Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudo-transient continuation and differential-algebraic equations

Pseudo-transient continuation is a practical technique for globalizing the computation of steady-state solutions of nonlinear differential equations. The technique employs adaptive time-stepping to integrate an initial value problem derived from an underlying ODE or PDE boundary value problem until sufficient accuracy in the desired steady-state root is achieved to switch over to Newton’s method and gain a rapid asymptotic convergence. The existing theory for pseudo-transient continuation includes a global convergence result for differential equations written in semidiscretized method-of-lines form. However, many problems are better formulated or can only sensibly be formulated as differentialalgebraic equations (DAEs). These include systems in which some of the equations represent algebraic constraints, perhaps arising from the spatial discretization of a PDE constraint. Multirate systems, in particular, are often formulated as differential-algebraic systems to suppress fast time scales (acoustics, gravity waves, Alfven waves, near equilibrium chemical oscillations, etc.) that are irrelevant on the dynamical time scales of interest. In this paper we present a global convergence result for pseudo-transient continuation applied to DAEs of index 1, and we illustrate it with numerical experiments on model incompressible flow and reacting flow problems, in which a constraint is employed to step over acoustic waves.
Setting the Research Agenda in Automated Timetabling: The Second International Timetabling Competition

The Second International Timetabling Competition (TTC2007) opened in August 2007. Building on the success of the first competition in 2002, this sequel aimed to further develop research activity in the area of educational timetabling. The broad aim of the competition was to create better understanding between researchers and practitioners by allowing emerging techniques to be developed and tested on real-world models of timetabling problems. To support this, a primary goal was to provide researchers with models of problems faced by practitioners through incorporating a significant number of real-world constraints. Another objective of the competition was to stimulate debate within the widening timetabling research community. The competition was divided into three tracks to reflect the important variations that exist in educational timetabling within higher education. Because these formulations incorporate an increased number of “real-world” issues, it is anticipated that the competition will now set the research agenda within the field. After finishing in January 2008, final results were made available in May 2008. Along with background to the competition, the competition tracks are described here along with a brief overview of the techniques used by the competition winners.
Prospective Associations of Systemic and Urinary Choline Metabolites with Incident Type 2 Diabetes.

BACKGROUND Several compounds in the choline oxidation pathway are associated with insulin resistance and prevalent diabetes; however, prospective data are scarce.We explored the relationships between systemic and urinary choline-related metabolites and incident type 2 diabetes in an observational prospective study among Norwegian patients. METHODS We explored risk associations by logistic regression among 3621 nondiabetic individuals with suspected stable angina pectoris, of whom 3242 provided urine samples. Reclassification of patients was investigated according to continuous net reclassification improvement (NRI >0). RESULTS After median (25th to 75th percentile) follow-up of 7.5 (6.4-8.7) years, 233 patients (6.4%) were registered with incident type 2 diabetes. In models adjusted for age, sex, and fasting status, plasma betaine was inversely related to new-onset disease [odds ratio (OR) per 1 SD, 0.72; 95% CI, 0.62-0.83; P < 0.00001], whereas positive associations were observed for urine betaine (1.25; 1.09-1.43; P = 0.001), dimethylglycine (1.22; 1.06-1.40; P = 0.007), and sarcosine (1.30; 1.13-1.49; P < 0.001). The associations were maintained in a multivariable model adjusting for body mass index, hemoglobin A1c, urine albumin-to-creatinine ratio, estimated glomerular filtration rate, C-reactive protein, HDL cholesterol, and medications. Plasma betaine and urine sarcosine, the indices most strongly related to incident type 2 diabetes, improved reclassification [NRI >0 (95% CI) 0.33 (0.19-0.47) and 0.16 (0.01-0.31), respectively] and showed good within-person reproducibility. CONCLUSIONS Systemic and urinary concentrations of several choline metabolites were associated with risk of incident type 2 diabetes, and relevant biomarkers may improve risk prediction.
Abnormal chromatographic patterns of porphyrins in urine.

Urine is the most frequent specimen used in the initial evaluation of adult patients who present with photosensitivity. When urine porphyrins are abnormal, characterization of the chromatogram is facilitated by calculation of uroporphyrin-to-heptacarboxylate porphyrin (uro/hepta) and uroporphyrin-to-isocoproporphyrin (uro/iso) ratios. The most frequent abnormal pattern, and that most consistent with porphyria cutanea tarda (PCT), is an uro/hepta ratio < or =2.0 and an uro/iso ratio < or =18. When the uro/hepta or uro/iso ratios are less consistent with PCT, other less common porphyrin disorders should be considered. These include variegate porphyria, coproporphyria with manifestations of photosensitivity only, adult onset congenital porphyria, mixed porphyrias, and other less frequent porphyrin disorders. After initial evaluation, the diagnosis should ideally be confirmed by additional testing of blood and fecal specimens. Most attacks of the acute porphyrias are associated with a uro/hepta ratio >4, and can be confirmed by an elevated urine porphobilinogen concentration.
Incremental Value of Plaque Enhancement in Patients with Moderate or Severe Basilar Artery Stenosis: 3.0 T High-Resolution Magnetic Resonance Study

Aim To investigate the clinical relevance of plaque's morphological characteristics and distribution pattern using 3.0 T high-resolution magnetic resonance imaging (HRMRI) in patients with moderate or severe basilar artery (BA) atherosclerosis stenosis. Materials and Methods Fifty-seven patients (33 symptomatic patients and 24 asymptomatic patients) were recruited for 3.0 T HRMRI scan; all of them had >50% stenosis on the BA. The intraplaque hemorrhage (IPH), contrast-enhancement pattern, and distribution of BA plaques were compared between the symptomatic and asymptomatic groups. Factors potentially associated with posterior ischemic stroke were calculated by multivariate analyses. Results Enhancement of BA plaque was more frequently observed in symptomatic than in asymptomatic patients (27/33, 81.8% versus 11/24, 45.8%; p < 0.01). In multivariate regression analysis, plaque enhancement (OR = 7.193; 95% CI: 1.880–27.517; p = 0.004) and smoking (OR = 4.402; 95% CI: 2.218–15.909; p = 0.024) were found to be independent risk factors of posterior ischemic events in patients with BA stenosis >50%. Plaques were mainly distributed at the ventral site (39.3%) or involved more than two arcs (21.2%) in the symptomatic group but were mainly distributed at left (33.3%) and right (25.0%) sites in the asymptomatic group.
Circulating levels of sclerostin but not DKK1 associate with laboratory parameters of CKD-MBD

Introduction Mounting evidence indicates that a disturbed Wnt–β-catenin signaling may be involved in the pathogenesis of chronic kidney disease-mineral and bone and mineral disorder (CKD-MBD). Data on the impact of CKD on circulating levels of the Wnt antagonists sclerostin and Dickkopf related protein 1 (DKK1) and the relationship with laboratory parameters of CKD-MBD are incomplete. Methods We analyzed serum sclerostin and DKK1 in 308 patients across the stages of chronic kidney disease (kDOQI stage 1–2 n = 41; CKD stage 3 n = 54; CKD stage 4–5 n = 54; hemodialysis n = 100; peritoneal dialysis n = 59) as well as in 49 healthy controls. We investigated associations with demographics, renal function, parameters of mineral metabolism including 25(OH) vitamin D, 1,25(OH)2 vitamin D, biointact fibroblast growth factor 23 (FGF23), and parathyroid hormone (PTH), and bone turnover markers. Results Serum sclerostin, but not DKK1, increases in more advanced stages of CKD and associates with PTH, phosphate, and 1,25(OH)2 vitamin D concentrations. Bone turnover markers are highest in hemodialysis patients presenting the combination of high PTH with low sclerostin level. Serum DKK1 levels are lower in CKD patients than in controls and are not associated with laboratory parameters of mineral metabolism. Interestingly, a direct association between DKK1 and platelet count was observed. Conclusion In CKD, serum levels of the Wnt inhibitors DKK1 and sclerostin are unrelated, indicating different sites of origin and/ or different regulatory mechanisms. Sclerostin, as opposed to DKK1, may qualify as a biomarker of CKD-MBD, particularly in dialysis patients. DKK1 serum levels, remarkably, correlate almost uniquely with blood platelet counts.
Maintaining cooperation in complex social dilemmas using deep reinforcement learning

Social dilemmas are situations where individuals face a temptation to increase their payoffs at a cost to total welfare. Building artificially intelligent agents that achieve good outcomes in these situations is important because many real world interactions include a tension between selfish interests and the welfare of others. We show how to modify modern reinforcement learning methods to construct agents that act in ways that are simple to understand, nice (begin by cooperating), provokable (try to avoid being exploited), and forgiving (try to return to mutual cooperation). We show both theoretically and experimentally that such agents can maintain cooperation in Markov social dilemmas. Our construction does not require training methods beyond a modification of self-play, thus if an environment is such that good strategies can be constructed in the zero-sum case (eg. Atari) then we can construct agents that solve social dilemmas in this environment.
Exercise and Mitochondrial Dynamics: Keeping in Shape with ROS and AMPK

Exercise is a robust stimulus for mitochondrial adaptations in skeletal muscle which consequently plays a central role in enhancing metabolic health. Despite this, the precise molecular events that underpin these beneficial effects remain elusive. In this review, we discuss molecular signals generated during exercise leading to altered mitochondrial morphology and dynamics. In particular, we focus on the interdependence between reactive oxygen species (ROS) and redox homeostasis, the sensing of cellular bioenergetic status via 5’ adenosine monophosphate (AMP)-activated protein kinase (AMPK), and the regulation of mitochondrial fission and fusion. Precisely how exercise regulates the network of these responses and their effects on mitochondrial dynamics is not fully understood at present. We highlight the limitations that exist with the techniques currently available, and discuss novel molecular tools to potentially advance the fields of redox biology and mitochondrial bioenergetics. Ultimately, a greater understanding of these processes may lead to novel mitochondria-targeted therapeutic strategies to augment or mimic exercise in order to attenuate or reverse pathophysiology.
A greedy approach to sparse canonical correlation analysis

We consider the problem of sparse canonical correlation analysis (CCA), i.e., the search for two linear combinations, one for each multivariate, that yield maximum correlation using a specified number of variables. We propose an efficient numerical approximation based on a direct greedy approach which bounds the correlation at each stage. The method is specifically designed to cope with large data sets and its computational complexity depends only on the sparsity levels. We analyze the algorithm's performance through the tradeoff between correlation and parsimony. The results of numerical simulation suggest that a significant portion of the correlation may be captured using a relatively small number of variables. In addition, we examine the use of sparse CCA as a regularization method when the number of available samples is small compared to the dimensions of the multivariates.
Multi-module learning system for behavior acquisition in multi-agent environment

The conventional reinforcement learning approaches have difficulties in handling the policy alternation of the opponents because it may cause dynamic changes of state transition probabilities of which stability is necessary for the learning to converge. A multiple learning module approach would provide one solution for this problem. If we can assign multiple learning modules to different situations in which each of the module can regard the state transition probabilities as consistent, then the system would provide reasonable performance. This paper presents a method of multi-module reinforcement learning in a multi-agent environment, by which the learning agent can adapt its behaviors to the situations as results of the other agent's behaviors. We show a preliminary result of a simple soccer situation.
The Risk and Intensity of Sperm Ejection in Female Birds

The way females utilize the gametes of different males has important consequences for sexual selection, sexual conflict, and intersexual coevolution in natural populations. However, patterns of sperm utilization by females are difficult to demonstrate, and their functional significance remains unclear. Here, we experimentally study sperm ejection in the fowl Gallus gallus domesticus, where females eject preferentially the sperm of socially subordinate males. We study two measures of sperm ejection, (i) the probability that an ejaculate is ejected (“risk”) and (ii) the proportion of semen ejected (“intensity”), and show that both measures are strongly nonrandom with respect to characteristics of the ejaculate, the male, and the female. Sperm ejection neutralized on average 80% of an ejaculate, and while larger ejaculates suffered a higher ejection risk, smaller ejaculates suffered more intense ejection. After controlling for ejaculate volume, we found socially subdominant males suffered higher ejection intensity. After controlling for male and ejaculate effects, we found ejection risk increased and intensity declined as females mated with successive males. Collectively, these results reveal that sperm ejection risk and intensity are at least partly actively caused by female behavior and generate independent selective pressures on male and ejaculate phenotypes.
Host race or species? Allozyme characterization of the ‘flowering dogwood fly’, a member of the Rhagoletis pomonella complex

The term ‘flowering dogwood fly’ has been used in the literature for a poorly understood member of the Rhagoletis pomonella sibling species complex infesting the fruits of flowering dogwood (Cornus florida). Electrophoretic analysis of 17 allozyme loci in 21 populations reveals significant frequency differences between the flowering dogwood fly and its closest relative the apple maggot fly, R. pomonella, and between it and the somewhat more distant ‘sparkleberry fly’. Frequency differences between the flowering dogwood fly and R. pomonella are as great as 0.817 in the north, but are less in the south, with a maximum difference at one site of only 0.328. No fixed allozyme differences distinguish the flowering dogwood fly anywhere; its only consistent, unique feature is the highest frequency of Aat-259 in the pomonella species group. Population structure of the flowering dogwood fly is moderate with FST=0.084 and fewer latitudinal clines than R. pomonella. The conclusion from the allozyme and life history data is that the flowering dogwood fly is a species, although some interspecific gene flow may be occurring. Additional issues discussed include how to estimate interspecific gene flow when genetic markers are under divergent selection, the appropriate species concept when there is gene flow, and the future of the flowering dogwood fly in the face of the dogwood anthracnose epidemic. The possible utility of a new species concept for phytophagous insects, using as a criterion the capacity of a host race to regenerate the ancestral population, is also discussed.
Comparing the Duration of the Analgesic Effects of Intravenous and Rectal Acetaminophen Following Tonsillectomy in Children

Background: Postoperative pain control (especially, after adenotonsillectomy) has a very important effect on recovery time, hospitalization duration, hemodynamic disorders, bleeding, nausea, vomiting and medical costs. Objectives: The aim of this study was to investigate and compare the effects of intravenous and rectal acetaminophen on controlling post-adenotonsillectomy pain in children, and duration of their analgesic effects. Patients and Methods: In this randomized double-blinded clinical trial, 96 children aged 4 - 10 years old with ASA physical status I or II who were candidates for adenotonsillectomy surgery in Amir-al-Momenin Hospital, Rasht, Iran were entered into the study and randomly divided into two equal groups. Anesthesia in both groups was induced injecting fentanyl-thiopental and at racurium; afterwards is of lurane was used to maintain anesthesia. After anesthesia induction, one group received intravenous and the other one, rectal acetaminophen, and were later compared based on CHIPPS criteria. Results: Data analysis indicated a significant relationship between reduction of postoperative pain and the use of intravenous or rectal acetaminophen (P = 0.0001); in group receiving IV acetaminophen, only 10.4% of patients had no pain whereas in group receiving rectal acetaminophen, this number reached 43.8%. Also, on 4 and 6 hour time intervals, pain in rectal acetaminophen receiving group was less than that in IV acetaminophen receiving group (P < 0.05). Demand for additional analgesic medication in rectal acetaminophen receiving group was less than that in IV group (P = 0.0001). Conclusions: Post-operative pain in rectal acetaminophen group was less than that in intravenous acetaminophen group, and rectal acetaminophen group demanded their first additional analgesic medication later.
Anti‐EGFR Monoclonal Antibodies for Treatment of Colorectal Cancers: Development of Cetuximab and Panitumumab

Over the last decade, anti‐epidermal growth factor receptor (EGFR) monoclonal antibodies (mAbs) have been firmly established as essential drugs for the treatment of metastatic colorectal cancer (CRC). Cetuximab and panitumumab have been approved by American and European drug agencies. This review aims at exploring the main outcomes of clinical studies performed during their clinical development, from phase I to III trials, and hence at giving a comprehensive review of the scientific rational and up‐to‐date evidence sustaining the use of these drugs. Many areas are still under active investigation such as administration schedules, their efficacy in comparison with bevacizumab, their role in adjuvant therapy, molecular predictors, and management of side effects.
Mechanisms for collaboration: A design and evaluation framework for multi-user interfaces

Multi-user interfaces are said to provide “natural” interaction in supporting collaboration, compared to individual and noncolocated technologies. We identify three mechanisms accounting for the success of such interfaces: high awareness of others' actions and intentions, high control over the interface, and high availability of background information. We challenge the idea that interaction over such interfaces is necessarily “natural” and argue that everyday interaction involves constraints on awareness, control, and availability. These constraints help people interact more smoothly. We draw from social developmental psychology to characterize the design of multi-user interfaces in terms of how constraints on these mechanisms can be best used to promote collaboration. We use this framework of mechanisms and constraints to explain the successes and failures of existing designs, then apply it to three case studies of design, and finally derive from them a set of questions to consider when designing and analysing multi-user interfaces for collaboration.
Phase IIa Clinical Trial of Trans-1-Amino-3-18F-Fluoro-Cyclobutane Carboxylic Acid in Metastatic Prostate Cancer

Objective(s): We performed a phase IIa clinical trial of trans-1-amino-3-18F-fluoro-cyclobutane carboxylic acid (anti-18F-FACBC), a synthetic amino acid analog for PET, in patients with metastatic prostate cancer. Methods: The study subjects consisted of 10 untreated prostate cancer patients having lymph node and/or bone metastasis. Five patients underwent whole-body PET 5 and 30 min after intravenous injection of anti-18F-FACBC. The other five patients underwent 60 min dynamic PET of the pelvis. Safety assessment was performed before and 24 h after injection. PET/CT images were assessed visually, and time courses of anti-18F-FACBC uptake were evaluated from dynamic imaging. Results: Two mild adverse events were observed and resolved without treatment. All 10 patients showed increased accumulation of anti-18F-FACBC in the primary prostate lesion. CT revealed five enlarged lymph nodes indicating metastasis, and all showed increased uptake. Additionally, anti-18F-FACBC PET delineated unenlarged lymph nodes as hot spots. Anti-18F-FACBC PET demonstrated metastatic bone lesions, similar to conventional imaging. In one of two patients with lung metastasis, some lesions showed increased uptake. Regarding the time course, increased uptake of anti-18F-FACBC in the lesion was demonstrated immediately after injection, followed by gradual washout. Conclusion: The results of this phase IIa clinical trial indicated the safety of anti-18F-FACBC in patients with prostate cancer and the potential of anti-18F-FACBC PET to delineate primary prostate lesions and metastatic lesions. This clinical trial was registered as JapicCTI-101326.