Miracle-dz/UniFAR-FTUs huggingface dataset:
Directional Sparsity in Optimal Control of Partial Differential Equations

We study optimal control problems in which controls with certain sparsity patterns are preferred. For time-dependent problems the approach can be used to find locations for control devices that allow controlling the system in an optimal way over the entire time interval. The approach uses a nondifferentiable cost functional to implement the sparsity requirements; additionally, bound constraints for the optimal controls can be included. We study the resulting problem in appropriate function spaces and present two solution methods of Newton type, based on different formulations of the optimality system. Using elliptic and parabolic test problems we research the sparsity properties of the optimal controls and analyze the behavior of the proposed solution algorithms.
Reuse-aware modulo scheduling for stream processors

This paper presents reuse-aware modulo scheduling to maximizing stream reuse and improving concurrency for stream-level loops running on stream processors. The novelty lies in the development of a new representation for an unrolled and software-pipelined stream-level loop using a set of reuse equations, resulting in simultaneous optimization of two performance objectives for the loop, reuse and concurrency, in a unified framework. We have implemented this work in the compiler developed for our 64-bit FT64 stream processor. Our experimental results obtained on FT64 and by simulation using nine representative stream applications demonstrate the effectiveness of the proposed approach.
Endurance, Refuge, and Reemergence of Dengue Virus Type 2, Puerto Rico, 1986–2007

To study the evolution of dengue virus (DENV) serotype 2 in Puerto Rico, we examined the genetic composition and diversity of 160 DENV-2 genomes obtained through 22 consecutive years of sampling. A clade replacement took place in 1994–1997 during a period of high incidence of autochthonous DENV-2 and frequent, short-lived reintroductions of foreign DENV-2. This unique clade replacement was complete just before DENV-3 emerged. By temporally and geographically defining DENV-2 lineages, we describe a refuge of this virus through 4 years of low genome diversity. Our analyses may explain the long-term endurance of DENV-2 despite great epidemiologic changes in disease incidence and serotype distribution.
Busemann Points of Artin Groups of dihedral Type

We study the horofunction boundary of an Artin group of dihedral type with its word metric coming from either the usual Artin generators or the dual generators. In both cases, we determine the horoboundary and say which points are Busemann points, that is, the limits of geodesic rays. In the case of the dual generators, it turns out that all boundary points are Busemann points, but this is not true for the Artin generators. We also characterize the geodesics with respect to the dual generators, which allows us to calculate the associated geodesic growth series.
Maize Varieties Released in Different Eras Have Similar Root Length Density Distributions in the Soil, Which Are Negatively Correlated with Local Concentrations of Soil Mineral Nitrogen

Larger, and deeper, root systems of new maize varieties, compared to older varieties, are thought to have enabled improved acquisition of soil resources and, consequently, greater grain yields. To compare the spatial distributions of the root systems of new and old maize varieties and their relationships with spatial variations in soil concentrations of available nitrogen (N), phosphorus (P) and potassium (K), two years of field experiments were performed using six Chinese maize varieties released in different eras. Vertical distributions of roots, and available N, P and K in the 0–60 cm soil profile were determined in excavated soil monoliths at silking and maturity. The results demonstrated that new maize varieties had larger root dry weight, higher grain yield and greater nutrient accumulation than older varieties. All varieties had similar total root length and vertical root distribution at silking, but newer varieties maintained greater total root length and had more roots in the 30–60 cm soil layers at maturity. The spatial variation of soil mineral N (Nmin) in each soil horizon was larger than that of Olsen-P and ammonium-acetate-extractable K, and was inversely correlated with root length density (RLD), especially in the 0–20 cm soil layer. It was concluded that greater acquisition of mineral nutrients and higher yields of newer varieties were associated with greater total root length at maturity. The negative relationship between RLD and soil Nmin at harvest for all varieties suggests the importance of the spatial distribution of the root system for N uptake by maize.
Effects of acute supine rest on mid‐thigh cross‐sectional area as measured by computed tomography

The loss of hydrostatic pressure that occurs as a person moves from the standing to the supine position causes a fluid redistribution that may confound the measurement of thigh cross‐sectional area (CSA) if data are obtained while tissue fluid content is in flux. To determine the effects of changing postural position on thigh tissue CSA, mid‐thigh axial scans of 13 older women were obtained at 5, 10 and 15 min of supine rest using computed tomography (CT). Scans were analysed for changes in CSA of subcutaneous fat (SF), low density muscle (LDM) and normal density muscle (NDM). A significant decrease from baseline was found in the CSA of NDM at 15 min [2.3 ± 0.8 cm2 (±SE), 1.6%, P<0.05], with no change in LDM or SF CSA among any of the time intervals. The results of the current study suggest that potential measurement error can be minimized when baseline and follow‐up CT‐derived images of mid‐thigh CSA are obtained within the first 10 min the subject assumes the supine position and that the CSA of NDM and LDM may be affected differently by supine rest.
Büchi Complementation and Size-Change Termination

We compare tools for complementing nondeterministic Buchi automata with a recent termination-analysis algorithm. Complementation of Buchi automata is a key step in program verification. Early constructions using a Ramsey-based argument have been supplanted by rank-based constructions with exponentially better bounds. In 2001 Lee et al. presented the size-change termination (SCT) problem, along with both a reduction to Buchi automata and a Ramsey-based algorithm. This algorithm strongly resembles the initial complementation constructions for Buchi automata. We prove that the SCT algorithm is a specialized realization of the Ramsey-based complementation construction. Surprisingly, empirical analysis suggests Ramsey-based approaches are superior over the domain of SCT problems. Upon further analysis we discover an interesting property of the problem space that both explains this result and provides a chance to improve rank-based tools. With these improvements, we show that theoretical gains in efficiency are mirrored in empirical performance.
Relationship status and perceived support in the social regulation of neural responses to threat

Abstract Strong social ties correspond with better health and well being, but the neural mechanisms linking social contact to health remain speculative. This study extends work on the social regulation of brain activity by supportive handholding in 110 participants (51 female) of diverse racial and socioeconomic origins. In addition to main effects of social regulation by handholding, we assessed the moderating effects of both perceived social support and relationship status (married, cohabiting, dating or platonic friends). Results suggest that, under threat of shock, handholding by familiar relational partners attenuates both subjective distress and activity in a network associated with salience, vigilance and regulatory self-control. Moreover, greater perceived social support corresponded with less brain activity in an extended network associated with similar processes, but only during partner handholding. In contrast, we did not observe any regulatory effects of handholding by strangers, and relationship status did not moderate the regulatory effects of partner handholding. These findings suggest that contact with a familiar relational partner is likely to attenuate subjective distress and a variety of neural responses associated with the presence of threat. This effect is likely enhanced by an individual’s expectation of the availability of support from their wider social network.
Relationship of blood monocytes with chronic lymphocytic leukemia aggressiveness and outcomes: a multi‐institutional study

Monocyte‐derived cells, constituents of the cancer microenvironment, support chronic lymphocytic leukemia (CLL) cell survival in vitro via direct cell‐cell interaction and secreted factors. We hypothesized that circulating absolute monocyte count (AMC) reflects the monocyte‐derived cells in the microenvironment, and that higher AMC is associated with increased CLL cell survival in vivo and thus inferior CLL patient outcomes. We assessed the extent to which AMC at diagnosis of CLL is correlated with clinical outcomes, and whether this information adds to currently used prognostic markers. We evaluated AMC, clinically used prognostic markers, and time to event data from 1,168 CLL patients followed at the Mayo Clinic, the Duke University Medical Center, and the Durham VA Medical Center. Elevated AMC was significantly associated with inferior clinical outcomes, including time to first therapy (TTT) and overall survival (OS). AMC combined with established clinical and molecular prognostic markers significantly improved risk‐stratification of CLL patients for TTT. As an elevated AMC at diagnosis is associated with accelerated disease progression, and monocyte‐derived cells in the CLL microenvironment promote CLL cell survival and proliferation, these findings suggest that monocytes and monocyte‐derived cells are rational therapeutic targets in CLL. Am. J. Hematol. 91:687–691, 2016. © 2016 Wiley Periodicals, Inc.
The impact of global elevated CO2 concentration on photosynthesis and plant productivity

The alarming and unprecedented rise in the atmospheric concentration of greenhouse gases under global climate change warrants an urgent need to understand the synergistic and holistic mechanisms associated with plant growth and productivity. Photosynthesis is a major process of sequestration and turnover of the total carbon on the planet. The extensive literature on the impacts of climate change demonstrates both positive and negative effects of rising CO 2 on photosynthesis in different groups of higher plants. Significant variation exists in the physiological, biochemical and molecular responsiveness to elevated CO 2 atmosphere, among terrestrial plant species including those with C 3 , C 4 and crassulacean acid metabolic (CAM) pathways. However, the regulatory events associated with the inter- and intraspecific metabolic plasticity governed by genetic organization in different plants are little understood. The adaptive acclimation responses of plants to changing climate remain contradictory. This review focuses primarily on the impacts of global climate change on plant growth and productivity with special reference to adaptive photosynthetic acclimative responses to elevated CO 2 concentration. The effects of elevated CO 2 concentration on plant growth and development, source-sink balance as well as its interactive mechanisms with other environmental factors including water availability, temperature and mineral nutrition are discussed.
Analog front-end circuit with low-noise amplifier and high-pass sigma-delta modulator for an EEG or ECoG acquisition system

The present paper proposes an analog front-end (AFE) circuit, including only one low-noise amplifier with chopping techniques and one high-pass sigma-delta modulator (HPSDM), which can be applied as a sensing circuit for electroencephalogram or electrocorticogram (ECoG) signal acquisition systems. The low-noise amplifier, which has a close-loop gain of 20 V/V and CMRR of 109.6 dB, is implemented by a differential difference amplifier with feedback pseudo-resistors and capacitors. The HPSDM is implemented in a feed-forward architecture with an order of 3, an oversampling ratio of 128, and a 1-bit quantizer under a sampling frequency of 51.2 kHz. The TSMC 0.18 μm 1P6M CMOS process is used in the entire AFE circuit with a supply voltage of 1.2 V and power consumption of 28.7 μW. Within the maximum range of ECoG signals, the simulated SNR and SFDR of the entire AFE circuits are 70.8 and 73 dB, respectively.
Genetic organization of the yersiniabactin biosynthetic region and construction of avirulent mutants in Yersinia pestis

We have identified an approximately 22-kb region of the pgm locus of Yersinia pestis KIM6+ which encodes a number of iron-regulated proteins involved in the biosynthesis of the Y. pestis cognate siderophore, yersiniabactin (Ybt), and which is located immediately upstream of the pesticin/yersiniabactin receptor gene (psn). Sequence analysis and the construction of insertion and deletion mutants allowed us to determine the putative location of the irp1 gene and the positions of irp2, ybtT, and ybtE within the ybt operon. Mutations in the irp1, irp2, or ybtE gene yielded strains defective in siderophore production. Mutant strains were unable to grow on iron-deficient media at 37 degrees C but could be cross-fed by culture supernatants from yersiniabactin-producing strains of Y. pestis grown under iron-limiting conditions. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of whole-cell extracts from Ybt+ and Ybt- strains grown in iron-deficient media revealed that expression of ybt-encoded proteins is not only iron regulated but also influenced by the presence of the siderophore itself. Finally, Y. pestis strains with mutations in either the psn or irp2 gene were avirulent in mice when inoculated subcutaneously.
Polynomial bounds for decoupling, with applications

Let f(x) = f(x_1, ., x_n) = \sum_{|S| <= k} a_S \prod_{i \in S} x_i be an n-variate real multilinear polynomial of degree at most k, where S \subseteq [n] = {1, 2, . , n}. For its "one-block decoupled" version, f~(y,z) = \sum_{|S| <= k} a_S \sum_{i \in S} y_i \prod_{j \in S\i} z_j, we show tail-bound comparisons of the form Pr[|f~(y,z)| > C_k t] t]. Our constants C_k, D_k are significantly better than those known for "full decoupling". For example, when x, y, z are independent Gaussians we obtain C_k = D_k = O(k); when x, y, z, Rademacher random variables we obtain C_k = O(k^2), D_k = k^{O(k)}. By contrast, for full decoupling only C_k = D_k = k^{O(k)} is known in these settings. We describe consequences of these results for query complexity (related to conjectures of Aaronson and Ambainis) and for analysis of Boolean functions (including an optimal sharpening of the DFKO Inequality).
The Effect of Molecular Structure and Environment on the Miscibility and Diffusivity in Polythiophene-Methanofullerene Bulk Heterojunctions: Theory and Modeling with the RISM Approach

Although better means to model the properties of bulk heterojunction molecular blends are much needed in the field of organic optoelectronics, only a small subset of methods based on molecular dynamics- and Monte Carlo-based approaches have been hitherto employed to guide or replace empirical characterization and testing. Here, we present the first use of the integral equation theory of molecular liquids in modelling the structural properties of blends of phenyl-C61-butyric acid methyl ester (PCBM) with poly(3-hexylthiophene) (P3HT) and a carboxylated poly(3-butylthiophene) (P3BT), respectively. For this, we use the Reference Interaction Site Model (RISM) with the Universal Force Field (UFF) to compute the microscopic structure of blends and obtain insight into the miscibility of its components. Input parameters for RISM, such as optimized molecular geometries and charge distribution of interaction sites, are derived by the Density Functional Theory (DFT) methods. We also run Molecular Dynamics (MD) simulation to compare the diffusivity of the PCBM in binary blends with P3HT and P3BT, respectively. A remarkably good agreement with available experimental data and results of alternative modelling/simulation is observed for PCBM in the P3HT system. We interpret this as a step in the validation of the use of our approach for organic photovoltaics and support of its results for new systems that do not have reference data for comparison or calibration. In particular, for the less-studied P3BT, our results show that expectations about its performance in binary blends with PCBM may be overestimated, as it does not demonstrate the required level of miscibility and short-range structural organization. In addition, the simulated mobility of PCBM in P3BT is somewhat higher than what is expected for polymer blends and falls into a range typical for fluids. The significance of our predictive multi-scale modelling lies in the insights it offers into nanoscale morphology and charge transport behaviour in multi-component organic semiconductor blends.
Essential Role of D1 But Not D2 Receptors in the NMDA Receptor-Dependent Long-Term Potentiation at Hippocampal-Prefrontal Cortex Synapses In Vivo

An intact mesocortical dopaminergic (DA) input to the prefrontal cortex (PFC) has been reported to be necessary for long-term potentiation (LTP) to occur at hippocampal-prefrontal cortex synapses. Here, we investigated the role of D1 and D2 receptors in this NMDA receptor-dependent LTP. Local infusion of the D1 agonist SKF81297 at an optimal dose induced a sustained enhancement of hippocampal-PFC LTP, whereas the D1 antagonist SCH23390 caused a dose-related impairment of its induction. The D1 agonist effect was mimicked by infusion of a low dose of the adenylyl cyclase activator forskolin, whereas LTP was severely attenuated with a protein kinase A inhibitor, Rp-cAMPS. To further assess the complex interplay between DA and NMDA receptors, changes in extracellular DA levels in the PFC were estimated during LTP, and a significant increase was observed immediately after tetanus. Taken together, these data suggest that D1 but not D2 receptors are crucial for the DA control of the NMDA receptor-mediated synaptic response on a specific excitatory input to the PFC. The interactions of these receptors may play a crucial role in the storage and transfer of hippocampal information in the PFC.
Promoting Freedom, Responsibility, and Learning in the Classroom: The Learning Covenant a Decade Later

This essay discusses an approach to teaching religious studies in a general education or core curricu- lum that I have experimented with for the last decade, which I call the "Learning Covenant. " The Learning Covenant brings together various pedagogical theories, including transformational, experiential, contract, and cooperative learning, in an attempt to address diverse learning styles, multiple intelligences, and student learn- ing assessment. It has advantages over more traditional teacher-directed approaches to teaching, including meeting student resistance to "required" courses head-on by inviting them to identify learning needs regardless of chosen vocation and meeting them in the context of a religious studies course, recognizing the multiple ways in which students learn and providing a variety of opportunities for students to express their learning, and allowing students opportunity to take increased responsibility for their own learning. The essay will focus on the Learning Covenant's develop- ment, components, strengths, and drawbacks.
PROGNOSTIC FACTORS AND SURVIVAL ANALYSIS IN ESOPHAGEAL CARCINOMA

ABSTRACT Background: Despite recent advances in diagnosis and treatment, esophageal cancer still has high mortality. Prognostic factors associated with patient and with disease itself are multiple and poorly explored. Aim: Assess prognostic variables in esophageal cancer patients. Methods: Retrospective review of all patients with esophageal cancer in an oncology referral center. They were divided according to histological diagnosis (444 squamous cell carcinoma patients and 105 adenocarcinoma), and their demographic, pathological and clinical characteristics were analyzed and compared to clinical stage and overall survival. Results: No difference was noted between squamous cell carcinoma and esophageal adenocarcinoma overall survival curves. Squamous cell carcinoma presented 22.8% survival after five years against 20.2% for adenocarcinoma. When considering only patients treated with curative intent resection, after five years squamous cell carcinoma survival rate was 56.6 and adenocarcinoma, 58%. In patients with squamous cell carcinoma, poor differentiation histology and tumor size were associated with worse oncology stage, but this was not evidenced in adenocarcinoma. Conclusion: Weight loss (kg), BMI variation (kg/m²) and percentage of weight loss are factors that predict worse stage at diagnosis in the squamous cell carcinoma. In adenocarcinoma, these findings were not statistically significant.
Code Reuse in Open Source Software

Code reuse is a form of knowledge reuse in software development that is fundamental to innovation in many fields. However, to date there has been no systematic investigation of code reuse in open source software projects. This study uses quantitative and qualitative data gathered from a sample of six open source software projects to explore two sets of research questions derived from the literature on software reuse in firms and open source software development. We find that code reuse is extensive across the sample and that open source software developers, much like developers in firms, apply tools that lower their search costs for knowledge and code, assess the quality of software components, and have incentives to reuse code. Open source software developers reuse code because they want to integrate functionality quickly, because they want to write preferred code, because they operate under limited resources in terms of time and skills, and because they can mitigate development costs through code reuse.
Swifter: Chunked Network Coding for Peer-to-Peer Content Distribution

The benefit of network coding with respect to simplifying scheduling overhead for content distribution has been extensively studied in previous literature. However, the complexity of network coding increases as the content size scales up. In this paper, we study the tradeoff between scheduling overhead and coding overhead. To this end, we propose Swifter, a P2P content distribution scheme, which employs local-rarest-first segment scheduling and chunked network coding algorithms. In Swifter, content is divided into segments, which are further divided into blocks. Each peer schedules a local-rarest segment request from its neighbors. Network coding is then used for generating a reply block within the requested segment. Leveraging our real-world implementation and experiments, we find that Swifter has low coding overhead and can reduce average download time by up to 40% compared to existing work.