a multi-domain lifestyle intervention, including CCT. The measure of adherence was the number of completed CCT sessions (max = 144) as continuous measure. Due to a substantial proportion of participants with 0 sessions, the zero inflated negative binomial regression analyses were used to enable assessment of both predictors of starting the training and predictors of completing a higher number of training sessions. Several cognitive, demographic, lifestyle, and health-related variables were examined as potential predictors of adherence to CCT. Altogether, 63% of the participants participated in the CCT at least once, 20% completed at least half of the training, and 12% completed all sessions. Previous experience with computers, being married or cohabiting, better memory performance, and positive expectations toward the study predicted greater odds for starting CCT. Previous computer use was the only factor associated with a greater number of training sessions completed. Our study shows that there is a large variation in adherence to a long-lasting CCT among older adults with an increased risk of dementia. The results indicate that encouraging computer use, and taking into account the level of cognitive functioning, may help boost adherence to CCT.
Effects of White Potatoes Consumed With Eggs on Satiety, Food Intake, and Glycemic Response in Children and Adolescents

Abstract Objective: Short-term studies in adults have shown that white potatoes increase satiety and suppress food intake (FI) compared with several other carbohydrate-containing foods; however, studies are limited in children. The objective was to compare the effects of white potatoes in mixed meals on satiety, FI, and glycemic response in 9-14-year-old children and adolescents. Methods: Using a within-subject, repeated-measures design, 21 children completed five counter-balanced test sessions. After an overnight fast, children consumed one of four isocaloric treatment meals (450 kcal) of French fries, mashed potatoes, or white beans served with a fixed portion of egg omelet (30 g of protein), a control meal with cereal, milk, and bread, or continued to fast (i.e., meal skipping). Subjective appetite was measured using visual analogue scales. FI at an ad libitum pizza meal at 180 min and rest of day diet record were used to measure lunch FI and rest of day energy intake, respectively. Total daily energy intake was calculated by adding the energy intake from the treatment meal, the ad libitum pizza lunch, and rest of day food record. Capillary blood samples were collected to assess glycemic response over 180 min. Results: Change from baseline subjective average appetite scores were lower after mashed potatoes compared with all other treatment conditions (p < 0.001), and higher after French fries compared with white beans (p = 0.04). Lunch FI (kcal) was significantly lower (p < 0.001) after French fries (1010±73) and mashed potatoes (1039±74) compared with the control meal (1257±92) and meal skipping (1235±74). Total daily energy intake (kcal) was lower after French fries compared with the control meal (2228±141 vs. 2624±137; p = 0.04). Change from baseline blood glucose was lower after white beans and French fries compared with mashed potatoes (p < 0.05) and the control meal (p < 0.001). Conclusion: In conclusion, white potatoes with eggs increased satiety, decreased short-term FI, and resulted in similar energy intakes compared with meal skipping.
The domain architecture of the protozoan protein J-DNA–binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity

J-DNA–binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-d-glucosyl-hydroxymethyluracil), an epigenetic modification of thymidine (T) confined to pathogenic protozoa such as Trypanosoma and Leishmania. JBP1 has two known functional domains: an N-terminal T hydroxylase (TH) homologous to the 5-methylcytosine hydroxylase domain in TET proteins and a J-DNA–binding domain (JDBD) that resides in the middle of JBP1. Here, we show that removing JDBD from JBP1 results in a soluble protein (Δ-JDBD) with the N- and C-terminal regions tightly associated together in a well-ordered structure. We found that this Δ-JDBD domain retains TH activity in vitro but displays a 15-fold lower apparent rate of hydroxylation compared with JBP1. Small-angle X-ray scattering (SAXS) experiments on JBP1 and JDBD in the presence or absence of J-DNA and on Δ-JDBD enabled us to generate low-resolution three-dimensional models. We conclude that Δ-JDBD, and not the N-terminal region of JBP1 alone, is a distinct folding unit. Our SAXS-based model supports the notion that binding of JDBD specifically to J-DNA can facilitate T hydroxylation 12–14 bp downstream on the complementary strand of the J-recognition site. We postulate that insertion of the JDBD module into the Δ-JDBD scaffold during evolution provided a mechanism that synergized J recognition and T hydroxylation, ensuring inheritance of base J in specific sequence patterns following DNA replication in kinetoplastid parasites.
An upper bound computational model for investigation of fusion effects on adjacent segment biomechanics of the lumbar spine

Abstract Prediction of the biomechanical effects of fusion surgery on adjacent segments is a challenge in computational biomechanics of the spine. In this study, a two-segment L3-L4-L5 computational model was developed to simulate the effects of spinal fusion on adjacent segment biomechanical responses under a follower load condition. The interaction between the degenerative segment (L4-5) and the adjacent segment (L3-4) was simulated using an equivalent follower spring. The spring stiffness was calibrated using a rigid fusion of a completely degenerated disc model at the L4-5 level, resulting in an upper bound response at the adjacent (L3-4) segment. The obtained upper bound equivalent follower spring was used to simulate the upper bound biomechanical responses of fusion of the disc with different degeneration grades. It was predicted that as the disc degeneration grade at the degenerative segment decreased, the effect on the adjacent segment responses decreased accordingly after fusion. The data indicated that the upper bound computational model can be a useful computational tool for evaluation of the interaction between segments and for investigation of the biomechanical mechanisms of adjacent segment degeneration after fusion.
Diagnosing type 2 myocardial infarction in clinical routine. A validation study

Abstract Objective. Since 2010, myocardial infarction (MI) patients reported to the Swedish registry for MI (SWEDEHEART) are routinely classified into MI subtypes. The registry has been used to study the type 2 MI population but the MI-classification in the registry has not previously been validated. The aim of this study was to validate the type 2 MI classification in the registry. Design. A total of 772 patients diagnosed with MI in 2011 and reported to the SWEDEHEART registry were included in the study. All patients were retrospectively classified into MI type 1–5 or myocardial injury by independent reviewers strictly adhering to The Third Universal Definition of MI. This gold standard classification was compared with the classification in the registry. Results. Forty-eight (6.2%) patients were classified as type 2 MI in the registry compared with 93 (12.0%) according to the gold standard classification. A type 2 MI diagnosis was confirmed in 30 out of the 48 type 2 MI patients in the registry (PPV: 62.5%). There was a moderate rate of agreement (κ: 0.43) between the gold standard classification and the classification in SWEDEHEART in deciding a type 2 MI diagnosis. Conclusion. The SWEDEHEART registry agreed moderately with the gold standard in classifying patients with type 2 MI diagnosis. Thus, studies on patients with type 2 MI in the registry should be interpreted with caution. Since the prevalence of type 2 MI is substantially underestimated in SWEDEHEART, the registry should not be used to study the prevalence of type 2 MI.
Traffic management for tcp/ip over asynchronous transfer mode (atm) networks

The problem of traffic management has been widely recognized as critical to the development of an operational Internet. The goal of traffic management is to efficiently allocate network resources including buffers and bandwidth, and provide the negotiated QoS guarantees to users. This thesis studies the problem of traffic management for the Transmission Control Protocol/Internet Protocol (TCP/IP) suite over Asynchronous Transfer Mode (ATM) networks. The ATM Unspecified Bit Rate (UBR), Guaranteed Frame Rate (GFR) and Available Bit Rate (ABR) service categories are intended for data applications. The main focus of this research is to analyze and improve the performance of TCP over UBR, GFR and ABR. This thesis proposes buffer management algorithms for the UBR and GFR services, and a feedback control algorithm for the ABR service. A buffer management scheme called Selective Drop is presented for the UBR service. An analysis of the relative performance of three TCP flavors—slow start and congestion avoidance (Vanilla), fast retransmit and recovery (Reno), and selective acknowledgments (SACK), with three buffer management policies—Tail Drop, Early Packet Discard (EPD), and Selective Drop, is then presented for LAN, WAN and satellite networks. The results show that for LANs, TCP performance over UBR can be improved by using intelligent buffer management policies. As the propagation delay increases, the TCP policies become more significant than buffer management—SACK performs the best while Reno performs the worst. In the presence of high priority variable bit rate traffic, guaranteed rate can be provided to the UBR service to prevent bandwidth starvation. This research proposes the Differential Fair Buffer Allocation (DFBA) scheme for the GFR service. DFBA provides minimum rate guarantees to VCs carrying TCP traffic by allocating buffers in proportion to the guaranteed rates and probabilistically dropping packets. Finally, the thesis proposes a virtual source virtual destination scheme for ABR that can be used to limit the buffer requirements of terrestrial networks connected to long delay satellite networks. The experiments and analysis in this research provide valuable insight into designing traffic management solutions for broadband networks.
Pembrolizumab After Completion of Locally Ablative Therapy for Oligometastatic Non-Small Cell Lung Cancer: A Phase 2 Trial.

Importance Patients with oligometastatic non-small cell lung cancer (NSCLC) may benefit from locally ablative therapy (LAT) such as surgery or stereotactic radiotherapy. Prior studies were conducted before the advent of immunotherapy, and a strong biological rationale for the use of immunotherapy exists in a minimal residual disease state. Objective To evaluate whether the addition of pembrolizumab after LAT improves outcomes for patients with oligometastatic NSCLC. Design, Setting, and Participants This single-arm phase 2 trial of pembrolizumab therapy was performed from February 1, 2015, through September 30, 2017, at an academic referral cancer center. The 51 eligible patients enrolled had oligometastatic NSCLC (≤4 metastatic sites) and had completed LAT to all known sites of disease. Data were analyzed from February 1, 2015, to August 23, 2018. Interventions Within 4 to 12 weeks of completing LAT, patients began intravenous pembrolizumab therapy, 200 mg every 21 days, for 8 cycles, with provision to continue to 16 cycles in the absence of progressive disease or untoward toxic effects. Main Outcomes and Measures The 2 primary efficacy end points were progression-free survival (PFS) from the start of LAT (PFS-L), which preceded enrollment in the trial, and PFS from the start of pembrolizumab therapy (PFS-P). The study was powered for comparison with historical data on the first efficacy end point. Secondary outcomes included overall survival, safety, and quality of life as measured by the Functional Assessment of Cancer Therapy-Lung instrument. Results Of 51 patients enrolled, 45 (24 men [53%]; median age, 64 years [range, 46-82 years]) received pembrolizumab. At the time of analysis, 24 patients had progressive disease or had died. Median PFS-L was 19.1 months (95% CI, 9.4-28.7 months), significantly greater than the historical median of 6.6 months (P = .005). Median PFS-P was 18.7 months (95% CI, 10.1-27.1 months). Eleven patients died. Overall mean (SE) survival rate at 12 months was 90.9% (4.3%); at 24 months, 77.5% (6.7%). Neither programmed death ligand 1 expression nor CD8 T-cell tumor infiltration was associated with PFS-L. Pembrolizumab after LAT yielded no new safety signals and no reduction in quality of life. Conclusions and Relevance Pembrolizumab after LAT for oligometastatic NSCLC appears to improve PFS with no reduction in quality of life. Trial Registration ClinicalTrials.gov identifier: NCT02316002.